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  <doc>
    <id>7571</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>19344</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>9</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">pKa of opioid ligands as a discriminating factor for side effects</title>
    <abstract language="eng">The non-selective activation of central and peripheral opioid receptors is a major shortcoming of currently available opioids. Targeting peripheral opioid receptors is a promising strategy to preclude side effects. Recently, we showed that fentanyl-derived μ-opioid receptor (MOR) agonists with reduced acid dissociation constants (pKa) due to introducing single fluorine atoms produced injury-restricted antinociception in rat models of inflammatory, postoperative and neuropathic pain. Here, we report that a new double-fluorinated compound (FF6) and fentanyl show similar pKa, MOR affinity and [35S]-GTPγS binding at low and physiological pH values. In vivo, FF6 produced antinociception in injured and non-injured tissue, and induced sedation and constipation. The comparison of several fentanyl derivatives revealed a correlation between pKa values and pH-dependent MOR activation, antinociception and side effects. An opioid ligand's pKa value may be used as discriminating factor to design safer analgesics.</abstract>
    <parentTitle language="eng">Scientific Reports</parentTitle>
    <identifier type="doi">10.1038/s41598-019-55886-1</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Giovanna Del Vecchio</author>
    <submitter>Marcus Weber</submitter>
    <author>Dominika Labuz</author>
    <author>Julia Temp</author>
    <author>Viola Seitz</author>
    <author>Michael Kloner</author>
    <author>Roger Negrete</author>
    <author>Antonio Rodriguez-Gaztelumendi</author>
    <author>Marcus Weber</author>
    <author>Halina Machelska</author>
    <author>Christoph Stein</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
  </doc>
  <doc>
    <id>7565</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1900501</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>13</issue>
    <volume>6</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces</title>
    <abstract language="eng">Mussel glue‐proteins undergo structural transitions at material interfaces to optimize adhesive surface contacts. Those intriguing structure responses are mimicked by a mussel‐glue mimetic peptide (HSY*SGWSPY*RSG (Y* = l‐Dopa)) that was previously selected by phage‐display to adhere to Al2O3 after enzymatic activation. Molecular level insights into the full‐length adhesion domain at Al2O3 surfaces are provided by a divergent‐convergent analysis, combining nuclear Overhauser enhancement based 2D NOESY and saturation transfer difference NMR analysis of submotifs along with molecular dynamics simulations of the full‐length peptide. The peptide is divided into two submotifs, each containing one Dopa “anchor” (Motif‐1 and 2). The analysis proves Motif‐1 to constitute a dynamic Al2O3 binder and adopting an “M”‐structure with multiple surface contacts. Motif‐2 binds stronger by two surface contacts, forming a compact “C”‐structure. Taking these datasets as constraints enables to predict the structure and propose a binding process model of the full‐length peptide adhering to Al2O3.</abstract>
    <parentTitle language="eng">Advanced Materials Interfaces</parentTitle>
    <identifier type="doi">10.1002/admi.201900501</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Narendra Lagumaddepalli Venkatareddy</author>
    <submitter>Marcus Weber</submitter>
    <author>Patrick Wilke</author>
    <author>Natalia Ernst</author>
    <author>Justus Horch</author>
    <author>Marcus Weber</author>
    <author>Andre Dallmann</author>
    <author>Hans G. Börner</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
    <collection role="persons" number="ernst">Ernst, Natalia</collection>
  </doc>
  <doc>
    <id>7564</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>551</pageFirst>
    <pageLast>557</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>7</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung</title>
    <parentTitle language="deu">KA Korrespondenz Abwasser, Abfall</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Marcus Weber</author>
    <submitter>Marcus Weber</submitter>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
  </doc>
  <doc>
    <id>7563</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>46</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>7</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC</title>
    <abstract language="eng">In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies.</abstract>
    <parentTitle language="eng">Computation</parentTitle>
    <identifier type="doi">10.3390/computation7030046</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2019-08-16</enrichment>
    <author>Franziska Erlekam</author>
    <submitter>Marcus Weber</submitter>
    <author>Sinaida Igde</author>
    <author>Susanna Röblitz</author>
    <author>Laura Hartmann</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>7314</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>174103</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>150</issue>
    <volume>17</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Generalized Markov modeling of nonreversible molecular kinetics</title>
    <abstract language="eng">Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems. Thus, we generalized the common Robust Perron Cluster Cluster Analysis (PCCA+) method to enable straightforward modeling of nonequilibrium systems as well. The resulting Generalized PCCA (G-PCCA) method readily handles equilibrium as well as nonequilibrium data by utilizing real Schur vectors instead of eigenvectors. This is implemented in the G-PCCA algorithm that enables the semiautomatic coarse graining of molecular kinetics. G-PCCA is not limited to the detection of metastable states but also enables the identification and modeling of cyclic processes. This is demonstrated by three typical examples of nonreversible systems.</abstract>
    <parentTitle language="eng">The Journal of Chemical Physics</parentTitle>
    <identifier type="doi">10.1063/1.5064530</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Bernhard Reuter</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>7315</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>904</pageFirst>
    <pageLast>911</pageLast>
    <pageNumber/>
    <edition/>
    <issue>11</issue>
    <volume>45</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes</title>
    <abstract language="eng">Molecular simulations are often used to analyse the stability of protein–ligand complexes. The stability can be characterised by exit rates or using the exit time approach, i.e. by computing the expected holding time of the complex before its dissociation. However determining exit rates by straightforward molecular dynamics methods can be challenging for stochastic processes in which the exit event occurs very rarely. Finding a low variance procedure for collecting rare event statistics is still an open problem. In this work we discuss a novel method for computing exit rates which uses results of Robust Perron Cluster Analysis (PCCA+). This clustering method gives the possibility to define a fuzzy set by a membership function, which provides additional information of the kind ‘the process is being about to leave the set’. Thus, the derived approach is not based on the exit event occurrence and, therefore, is also applicable in case of rare events. The novel method can be used to analyse the temperature effect of protein–ligand systems through the differences in exit rates, and, thus, open up new drug design strategies and therapeutic applications.</abstract>
    <parentTitle language="eng">Molecular Simulation</parentTitle>
    <identifier type="doi">10.1080/08927022.2019.1610949</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Natalia Ernst</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Andrea Volkamer</author>
    <author>Oliver Opatz</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
    <collection role="persons" number="ernst">Ernst, Natalia</collection>
  </doc>
  <doc>
    <id>7223</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>012101</pageFirst>
    <pageLast>012101</pageLast>
    <pageNumber>11</pageNumber>
    <edition/>
    <issue/>
    <volume>29</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">From metastable to coherent sets - Time-discretization schemes</title>
    <abstract language="eng">In this article, we show that these well-established spectral algorithms (like PCCA+, Perron Cluster Cluster Analysis) also identify coherent sets of non-autonomous dynamical systems. For the identification of coherent sets, one has to compute a discretization (a matrix T) of the transfer operator of the process using a space-time-discretization scheme. The article gives an overview about different time-discretization schemes and shows their applicability in two different fields of application.</abstract>
    <parentTitle language="eng">Chaos: An Interdisciplinary Journal of Nonlinear Science</parentTitle>
    <identifier type="doi">10.1063/1.5058128</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2019-01-28</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-66074</enrichment>
    <author>Konstantin Fackeldey</author>
    <submitter>Marcus Weber</submitter>
    <author>Peter Koltai</author>
    <author>Peter Nevir</author>
    <author>Henning Rust</author>
    <author>Axel Schild</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>7176</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>47</pageFirst>
    <pageLast>60</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>152</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays</title>
    <abstract language="eng">The assessment of water quality is crucial for safeguarding drinking water resources and ecosystem integrity. To this end, sample preparation and extraction is critically important, especially when investigating emerging contaminants and the toxicity of water samples. As extraction methods are rarely optimised for bioassays but rather adopted from chemical analysis, this may result in a misrepresentation of the actual toxicity.&#13;
&#13;
In this study, surface water, groundwater, hospital and municipal wastewater were used to characterise the impacts of common sample preparation techniques (acidification, filtration and solid phase extraction (SPE)) on the outcomes of eleven in vitro bioassays. The latter covered endocrine activity (reporter gene assays for estrogen, androgen, aryl-hydrocarbon, retinoic acid, retinoid X, vitamin D, thyroid receptor), mutagenicity (Ames fluctuation test), genotoxicity (umu test) and cytotoxicity. Water samples extracted using different SPE sorbents (Oasis HLB, Supelco ENVI-Carb+, Telos C18/ENV) at acidic and neutral pH were compared for their performance in recovering biological effects.&#13;
&#13;
