@article{AbendrothSollederWelkeretal.2015, author = {Abendroth, Frank and Solleder, Marthe and Welker, Pia and Licha, Kai and Weber, Marcus and Seitz, Oliver and Mangoldt, Dorothea}, title = {High affinity flourescence labelled ligands for the estrogen receptor}, volume = {2015}, journal = {Eur. J. Org. Chem.}, number = {10}, pages = {2157 -- 2166}, year = {2015}, language = {en} } @article{WeberZoschkeSedighietal.2014, author = {Weber, Marcus and Zoschke, Christian and Sedighi, Amir and Fleige, Emanuel and Haag, Rainer and Sch{\"a}fer-Korting, Monika}, title = {Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters}, volume = {5}, journal = {J Nanomed Nanotechnol}, number = {5}, doi = {10.4172/2157-7439.1000234}, pages = {234}, year = {2014}, language = {en} } @misc{SteinWeberZoellneretal.2013, author = {Stein, Christoph and Weber, Marcus and Z{\"o}llner, Christian and Scharkoi, Olga}, title = {Fentanyl derivatives as pH-dependent opioid receptor agonists}, journal = {European Patent Application, Bulletin 2013/08}, year = {2013}, language = {en} } @misc{SteinWeberScharkoietal.2013, author = {Stein, Christoph and Weber, Marcus and Scharkoi, Olga and Deuflhard, Peter}, title = {Method and system for identifying compounds that bind and preferably activate a target opioid receptor in a pH-dependent manner}, journal = {European Patent Application, Bulletin 2013/28}, year = {2013}, language = {en} } @article{ZhangWangHartmannetal.2014, author = {Zhang, Wei and Wang, Han and Hartmann, Carsten and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Applications of the cross-entropy method to importance sampling and optimal control of diffusions}, volume = {36}, journal = {Siam Journal on Scientific Computing}, number = {6}, doi = {10.1137/14096493X}, pages = {A2654 -- A2672}, year = {2014}, language = {en} } @article{AndraeMerkelDurmazetal.2014, author = {Andrae, Karsten and Merkel, Stefan and Durmaz, Vedat and Fackeldey, Konstantin and K{\"o}ppen, Robert and Weber, Marcus and Koch, Matthias}, title = {Investigation of the Ergopeptide Epimerization Process}, volume = {2}, journal = {Computation}, number = {3}, doi = {10.3390/computation2030102}, pages = {102 -- 111}, year = {2014}, abstract = {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.}, language = {en} } @misc{DeuflhardWeber2014, author = {Deuflhard, Peter and Weber, Marcus}, title = {Mathematics without pain}, volume = {1}, journal = {MATHEON-Mathematics for Key Technologies}, editor = {Deuflhard, Peter and Gr{\"o}tschel, Martin and H{\"o}mberg, Dietmar and Horst, Ulrich and Kramer, J{\"u}rg and Mehrmann, Volker and Polthier, Konrad and Schmidt, Frank and Skutella, Martin and Sprekels, J{\"u}rgen}, publisher = {European Mathematical Society}, doi = {10.4171/137}, pages = {26 -- 28}, year = {2014}, language = {en} } @article{SchuetteNielsenWeber2015, author = {Sch{\"u}tte, Christof and Nielsen, Adam and Weber, Marcus}, title = {Markov State Models and Molecular Alchemy}, volume = {113}, journal = {Molecular Physics}, number = {1}, doi = {10.1080/00268976.2014.944597}, pages = {69 -- 78}, year = {2015}, abstract = {In recent years Markov State Models (MSMs) have attracted a consid- 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- 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.}, language = {en} } @article{WeberFackeldey2014, author = {Weber, Marcus and Fackeldey, Konstantin}, title = {Computing the Minimal Rebinding Effect Included in a Given Kinetics}, volume = {12}, journal = {Multiscale Model. Simul.}, number = {1}, doi = {10.1137/13091124X}, pages = {318 -- 334}, year = {2014}, abstract = {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.