TY - GEN A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 N2 - Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodefficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs. T3 - ZIB-Report - 13-34 KW - information costs KW - hidden state KW - bellmann equation KW - optimal therapeutic policies KW - diagnostic frequency KW - resource-poor KW - resource-rich Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41955 SN - 1438-0064 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - Identification of Molecular Conformations via Statistical Analysis of Simulation Data JF - Comp. Chem. Y1 - 1999 VL - 20 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Conrad, Tim A1 - Genzel, Martin A1 - Cvetkovic, Nada A1 - Wulkow, Niklas A1 - Vybiral, Jan A1 - Kutyniok, Gitta A1 - Schütte, Christof T1 - Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data JF - BMC Bioinformatics N2 - Motivation: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested how MS spectra dier between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust to noise and outliers, and the identied feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of Compressed Sensing that allows to identify a minimal discriminating set of features from mass spectrometry data-sets. We show how our method performs on artificial and real-world data-sets. Y1 - 2017 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 18 IS - 160 SP - 1 EP - 20 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Eisert, Jens A1 - Schütte, Christof T1 - Multidimensional Approximation of Nonlinear Dynamical Systems JF - Journal of Computational and Nonlinear Dynamics N2 - A key task in the field of modeling and analyzing nonlinear dynamical systems is the recovery of unknown governing equations from measurement data only. There is a wide range of application areas for this important instance of system identification, ranging from industrial engineering and acoustic signal processing to stock market models. In order to find appropriate representations of underlying dynamical systems, various data-driven methods have been proposed by different communities. However, if the given data sets are high-dimensional, then these methods typically suffer from the curse of dimensionality. To significantly reduce the computational costs and storage consumption, we propose the method multidimensional approximation of nonlinear dynamical systems (MANDy) which combines data-driven methods with tensor network decompositions. The efficiency of the introduced approach will be illustrated with the aid of several high-dimensional nonlinear dynamical systems. Y1 - 2019 U6 - https://doi.org/10.1115/1.4043148 VL - 14 IS - 6 ER - TY - JOUR A1 - Koltai, Péter A1 - Schütte, Christof T1 - A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics JF - SIAM J. Multiscale Model. Simul. N2 - We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one. Y1 - 2018 U6 - https://doi.org/10.1137/17M1146403 VL - 16 IS - 4 SP - 1455 EP - 1485 PB - SIAM ER - TY - JOUR A1 - Klus, Stefan A1 - Bittracher, Andreas A1 - Schuster, Ingmar A1 - Schütte, Christof T1 - A kernel-based approach to molecular conformation analysis JF - Journal of Chemical Physics N2 - We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for analyzing dynamical systems in order to identify conformation dynamics based on molecular dynamics simulation data. We show that many of the prominent methods like Markov State Models, EDMD, and TICA can be regarded as special cases of this approach and that new efficient algorithms can be constructed based on this derivation. The results of these new powerful methods will be illustrated with several examples, in particular the alanine dipeptide and the protein NTL9. Y1 - 2018 U6 - https://doi.org/10.1063/1.5063533 VL - 149 IS - 24 ER - TY - JOUR A1 - Shao, Borong A1 - Bjaanaes, Maria A1 - Helland, Aslaug A1 - Schütte, Christof A1 - Conrad, Tim T1 - EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma JF - PLOS ONE N2 - Various feature selection algorithms have been proposed to identify cancer prognostic biomarkers. In recent years, however, their reproducibility is criticized. The performance of feature selection algorithms is shown to be affected by the datasets, underlying networks and evaluation metrics. One of the causes is the curse of dimensionality, which makes it hard to select the features that generalize well on independent data. Even the integration of biological networks does not mitigate this issue because the networks are large and many of their components are not relevant for the phenotype of interest. With the availability of multi-omics data, integrative approaches are being developed to build more robust predictive models. In this scenario, the higher data dimensions create greater challenges. We proposed a phenotype relevant network-based feature selection (PRNFS) framework and demonstrated its advantages in lung cancer prognosis prediction. We constructed cancer prognosis relevant networks based on epithelial mesenchymal transition (EMT) and integrated them with different types of omics data for feature selection. With less than 2.5% of the total dimensionality, we obtained EMT prognostic signatures that achieved remarkable prediction performance (average AUC values above 0.8), very significant sample stratifications, and meaningful biological interpretations. In addition to finding EMT signatures from different omics data levels, we combined these single-omics signatures into multi-omics signatures, which improved sample stratifications significantly. Both single- and multi-omics EMT signatures were tested on independent multi-omics lung cancer datasets and significant sample stratifications were obtained. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0204186 VL - 14 IS - 1 ER - TY - JOUR A1 - Gupta, Pooja A1 - Peter, Sarah A1 - Jung, Markus A1 - Lewin, Astrid A1 - Hemmrich-Stanisak, Georg A1 - Franke, Andre A1 - von Kleist, Max A1 - Schütte, Christof A1 - Einspanier, Ralf A1 - Sharbati, Soroush A1 - zur Bruegge, Jennifer T1 - Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections JF - Scientific Reports in Nature N2 - Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-018-38141-x VL - 9 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - A hybrid Galerkin-Monte-Carlo approach to higher-dimensional population balances in polymerization kinetics JF - Macromol. React. Eng. Y1 - 2010 VL - 4 SP - 562 EP - 577 ER - TY - BOOK A1 - Schütte, Christof A1 - Sarich, Marco T1 - Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches Y1 - 2013 N1 - Courant Lecture Notes No. 32, American Mathematical Society PB - American Mathematical Society ER - TY - JOUR A1 - Paulus, Florian A1 - Weiss, Maximilian A1 - Steinhilber, Dirk A1 - Nikitin, Anatoly A1 - Schütte, Christof A1 - Haag, Rainer T1 - Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights JF - Macromolecules Y1 - 2013 U6 - https://doi.org/10.1021/ma401712w VL - 46 IS - 21 SP - 8458 EP - 8466 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010350 VL - 16 IS - 1 SP - 350 EP - 376 ER - TY - JOUR A1 - Sarich, Marco A1 - Banisch, Ralf A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Markov State Models for Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010258 VL - 16 IS - 1 SP - 258 EP - 286 ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Linear response theory and optimal control for a molecular system under nonequilibrium conditions JF - Molecular Physics Y1 - 2013 UR - http://publications.imp.fu-berlin.de/1297/ U6 - https://doi.org/10.1080/00268976.2013.844370 VL - 111 SP - 3555 EP - 3564 ER - TY - JOUR A1 - Nikitin, B. A. A1 - Wulkow, Michael A1 - Schütte, Christof T1 - Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique JF - Macromolecular Theory and Simulation Y1 - 2013 U6 - https://doi.org/10.1002/mats.201300125 VL - 22 IS - 9 SP - 475 EP - 489 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study JF - Molecular Physics Y1 - 2013 U6 - https://doi.org/10.1080/00268976.2013.827254 VL - 111 IS - 22-23 SP - 3363 EP - 3371 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - Delle Site, Luigi T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation Y1 - 2014 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 10 IS - 4 SP - 1376 EP - 1386 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 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling N2 - Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest. We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models (MSM) as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented. T3 - ZIB-Report - 16-60 KW - reaction-diffusion KW - stochastic chemical kinetics KW - chemical master equation Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60999 SN - 1438-0064 ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Empirical Bayes Methods, Reference Priors, Cross Entropy and the EM Algorithm N2 - When estimating a probability density within the empirical Bayes framework, the non-parametric maximum likelihood estimate (NPMLE) usually tends to overfit the data. This issue is usually taken care of by regularization - a penalization term is subtracted from the marginal log-likelihood before the maximization step, so that the estimate favors smooth solutions, resulting in the so-called maximum penalized likelihood estimation (MPLE). The majority of penalizations currently in use are rather arbitrary brute-force solutions, which lack invariance under transformation of the parameters(reparametrization) and measurements. This contradicts the principle that, if the underlying model has several equivalent formulations, the methods of inductive inference should lead to consistent results. Motivated by this principle and using an information-theoretic point of view, we suggest an entropy-based penalization term that guarantees this kind of invariance. The resulting density estimate can be seen as a generalization of reference priors. Using the reference prior as a hyperprior, on the other hand, is argued to be a poor choice for regularization. We also