Acidification, commonly used for stabilisation, significantly altered the endocrine activity and toxicity of most (waste)water samples. Sample filtration did not affect the majority of endpoints but in certain cases affected the (anti-)estrogenic and dioxin-like activities. SPE extracts (10.4 × final concentration), including WWTP effluents, induced significant endocrine effects that were not detected in aqueous samples (0.63 × final concentration), such as estrogenic, (anti-)androgenic and dioxin-like activities. When ranking the SPE methods using multivariate Pareto optimisation an extraction with Telos C18/ENV at pH 7 was most effective in recovering toxicity. At the same time, these extracts were highly cytotoxic masking the endpoint under investigation. Compared to that, extraction at pH 2.5 enriched less cytotoxicity.&#13;
&#13;
In summary, our study demonstrates that sample preparation and extraction critically affect the outcome of bioassays when assessing the toxicity of water samples. Depending on the water matrix and the bioassay, these methods need to be optimised to accurately assess water quality.</abstract>
    <parentTitle language="eng">Water Research</parentTitle>
    <identifier type="doi">10.1016/j.watres.2018.12.049</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Aennes Abbas</author>
    <submitter>Marcus Weber</submitter>
    <author>Ilona Schneider</author>
    <author>Anna Bollmann</author>
    <author>Jan Funke</author>
    <author>Jörg Oehlmann</author>
    <author>Carsten Prasse</author>
    <author>Ulrike Schulte-Oehlmann</author>
    <author>Wolfram Seitz</author>
    <author>Thomas Ternes</author>
    <author>Marcus Weber</author>
    <author>Henning Wesely</author>
    <author>Martin Wagner</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>7164</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>108</pageFirst>
    <pageLast>117</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>436</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Structural characterization of synthetic peptides using electronspray ion mobility spectrometry and molecular dynamics simulations</title>
    <abstract language="eng">Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540–3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF).</abstract>
    <parentTitle language="eng">International Journal of Mass Spectrometry</parentTitle>
    <identifier type="doi">10.1016/j.ijms.2018.10.036</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018/10/27</enrichment>
    <author>José Villatoro</author>
    <submitter>Marcus Weber</submitter>
    <author>Marcus Weber</author>
    <author>Martin Zühlke</author>
    <author>Andreas Lehmann</author>
    <author>Karl Zechiowski</author>
    <author>Daniel Riebe</author>
    <author>Toralf Beitz</author>
    <author>Hans-Gerd Löhmannsröben</author>
    <author>Oliver Kreuzer</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SALSA-IR-MALDI">SALSA-IR-MALDI</collection>
  </doc>
  <doc>
    <id>7163</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>e0207718</pageFirst>
    <pageLast>e0207718</pageLast>
    <pageNumber>23</pageNumber>
    <edition/>
    <issue>12</issue>
    <volume>13</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Prediction of perturbed proton transfer networks</title>
    <abstract language="eng">The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80%, while important network properties are maintained in most predictions.</abstract>
    <parentTitle language="eng">PLoS ONE</parentTitle>
    <identifier type="doi">https://doi.org/10.1371/journal.pone.0207718</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Marco Reidelbach</author>
    <submitter>Marcus Weber</submitter>
    <author>Marcus Weber</author>
    <author>Petra Imhof</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>7065</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>425201</pageFirst>
    <pageLast>425201</pageLast>
    <pageNumber/>
    <edition/>
    <issue>42</issue>
    <volume>30</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Estimation of the infinitesimal generator by square-root approximation</title>
    <abstract language="eng">In recent years, for the analysis of molecular processes, the estimation of time-scales and transition rates has become fundamental. Estimating the transition rates between molecular conformations is—from a mathematical point of view—an invariant subspace projection problem. We present a method to project the infinitesimal generator acting on function space to a low-dimensional rate matrix. This projection can be performed in two steps. First, we discretize the conformational space in a Voronoi tessellation, then the transition rates between adjacent cells is approximated by the geometric average of the Boltzmann weights of the Voronoi cells. This method demonstrates that there is a direct relation between the potential energy surface of molecular structures and the transition rates of conformational changes. We will show also that this approximation is correct and converges to the generator of the Smoluchowski equation in the limit of infinitely small Voronoi cells. We present results for a two dimensional diffusion process and alanine dipeptide as a high-dimensional system.</abstract>
    <parentTitle language="eng">J. Phys.: Condens. Matter</parentTitle>
    <identifier type="doi">10.1088/1361-648X/aadfc8</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018-09-07</enrichment>
    <author>Luca Donati</author>
    <submitter>Marcus Weber</submitter>
    <author>Martin Heida</author>
    <author>Bettina G. Keller</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="persons" number="donati">Donati, Luca</collection>
  </doc>
  <doc>
    <id>7040</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>6376</pageFirst>
    <pageLast>6391</pageLast>
    <pageNumber/>
    <edition/>
    <issue>5</issue>
    <volume>37</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Spectral Clustering for Non-Reversible Markov Chains</title>
    <abstract language="eng">Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e., generalized PCCA), since it includes the case of non-reversible processes. We also apply the method to real-world eye-tracking data.</abstract>
    <parentTitle language="eng">Computational and Applied Mathematics</parentTitle>
    <identifier type="doi">https://doi.org/10.1007/s40314-018-0697-0</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018/08/22</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-70218</enrichment>
    <author>Konstantin Fackeldey</author>
    <submitter>Marcus Weber</submitter>
    <author>Alexander Sikorski</author>
    <author>Marcus Weber</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Spectral clustering</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov chain</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Non-reversible</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Schur decomposition</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>GenPCCA</value>
    </subject>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="persons" number="sikorski">Sikorski, Alexander</collection>
  </doc>
  <doc>
    <id>7021</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2018-08-24</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Spectral Clustering for Non-reversible Markov Chains</title>
    <abstract language="eng">Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g. the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA  (i.e.&#13;
Generalized PCCA), since it includes the case of non reversible processes. &#13;
We also apply the method to real world eye tracking data.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-70218</identifier>
    <enrichment key="AcceptedDate">01.07.2018</enrichment>
    <enrichment key="SourceTitle">Comp. Appl. Math., pp 1-16, https://doi.org/10.1007/s40314-018-0697-0</enrichment>
    <author>Konstantin Fackeldey</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Alexander Sikorski</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>18-48</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>spectral clustering</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov chain</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Schur decomposition</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>non-reversible</value>
    </subject>
    <collection role="ccs" number="G.1.3">Numerical Linear Algebra</collection>
    <collection role="pacs" number="05.00.00">Statistical physics, thermodynamics, and nonlinear dynamical systems (see also 02.50.-r Probability theory, stochastic processes, and statistics)</collection>
    <collection role="msc" number="15A21">Canonical forms, reductions, classification</collection>
    <collection role="msc" number="62H30">Classification and discrimination; cluster analysis [See also 68T10]</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
    <collection role="persons" number="sikorski">Sikorski, Alexander</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/7021/GenPCCA_FSW.pdf</file>
  </doc>
  <doc>
    <id>6922</id>
    <completedYear>2018</completedYear>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>3579</pageFirst>
    <pageLast>3594</pageLast>
    <pageNumber/>
    <edition/>
    <issue>7</issue>
    <volume>14</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-05-29</completedDate>
    <publishedDate>2018-07-10</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field</title>
    <abstract language="eng">Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very&#13;
well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a&#13;
detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with&#13;
general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems.&#13;
To overcome this limitation, we developed a generalization of the common robust Perron Cluster Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles equilibrium and nonequilibrium simulation data, utilizing Schur vectors instead of eigenvectors. G-PCCA is not limited to the detection of metastable states but enables the identification of dominant structures in a general sense, unraveling cyclic processes. This is exemplified by application of G-PCCA on nonequilibrium molecular dynamics data of the Amyloid β (1−40) peptide, periodically driven by an oscillating electric field.</abstract>
    <parentTitle language="eng">Journal of Chemical Theory and Computation</parentTitle>
    <identifier type="doi">10.1021/acs.jctc.8b00079</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">29.05.2018</enrichment>
    <author>Bernhard Reuter</author>
    <submitter>Bernhard Reuter</submitter>
    <author>Marcus Weber</author>
    <author>Konstantin Fackeldey</author>
    <author>Susanna Röblitz</author>
    <author>Martin E. Garcia</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
  </doc>
  <doc>
    <id>6899</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung</title>
    <parentTitle language="deu">KA Korrespondenz Abwasser, Abfall</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SubmissionStatus">accepted for publication</enrichment>
    <enrichment key="AcceptedDate">2018-06-04</enrichment>
    <author>Marcus Weber</author>
    <submitter>Marcus Weber</submitter>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>6898</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>8965</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>8</volume>
    <type>article</type>
    <publisherName>Springer Nature</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2018-06-12</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist</title>