}, language = {en} } @masterthesis{Solleder2014, type = {Bachelor Thesis}, author = {Solleder, Marthe}, title = {Bewertung von Transformationsprodukten im Wasserkreislauf durch Computersimulationen}, year = {2014}, language = {de} } @masterthesis{Schmiedel2013, type = {Bachelor Thesis}, author = {Schmiedel, Jessica}, title = {Singul{\"a}rwertzerlegung mit Zufallsalgorithmen}, year = {2013}, language = {de} } @masterthesis{Toudic2013, type = {Bachelor Thesis}, author = {Toudic, Remi}, title = {Confjump: A method for biomolecular sampling}, year = {2013}, language = {de} } @misc{Pommer2013, type = {Master Thesis}, author = {Pommer, Daniel}, title = {Konditionsverbesserung von Markov-Modellen}, year = {2013}, language = {de} } @misc{Riesland2012, type = {Master Thesis}, author = {Riesland, Mark Daniel}, title = {Anwendbarkeit von Thermostaten in der molek{\"u}ldynamischen Simulation}, year = {2012}, language = {de} } @masterthesis{Jeschke2012, type = {Bachelor Thesis}, author = {Jeschke, Bj{\"o}rn-Marcel}, title = {Spezielle Eigenschaften von Simulated Annealing}, year = {2012}, language = {de} } @misc{Josten2012, type = {Master Thesis}, author = {Josten, Jan-Martin}, title = {{\"O}strogenit{\"a}ts-Approximation mittels physikochemischem Oberfl{\"a}chenvergleich}, year = {2012}, language = {de} } @misc{Lie2012, type = {Master Thesis}, author = {Lie, Han Cheng}, title = {A Meshless Method for Conformational Analysis}, year = {2012}, language = {en} } @misc{Haack2009, type = {Master Thesis}, author = {Haack, Fiete}, title = {Representative Spectral Clustering for Large Data Sets applied to Gene Expression Data}, year = {2009}, language = {en} } @misc{NielsenWeber2014, author = {Nielsen, Adam and Weber, Marcus}, title = {Computing the nearest reversible Markov chain}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53292}, year = {2014}, abstract = {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.}, language = {en} } @article{NielsenWeber2015, author = {Nielsen, Adam and Weber, Marcus}, title = {Computing the nearest reversible Markov chain}, volume = {22}, journal = {Numerical Linear Algebra with Applications}, number = {3}, doi = {10.1002/nla.1967}, pages = {483 -- 499}, year = {2015}, abstract = {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.}, language = {en} } @article{WeberFackeldeySchuette2017, author = {Weber, Marcus and Fackeldey, Konstantin and Sch{\"u}tte, Christof}, title = {Set-Free Markov State Model Building}, volume = {146}, journal = {Journal of Chemical Physics}, number = {12}, doi = {10.1063/1.4978501}, year = {2017}, language = {en} } @article{QuerLie2017, author = {Quer, Jannes and Lie, Han Cheng}, title = {Some connections between importance sampling and enhanced sampling methods in molecular dynamics}, journal = {Journal of Chemical Physics}, year = {2017}, abstract = {Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Sch{\"u}tte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling.}, language = {en} } @article{FackeldeyNiknejadWeber2017, author = {Fackeldey, Konstantin and Niknejad, Amir and Weber, Marcus}, title = {Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation}, journal = {Special Matrices}, number = {5/1}, doi = {10.1515/spma-2017-0006}, pages = {73 -- 81}, year = {2017}, language = {en} } @article{FackeldeyWeber2017, author = {Fackeldey, Konstantin and Weber, Marcus}, title = {GenPCCA -- Markov State Models for Non-Equilibrium Steady States}, journal = {Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29}, doi = {10.20347/WIAS.REPORT.29}, pages = {70 -- 80}, year = {2017}, language = {en} } @inproceedings{FackeldeyBujotzek2014, author = {Fackeldey, Konstantin and Bujotzek, Alexander}, title = {Local Quantum-Like Updates in Classical Molecular Simulation Realized Within an Uncoupling-Coupling Approach}, volume = {19}, booktitle = {Progress in Industrial Mathematics at ECMI 2012}, doi = {10.1007/978-3-319-05365-3_42}, pages = {309 -- 313}, year = {2014}, abstract = {In this article a method to improve the precision of the classical molecular dynamics force field by solving an approximation problem with scattered quantum mechanical data is presented. This novel technique is based on two steps. In the first step a partition of unity scheme is used for partitioning the state space by meshfree basis functions. As a consequence the potential can be localized for each basis function. In a second step, for one state in each meshfree basis function, the precise QM-based charges are computed. These local QM-based charges are then used, to optimize the local potential function. The performance of this method is shown for the alanine tripeptide.