present an insightful connection between the NPMLE, the cross entropy and the principle of minimum discrimination information suggesting another method of inference that contains the doubly-smoothed maximum likelihood estimation as a special case. T3 - ZIB-Report - 16-56 KW - parameter estimation KW - Bayesian inference KW - Bayesian hierarchical modeling KW - hyperparameter KW - hyperprior KW - EM algorithm KW - NPMLE KW - MPLE KW - DS-MLE KW - principle of maximum entropy KW - cross entropy KW - minimum discrimination information KW - reference prior KW - Jeffreys prior Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61230 SN - 1438-0064 ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Empirical Bayes Methods for Prior Estimation in Systems Medicine N2 - One of the main goals of mathematical modelling in systems medicine related to medical applications is to obtain patient-specific parameterizations and model predictions. In clinical practice, however, the number of available measurements for single patients is usually limited due to time and cost restrictions. This hampers the process of making patient-specific predictions about the outcome of a treatment. On the other hand, data are often available for many patients, in particular if extensive clinical studies have been performed. Therefore, before applying Bayes’ rule separately to the data of each patient (which is typically performed using a non-informative prior), it is meaningful to use empirical Bayes methods in order to construct an informative prior from all available data. We compare the performance of four priors - a non-informative prior and priors chosen by nonparametric maximum likelihood estimation (NPMLE), by maximum penalized lilelihood estimation (MPLE) and by doubly-smoothed maximum likelihood estimation (DS-MLE) - by applying them to a low-dimensional parameter estimation problem in a toy model as well as to a high-dimensional ODE model of the human menstrual cycle, which represents a typical example from systems biology modelling. T3 - ZIB-Report - 16-57 KW - Parameter estimation KW - Bayesian inference KW - Bayesian hierarchical modelling KW - NPMLE KW - MPLE KW - DS-MLE KW - EM algorithm KW - Jeffreys prior KW - reference prior KW - hyperparameter KW - hyperprior KW - principle of maximum entropy Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61307 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 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling JF - Journal of Chemical Physics N2 - Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest.We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models (MSM) as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented. Y1 - 2016 U6 - https://doi.org/10.1063/1.4971163 VL - 145 IS - 21 ER - TY - JOUR A1 - Duwal, Sulav A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings JF - PloS Computational Biology N2 - An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment-for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pcbi.1004200 VL - 11 IS - 4 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 VL - 20 IS - 16 SP - 1760 EP - 1774 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 - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-01-03 IS - 24 SP - 235 EP - 259 PB - Springer ER - TY - JOUR A1 - Metzner, Ph. A1 - Weber, Marcus A1 - Schütte, Christof T1 - Observation uncertainty in reversible Markov chains JF - Phys. Rev. E Y1 - 2010 U6 - https://doi.org/10.1103/PhysRevE.82.031114 VL - 82 IS - 3 SP - 031114 PB - American Physical Society ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo JF - J. Comput. Phys. Y1 - 1999 UR - http://www.zib.de/PaperWeb/abstracts/SC-98-45 VL - 151 SP - 146 EP - 168 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter ED - Fiedler, Bernold T1 - Transfer operator approach to conformational dynamics in biomolecular systems T2 - Ergodic theory, analysis, and efficient simulation of dynamical systems Y1 - 2001 SP - 191 EP - 223 PB - Berlin: Springer ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique JF - Phys. Rev. X Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevX.3.011018 VL - 3 SP - 011018 ER - TY - JOUR A1 - Sarich, Marco A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Sharon A1 - Conrad, Tim A1 - Schütte, Christof T1 - Modularity revisited: A novel dynamics-based concept for decomposing complex networks JF - Journal of Computational Dynamics Y1 - 2014 UR - http://publications.mi.fu-berlin.de/1127/ U6 - https://doi.org/10.3934/jcd.2014.1.191 VL - 1 IS - 1 SP - 191 EP - 212 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Efficient rare event simulation by optimal nonequilibrium forcing JF - J. Stat. Mech. Theor. Exp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1153/ U6 - https://doi.org/10.1088/1742-5468/2012/11/P11004 VL - 2012 SP - P11004 ER - TY - JOUR A1 - Sarich, Marco A1 - Schütte, Christof T1 - Approximating Selected Non-dominant Timescales by Markov State Models JF - Comm. Math. Sci. Y1 - 2012 U6 - https://doi.org/10.4310/CMS.2012.v10.n3.a14 