    <abstract language="eng">Novel pain killers without adverse effects are urgently needed.</abstract>
    <parentTitle language="eng">Scientific Reports</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018-06-01</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Viola Spahn</author>
    <submitter>Marcus Weber</submitter>
    <author>Giovanna Del Vecchio</author>
    <author>Antonio Rodriguez-Gaztelumendi</author>
    <author>Julia Temp</author>
    <author>Dominika Labuz</author>
    <author>Michael Kloner</author>
    <author>Marco Reidelbach</author>
    <author>Halina Machelska</author>
    <author>Marcus Weber</author>
    <author>Christoph Stein</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
  </doc>
  <doc>
    <id>6897</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>6963</pageFirst>
    <pageLast>6975</pageLast>
    <pageNumber/>
    <edition/>
    <issue>23</issue>
    <volume>34</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-10-03</completedDate>
    <publishedDate>2018-10-03</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Role of Counterions in Molecularly Imprinted Polymers for Anionic Species</title>
    <abstract language="eng">Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-L/D-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme–substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-x-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development.</abstract>
    <parentTitle language="eng">Langmuir</parentTitle>
    <identifier type="doi">10.1021/acs.langmuir.8b00500</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018-05-23</enrichment>
    <author>Sabine Wagner</author>
    <submitter>Marcus Weber</submitter>
    <author>Carlos Zapata</author>
    <author>Wei Wan</author>
    <author>Kornelia Gawlitza</author>
    <author>Marcus Weber</author>
    <author>Knut Rurack</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="MIP_FORMATION">MIP_FORMATION</collection>
  </doc>
  <doc>
    <id>6713</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>researchdata</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Supplementary simulation data for Science Manuscript ai8636</title>
    <abstract language="eng">The simulation data has been produced by Vedat Durmaz, Peggy Sabri and Marco Reidelbach inside the "Computational Molecular Design" Group headed by Marcus Weber at Zuse-Institut Berlin, Takustr. 7, D-14195 Berlin, Germany.&#13;
&#13;
The file contains classical simulation data for different fentanyl derivates in the MOR binding pocket at different pHs. It also includes instruction files for quantum-chemical pKa-value estimations and a description of how we derived the pKa-values from the Gaussian09 log-files.</abstract>
    <identifier type="doi">10.12752/5.MWB.1.0</identifier>
    <note>GROMACS trajectories and GAUSSIAN files of MOR and fentanyl derivates</note>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="ScientificResourceTypeGeneral">Dataset</enrichment>
    <enrichment key="ScientificGeolocation">Berlin</enrichment>
    <enrichment key="ScientificDateCollected">2016</enrichment>
    <enrichment key="ScientificDateCreated">2017</enrichment>
    <enrichment key="zib_relatedIdentifier">https://doi.org/10.1126/science.aai8636</enrichment>
    <enrichment key="zib_DownloadUrl">http://www.zib.de/ext-data/selective-opioids/data_4manuscript.tar</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Marcus Weber</author>
    <submitter>Marcus Weber</submitter>
    <author>Vedat Durmaz</author>
    <author>Peggy Sabri</author>
    <author>Marco Reidelbach</author>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
  </doc>
  <doc>
    <id>6714</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>researchdata</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Supplementary: Implications of PCCA+ in Molecular Simulation</title>
    <abstract language="eng">Matlab-software and data sets to recapitulate the presented results in M. Weber: Implications of PCCA+ in Molecular Simulation. Computation, 6(1):20, 2018.</abstract>
    <note>This data set includes one folder per published figure. The folders contain all needed resources to recapitulate the presented results.</note>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="ScientificResourceTypeGeneral">Software</enrichment>
    <enrichment key="ScientificGeolocation">Berlin</enrichment>
    <enrichment key="ScientificDateCollected">2017</enrichment>
    <enrichment key="ScientificDateCreated">2018</enrichment>
    <enrichment key="SoftwareDescription">MATLAB-files</enrichment>
    <enrichment key="zib_relatedIdentifier">https://doi.org/10.3390/computation6010020</enrichment>
    <enrichment key="zib_DownloadUrl">http://www.mdpi.com/2079-3197/6/1/20/s1</enrichment>
    <licence>Creative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International</licence>
    <author>Marcus Weber</author>
    <submitter>Marcus Weber</submitter>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>6710</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>20</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>1</issue>
    <volume>6</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Implications of PCCA+ in Molecular Simulation</title>
    <abstract language="eng">Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ’bound’ vs. ’unbound’), although the process itself takes place in a continuous space. In this context, the formula chi=XA connects the micro-dynamics of the molecular system to its macro-dynamics. Chi can be understood as a clustering of micro-states of a molecular system into a few macro-states. X is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation A between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences.</abstract>
    <parentTitle language="eng">Computation</parentTitle>
    <identifier type="doi">10.3390/computation6010020</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Marcus Weber</author>
    <submitter>Marcus Weber</submitter>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>6709</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>7</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mathematical modeling of the spreading of innovations in the ancient world</title>
    <parentTitle language="eng">eTopoi. Journal for Ancient Studies</parentTitle>
    <identifier type="issn">ISSN 2192-2608</identifier>
    <identifier type="doi">10.17171/4-7-1</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="FulltextUrl">http://journal.topoi.org/index.php/etopoi/index</enrichment>
    <author>Natasa Djurdjevac Conrad</author>
    <submitter>Erlinda Koernig</submitter>
    <author>Daniel Fuerstenau</author>
    <author>Ana Grabundzija</author>
    <author>Luzie Helfmann</author>
    <author>Martin Park</author>
    <author>Wolfram Schier</author>
    <author>Brigitta Schütt</author>
    <author>Christof Schütte</author>
    <author>Marcus Weber</author>
    <author>Niklas Wulkow</author>
    <author>Johannes Zonker</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="persons" number="natasa.conrad">Conrad, Natasa</collection>
    <collection role="projects" number="INNOSPREAD">INNOSPREAD</collection>
  </doc>
  <doc>
    <id>6663</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>e0191423</pageFirst>
    <pageLast>e0191423</pageLast>
    <pageNumber>30</pageNumber>
    <edition/>
    <issue>1</issue>
    <volume>13</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">An AKAP-Lbc-RhoA interaction inhibitor promotes the translocation of aquaporin-2 to the plasma membrane of renal collecting duct principal cells</title>
    <abstract language="eng">Stimulation of renal collecting duct principal cells with antidiuretic hormone (arginine-vasopressin, AVP) results in inhibition of the small GTPase RhoA and the enrichment of the water channel aquaporin-2 (AQP2) in the plasma membrane. The membrane insertion facilitates water reabsorption from primary urine and fine-tuning of body water homeostasis. Rho guanine nucleotide exchange factors (GEFs) interact with RhoA, catalyze the exchange of GDP for GTP and thereby activate the GTPase. However, GEFs involved in the control of AQP2 in renal principal cells are unknown. The A-kinase anchoring protein, AKAP-Lbc, possesses GEF activity, specifically activates RhoA, and is expressed in primary renal inner medullary collecting duct principal (IMCD) cells. Through screening of 18,431 small molecules and synthesis of a focused library around one of the hits, we identified an inhibitor of the interaction of AKAP-Lbc and RhoA. This molecule, Scaff10-8, bound to RhoA, inhibited the AKAP-Lbc-mediated RhoA activation but did not interfere with RhoA activation through other GEFs or activities of other members of the Rho family of small GTPases, Rac1 and Cdc42. Scaff10-8 promoted the redistribution of AQP2 from intracellular vesicles to the periphery of IMCD cells. Thus, our data demonstrate an involvement of AKAP-Lbc-mediated RhoA activation in the control of AQP2 trafficking.</abstract>
    <parentTitle language="eng">PLOS ONE</parentTitle>
    <identifier type="doi">10.1371/journal.pone.0191423</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Katharina Schrade</author>
    <submitter>Marcus Weber</submitter>
    <author>Jessica Tröger</author>
    <author>Adeep Eldashan</author>
    <author>Kerstin Zühlke</author>
    <author>Kamal R. Abdul Azees</author>
    <author>Jonathan M. Elkins</author>
    <author>Martin Neuenschwander</author>
    <author>Andreas Oder</author>
    <author>Mohamed Elkewedi</author>
    <author>Sarah Jaksch</author>
    <author>Karsten Andrae</author>
    <author>Jinliang Li</author>
    <author>Jaoa Fernandes</author>
    <author>Paul Markus Müller</author>
    <author>Stephan Grunwald</author>
    <author>Stephen F. Marino</author>
    <author>Tanja Vukicevic</author>
    <author>Jenny Eichhorst</author>
    <author>Burkhard Wiesner</author>
    <author>Marcus Weber</author>
    <author>Michael Kapiloff</author>
    <author>Oliver Rocks</author>
    <author>Oliver Daumke</author>
    <author>Thomas Wieland</author>
    <author>Stefan Knapp</author>
    <author>Jens Peter von Kries</author>
    <author>Enno Klussmann</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
  </doc>
  <doc>
    <id>6646</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1700198</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>12</issue>
    <volume>17</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH</title>
    <parentTitle language="eng">Marcomolecular Bioscience</parentTitle>
    <identifier type="doi">10.1002/mabi.201700198</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sinaida Igde</author>
    <submitter>Marcus Weber</submitter>
    <author>Susanna Röblitz</author>
    <author>Anne Müller</author>
    <author>Katharina Kolbe</author>
    <author>Sophia Boden</author>
    <author>Claudia Fessele</author>
    <author>Thisbe Lindhorst</author>
    <author>Marcus Weber</author>
    <author>Laura Hartmann</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>6607</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-12-08</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">From Metastable to Coherent Sets - time-discretization schemes</title>
