@misc{WinkelmannSchuettevonKleist2013, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1}, issn = {1438-0064}, doi = {10.4310/CMS.2014.v12.n5.a4}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41955}, year = {2013}, abstract = {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.}, language = {en} } @article{HuisingaBestCordesetal.1999, author = {Huisinga, Wilhelm and Best, Christoph and Cordes, Frank and Roitzsch, Rainer and Sch{\"u}tte, Christof}, title = {Identification of Molecular Conformations via Statistical Analysis of Simulation Data}, volume = {20}, journal = {Comp. Chem.}, pages = {1760 -- 1774}, year = {1999}, language = {en} } @article{GelssKlusEisertetal.2019, author = {Gelß, Patrick and Klus, Stefan and Eisert, Jens and Sch{\"u}tte, Christof}, title = {Multidimensional Approximation of Nonlinear Dynamical Systems}, volume = {14}, journal = {Journal of Computational and Nonlinear Dynamics}, number = {6}, doi = {10.1115/1.4043148}, year = {2019}, abstract = {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.}, language = {en} } @article{KoltaiSchuette2018, author = {Koltai, P{\´e}ter and Sch{\"u}tte, Christof}, title = {A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics}, volume = {16}, journal = {SIAM J. Multiscale Model. Simul.}, number = {4}, publisher = {SIAM}, doi = {10.1137/17M1146403}, pages = {1455 -- 1485}, year = {2018}, abstract = {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.}, language = {en} } @article{KlusBittracherSchusteretal.2018, author = {Klus, Stefan and Bittracher, Andreas and Schuster, Ingmar and Sch{\"u}tte, Christof}, title = {A kernel-based approach to molecular conformation analysis}, volume = {149}, journal = {Journal of Chemical Physics}, number = {24}, doi = {10.1063/1.5063533}, year = {2018}, abstract = {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.}, language = {en} } @article{ShaoBjaanaesHellandetal.2019, author = {Shao, Borong and Bjaanaes, Maria and Helland, Aslaug and Sch{\"u}tte, Christof and Conrad, Tim}, title = {EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma}, volume = {14}, journal = {PLOS ONE}, number = {1}, doi = {10.1371/journal.pone.0204186}, year = {2019}, abstract = {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.}, language = {en} } @article{GuptaPeterJungetal.2019, author = {Gupta, Pooja and Peter, Sarah and Jung, Markus and Lewin, Astrid and Hemmrich-Stanisak, Georg and Franke, Andre and von Kleist, Max and Sch{\"u}tte, Christof and Einspanier, Ralf and Sharbati, Soroush and zur Bruegge, Jennifer}, title = {Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections}, volume = {9}, journal = {Scientific Reports in Nature}, doi = {10.1038/s41598-018-38141-x}, year = {2019}, abstract = {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.}, language = {en} } @article{SchuetteWulkow2010, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {A hybrid Galerkin-Monte-Carlo approach to higher-dimensional population balances in polymerization kinetics}, volume = {4}, journal = {Macromol. React. Eng.}, pages = {562 -- 577}, year = {2010}, language = {en} } @book{SchuetteSarich2013, author = {Sch{\"u}tte, Christof and Sarich, Marco}, title = {Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches}, publisher = {American Mathematical Society}, year = {2013}, language = {en} } @article{PaulusWeissSteinhilberetal.2013, author = {Paulus, Florian and Weiss, Maximilian and Steinhilber, Dirk and Nikitin, Anatoly and Sch{\"u}tte, Christof and Haag, Rainer}, title = {Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights}, volume = {46}, journal = {Macromolecules}, number = {21}, doi = {10.1021/ma401712w}, pages = {8458 -- 8466}, year = {2013}, language = {en} } @article{HartmannBanischSarichetal.2013, author = {Hartmann, Carsten and Banisch, Ralf and Sarich, Marco and Badowski, Thomas and Sch{\"u}tte, Christof}, title = {Characterization of Rare Events in Molecular Dynamics}, volume = {16}, journal = {Entropy (Special Issue)}, number = {1}, doi = {10.3390/e16010350}, pages = {350 -- 376}, year = {2013}, language = {en} } @article{SarichBanischHartmannetal.2013, author = {Sarich, Marco and Banisch, Ralf and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Markov State Models for Rare Events in Molecular Dynamics}, volume = {16}, journal = {Entropy (Special Issue)}, number = {1}, doi = {10.3390/e16010258}, pages = {258 -- 286}, year = {2013}, language = {en} } @article{WangHartmannSchuette2013, author = {Wang, Han and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Linear response theory and optimal control for a molecular system under nonequilibrium conditions}, volume = {111}, journal = {Molecular Physics}, doi = {10.1080/00268976.2013.844370}, pages = {3555 -- 3564}, year = {2013}, language = {en} } @article{NikitinWulkowSchuette2013, author = {Nikitin, B. A. and Wulkow, Michael and Sch{\"u}tte, Christof}, title = {Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique}, volume = {22}, journal = {Macromolecular Theory and Simulation}, number = {9}, doi = {10.1002/mats.201300125}, pages = {475 -- 489}, year = {2013}, language = {en} } @article{EncisoSchuetteDelleSite2013, author = {Enciso, Marta and Sch{\"u}tte, Christof and Delle Site, Luigi}, title = {pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study}, volume = {111}, journal = {Molecular Physics}, number = {22-23}, doi = {10.1080/00268976.2013.827254}, pages = {3363 -- 3371}, year = {2013}, language = {en} } @article{WangSchuetteCiccottietal.2014, author = {Wang, Han and Sch{\"u}tte, Christof and Ciccotti, Giovanni and Delle Site, Luigi}, title = {Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation}, volume = {10}, journal = {Journal of Chemical Theory and Computation}, number = {4}, doi = {10.1186/s12859-017-1565-4}, pages = {1376 -- 1386}, year = {2014}, language = {en} } @misc{WeberFackeldeySchuette2017, author = {Weber, Marcus and Fackeldey, Konstantin and Sch{\"u}tte, Christof}, title = {Set-free Markov State Building}, issn = {1438-0064}, doi = {10.1063/1.4978501}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62167}, year = {2017}, abstract = {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.}, language = {en} } @misc{WinkelmannSchuette2016, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof}, title = {The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60999}, year = {2016}, abstract = {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.}, language = {en} } @misc{KlebanovSikorskiSchuetteetal.2016, author = {Klebanov, Ilja and Sikorski, Alexander and Sch{\"u}tte, Christof and R{\"o}blitz, Susanna}, title = {Empirical Bayes Methods, Reference Priors, Cross Entropy and the EM Algorithm}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61230}, year = {2016}, abstract = {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.}, language = {en} } @misc{KlebanovSikorskiSchuetteetal.2016, author = {Klebanov, Ilja and Sikorski, Alexander and Sch{\"u}tte, Christof and R{\"o}blitz, Susanna}, title = {Empirical Bayes Methods for Prior Estimation in Systems Medicine}, issn = {1438-0064}, arxiv = {http://arxiv.org/abs/1612.01403}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61307}, year = {2016}, abstract = {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.}, language = {en} } @article{HartmannSchuetteWeberetal.2017, author = {Hartmann, Carsten and Sch{\"u}tte, Christof and Weber, Marcus and Zhang, Wei}, title = {Importance sampling in path space for diffusion processes with slow-fast variables}, journal = {Probability Theory and Related Fields}, doi = {10.1007/s00440-017-0755-3}, pages = {1 -- 52}, year = {2017}, abstract = {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.}, language = {en} } @article{WinkelmannSchuette2016, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof}, title = {The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling}, volume = {145}, journal = {Journal of Chemical Physics}, number = {21}, doi = {10.1063/1.4971163}, year = {2016}, abstract = {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.