TY - JOUR A1 - Rosenberg, Marjorie A1 - Agarwala, Richa A1 - Bouffard, Gerard A1 - Davis, Joie A1 - Fiermonte, Giuseppe A1 - Hilliard, Mark A1 - Koch, Thorsten A1 - Kalikin, Linda A1 - Makalowska, Izabela A1 - Morton, D. A1 - Petty, Elizabeth A1 - Weber, James A1 - Palmieri, Ferdinando A1 - Kelley, Richard A1 - Schäffer, Alejandro A1 - Biesecker, Leslie T1 - Mutant deoxynucleotide carrier DNC is associated with congenital microcephaly JF - Nature Genetics Y1 - 2002 U6 - https://doi.org/10.1038/ng948 VL - 32 IS - 1 SP - 175 EP - 179 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 - GEN A1 - Quer, Jannes A1 - Donati, Luca A1 - Keller, Bettina A1 - Weber, Marcus T1 - An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates N2 - 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. T3 - ZIB-Report - 17-09 KW - Adaptive Importance Sampling KW - Molecular Dynamics KW - Metastability KW - Variance Reduction KW - Non Equilibrium Sampling KW - Metadynamics KW - Girsanov Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62075 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 A1 - Fackeldey, Konstantin A1 - Schütte, Christof T1 - Set-free Markov State Building N2 - Molecular dynamics (MD) simulations face challenging problems since the timescales of interest often are much longer than what is possible to simulate and even if sufficiently long simulation are possible the complex nature of the resulting simulation data makes interpretation difficult. Markov State Models (MSMs) help to overcome these problems by making experimentally relevant timescales accessible via coarse grained representations that also allows for convenient interpretation. However, standard set-based MSMs exhibit some caveats limiting their approximation quality and statistical significance. One of the main caveats results from the fact that typical MD trajectories repeatedly re-cross the boundary between the sets used to build the MSM which causes statistical bias in estimating the transition probabilities between these sets. In this article, we present a set-free approach to MSM building utilizing smooth overlapping ansatz functions instead of sets and an adaptive refinement approach. This kind of meshless discretization helps to overcome the recrossing problem and yields an adaptive refinement procedure that allows to improve the quality of the model while exploring state space and inserting new ansatz functions into the MSM. T3 - ZIB-Report - 17-10 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62167 SN - 1438-0064 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 - 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 -