    <abstract language="eng">Given a time-dependent stochastic process with trajectories x(t) in a space $\Omega$, there may be sets such that the corresponding trajectories only very rarely cross the boundaries of these sets. We can analyze such a process in terms of metastability or coherence. Metastable sets M are defined in space $M\subset\Omega$, coherent sets $M(t)\subset\Omega$ are defined in space and time. Hence, if we extend the space by the time-variable t, coherent sets are metastable sets in  $\Omega\times[0,\infty]$. This relation can be exploited, because there already exist spectral algorithms for the identification of metastable sets. In this article we show that these well-established spectral algorithms (like PCCA+) also identify coherent sets of non-autonomous dynamical systems. For the identification of coherent sets, one has to compute a discretization (a matrix T) of the transfer operator of the process using a space-timediscretization scheme. The article gives an overview about different time-discretization schemes and shows their applicability in two different fields of application.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-66074</identifier>
    <author>Konstantin Fackeldey</author>
    <submitter>Paulina Bressel</submitter>
    <author>Péter Koltai</author>
    <author>Peter Névir</author>
    <author>Henning Rust</author>
    <author>Axel Schild</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-74</number>
    </series>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6607/ZIB-Report_17-74.pdf</file>
  </doc>
  <doc>
    <id>6595</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>A653</pageFirst>
    <pageLast>A670</pageLast>
    <pageNumber>18</pageNumber>
    <edition/>
    <issue>2</issue>
    <volume>40</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-03-01</completedDate>
    <publishedDate>2018-02-01</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates</title>
    <abstract language="eng">In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities.</abstract>
    <parentTitle language="eng">SIAM Journal on Scientific Computing</parentTitle>
    <identifier type="doi">10.1137/17m1124772</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-62075</enrichment>
    <enrichment key="AcceptedDate">2017-11-17</enrichment>
    <author>Jannes Quer</author>
    <submitter>Julia Boltze</submitter>
    <author>Luca Donati</author>
    <author>Bettina Keller</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="persons" number="quer">Quer, jannes</collection>
    <collection role="persons" number="donati">Donati, Luca</collection>
  </doc>
  <doc>
    <id>6395</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>70</pageFirst>
    <pageLast>80</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">GenPCCA -- Markov State Models for Non-Equilibrium Steady States</title>
    <parentTitle language="eng">Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29</parentTitle>
    <identifier type="doi">10.20347/WIAS.REPORT.29</identifier>
    <enrichment key="PeerReviewed">Yes</enrichment>
    <author>Konstantin Fackeldey</author>
    <submitter>Julia Boltze</submitter>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>6392</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>73</pageFirst>
    <pageLast>81</pageLast>
    <pageNumber/>
    <edition/>
    <issue>5/1</issue>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation</title>
    <parentTitle language="eng">Special Matrices</parentTitle>
    <identifier type="doi">10.1515/spma-2017-0006</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Konstantin Fackeldey</author>
    <submitter>Julia Boltze</submitter>
    <author>Amir Niknejad</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>6262</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>12</issue>
    <volume>146</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Set-Free Markov State Model Building</title>
    <parentTitle language="eng">Journal of Chemical Physics</parentTitle>
    <identifier type="doi">10.1063/1.4978501</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-62167</enrichment>
    <author>Marcus Weber</author>
    <submitter>Erlinda Körnig</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Christof Schütte</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>6219</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-03-09</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Eigenvalues of non-reversible Markov chains – A case study</title>
    <abstract language="eng">Finite reversible Markov chains are characterized by a transition matrix P that has real eigenvalues and pi-orthogonal eigenvectors, where pi is the stationary distribution of P. This means, that a transition matrix with complex eigenvalues corresponds to a non-reversible Markov chain. This observation leads to the question, whether the imaginary part of that eigendecomposition corresponds to or indicates the “pattern” of the nonreversibility. This article shows that the direct relation between imaginary parts of eigendecompositions and the non-reversibility of a transition matrix is not given. It is proposed to apply the Schur decomposition of P instead of the eigendecomposition in order to characterize its nonreversibility.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-62191</identifier>
    <author>Marcus Weber</author>
    <submitter>Regine Kossick</submitter>
    <series>
      <title>ZIB-Report</title>
      <number>17-13</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>non-reversible</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>transition matrix</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>detailed balance</value>
    </subject>
    <collection role="msc" number="60J10">Markov chains (discrete-time Markov processes on discrete state spaces)</collection>
    <collection role="msc" number="65F15">Eigenvalues, eigenvectors</collection>
    <collection role="msc" number="82C35">Irreversible thermodynamics, including Onsager-Machlup theory</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6219/ZR-17-13.pdf</file>
  </doc>
  <doc>
    <id>6216</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-03-03</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Set-free Markov State Building</title>
    <abstract language="eng">Molecular dynamics (MD) simulations face challenging problems since&#13;
the timescales of interest often are much longer than what is possible&#13;
to simulate and even if sufficiently long simulation are possible the complex&#13;
nature of the resulting simulation data makes interpretation difficult.&#13;
Markov State Models (MSMs) help to overcome these problems by making&#13;
experimentally relevant timescales accessible via coarse grained representations&#13;
that also allows for convenient interpretation. However, standard&#13;
set-based MSMs exhibit some caveats limiting their approximation quality&#13;
and statistical significance. One of the main caveats results from the fact&#13;
that typical MD trajectories repeatedly re-cross the boundary between&#13;
the sets used to build the MSM which causes statistical bias in estimating&#13;
the transition probabilities between these sets. In this article, we present&#13;
a set-free approach to MSM building utilizing smooth overlapping ansatz&#13;
functions instead of sets and an adaptive refinement approach. This kind&#13;
of meshless discretization helps to overcome the recrossing problem and&#13;
yields an adaptive refinement procedure that allows to improve the quality&#13;
of the model while exploring state space and inserting new ansatz&#13;
functions into the MSM.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-62167</identifier>
    <identifier type="doi">10.1063/1.4978501</identifier>
    <enrichment key="SourceTitle">Appeared in: Journal of Chemical Physics 146/12 (2017)</enrichment>
    <author>Marcus Weber</author>
    <submitter>Julia Boltze</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-10</number>
    </series>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6216/ZR-17-10.pdf</file>
  </doc>
  <doc>
    <id>6214</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>966</pageFirst>
    <pageLast>969</pageLast>
    <pageNumber/>
    <edition/>
    <issue>6328</issue>
    <volume>355</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A nontoxic pain killer designed by modeling of pathological receptor conformations</title>
    <parentTitle language="eng">Science</parentTitle>
    <identifier type="doi">10.1126/science.aai8636</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Viola Spahn</author>
    <submitter>Marcus Weber</submitter>
    <author>Giovanna Del Vecchio</author>
    <author>Dominika Labuz</author>
    <author>Antonio Rodriguez-Gaztelumendi</author>
    <author>N. Massaly</author>
    <author>Julia Temp</author>
    <author>Vedat Durmaz</author>
    <author>P. Sabri</author>
    <author>Marco Reidelbach</author>
    <author>Halina Machelska</author>
    <author>Marcus Weber</author>
    <author>Christoph Stein</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>6207</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-01-03</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates</title>
    <abstract language="eng">In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine  a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-62075</identifier>
    <author>Jannes Quer</author>
    <submitter>Jannes Quer</submitter>
    <author>Luca Donati</author>
    <author>Bettina Keller</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>17-09</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Adaptive Importance Sampling</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Molecular Dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Metastability</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Variance Reduction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Non Equilibrium Sampling</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Metadynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Girsanov</value>
    </subject>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="msc" number="37-XX">DYNAMICAL SYSTEMS AND ERGODIC THEORY [See also 26A18, 28Dxx, 34Cxx, 34Dxx, 35Bxx, 46Lxx, 58Jxx, 70-XX]</collection>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="65-XX">NUMERICAL ANALYSIS</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="persons" number="quer">Quer, jannes</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6207/AISZIB.pdf</file>
  </doc>
  <doc>
    <id>6177</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>52</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Importance sampling in path space for diffusion processes with slow-fast variables</title>
    <abstract language="eng">Importance sampling is a widely used technique to reduce the variance of a Monte Carlo estimator by an appropriate change of measure. In this work, we study importance sampling in the framework of diffusion process and consider the change of measure which is realized by adding a control force to the original dynamics. For certain exponential type expectation, the corresponding control force of the optimal change of measure leads to a zero-variance estimator and is related to the solution of a Hamilton–Jacobi–Bellmann equation. We focus on certain diffusions with both slow and fast variables, and the main result is that we obtain an upper bound of the relative error for the importance sampling estimators with control obtained from the limiting dynamics. We demonstrate our approximation strategy with an illustrative numerical example.</abstract>