}, language = {en} } @article{DuwalWinkelmannSchuetteetal.2015, author = {Duwal, Sulav and Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings}, volume = {11}, journal = {PloS Computational Biology}, number = {4}, doi = {10.1371/journal.pcbi.1004200}, year = {2015}, abstract = {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.}, language = {en} } @article{HuisingaBestRoitzschetal.1999, author = {Huisinga, Wilhelm and Best, Christoph and Roitzsch, Rainer and Sch{\"u}tte, Christof and Cordes, Frank}, title = {From Simulation Data to Conformational Ensembles}, volume = {20}, journal = {J. Comp. Chem.}, number = {16}, pages = {1760 -- 1774}, year = {1999}, language = {en} } @article{FischerCordesSchuette1998, author = {Fischer, Alexander and Cordes, Frank and Sch{\"u}tte, Christof}, title = {Hybrid Monte Carlo with Adaptive Temperature in Mixed-Canonical Ensemble: Efficient conformational analysis of RNA}, volume = {19}, journal = {J. Comp. Chem.}, number = {15}, doi = {10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J}, pages = {1689 -- 1697}, year = {1998}, language = {en} } @inproceedings{FischerSchuetteDeuflhardetal.2002, author = {Fischer, Alexander and Sch{\"u}tte, Christof and Deuflhard, Peter and Cordes, Frank}, title = {Hierarchical Uncoupling-Coupling of Metastable Conformations}, booktitle = {Computational Methods for Macromolecules}, number = {24}, editor = {Schlick, T. and Gan, H.}, publisher = {Springer}, pages = {235 -- 259}, year = {2002}, language = {en} } @article{MetznerWeberSchuette2010, author = {Metzner, Ph. and Weber, Marcus and Sch{\"u}tte, Christof}, title = {Observation uncertainty in reversible Markov chains}, volume = {82}, journal = {Phys. Rev. E}, number = {3}, publisher = {American Physical Society}, doi = {10.1103/PhysRevE.82.031114}, pages = {031114}, year = {2010}, language = {en} } @article{SchuetteFischerHuisingaetal.1999, author = {Sch{\"u}tte, Christof and Fischer, Alexander and Huisinga, Wilhelm and Deuflhard, Peter}, title = {A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo}, volume = {151}, journal = {J. Comput. Phys.}, pages = {146 -- 168}, year = {1999}, language = {en} } @incollection{SchuetteHuisingaDeuflhard2001, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm and Deuflhard, Peter}, title = {Transfer operator approach to conformational dynamics in biomolecular systems}, booktitle = {Ergodic theory, analysis, and efficient simulation of dynamical systems}, editor = {Fiedler, Bernold}, publisher = {Berlin: Springer}, pages = {191 -- 223}, year = {2001}, language = {en} } @article{WangHartmannSchuetteetal.2013, author = {Wang, Han and Hartmann, Carsten and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique}, volume = {3}, journal = {Phys. Rev. X}, doi = {10.1103/PhysRevX.3.011018}, pages = {011018}, year = {2013}, language = {en} } @article{SarichDjurdjevacConradBruckneretal.2014, author = {Sarich, Marco and Djurdjevac Conrad, Natasa and Bruckner, Sharon and Conrad, Tim and Sch{\"u}tte, Christof}, title = {Modularity revisited: A novel dynamics-based concept for decomposing complex networks}, volume = {1}, journal = {Journal of Computational Dynamics}, number = {1}, doi = {10.3934/jcd.2014.1.191}, pages = {191 -- 212}, year = {2014}, language = {en} } @article{HartmannSchuette2012, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Efficient rare event simulation by optimal nonequilibrium forcing}, volume = {2012}, journal = {J. Stat. Mech. Theor. Exp.}, doi = {10.1088/1742-5468/2012/11/P11004}, pages = {P11004}, year = {2012}, language = {en} } @article{SarichSchuette2012, author = {Sarich, Marco and Sch{\"u}tte, Christof}, title = {Approximating Selected Non-dominant Timescales by Markov State Models}, volume = {10}, journal = {Comm. Math. Sci.}, number = {3}, doi = {10.4310/CMS.2012.v10.n3.a14}, pages = {1001 -- 1013}, year = {2012}, language = {en} } @article{WangSchuetteZhang2012, author = {Wang, Han and Sch{\"u}tte, Christof and Zhang, P.