TY - GEN A1 - Weber, Marcus T1 - A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator N2 - Supercomputers can simulate complex molecular systems. However, there is a very large gap between the fastest oscillations of covalent bonds of a molecule and the time-scale of the dominant processes. In order to extract the dominant time-scales and to identify the dominant processes, a clustering of information is needed. This thesis shows that only the subspace-based Robust Perron Cluster Analysis (PCCA+) can solve this problem correctly by the construction of a Markov State Model. PCCA+ allows for time-extrapolation in molecular kinetics. This thesis shows the difference between molecular dynamics and molecular kinetics. Only in the molecular kinetics framework a definition of transition rates is possible. In this context, the existence of an infinitesimal generator of the dynamical processes is discussed. If the existence is assumed, the Theorem of Gauß can be applied in order to compute transition rates efficiently. Molecular dynamics, however, is not able to provide a suitable statistical basis for the determination of the transition pattern. T3 - ZIB-Report - 09-27 KW - Robuste Perron Cluster Analyse KW - Molekülkinetik KW - Übergangsraten KW - Robust Perron cluster analysis KW - molecular kinetics KW - transition rates Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11432 SN - 1438-0064 ER - TY - GEN A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Scharkoi, Olga A1 - Weber, Marcus T1 - Soft Versus Hard Metastable Conformations in Molecular Simulations N2 - Particle methods have become indispensible in conformation dynamics to compute transition rates in protein folding, binding processes and molecular design, to mention a few. Conformation dynamics requires at a decomposition of a molecule's position space into metastable conformations. In this paper, we show how this decomposition can be obtained via the design of either ``soft'' or ``hard'' molecular conformations. We show, that the soft approach results in a larger metastabilitiy of the decomposition and is thus more advantegous. This is illustrated by a simulation of Alanine Dipeptide. T3 - ZIB-Report - 11-27 KW - Proteins, Conformation Space, Meshfree Methods Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-13189 ER - TY - THES A1 - Weber, Marcus T1 - A Subspace Approach to Molecular Markov State Models via a New Infinitesimal Generator N2 - Supercomputers can simulate complex molecular systems. However, there is a very large gap between the fastest oscillations of covalent bonds of a molecule and the time-scale of the dominant processes. In order to extract the dominant time-scales and to identify the dominant processes, a clustering of information is needed. This thesis shows that only the subspace-based Robust Perron Cluster Analysis (PCCA+) can solve this problem correctly by the construction of a Markov State Model. PCCA+ allows for time-extrapolation in molecular kinetics. This thesis shows the difference between molecular dynamics and molecular kinetics. Only in the molecular kinetics framework a definition of transition rates is possible. In this context, the existence of an infinitesimal generator of the dynamical processes is discussed. If the existence is assumed, the Theorem of Gauß can be applied in order to compute transition rates efficiently. Molecular dynamics, however, is not able to provide a suitable statistical basis for the determination of the transition pattern. KW - Conformation Dynamics KW - Molecular Kinetics KW - Transition Rates KW - Markov State Models Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14025 ER - TY - GEN A1 - Weber, Marcus T1 - The funnel trap paradox N2 - In this article, an illustrative example is given for the coarse-graining of a Markov process which leads to a shift in the statistical weights of a two-states-system. The example is based on a 2D-funnel trap. The funnel trap is constructed in such a way, that the area inside and outside of the trap is identical. However, observing the flight of the insect as a Markov process, the probability for being “in the trap” is higher. This example can be transferred to several kinds of processes (like receptor-ligandbinding processes in chemistry) and