    <parentTitle language="eng">Probability Theory and Related Fields</parentTitle>
    <identifier type="doi">10.1007/s00440-017-0755-3</identifier>
    <identifier type="url">http://rdcu.be/oA51</identifier>
    <note>If you are not subscribing to the journal please use the http link below as part of the Springer Nature SharedIt initiative</note>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Carsten Hartmann</author>
    <submitter>Regine Kossick</submitter>
    <author>Christof Schütte</author>
    <author>Marcus Weber</author>
    <author>Wei Zhang</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>6053</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>197</pageFirst>
    <pageLast>297</pageLast>
    <pageNumber/>
    <edition/>
    <issue>19/4</issue>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector</title>
    <parentTitle language="eng">International Journal for Ion Mobility Spectrometry</parentTitle>
    <identifier type="doi">10.1007/s12127-016-0208-1</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>José Villatoro</author>
    <submitter>Regine Kossick</submitter>
    <author>Martin Zühlke</author>
    <author>Daniel Riebe</author>
    <author>Toralf Beitz</author>
    <author>Marcus Weber</author>
    <author>Jens Riedel</author>
    <author>Hans-Gerd Löhmannsröben</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SALSA-IR-MALDI">SALSA-IR-MALDI</collection>
  </doc>
  <doc>
    <id>6035</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-05-09</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes</title>
    <abstract language="eng">In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-60353</identifier>
    <identifier type="doi">10.1137/16M1091162</identifier>
    <author>Jakob Witzig</author>
    <submitter>Jakob Witzig</submitter>
    <author>Isabel Beckenbach</author>
    <author>Leon Eifler</author>
    <author>Konstantin Fackeldey</author>
    <author>Ambros Gleixner</author>
    <author>Andreas Grever</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-39</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Non-reversible Markov Processes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>NESS</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Mixed-Integer Programming</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov State Models</value>
    </subject>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="62-XX">STATISTICS</collection>
    <collection role="msc" number="82-XX">STATISTICAL MECHANICS, STRUCTURE OF MATTER</collection>
    <collection role="msc" number="90-XX">OPERATIONS RESEARCH, MATHEMATICAL PROGRAMMING</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="optimization">Mathematical Optimization</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="mip">Mathematical Optimization Methods</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="persons" number="beckenbach">Beckenbach, Isabel</collection>
    <collection role="projects" number="MIP-ZIBOPT">MIP-ZIBOPT</collection>
    <collection role="projects" number="MODAL-SynLab">MODAL-SynLab</collection>
    <collection role="projects" number="SparseApproxiTN">SparseApproxiTN</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
    <collection role="institutes" number="aopt">Applied Optimization</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6035/ZR-16-39-revised2.pdf</file>
  </doc>
  <doc>
    <id>6034</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC</title>
    <abstract language="eng">Multivalent sugar/protein interactions are well-known to proceed through different binding modes 1-5 which in turn can be described by their binding kinetics 3-5. This study provides additional insight into the association and dissociation reaction rates of complex multivalent sugar/protein interactions. Binding kinetics of recently introduced multivalent precision glycomacromolecules 6-8 to Concanavalin A (Con A) were studied by " kinetic Isothermal Titration Calorimetry " (kinITC) 9-11. The effect of multivalency is evaluated by comparing rate constants of glycomacromolecules obtaining the same and different valency of mannose ligands and by variation of the overall backbone properties, such as hydrophilic/ hydrophoboc. In addition, binding kinetics were studied using different conformations of Con A (homodimer vs.-tetramer) and thus a different protein valency. Our results show that precision glycomacromolecule/Con A binding proceeds non-cooperatively. Further, association and dissociation rates are mainly described by intermolecular complex formation. Together with the so-called functional valency, we can discriminate between " bound " and " unbound " states for macroscopic on-and off-rates, even for such complex glycooligomer/protein systems. By comparing e.g. a mono-to a divalent glycomacromolecule for their binding to dimeric Con A, we see a lower dissociation rate for the latter. As both bind monovalently to Con A, this is a strong indication for a statistical rebinding event. Further, there is a strong dependence of multivalent binding kinetics on the ligand density of glycomacromolecules as well as the Con A conformation and thus the overall on-and off-rates.</abstract>
    <parentTitle language="eng">Münster Symposium on Cooperative Effects 2015 - SFB 858, at Westfälische Wilhelms-Universität Münster, 2015</parentTitle>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Sinaida Igde</author>
    <submitter>Regine Kossick</submitter>
    <author>Hendrik Wölk</author>
    <author>Susanna Röblitz</author>
    <author>Marco Reidelbach</author>
    <author>Marcus Weber</author>
    <author>Laura Hartmann</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>6029</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>248</pageFirst>
    <pageLast>265</pageLast>
    <pageNumber/>
    <edition/>
    <issue>1</issue>
    <volume>16</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-02-15</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes</title>
    <abstract language="eng">In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.</abstract>
    <parentTitle language="eng">Multiscale Modeling and Simulation</parentTitle>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="doi">10.1137/16M1091162</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-60353</enrichment>
    <enrichment key="SourceTitle">Multiscale Modeling and Simulation</enrichment>
    <enrichment key="AcceptedDate">2017-10-18</enrichment>
    <author>Jakob Witzig</author>
    <submitter>Jakob Witzig</submitter>
    <author>Isabel Beckenbach</author>
    <author>Leon Eifler</author>
    <author>Konstantin Fackeldey</author>
    <author>Ambros Gleixner</author>
    <author>Andreas Grever</author>
    <author>Marcus Weber</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov State Models</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>NESS</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Non-reversible Markov Processes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Mixed-Integer Programming</value>
    </subject>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="82-XX">STATISTICAL MECHANICS, STRUCTURE OF MATTER</collection>
    <collection role="msc" number="90-XX">OPERATIONS RESEARCH, MATHEMATICAL PROGRAMMING</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="optimization">Mathematical Optimization</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="mip">Mathematical Optimization Methods</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="persons" number="beckenbach">Beckenbach, Isabel</collection>
    <collection role="projects" number="MIP-ZIBOPT">MIP-ZIBOPT</collection>
    <collection role="projects" number="MODAL-RailLab">MODAL-RailLab</collection>
    <collection role="projects" number="MODAL-SynLab">MODAL-SynLab</collection>
    <collection role="projects" number="SparseApproxiTN">SparseApproxiTN</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
    <collection role="institutes" number="aopt">Applied Optimization</collection>
  </doc>
  <doc>
    <id>5882</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>15475</pageFirst>
    <pageLast>15484</pageLast>
    <pageNumber/>
    <edition/>
    <issue>43</issue>
    <volume>22</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements</title>
    <parentTitle language="eng">Chem. Eur. J.</parentTitle>
    <identifier type="doi">10.1002/chem.201603098</identifier>
    <note>Has been announced under the title: Cooperativity in Multivalent Binding: A Detailed Experimental and Theoretical Thermochemical Study of Divalent Crown Ether-Ammonium Complexes</note>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Larissa K. S. Krebek, von</author>
    <submitter>Regine Kossick</submitter>
    <author>Andreas J. Achazi</author>
    <author>Marthe Solleder</author>
    <author>Marcus Weber</author>
    <author>Beate Paulus</author>
    <author>Christoph A. Schalley</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>5879</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>poster</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales</title>
    <abstract language="eng">Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects.&#13;
&#13;
The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function.&#13;
&#13;
The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models.</abstract>
    <parentTitle language="eng">Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany</parentTitle>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Stefan Bojarovski</author>
    <submitter>Hans-Christian Hege</submitter>
    <author>Hans-Christian Hege</author>
    <author>Han Cheng Lie</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="projects" number="TopoMol">TopoMol</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5794</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1319</pageFirst>
    <pageLast>1340</pageLast>
    <pageNumber/>
    <edition/>
    <issue>4</issue>
    <volume>14</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Finding dominant structures of nonreversible Markov processes</title>
    <parentTitle language="eng">Multiscale Modeling and Simulation</parentTitle>
    <identifier type="doi">10.1137/15M1032272</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-55739</enrichment>
    <author>Natasa Djurdjevac Conrad</author>
    <submitter>Regine Kossick</submitter>
    <author>Marcus Weber</author>
    <author>Christof Schütte</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="MODAL-MedLab">MODAL-MedLab</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
    <collection role="persons" number="natasa.conrad">Conrad, Natasa</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
  </doc>
  <doc>
    <id>5662</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2015-11-26</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Estimating exit rates in rare event dynamical systems via extrapolation</title>