}, title = {Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems}, volume = {86}, journal = {Phys. Rev. E}, number = {02}, doi = {10.1103/PhysRevE.86.026704}, pages = {026704}, year = {2012}, language = {en} } @article{SchuetteWinkelmannHartmann2012, author = {Sch{\"u}tte, Christof and Winkelmann, Stefanie and Hartmann, Carsten}, title = {Optimal control of molecular dynamics using Markov state models}, volume = {134}, journal = {Math. Program. (Series B)}, number = {1}, doi = {10.1007/s10107-012-0547-6}, pages = {259 -- 282}, year = {2012}, language = {en} } @article{WangZhangSchuette2012, author = {Wang, Han and Zhang, P. and Sch{\"u}tte, Christof}, title = {On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems}, volume = {8}, journal = {J. Chem. Theo. Comp.}, number = {9}, doi = {10.1021/ct300343y}, pages = {3243 -- 3256}, year = {2012}, language = {en} } @article{EncisoSchuetteSite2013, author = {Enciso, Marta and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {A pH-dependent coarse-grained model of peptides}, volume = {9}, journal = {Soft Matter}, number = {26}, doi = {10.1039/C3SM27893J}, pages = {6118 -- 6127}, year = {2013}, language = {en} } @article{DuwalSchuettevonKleist2012, author = {Duwal, Sulav and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir \& Prophylactic Efficacy against HIV-1 Infection.}, volume = {7}, journal = {PLoS One}, number = {7}, doi = {10.1371/journal.pone.0040382}, pages = {e40382}, year = {2012}, language = {en} } @article{vonKleistMetznerMarquetetal.2012, author = {von Kleist, Max and Metzner, Ph. and Marquet, R. and Sch{\"u}tte, Christof}, title = {Polymerase Inhibition by Nucleoside Analogs}, volume = {8}, journal = {Plos Computational Biology}, number = {1}, doi = {10.1371/journal.pcbi.1002359}, pages = {e1002359}, year = {2012}, language = {en} } @article{MeerbachLatorreSchuette2012, author = {Meerbach, E. and Latorre, J. and Sch{\"u}tte, Christof}, title = {Sequential Change Point Detection in Molecular Dynamics Trajectories}, volume = {10}, journal = {Multicale Model. Sim.}, number = {4}, doi = {10.1137/110850621}, pages = {1263 -- 1291}, year = {2012}, language = {en} } @article{SchaeferBungHartmannSchmidtetal.2011, author = {Sch{\"a}fer-Bung, B. and Hartmann, Carsten and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Dimension reduction by balanced truncation}, volume = {135}, journal = {J. Chem. Phys.}, number = {1}, pages = {014112}, year = {2011}, language = {en} } @article{SchuetteNoeLuetal.2011, author = {Sch{\"u}tte, Christof and No{\´e}, Frank and Lu, Jianfeng and Sarich, Marco and Vanden-Eijnden, E.}, title = {Markov State Models Based on Milestoning}, volume = {134}, journal = {J. Chem. Phys.}, number = {20}, doi = {10.1063/1.3590108}, pages = {204105}, year = {2011}, language = {en} } @article{PrinzWuSarichetal.2011, author = {Prinz, J.-H. and Wu, Hao and Sarich, Marco and Keller, B. and Fischbach, M. and Held, M. and Chodera, J. and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Markov models of molecular kinetics}, volume = {134}, journal = {J. Chem. Phys.}, doi = {10.1063/1.3565032}, pages = {174105}, year = {2011}, language = {en} } @article{vonKleistMenzStockeretal.2011, author = {von Kleist, Max and Menz, Stephan and Stocker, Hartmut and Arasteh, Keikawus and Huisinga, Wilhelm and Sch{\"u}tte, Christof}, title = {HIV Quasispecies Dynamics during Pro-active Treatment Switching}, volume = {6}, journal = {Plos One}, number = {3}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0018204}, pages = {e18204}, year = {2011}, language = {en} } @article{FrankvonKleistKunzetal.2011, author = {Frank, M. and von Kleist, Max and Kunz, A. and Harms, G. and Sch{\"u}tte, Christof and Kloft, Ch.}, title = {Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1}, volume = {55}, journal = {Antimicrob. Agents Chemother.}, number = {12}, pages = {5529 -- 5540}, year = {2011}, language = {en} } @incollection{BernhardZoukraSchuette2011, author = {Bernhard, Stefan and Zoukra, Kristine Al and Sch{\"u}tte, Christof}, title = {Statistical parameter estimation and signal classification in cardiovascular diagnosis}, volume = {IX}, booktitle = {Modelling in Medicine and Biology}, number = {15}, editor = {Knets, I. and Brebbia, C. and Miftahof, R. and Kasyanov, V. and Popov, V.