describes the influence of “re-entering events”. T3 - ZIB-Report - 12-12 KW - Markov process KW - Robust Perron Cluster Analysis KW - Conformation Dynamics Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14765 SN - 1438-0064 ER - TY - GEN A1 - Fackeldey, Konstantin T1 - Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach N2 - In contrast to the well known meshbased methods like the finite element method, meshfree methods do not rely on a mesh. However besides their great applicability, meshfree methods are rather time consuming. Thus, it seems favorable to combine both methods, by using meshfree methods only in a small part of the domain, where a mesh is disadvantageous, and a meshbased method for the rest of the domain. We motivate, that this coupling between the two simulation techniques can be considered as saddle point problem and show the stability of this coupling. Thereby a novel transfer operator is introduced, which interacts in the transition zone, where both methods coexist. T3 - ZIB-Report - 10-12 KW - Gitterlose Methoden KW - inf-sup-Bedingung KW - Kopplung KW - meshfree KW - meshbased KW - inf-sup-Condition Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11755 SN - 1438-0064 ER - TY - GEN A1 - Tunga, Burcu A1 - Weber, Marcus T1 - Free Energy Calculation Using Mayer Cluster Expansion and Fluctuation Free Integration N2 - This work aims to develop a new algorithm to calculate the free energy of water molecules by using a deterministic way. For this purpose, we assume a closed system confined to a physical volume, having water molecules in gas phase. To calculate the free energy of this sytem we utilized Mayer cluster expansion and the fluctuation free integration method. T3 - ZIB-Report - 12-35 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16031 SN - 1438-0064 ER - TY - GEN A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Computing the Minimal Rebinding Effect Included in a Given Kinetics N2 - 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. T3 - ZIB-Report - 13-12 KW - Rebinding KW - Molecular Kinetics KW - Conformation Dynamics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17796 SN - 1438-0064 ER - TY - GEN A1 - Lie, Han Cheng A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - A square root approximation of transition rates for a Markov State Model N2 - 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. T3 - ZIB-Report - 13-43 KW - Markov State Models KW - Markov chains KW - meshfree methods KW - metastability KW - Voronoi KW - linear programming Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42195 SN - 1438-0064 ER - TY - GEN A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - On a Generalized Transfer Operator N2 - 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. T3 - ZIB-Report - 13-74 KW - Transfer Operator KW - Pre Kernel KW - Perron Frobenius Generalization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43162 SN - 1438-0064 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Koltai, Peter A1 - Nevir, Peter A1 - Rust, Henning A1 - Schild, Axel A1 - Weber, Marcus T1 - From metastable to coherent sets - Time-discretization schemes JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1063/1.5058128 VL - 29 SP - 012101 EP - 012101 ER - TY - JOUR A1 - Abbas, Aennes A1 - Schneider, Ilona A1 - Bollmann, Anna A1 - Funke, Jan A1 - Oehlmann, Jörg A1 - Prasse, Carsten A1 - Schulte-Oehlmann, Ulrike A1 - Seitz, Wolfram A1 - Ternes, Thomas A1 - Weber, Marcus A1 - Wesely, Henning A1 - Wagner, Martin T1 - What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays JF - Water Research N2 - 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. 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. 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. 