    <abstract language="eng">In this article we present a new idea for approximating exit rates for diffusion processes living in a craggy landscape. We are especially interested in the exit rates of a process living in a metastable regions. Due to the fact that Monte Carlo simulations perform quite poor and are very computational expensive in this setting we create several similar situations with a smoothed potential. For this we introduce a new parameter $\lambda \in [0,1]$ ($\lambda = 1$ very smoothed potential, $\lambda=0$ original potential) into the potential which controls the influence the smoothing. We then sample the exit rate for different parameters $\lambda$ the exit rate from a given region. Due to the fact that $\lambda$ is connected to the exit rate we can use this dependency to approximate the real exit rate. The method can be seen as something between hyperdynamics and temperature accelerated MC.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-56622</identifier>
    <author>Marcus Weber</author>
    <submitter>Jannes Quer</submitter>
    <author>Jannes Quer</author>
    <series>
      <title>ZIB-Report</title>
      <number>15-54</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>rare event sampling, smoothing, membership functions, perturbed potential</value>
    </subject>
    <collection role="ccs" number="G.3">PROBABILITY AND STATISTICS</collection>
    <collection role="pacs" number="31.00.00">Electronic structure of atoms and molecules: theory</collection>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="82-XX">STATISTICAL MECHANICS, STRUCTURE OF MATTER</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
    <collection role="persons" number="quer">Quer, jannes</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5662/Homotopy.pdf</file>
    <file>https://opus4.kobv.de/opus4-zib/files/5662/ConExitTimes-2.pdf</file>
  </doc>
  <doc>
    <id>5594</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>264</pageFirst>
    <pageLast>267</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>3/15</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix</title>
    <parentTitle language="deu">KA Korrespondenz Abwasser, Abfall</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Vedat Durmaz</author>
    <submitter>Marcus Weber</submitter>
    <author>Marcus Weber</author>
    <author> Meyer</author>
    <author> Mückter</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>5593</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>837</pageFirst>
    <pageLast>847</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>11</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands</title>
    <parentTitle language="eng">Beilstein J. Org. Chem.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author> Koschek</author>
    <submitter>Marcus Weber</submitter>
    <author>Vedat Durmaz</author>
    <author> Krylova</author>
    <author> Wieczorek</author>
    <author>Pooja Gupta</author>
    <author> Richter</author>
    <author>Alexander Bujotzek</author>
    <author> Fischer</author>
    <author>Rainer Haag</author>
    <author> Freund</author>
    <author>Marcus Weber</author>
    <author> Rademann</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>5592</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>2157</pageFirst>
    <pageLast>2166</pageLast>
    <pageNumber/>
    <edition/>
    <issue>10</issue>
    <volume>2015</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">High affinity flourescence labelled ligands for the estrogen receptor</title>
    <parentTitle language="eng">Eur. J. Org. Chem.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Frank Abendroth</author>
    <submitter>Marcus Weber</submitter>
    <author>Marthe Solleder</author>
    <author>Pia Welker</author>
    <author>Kai Licha</author>
    <author>Marcus Weber</author>
    <author>Oliver Seitz</author>
    <author>Dorothea Mangoldt</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>5573</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2015-08-19</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Finding dominant structures of nonreversible Markov processes</title>
    <abstract language="eng">Finding metastable sets as dominant structures of Markov processes has been shown to be especially useful in modeling interesting slow dynamics of various real world complex processes. Furthermore, coarse graining of such processes based on their dominant structures leads to better understanding and dimension reduction of observed systems. However, in many cases, e.g. for nonreversible Markov processes, dominant structures are often not formed by metastable sets but by important cycles or mixture of both. This paper aims at understanding and identifying these different types of dominant structures for reversible as well as nonreversible ergodic Markov processes. Our algorithmic approach generalizes spectral based methods for reversible process by using Schur decomposition techniques which can tackle also nonreversible cases. We illustrate the mathematical construction of our new approach by numerical experiments.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-55739</identifier>
    <identifier type="doi">10.1137/15M1032272</identifier>
    <enrichment key="SourceTitle">Appeared in: Multiscale Modeling and Simulation 14(4): 1319-1340</enrichment>
    <author>Natasa Djurdjevac Conrad</author>
    <submitter>Erlinda Koernig</submitter>
    <author>Marcus Weber</author>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>15-40</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>nonreversible Markov processes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metastable sets</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cycle decomposition</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Schur decomposition</value>
    </subject>
    <collection role="msc" number="60J20">Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) [See also 90B30, 91D10, 91D35, 91E40]</collection>
    <collection role="msc" number="65C40">Computational Markov chains</collection>
    <collection role="msc" number="82C26">Dynamic and nonequilibrium phase transitions (general)</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
    <collection role="persons" number="natasa.conrad">Conrad, Natasa</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5573/ZIB-Report_15-40.pdf</file>
  </doc>
  <doc>
    <id>5550</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">G-PCCA: Spectral Clustering for Non-reversible Markov Chains</title>
    <abstract language="eng">Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We extend this spectral clustering method also to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension, non-reversible Markov chains can be analyzed. Furthermore, the chains need not have a positive stationary distribution. And additionally to metastabilities, dominant cycles and sinks can be identified, too.</abstract>
    <identifier type="urn">urn:nbn:de:0297-zib-55505</identifier>
    <author>Marcus Weber</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Konstantin Fackeldey</author>
    <series>
      <title>ZIB-Report</title>
      <number>15-35</number>
    </series>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5550/ZR-15-35.pdf</file>
  </doc>
  <doc>
    <id>5428</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>234</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>5</issue>
    <volume>5</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters</title>
    <parentTitle language="eng">J Nanomed Nanotechnol</parentTitle>
    <identifier type="doi">10.4172/2157-7439.1000234</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Marcus Weber</author>
    <submitter>Marcus Weber</submitter>
    <author>Christian Zoschke</author>
    <author>Amir Sedighi</author>
    <author>Emanuel Fleige</author>
    <author>Rainer Haag</author>
    <author>Monika Schäfer-Korting</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
  </doc>
  <doc>
    <id>5330</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>483</pageFirst>
    <pageLast>499</pageLast>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>22</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computing the nearest reversible Markov chain</title>
    <abstract language="eng">Reversible Markov chains are the basis of many applications. However, computing transition probabilities by a finite sampling of a Markov chain can lead to truncation errors. Even if the original Markov chain is reversible, the approximated Markov chain might be non-reversible and will lose important properties, like the real valued spectrum. In this paper, we show how to find the closest reversible Markov chain to a given transition matrix. It turns out that this matrix can be computed by solving a convex minimization problem.</abstract>
    <parentTitle language="eng">Numerical Linear Algebra with Applications</parentTitle>
    <identifier type="doi">10.1002/nla.1967</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-53292</enrichment>
    <author>Adam Nielsen</author>
    <submitter>Adam Nielsen</submitter>
    <author>Marcus Weber</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Reversible Markov Chain</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Convex Optimization</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>MSM</value>
    </subject>
    <collection role="msc" number="15-XX">LINEAR AND MULTILINEAR ALGEBRA; MATRIX THEORY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
  </doc>
  <doc>
    <id>5329</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2014-12-10</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computing the nearest reversible Markov chain</title>
    <abstract language="eng">Reversible Markov chains are the basis of many applications. However, computing transition probabilities by a finite sampling of a Markov chain can lead to truncation errors. Even if the original Markov chain is reversible, the approximated Markov chain might be non-reversible and will lose important properties, like the real valued spectrum. In this paper, we show how to find the closest reversible Markov chain to a given transition matrix. It turns out that this matrix can be computed by solving a convex minimization problem.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-53292</identifier>
    <author>Adam Nielsen</author>
    <submitter>Adam Nielsen</submitter>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>14-48</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Reversible Markov Chain</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Convex Optimization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>MSM</value>
    </subject>
    <collection role="msc" number="15-XX">LINEAR AND MULTILINEAR ALGEBRA; MATRIX THEORY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5329/ZR-14-48.pdf</file>
  </doc>
  <doc>
    <id>5233</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>26</pageFirst>
    <pageLast>28</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>1</volume>
    <type>incollection</type>
    <publisherName>European Mathematical Society</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mathematics without pain</title>
    <parentTitle language="eng">MATHEON-Mathematics for Key Technologies</parentTitle>
    <identifier type="doi">10.4171/137</identifier>
    <enrichment key="Series">Series in Industrial and Applied Mathematics</enrichment>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Peter Deuflhard</author>
    <editor>Peter Deuflhard</editor>
    <submitter>Erlinda Körnig</submitter>
    <author>Marcus Weber</author>