}, publisher = {WIT Press}, address = {Southampton \& Boston}, year = {2011}, language = {en} } @article{AicheReinertSchuetteetal.2012, author = {Aiche, Stephan and Reinert, Knut and Sch{\"u}tte, Christof and Hildebrand, Diana and Schl{\"u}ter, Hartmut and Conrad, Tim}, title = {Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs}, volume = {7}, journal = {PLoS ONE}, number = {7}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0040656}, pages = {e40656}, year = {2012}, language = {en} } @article{WeissPaulusSteinhilberetal.2012, author = {Weiss, Maximilian and Paulus, Florian and Steinhilber, D. and Nikitin, Anatoly and Haag, Rainer and Sch{\"u}tte, Christof}, title = {Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures}, volume = {21}, journal = {MACROMOLECULAR THEORY and SIMULATIONS}, number = {7}, doi = {10.1002/mats.201200003}, pages = {470 -- 481}, year = {2012}, language = {en} } @article{DjurdjevacConradBrucknerConradetal.2012, author = {Djurdjevac Conrad, Natasa and Bruckner, Stefanie and Conrad, Tim and Sch{\"u}tte, Christof}, title = {Random Walks on Complex Modular Networks}, volume = {6}, journal = {Journal of Numerical Analysis, Industrial and Applied Mathematics}, number = {1-2}, publisher = {European Society of Computational Methods in Sciences and Engineering}, pages = {29 -- 50}, year = {2012}, language = {en} } @article{WangSchuetteSite2012, author = {Wang, Han and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion.}, volume = {8}, journal = {J. Chem. Theo. Comp.}, number = {8}, doi = {10.1021/ct3003354}, pages = {2878 -- 2887}, year = {2012}, language = {en} } @article{SenneTrendelkampSchroerMeyetal.2012, author = {Senne, M. and Trendelkamp-Schroer, B. and Mey, A. and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {EMMA - A software package for Markov model building and analysis}, volume = {8}, journal = {Journal of Chemical Theory and Computation}, doi = {10.1021/ct300274u}, pages = {2223 -- 2238}, year = {2012}, language = {en} } @article{DjurdjevacConradSarichSchuette2012, author = {Djurdjevac Conrad, Natasa and Sarich, Marco and Sch{\"u}tte, Christof}, title = {Estimating the eigenvalue error of Markov State Models}, volume = {10}, journal = {Multiscale Modeling \& Simulation}, number = {1}, doi = {10.1137/100798910}, pages = {61 -- 81}, year = {2012}, language = {en} } @article{RathYousefKatzensteinetal.2013, author = {Rath, Barbara and Yousef, Kaveh and Katzenstein, D. and Shafer, R. and Sch{\"u}tte, Christof and von Kleist, Max and Merigan, T.}, title = {HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitor Induced Selective Pressure in vitro}, volume = {8}, journal = {PLoS ONE}, number = {4}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0061102}, pages = {e61102}, year = {2013}, language = {en} } @article{MenzLatorreSchuetteetal.2012, author = {Menz, Stephan and Latorre, J. and Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation}, volume = {10}, journal = {SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS)}, number = {4}, doi = {10.1137/110825716}, pages = {1232 -- 1262}, year = {2012}, language = {en} } @article{WinkelmannSchuettevonKleist2012, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control Processes with Rare State Observation}, volume = {12}, journal = {Communications in Mathematical Sciences}, number = {859}, year = {2012}, language = {en} } @article{WinkelmannSchuettevonKleist2012, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control with Rare State Observation}, journal = {International Journal of Biomathematics and Biostatistics}, year = {2012}, language = {en} } @article{SarichSchuetteVandenEijnden2010, author = {Sarich, Marco and Sch{\"u}tte, Christof and Vanden-Eijnden, E.}, title = {Optimal Fuzzy Aggregation of Networks}, volume = {8}, journal = {Multiscale Modeling and Simulation}, number = {4}, doi = {10.1137/090758519}, pages = {1535 -- 1561}, year = {2010}, language = {en} } @article{NoeSchuetteVandenEijndenetal.2009, author = {No{\´e}, Frank and Sch{\"u}tte, Christof and Vanden-Eijnden, E. and Reich, L. and Weikl, T.