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. Y1 - 2019 U6 - https://doi.org/10.1016/j.watres.2018.12.049 VL - 152 SP - 47 EP - 60 ER - TY - THES A1 - Helfmann, Luzie T1 - Stochastic Modeling of Interacting Agent Systems Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71887 ER - TY - JOUR A1 - Reuter, Bernhard A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Generalized Markov modeling of nonreversible molecular kinetics JF - The Journal of Chemical Physics N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1063/1.5064530 VL - 17 IS - 150 SP - 174103 ER - TY - JOUR A1 - Ernst, Natalia A1 - Fackeldey, Konstantin A1 - Volkamer, Andrea A1 - Opatz, Oliver A1 - Weber, Marcus T1 - Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes JF - Molecular Simulation N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1080/08927022.2019.1610949 VL - 45 IS - 11 SP - 904 EP - 911 ER - TY - JOUR A1 - Villatoro, José A1 - Weber, Marcus A1 - Zühlke, Martin A1 - Lehmann, Andreas A1 - Zechiowski, Karl A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd A1 - Kreuzer, Oliver T1 - Structural characterization of synthetic peptides using electronspray ion mobility spectrometry and molecular dynamics simulations JF - International Journal of Mass Spectrometry N2 - 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). Y1 - 2019 U6 - https://doi.org/10.1016/j.ijms.2018.10.036 VL - 436 SP - 108 EP - 117 ER - TY - THES A1 - Reuter, Bernhard T1 - Generalisierte Markov-Modellierung von Nichtgleichgewichtssystemen - Simulation und Modellierung der Amyloid-beta(1-40)-Konformationsdynamik unter Mikrowelleneinfluss Y1 - 2018 ER - TY - THES A1 - Quer, Jannes T1 - Importance Sampling for metastable dynamical systems in molecular dynamics Y1 - 2018 ER - TY - THES A1 - Klimm, Martina T1 - New Strategies in Conformation Dynamics Y1 - 2018 ER - TY - THES A1 - Villatoro, José T1 - A combined approach for the analysis of biomolecules using IR-MALDI ion mobility spectrometry and molecular dynamics simulations of peptide ions in the gas phase Y1 - 2018 ER - TY - JOUR A1 - Reidelbach, Marco A1 - Weber, Marcus A1 - Imhof, Petra T1 - Prediction of perturbed proton transfer networks JF - PLoS ONE N2 - 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. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1371/journal.pone.0207718 VL - 13 IS - 12 SP - e0207718 EP - e0207718 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - A Square Root Approximation of Transition Rates for a Markov State Model JF - SIAM. J. Matrix Anal. Appl. Y1 - 2013 U6 - https://doi.org/10.1137/120899959 VL - 34 IS - 2 SP - 738 EP - 756 ER - TY - JOUR A1 - Scharkoi, Olga A1 - Fackeldey, Konstantin A1 - Merkulow, Igor A1 - Andrae, Karsten A1 - Weber, Marcus A1 - Nehls, Irene T1 - Conformational Analysis of Alternariol on the Quantum Level JF - J. Mol. Model. Y1 - 2013 U6 - https://doi.org/10.1007/s00894-013-1803-2 VL - 19 IS - 6 SP - 2567 EP - 2572 ER - TY - GEN A1 - Bujotzek, Alexander A1 - Schütt, Ole A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Efficient Conformational Analysis by Partition-of-Unity Coupling T2 - Math Chem N2 - 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. T3 - ZIB-Report - 13-58 KW - Markov State Models KW - Meshfree KW - Molecular Simulation KW - Partition of Unity Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42570 SN - 1438-0064 ER - TY - JOUR A1 - Spahn, Viola A1 - Del Vecchio, Giovanna A1 - Labuz, Dominika A1 - Rodriguez-Gaztelumendi, Antonio A1 - Massaly, N. A1 - Temp, Julia A1 - Durmaz, Vedat A1 - Sabri, P. A1 - Reidelbach, Marco A1 - Machelska, Halina A1 - Weber, Marcus A1 - Stein, Christoph T1 - A nontoxic pain killer designed by modeling of pathological receptor conformations JF - Science Y1 - 2017 U6 - https://doi.org/10.1126/science.aai8636 VL - 355 IS - 6328 SP - 966 EP - 969 ER - TY - GEN A1 - Weber, Marcus T1 - Eigenvalues of non-reversible Markov chains – A case study N2 - 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. T3 - ZIB-Report - 17-13 KW - non-reversible KW - transition matrix KW - detailed balance Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62191 SN - 1438-0064 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Weber, Marcus A1 - Zhang, Wei T1 - Importance sampling in path space for diffusion processes with slow-fast variables JF - Probability Theory and Related Fields N2 - 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. Y1 - 2017 UR - http://rdcu.be/oA51 U6 - https://doi.org/10.1007/s00440-017-0755-3 N1 - If you are not subscribing to the journal please use the http link below as part of the Springer Nature SharedIt initiative SP - 1 EP - 52 ER - TY - JOUR A1 - Villatoro, José A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Weber, Marcus A1 - Riedel, Jens A1 - Löhmannsröben, Hans-Gerd T1 - IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector JF - International Journal for Ion Mobility Spectrometry Y1 - 2016 U6 - https://doi.org/10.1007/s12127-016-0208-1 IS - 19/4 SP - 197 EP - 297 ER - TY - JOUR A1 - Guerler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2008 UR - http://www.sciencedirect.com/science/article/pii/S0303264707001670 U6 - https://doi.org/DOI: 10.1016/j.biosystems.2007.11.004 VL - 92 IS - 1 SP - 42 EP - 48 ER - TY - THES A1 - Gürler, A. T1 - Selection and flexible optimization of binding modes from conformation ensembles. Y1 - 2006 ER - TY - JOUR A1 - Haack, Fiete A1 - Röblitz, Susanna A1 - Scharkoi, Olga A1 - Schmidt, Burkhard A1 - Weber, Marcus T1 - Adaptive Spectral Clustering for Conformation Analysis JF - AIP Conference Proceedings Y1 - 2010 UR - http://link.aip.org/link/?APC/1281/1585/1 U6 - https://doi.org/10.1063/1.3498116 VL - 1281 IS - 1 SP - 1585 EP - 1588 PB - AIP ER - TY - CHAP A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Weber, Marcus ED - Mode, Ch. T1 - A rapidly Mixing Monte Carlo Method for the Simulation of Slow Molecular Processes T2 - Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science Y1 - 2011 PB - InTech ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf T1 - Quadrature and Implementation of the Weak Coupling Method T2 - MMM 2008: Proceedings of the 4th International Conference on Multiscale Materials Modelling, 27-31 October 2008, Tallahassee, Fla. Y1 - 2008 SP - 62 EP - 65 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf T1 - Weak Coupling Algorithms in Multiscale Simulations T2 - Proceedings of the third Inter. Confer. on Comp. Meth. for Coupled Problems in Science and Engrg Y1 - 2009 SP - 1023pp ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf ED - Griebel, Michael ED - Schweitzer, M. T1 - Numerical Validation of Constraints Based Multiscale Methods T2 - Lecture Notes in Computational Science and Engineering Y1 - 2010 SP - 141 EP - 154 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf A1 - Lenzen, Christoph T1 - Coupling Molecular Dynamics and Continua with Weak Constraints JF - SIAM Multiscale Model. Simul. Y1 - 2011 U6 - https://doi.org//10.1137/100782097 N1 - also as MATHEON Preprint VL - 9 SP - 1459 EP - 1494 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf A1 - Schweitzer, M. ED - Griebel, Michael ED - Schweitzer, M. T1 - Stability of Energy Transfer in the Weak Coupling Method T2 - Meshfree Methods for Partial Differential Equations IV Y1 - 2008 VL - 65 SP - 111 EP - 121 ER - TY - JOUR A1 - Fackeldey, Konstantin T1 - Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach JF - IJPAM Y1 - 2011 VL - 69 IS - 2 SP - 185 EP - 202 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in Mixed–Canonical Ensemble: Efficient conformational analysis of RNA JF - J. Comp. Chem. Y1 - 1998 U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics JF - International Journal for Numerical Methods in Engineering Y1 - 2009 U6 - https://doi.org/10.1002/nme.2626 VL - 79 IS - 12 SP - 1517 EP - 1535 ER - TY - THES A1 - Fackeldey, Konstantin T1 - The Weak Coupling Method for Coupling Continuum Mechanics with Molecular Dynamics Y1 - 2009 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf ED - Widlund, Olof T1 - Solving Frictional Contact Problems with Multigrid Efficiency T2 - Proc.of the 16th International Conference on Domain Decomposition Methods Y1 - 2007 VL - 50 SP - 547 EP - 554 ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - Weak coupling in function space T2 - Proc. Appl. Math. Mech. Y1 - 2007 VL - 7 IS - 1 SP - 2020113pp ER - TY - CHAP A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - CM/MD Coupling - A Function Space Oriented Multiscale-Coupling Approach T2 - Proc. Appl. Math. Mech. Y1 - 2008 VL - 8 IS - 1 SP - 10495pp ER - TY - JOUR A1 - Gürler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2007 ER - TY - JOUR A1 - Kube, Susanna A1 - Weber, Marcus T1 - A Coarse Graining Method for the Identification of Transition rates between Molecular Conformations JF - Journal of Chemical Physics Y1 - 2007 U6 - https://doi.org/10.1063/1.2404953 VL - 126 IS - 2 ER - TY - JOUR A1 - Kümmel, S. A1 - Andrae, Karsten A1 - Reinhard, P.-G. 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