    <editor>Martin Grötschel</editor>
    <editor>Dietmar Hömberg</editor>
    <editor>Ulrich Horst</editor>
    <editor>Jürg Kramer</editor>
    <editor>Volker Mehrmann</editor>
    <editor>Konrad Polthier</editor>
    <editor>Frank Schmidt</editor>
    <editor>Martin Skutella</editor>
    <editor>Jürgen Sprekels</editor>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="deuflhard">Deuflhard, Peter</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
  </doc>
  <doc>
    <id>5173</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>318</pageFirst>
    <pageLast>334</pageLast>
    <pageNumber/>
    <edition/>
    <issue>1</issue>
    <volume>12</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computing the Minimal Rebinding Effect Included in a Given Kinetics</title>
    <abstract language="eng">The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing ''intermediate'' bound states. This allows us to define an indicator for the magnitude of rebinding and to formulate an optimization problem. The results form our examples show good agreement with data form laboratory.</abstract>
    <parentTitle language="eng">Multiscale Model. Simul.</parentTitle>
    <identifier type="doi">10.1137/13091124X</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-17796</enrichment>
    <author>Marcus Weber</author>
    <submitter>Adam Nielsen</submitter>
    <author>Konstantin Fackeldey</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>5172</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>102</pageFirst>
    <pageLast>111</pageLast>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>2</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Investigation of the Ergopeptide Epimerization Process</title>
    <abstract language="eng">Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that “folding” the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations.</abstract>
    <parentTitle language="eng">Computation</parentTitle>
    <identifier type="doi">10.3390/computation2030102</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Karsten Andrae</author>
    <submitter>Adam Nielsen</submitter>
    <author>Stefan Merkel</author>
    <author>Vedat Durmaz</author>
    <author>Konstantin Fackeldey</author>
    <author>Robert Köppen</author>
    <author>Marcus Weber</author>
    <author>Matthias Koch</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BAM-Ergoline">BAM-Ergoline</collection>
  </doc>
  <doc>
    <id>5167</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>A2654</pageFirst>
    <pageLast>A2672</pageLast>
    <pageNumber/>
    <edition/>
    <issue>6</issue>
    <volume>36</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Applications of the cross-entropy method to importance sampling and optimal control of diffusions</title>
    <parentTitle language="eng">Siam Journal on Scientific Computing</parentTitle>
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    <title language="eng">Markov State Models and Molecular Alchemy</title>
    <abstract language="deu">In recent years Markov State Models (MSMs) have attracted a consid-&#13;
erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic experiments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multivalent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular properties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con-&#13;
sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective energy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed.</abstract>
    <parentTitle language="eng">Molecular Physics</parentTitle>
    <identifier type="doi">10.1080/00268976.2014.944597</identifier>
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    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-46718</enrichment>
    <author>Christof Schütte</author>
    <submitter>Erlinda Körnig</submitter>
    <author>Adam Nielsen</author>
    <author>Marcus Weber</author>
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      <language>eng</language>
      <type>uncontrolled</type>
      <value>MSM</value>
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    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Reweighting</value>
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    <subject>
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      <type>uncontrolled</type>
      <value>Girsanov</value>
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    <parentTitle language="eng">MATHEON-Mathematics for Key Technologies</parentTitle>
    <enrichment key="Series">Series in Industrial and Applied Mathematics</enrichment>
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    <author>Christof Schütte</author>
    <editor>Peter Deuflhard</editor>
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    <editor>Volker Mehrmann</editor>
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    <editor>Frank Schmidt</editor>
    <editor>Christof Schütte</editor>
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    <title language="eng">Applications of the cross-entropy method to importance sampling and optimal control of diffusions</title>
    <abstract language="eng">We study the cross-entropy method for diffusions. One of the results is a versatile cross-entropy algorithm that can be used to design efficient importance sampling strategies for rare events or to solve optimal control problems. The approach is based on the minimization of a suitable cross-entropy functional, with a parametric family of exponentially tilted probability distributions. We illustrate the new algorithm with several numerical examples and discuss algorithmic issues and possible extensions of the method.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-49720</identifier>
    <identifier type="doi">10.1137/14096493X</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SourceTitle">Appeared in: Siam Journal on Scientific Computing 36 (2014) A 2654-A2672</enrichment>
    <author>Wei Zhang</author>
    <submitter>Erlinda Körnig</submitter>
    <author>Han Wang</author>
    <author>Carsten Hartmann</author>
    <author>Marcus Weber</author>
    <author>Christof Schütte</author>
    <series>
      <title>ZIB-Report</title>
      <number>14-10</number>
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    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>important sampling</value>
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    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>optimal control</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cross-entropy method</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>rare events</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>change of measure</value>
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    <title language="eng">Markov State Models and Molecular Alchemy</title>
    <abstract language="deu">In recent years Markov State Models (MSMs) have attracted a consid-&#13;
erable amount of attention with regard to modelling conformation changes&#13;
and associated function of biomolecular systems. They have been used&#13;
successfully, e.g., for peptides including time-resolved spectroscopic ex-&#13;
periments, protein function and protein folding , DNA and RNA, and&#13;
ligand-receptor interaction in drug design and more complicated multi-&#13;
valent scenarios. In this article a novel reweighting scheme is introduced&#13;
that allows to construct an MSM for certain molecular system out of an&#13;
MSM for a similar system. This permits studying how molecular proper-&#13;
ties on long timescales differ between similar molecular systems without&#13;
performing full molecular dynamics simulations for each system under con-&#13;
sideration. The performance of the reweighting scheme is illustrated for&#13;
simple test cases including one where the main wells of the respective en-&#13;
ergy landscapes are located differently and an alchemical transformation&#13;
of butane to pentane where the dimension of the state space is changed.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-46718</identifier>
    <identifier type="doi">10.1080/00268976.2014.944597</identifier>
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    <author>Christof Schütte</author>
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    <author>Adam Nielsen</author>
    <author>Marcus Weber</author>
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      <title>ZIB-Report</title>
      <number>14-05</number>
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    <subject>
      <language>deu</language>
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      <value>Girsanov Theorem</value>
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      <type>uncontrolled</type>
      <value>Stochastic Differential Equation</value>
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      <value>Importance Sampling</value>
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    <enrichment key="PeerReviewed">yes</enrichment>
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    <title language="eng">Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding</title>
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    <author>Min Shan</author>
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    <enrichment key="FulltextUrl">http://pubs.acs.org/doi/abs/10.1021/cb3006243</enrichment>
    <author>Min Shan</author>
    <submitter>Adam Nielsen</submitter>
    <author>Kathryn E. Carlson</author>
    <author>Alexander Bujotzek</author>
    <author>Anja Wellner</author>
    <author>Ronald Gust</author>
    <author>Marcus Weber</author>
    <author>John A. Katzenellenbogen</author>
    <author>Rainer Haag</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>4649</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>12307</pageFirst>
    <pageLast>12317</pageLast>
    <pageNumber/>
    <edition/>
    <issue>23</issue>
    <volume>117</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles</title>
    <parentTitle language="eng">J. Phys. Chem. C</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Rahul Tyagi</author>
    <submitter>Adam Nielsen</submitter>
    <author>Shashwat Malhotra</author>
    <author>Andreas F. Thünemann</author>
    <author>Amir Sedighi</author>
    <author>Marcus Weber</author>
    <author>Andreas Schäfer</author>
    <author>Rainer Haag</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>4648</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>2681</pageFirst>
    <pageLast>2688</pageLast>
    <pageNumber/>
    <edition/>
    <issue>10</issue>
    <volume>53</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens</title>
    <parentTitle language="eng">Journal of Chemical Information and Modeling</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="FulltextUrl">http://pubs.acs.org/doi/abs/10.1021/ci400392p</enrichment>
    <author>Vedat Durmaz</author>
    <submitter>Adam Nielsen</submitter>
    <author>Sebastian Schmidt</author>
    <author>Peggy Sabri</author>
    <author>Christian Piechotta</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BAM-Becker">BAM-Becker</collection>
    <collection role="projects" number="BAM-glycosidases">BAM-glycosidases</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>4639</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2014-03-25</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane</title>