}, title = {Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations}, volume = {106}, journal = {Proc. Natl. Acad. Sci. USA}, number = {45}, doi = {10.1073/pnas.0905466106}, pages = {19011 -- 19016}, year = {2009}, language = {en} } @article{SchuetteJahnke2009, author = {Sch{\"u}tte, Christof and Jahnke, Tobias}, title = {Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation}, volume = {43}, journal = {Mathematical Modelling and Numerical Analysis (ESAIM)}, number = {4}, publisher = {EDP Sciences}, doi = {10.1051/m2an/2009027}, pages = {721 -- 742}, year = {2009}, language = {en} } @article{SchuetteNoeMeerbachetal.2009, author = {Sch{\"u}tte, Christof and No{\´e}, Frank and Meerbach, E. and Metzner, Ph. and Hartmann, Carsten}, title = {Conformation Dynamics}, journal = {Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.),}, publisher = {EMS publishing house}, doi = {10.4171/056-1/15}, pages = {297 -- 335}, year = {2009}, language = {en} } @article{FiedlerLeichtleKaseetal.2009, author = {Fiedler, Georg Martin and Leichtle, Alexander Benedikt and Kase, Julia and Baumann, Sven and Ceglarek, Uta and Felix, Klaus and Conrad, Tim and Witzigmann, Helmut and Weimann, Arved and Sch{\"u}tte, Christof and Hauss, Johann and B{\"u}chler, Markus and Thiery, Joachim}, title = {Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer}, volume = {15}, journal = {Clinical Cancer Research}, number = {11}, publisher = {American Association for Cancer Research,}, doi = {10.1158/1078-0432.CCR-08-2701}, pages = {3812 -- 3819}, year = {2009}, language = {en} } @article{HartmannSchuetteKalibaevaetal.2009, author = {Hartmann, Carsten and Sch{\"u}tte, Christof and Kalibaeva, G. and Pierro, M. and Ciccotti, Giovanni}, title = {Fast Simulation of Polymer Chains}, volume = {130}, journal = {J. Chem. Phys.}, doi = {10.1063/1.3110603}, pages = {144101}, year = {2009}, language = {en} } @article{MetznerSchuetteVandenEijnden2009, author = {Metzner, Ph. and Sch{\"u}tte, Christof and Vanden-Eijnden, E.}, title = {Transition Path Theory for Markov Jump Processes}, volume = {7}, journal = {Mult. Mod. Sim.}, number = {3}, doi = {10.1137/070699500}, pages = {1192 -- 1219}, year = {2009}, language = {en} } @article{GraefeNordmeierSchuette2009, author = {Gr{\"a}fe, Ch. and Nordmeier, V. and Sch{\"u}tte, Christof}, title = {Computerspiel zum Thema Molek{\"u}ldynamik f{\"u}r Sch{\"u}ler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels}, volume = {1}, journal = {Jahrestagung 2008 der GDCP (Gesellschaft f{\"u}r Didaktik der Chemie und Physik)}, publisher = {LIT VERLAG Dr. W. Hopf}, pages = {77 -- 79}, year = {2009}, language = {en} } @article{MetznerNoeSchuette2009, author = {Metzner, Ph. and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {Estimating the Sampling Error}, volume = {80}, journal = {Phys. Rev. E}, number = {2}, publisher = {American Physical Society}, doi = {10.1103/PhysRevE.80.021106}, pages = {021106}, year = {2009}, language = {en} } @incollection{GraefeSchuetteNordmeier2009, author = {Gr{\"a}fe, Ch. and Sch{\"u}tte, Christof and Nordmeier, V.}, title = {"Learner as creator" - Sch{\"u}lerInnen generieren eigene Lernspiele}, booktitle = {Didaktik der Physik - Bochum 2009}, publisher = {Lehmanns Media}, address = {Berlin}, year = {2009}, language = {en} } @article{LatorreMetznerHartmannetal.2011, author = {Latorre, J. and Metzner, Ph. and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Structure-preserving numerical discretization of reversible diffusions}, volume = {9}, journal = {Commun. Math. Sci.}, number = {4}, pages = {1051 -- 1072}, year = {2011}, language = {en} } @incollection{BernhardZoukraSchuette2010, author = {Bernhard, Stefan and Zoukra, Kristine Al and Sch{\"u}tte, Christof}, title = {From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis}, booktitle = {Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine}, editor = {Daskalaki, A. and Lazakidou, A.