}, language = {en} } @misc{SchuetteDeuflhardNoeetal.2014, author = {Sch{\"u}tte, Christof and Deuflhard, Peter and No{\´e}, Frank and Weber, Marcus}, title = {Design of functional molecules}, volume = {1}, journal = {MATHEON-Mathematics for Key Technologies}, editor = {Deuflhard, Peter and Gr{\"o}tschel, Martin and H{\"o}mberg, Dietmar and Horst, Ulrich and Kramer, J{\"u}rg and Mehrmann, Volker and Polthier, Konrad and Schmidt, Frank and Sch{\"u}tte, Christof and Skutella, Martin and Sprekels, J{\"u}rgen}, publisher = {European Mathematical Society}, pages = {49 -- 65}, year = {2014}, language = {en} } @phdthesis{Bujotzek2013, author = {Bujotzek, Alexander}, title = {Molecular Simulation of Multivalent Ligand-Receptor Systems}, year = {2013}, language = {en} } @misc{WeberQuer2015, author = {Weber, Marcus and Quer, Jannes}, title = {Estimating exit rates in rare event dynamical systems via extrapolation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56622}, year = {2015}, abstract = {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.}, language = {en} } @article{BujotzekSchuettNielsenetal.2014, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling}, volume = {52}, journal = {Journal of Mathematical Chemistry}, number = {3}, doi = {10.1007/s10910-013-0265-1}, pages = {781 -- 804}, year = {2014}, language = {de} } @article{WeberFackeldey2014, author = {Weber, Marcus and Fackeldey, Konstantin}, title = {Local Refinements in Classical Molecular Dynamics Simulations}, volume = {490}, journal = {J. Phys. Conf. Ser.}, pages = {012016}, year = {2014}, language = {en} } @book{DieterGoetzKuemmereretal.2010, author = {Dieter, H. H. and G{\"o}tz, K. and K{\"u}mmerer, K. and Rechenberg, B. and Keil, F.}, title = {Handlungsm{\"o}glichkeiten zur Minderung des Eintrags von Humanarzneimitteln und ihren R{\"u}ckst{\"a}nden in das Roh- und Trinkwasser.}, editor = {Dieter, H.H. and G{\"o}tz, K. and K{\"u}mmerer, K. and Rechenberg, B. and Keil, F.}, publisher = {Umweltbundesamt}, year = {2010}, language = {de} } @misc{SchuetteNielsenWeber2014, author = {Sch{\"u}tte, Christof and Nielsen, Adam and Weber, Marcus}, title = {Markov State Models and Molecular Alchemy}, issn = {1438-0064}, doi = {10.1080/00268976.2014.944597}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-46718}, year = {2014}, abstract = {In recent years Markov State Models (MSMs) have attracted a consid- 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 ex- periments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multi- valent 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 proper- ties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective en- ergy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed.}, language = {en} } @article{AndraeDurmazFackeldeyetal.2013, author = {Andrae, Karsten and Durmaz, Vedat and Fackeldey, Konstantin and Scharkoi, Olga and Weber, Marcus}, title = {Medizin aus dem Computer}, volume = {62}, journal = {Der Anaesthesist}, number = {7}, publisher = {Springer}, doi = {10.1007/s00101-013-2202-x}, pages = {561 -- 557}, year = {2013}, language = {de} } @article{ScharkoiEsslingerBeckeretal.2011, author = {Scharkoi, O. and Esslinger, Susanne and Becker, Roland and Weber, Marcus and Nehls, Irene}, title = {Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites}, volume = {73}, journal = {Organohalogen Compounds}, pages = {730 -- 733}, year = {2011}, language = {de} } @article{DurmazSchmidtSabrietal.2013, author = {Durmaz, Vedat and Schmidt, Sebastian and Sabri, Peggy and Piechotta, Christian and Weber, Marcus}, title = {A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens}, volume = {53}, journal = {Journal of Chemical Information and Modeling}, number = {10}, pages = {2681 -- 2688}, year = {2013}, language = {en} } @article{TyagiMalhotraThuenemannetal.2013, author = {Tyagi, Rahul and Malhotra, Shashwat and Th{\"u}nemann, Andreas F. and Sedighi, Amir and Weber, Marcus and Sch{\"a}fer, Andreas and Haag, Rainer}, title = {Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles}, volume = {117}, journal = {J. Phys. Chem. C}, number = {23}, pages = {12307 -- 12317}, year = {2013}, language = {de} } @article{ShanCarlsonBujotzeketal.2013, author = {Shan, Min and Carlson, Kathryn E. and Bujotzek, Alexander and Wellner, Anja and Gust, Ronald and Weber, Marcus and Katzenellenbogen, John A. and Haag, Rainer}, title = {Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor}, volume = {8}, journal = {ACS Chem. Biol.}, number = {4}, pages = {707 -- 715}, year = {2013}, language = {en} } @article{Weber2013, author = {Weber, Marcus}, title = {Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization}, journal = {XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series}, pages = {147 -- 157}, year = {2013}, language = {de} } @article{FackeldeyRoeblitzScharkoietal.2011, author = {Fackeldey, Konstantin and R{\"o}blitz, Susanna and Scharkoi, O. and Weber, Marcus}, title = {Soft Versus Hard Metastable Conformations in Molecular Simulations}, journal = {Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.)}, pages = {899 -- 909}, year = {2011}, language = {de} } @article{ShanBujotzekAbendrothetal.2011, author = {Shan, Min and Bujotzek, Alexander and Abendroth, Frank and Seitz, Oliver and Weber, Marcus and Haag, Rainer}, title = {Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding}, journal = {ChemBioChem, 12(17)}, doi = {10.1002/cbic.201100529}, pages = {2587 -- 2598}, year = {2011}, language = {en} } @misc{Fackeldey2010, author = {Fackeldey, Konstantin}, title = {Challenges in Atomistic-to-Continuum Coupling}, volume = {2010}, journal = {ZIB Report}, edition = {10-12}, doi = {10.1155/2015/834517}, year = {2010}, abstract = {This paper is concerned with the design, analysis, and implementation of concurrent coupling approaches where different (atomic and continuous) models are used simultaneously within a single simulation process. Thereby, several problems or pitfalls can happen, for example, the reflection of molecular movements at the "boundary" between the atomic and continuum regions which leads to an unphysical increase in energy in the atomic model. We investigate the problems with the aim of giving an introduction into this field and preventing errors for scientists starting their research towards multiscale methods.}, language = {en} } @article{Durmaz2015, author = {Durmaz, Vedat}, title = {Markov model-based polymer assembly from force field-parameterized building blocks}, volume = {29}, journal = {Journal of Computer-Aided Molecular Design}, doi = {10.1007/s10822-014-9817-0}, pages = {225 -- 232}, year = {2015}, abstract = {A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very workintensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantumchemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers.}, language = {en} } @article{HeyeBeckerLuetkeEverslohetal.2016, author = {Heye, Katharina and Becker, Dennis and L{\"u}tke-Eversloh, Christian and Durmaz, Vedat and Ternes, Thomas and Oetken, Matthias and Oehlmann, J{\"o}rg}, title = {Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test}, volume = {98}, journal = {Water Research}, pages = {19 -- 27}, year = {2016}, abstract = {The antiepileptic drug carbamazepine (CBZ) and its main metabolites carbamazepine-10,11-epoxide (EP-CBZ) and 10,11-dihydro-10,11-dihydroxy-carbamazepine (DiOH-CBZ) were chosen as test substances to assess chronic toxicity on the non-biting midge Chironomus riparius. All three substances were tested in a 40-day sediment full life cycle test (according to OECD 233) in which mortality, emergence, fertility, and clutch size were evaluated. In addition, these parameters were integrated into the population growth rate to reveal population relevant effects. With an LC50 of 0.203 mg/kg (time-weighted mean), the metabolite EP-CBZ was significantly more toxic than the parent substance CBZ (LC50: 1.11 mg/kg). Especially mortality, emergence, and fertility showed to be sensitive parameters under the exposure to CBZ and EP-CBZ. By using classical molecular dynamics (MD) simulations, the binding of CBZ to the ecdysone receptor was investigated as one possible mode of action but showed to be unlikely. The second metabolite DiOH-CBZ did not show any effects within the tested concentration rage (0.171 - 1.22 mg/kg). Even though CBZ was less toxic compared to EP-CBZ, CBZ is found in the environment at much higher concentrations and causes therefore a higher potential risk for sediment dwelling organisms compared to its metabolites. Nevertheless, the current study illustrates the importance of including commonly found metabolites into the risk assessment of parent substances.}, language = {en} } @article{DjurdjevacConradWeberSchuette2016, author = {Djurdjevac Conrad, Natasa and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Finding dominant structures of nonreversible Markov processes}, volume = {14}, journal = {Multiscale Modeling and Simulation}, number = {4}, doi = {10.1137/15M1032272}, pages = {1319 -- 1340}, year = {2016}, language = {en} } @misc{BojarovskiHegeLieetal.2015, author = {Bojarovski, Stefan and Hege, Hans-Christian and Lie, Han Cheng and Weber, Marcus}, title = {Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales}, journal = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, year = {2015}, abstract = {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. 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. 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.}, language = {en} } @article{KrebekvonAchaziSollederetal.2016, author = {Krebek, von, Larissa K. S. and Achazi, Andreas J. and Solleder, Marthe and Weber, Marcus and Paulus, Beate and Schalley, Christoph A.}, title = {Allosteric and Chelate Cooperativity in Divalent Crown Ether-Ammonium Complexes with Strong Binding Enhancements}, volume = {22}, journal = {Chem. Eur. J.}, number = {43}, doi = {10.1002/chem.201603098}, pages = {15475 -- 15484}, year = {2016}, language = {en} } @phdthesis{Fackeldey2015, author = {Fackeldey, Konstantin}, title = {Crossing the Scales in Structural Mechanics and Molecular Research}, year = {2015}, language = {en} } @misc{Brust2017, type = {Master Thesis}, author = {Brust, Lisa}, title = {Molek{\"u}ldynamik-Simulation via eines Faltungsansatzes im Potential}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65198}, year = {2017}, language = {de} } @misc{Roehl2017, type = {Master Thesis}, author = {R{\"o}hl, Susanne}, title = {Computing the minimal rebinding effect for nonreversible processes}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65203}, year = {2017}, language = {en} } @misc{Roehm2017, type = {Master Thesis}, author = {R{\"o}hm, Jonas}, title = {Non-Negative Matrix Factorization for Raman Data Spectral Analysis}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65217}, year = {2017}, language = {en} } @misc{Grever2016, type = {Master Thesis}, author = {Grever, Andreas}, title = {Estimating Missing Entries of a Partial Mean First Passage Time Matrix}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65228}, year = {2016}, language = {en} }