    <parentTitle language="eng">Molecular Simulation</parentTitle>
    <identifier type="doi">10.1080/08927022.2014.898845</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <submitter>Adam Nielsen</submitter>
    <author>Olga Scharkoi</author>
    <author>Susanne Esslinger</author>
    <author>Roland Becker</author>
    <author>Marcus Weber</author>
    <author>Irene Nehls</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BAM-Becker">BAM-Becker</collection>
    <collection role="projects" number="BAM-glycosidases">BAM-glycosidases</collection>
    <collection role="projects" number="BB3R">BB3R</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>4647</id>
    <completedYear/>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>730</pageFirst>
    <pageLast>733</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>73</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites</title>
    <parentTitle language="deu">Organohalogen Compounds</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="FulltextUrl">http://www.dioxin20xx.org/pdfs/2011/1810.pdf</enrichment>
    <author>O. Scharkoi</author>
    <submitter>Adam Nielsen</submitter>
    <author>Susanne Esslinger</author>
    <author>Roland Becker</author>
    <author>Marcus Weber</author>
    <author>Irene Nehls</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>4645</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>561</pageFirst>
    <pageLast>557</pageLast>
    <pageNumber/>
    <edition/>
    <issue>7</issue>
    <volume>62</volume>
    <type>article</type>
    <publisherName>Springer</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Medizin aus dem Computer</title>
    <parentTitle language="deu">Der Anaesthesist</parentTitle>
    <identifier type="doi">10.1007/s00101-013-2202-x</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Karsten Andrae</author>
    <submitter>Adam Nielsen</submitter>
    <author>Vedat Durmaz</author>
    <author>Konstantin Fackeldey</author>
    <author>Olga Scharkoi</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="durmaz">Durmaz, Vedat</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="TransRisk">TransRisk</collection>
  </doc>
  <doc>
    <id>4640</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>110</pageFirst>
    <pageLast>194</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>139</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Adaptive spectral clustering with application to tripeptide conformation analysis</title>
    <parentTitle language="eng">The Journal of Chemical Physics</parentTitle>
    <identifier type="doi">10.1063/1.4830409</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Fiete Haack</author>
    <submitter>Adam Nielsen</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Susanna Röblitz</author>
    <author>Olga Scharkoi</author>
    <author>Marcus Weber</author>
    <author>Burkhard Schmidt</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
  </doc>
  <doc>
    <id>4614</id>
    <completedYear/>
    <publishedYear>2009</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>73</pageFirst>
    <pageLast>79</pageLast>
    <pageNumber/>
    <edition/>
    <issue>WIAS Report No. 26</issue>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Fuzzy Spectral Clustering by PCCA+</title>
    <parentTitle language="eng">Classification and Clustering: Models, Software and Applications</parentTitle>
    <identifier type="url">http://www.wias-berlin.de/publications/wias-publ/run.jsp?template=abstract&amp;type=Report&amp;year=2009&amp;number=26</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Susanna Röblitz</author>
    <submitter> Stötzel</submitter>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>4583</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>147</pageFirst>
    <pageLast>179</pageLast>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume>7</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification</title>
    <parentTitle language="eng">Advances in Data Analysis and Classification</parentTitle>
    <identifier type="doi">10.1007/s11634-013-0134-6</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Susanna Röblitz</author>
    <submitter> Stötzel</submitter>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
  </doc>
  <doc>
    <id>4316</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-11-26</completedDate>
    <publishedDate>2013-11-26</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">On a Generalized Transfer Operator</title>
    <abstract language="eng">We introduce a generalized operator for arbitrary stochastic processes by using a pre-kernel, which is a generalization of the Markov kernel. For deterministic processes, such an operator is already known as the Frobenius-Perron operator, which is defined for a large class of measures. For Markov processes, there exists transfer operators being only well defined for stationary measures in $L^2$. Our novel generalized transfer operator is well defined for arbitrary stochastic processes, in particular also for deterministic ones. We can show that this operator is acting on $L^1$. For stationary measures, this operator is also an endomorphism of $L^2$ and, therefore, allows for a mathematical analysis in Hilbert spaces.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-43162</identifier>
    <author>Adam Nielsen</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-74</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Transfer Operator</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Pre Kernel</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Perron Frobenius Generalization</value>
    </subject>
    <collection role="ccs" number="">Stochastic processes (NEW)</collection>
    <collection role="pacs" number="31.00.00">Electronic structure of atoms and molecules: theory</collection>
    <collection role="msc" number="37-XX">DYNAMICAL SYSTEMS AND ERGODIC THEORY [See also 26A18, 28Dxx, 34Cxx, 34Dxx, 35Bxx, 46Lxx, 58Jxx, 70-XX]</collection>
    <collection role="msc" number="47N30">Applications in probability theory and statistics</collection>
    <collection role="msc" number="60Gxx">Stochastic processes</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4316/NFW_13.pdf</file>
  </doc>
  <doc>
    <id>4257</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-09-27</completedDate>
    <publishedDate>2013-09-27</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Conformational Analysis by Partition-of-Unity Coupling</title>
    <abstract language="eng">Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.</abstract>
    <parentTitle language="eng">Math Chem</parentTitle>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42570</identifier>
    <author>Alexander Bujotzek</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Ole Schütt</author>
    <author>Adam Nielsen</author>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-58</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov State Models</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Meshfree</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Molecular Simulation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Partition of Unity</value>
    </subject>
    <collection role="ccs" number="G.4">MATHEMATICAL SOFTWARE</collection>
    <collection role="ccs" number="">Markov processes (NEW)</collection>
    <collection role="pacs" number="87.10.-e">General theory and mathematical aspects</collection>
    <collection role="msc" number="60Jxx">Markov processes</collection>
    <collection role="msc" number="92-08">Computational methods</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="MIP_FORMATION">MIP_FORMATION</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</collection>
    <collection role="projects" number="Salsa-Klimm">Salsa-Klimm</collection>
    <collection role="projects" number="SFB1114-A5">SFB1114-A5</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/4257/MolPyPUM.pdf</file>
  </doc>
  <doc>
    <id>4219</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-08-28</completedDate>
    <publishedDate>2013-08-28</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A square root approximation of transition rates for a Markov State Model</title>
    <abstract language="eng">Trajectory- or mesh-based methods for analyzing the dynamical behavior of large molecules tend to be impractical due to the curse of dimensionality - their computational cost increases exponentially with the size of the molecule. We propose a method to break the curse by a novel square root approximation of transition rates, Monte Carlo quadrature and a discretization approach based on solving linear programs. With randomly sampled points on the molecular energy landscape and randomly generated discretizations of the molecular configuration space as our initial data, we construct a matrix describing the transition rates between adjacent discretization regions. This transition rate matrix yields a Markov State Model of the molecular dynamics. We use Perron cluster analysis and coarse-graining techniques in order to identify metastable sets in configuration space and approximate the transition rates between the metastable sets. Application of our method to a simple energy landscape on a two-dimensional configuration space provides proof of concept and an example for which we compare the performance of different discretizations. We show that the computational cost of our method grows only polynomially with the size of the molecule. However, finding discretizations of higher-dimensional configuration spaces in which metastable sets can be identified remains a challenge.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="doi">10.1137/120899959</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42195</identifier>
    <enrichment key="SourceTitle">Appeared in: SIAM J. Matrix Anal. Appl. 34 (2013) pp. 738 - 756</enrichment>
    <author>Han Cheng Lie</author>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-43</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov State Models</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Markov chains</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>meshfree methods</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metastability</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Voronoi</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>linear programming</value>
    </subject>
    <collection role="ccs" number="G.">Mathematics of Computing</collection>
    <collection role="pacs" number="30.00.00">ATOMIC AND MOLECULAR PHYSICS</collection>
    <collection role="msc" number="60J10">Markov chains (discrete-time Markov processes on discrete state spaces)</collection>
    <collection role="msc" number="60J22">Computational methods in Markov chains [See also 65C40]</collection>
    <collection role="msc" number="82B80">Numerical methods (Monte Carlo, series resummation, etc.) [See also 65-XX, 81T80]</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
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    <pageFirst>1947</pageFirst>
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    <author>Susanna Kube</author>
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    <author>Susanna Kube</author>
    <author>Lionel Walter</author>
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