VL - 10 IS - 3 SP - 1001 EP - 1013 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Zhang, P. T1 - Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems JF - Phys. Rev. E Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1125/ U6 - https://doi.org/10.1103/PhysRevE.86.026704 VL - 86 IS - 02 SP - 026704 ER - TY - JOUR A1 - Schütte, Christof A1 - Winkelmann, Stefanie A1 - Hartmann, Carsten T1 - Optimal control of molecular dynamics using Markov state models JF - Math. Program. (Series B) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1107/ U6 - https://doi.org/10.1007/s10107-012-0547-6 VL - 134 IS - 1 SP - 259 EP - 282 ER - TY - JOUR A1 - Wang, Han A1 - Zhang, P. A1 - Schütte, Christof T1 - On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1181/ U6 - https://doi.org/10.1021/ct300343y VL - 8 IS - 9 SP - 3243 EP - 3256 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - A pH-dependent coarse-grained model of peptides JF - Soft Matter Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1192/ U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - JOUR A1 - Duwal, Sulav A1 - Schütte, Christof A1 - von Kleist, Max T1 - Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. JF - PLoS One Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1130/ U6 - https://doi.org/10.1371/journal.pone.0040382 VL - 7 IS - 7 SP - e40382 ER - TY - JOUR A1 - von Kleist, Max A1 - Metzner, Ph. A1 - Marquet, R. A1 - Schütte, Christof T1 - Polymerase Inhibition by Nucleoside Analogs JF - Plos Computational Biology Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1087/ U6 - https://doi.org/10.1371/journal.pcbi.1002359 VL - 8 IS - 1 SP - e1002359 ER - TY - JOUR A1 - Meerbach, E. A1 - Latorre, J. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Multicale Model. Sim. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1123/ U6 - https://doi.org/10.1137/110850621 VL - 10 IS - 4 SP - 1263 EP - 1291 ER - TY - JOUR A1 - Schäfer-Bung, B. A1 - Hartmann, Carsten A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Dimension reduction by balanced truncation JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1023/ VL - 135 IS - 1 SP - 014112 ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Lu, Jianfeng A1 - Sarich, Marco A1 - Vanden-Eijnden, E. T1 - Markov State Models Based on Milestoning JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1022/ U6 - https://doi.org/10.1063/1.3590108 VL - 134 IS - 20 SP - 204105 ER - TY - JOUR A1 - Prinz, J.-H. A1 - Wu, Hao A1 - Sarich, Marco A1 - Keller, B. A1 - Fischbach, M. A1 - Held, M. A1 - Chodera, J. A1 - Schütte, Christof A1 - Noé, Frank T1 - Markov models of molecular kinetics JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/944/ U6 - https://doi.org/10.1063/1.3565032 VL - 134 SP - 174105 ER - TY - JOUR A1 - von Kleist, Max A1 - Menz, Stephan A1 - Stocker, Hartmut A1 - Arasteh, Keikawus A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - HIV Quasispecies Dynamics during Pro-active Treatment Switching JF - Plos One Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1051/ U6 - https://doi.org/10.1371/journal.pone.0018204 VL - 6 IS - 3 SP - e18204 PB - Public Library of Science ER - TY - JOUR A1 - Frank, M. A1 - von Kleist, Max A1 - Kunz, A. A1 - Harms, G. A1 - Schütte, Christof A1 - Kloft, Ch. T1 - Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1 JF - Antimicrob. Agents Chemother. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1093/ VL - 55 IS - 12 SP - 5529 EP - 5540 ER - TY - CHAP A1 - Bernhard, Stefan A1 - Zoukra, Kristine Al A1 - Schütte, Christof ED - Knets, I. ED - Brebbia, C. ED - Miftahof, R. ED - Kasyanov, V. ED - Popov, V. T1 - Statistical parameter estimation and signal classification in cardiovascular diagnosis T2 - Modelling in Medicine and Biology Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1070/ VL - IX IS - 15 PB - WIT Press CY - Southampton & Boston ER - TY - JOUR A1 - Aiche, Stephan A1 - Reinert, Knut A1 - Schütte, Christof A1 - Hildebrand, Diana A1 - Schlüter, Hartmut A1 - Conrad, Tim T1 - Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs JF - PLoS ONE Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1143/ U6 - https://doi.org/10.1371/journal.pone.0040656 VL - 7 IS - 7 SP - e40656 PB - Public Library of Science ER - TY - JOUR A1 - Weiss, Maximilian A1 - Paulus, Florian A1 - Steinhilber, D. A1 - Nikitin, Anatoly A1 - Haag, Rainer A1 - Schütte, Christof T1 - Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures JF - MACROMOLECULAR THEORY and SIMULATIONS Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1142/ U6 - https://doi.org/10.1002/mats.201200003 VL - 21 IS - 7 SP - 470 EP - 481 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Stefanie A1 - Conrad, Tim A1 - Schütte, Christof T1 - Random Walks on Complex Modular Networks JF - Journal of Numerical Analysis, Industrial and Applied Mathematics Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1090/ VL - 6 IS - 1-2 SP - 29 EP - 50 PB - European Society of Computational Methods in Sciences and Engineering ER -