}, publisher = {Hershey, PA: Medical Information Science Reference}, year = {2010}, language = {en} } @article{HorenkoSchuette2010, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {On metastable conformational analysis of non-equilibrium biomolecular time series}, volume = {8}, journal = {Multiscale Modeling \& Simulation}, number = {2}, doi = {10.1137/080744347}, pages = {701 -- 716}, year = {2010}, language = {en} } @article{HartmannVulcanovSchuette2010, author = {Hartmann, Carsten and Vulcanov, V.-M. and Sch{\"u}tte, Christof}, title = {Balanced Truncation of Second Order Systems}, volume = {8}, journal = {Multiscale Model. Simul.}, number = {4}, doi = {10.1137/080732717}, pages = {1348 -- 1367}, year = {2010}, language = {en} } @article{LatorreHartmannSchuette2010, author = {Latorre, J. and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Free energy computation by controlled Langevin processes}, volume = {1}, journal = {Procedia Computer Science}, number = {1}, doi = {10.1016/j.procs.2010.04.179}, pages = {1591 -- 1600}, year = {2010}, language = {en} } @article{SchuetteWulkow2010, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {A Hybrid Galerkin-Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics}, volume = {4}, journal = {Macromol. React. Eng.}, number = {9-10}, doi = {10.1002/mren.200900073}, pages = {562 -- 577}, year = {2010}, language = {en} } @article{MarsalekFrigatoVandeVondeleetal.2010, author = {Marsalek, Ondrej and Frigato, Tomaso and VandeVondele, Joost and Bradforth, Stephen E. and Schmidt, Burkhard and Sch{\"u}tte, Christof and Jungwirth, Pavel}, title = {Hydrogen Forms in Water by Proton Transfer to a Distorted Electron}, volume = {114}, journal = {J. Phys. Chem. B}, number = {2}, doi = {10.1021/jp908986z}, pages = {915 -- 920}, year = {2010}, language = {en} } @inproceedings{DjurdjevacConradSarichSchuette2010, author = {Djurdjevac Conrad, Natasa and Sarich, Marco and Sch{\"u}tte, Christof}, title = {On Markov State Models for Metastable Processes}, booktitle = {Proceedings of the International Congress of Mathematics, Hyderabad, India, Section Invited Talks. (ICM) 2010}, year = {2010}, language = {en} } @article{SarichNoeSchuette2010, author = {Sarich, Marco and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {On the Approximation Quality of Markov State Models}, volume = {8}, journal = {Multiscale Model. Simul.}, number = {4}, doi = {10.1137/090764049}, pages = {1154 -- 1177}, year = {2010}, language = {en} } @article{HartmannSchuetteCiccotti2010, author = {Hartmann, Carsten and Sch{\"u}tte, Christof and Ciccotti, Giovanni}, title = {On the linear response of mechanical systems with constraints}, volume = {132}, journal = {J. Chem. Phys.}, number = {11}, doi = {10.1063/1.3354126}, pages = {111103}, year = {2010}, language = {en} } @article{FrigatoVandeVondeleSchmidtetal.2008, author = {Frigato, Tomaso and VandeVondele, Joost and Schmidt, Burkhard and Sch{\"u}tte, Christof and Jungwirth, Pavel}, title = {Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion}, volume = {112}, journal = {J. Phys. Chem. A}, number = {27}, doi = {10.1021/jp711545s}, pages = {6125 -- 6133}, year = {2008}, language = {en} } @article{HorenkoKleinDolaptchievetal.2008, author = {Horenko, Illia and Klein, Rupert and Dolaptchiev, S. and Sch{\"u}tte, Christof}, title = {Automated Generation of Reduced Stochastic Weather Models I}, volume = {6}, journal = {Mult. Mod. Sim.}, number = {4}, doi = {10.1137/060670535}, pages = {1125 -- 1145}, year = {2008}, language = {en} } @article{HartmannSchuette2008, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Balancing of partially-observed stochastic differential equations}, journal = {47th IEEE Conference on Decision and Control}, doi = {10.1109/CDC.2008.4739161}, pages = {4867 -- 4872}, year = {2008}, language = {en} } @article{HorenkoSchuette2008, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications}, journal = {Adv. Data Anal. Class., submitted}, year = {2008}, language = {en} } @article{HorenkoSchuette2008, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics}, volume = {7}, journal = {Mult. Mod. Sim.}, number = {2}, doi = {10.1137/070687451}, pages = {731 -- 773}, year = {2008}, language = {en} } @article{HorenkoDittmerLankasetal.2008, author = {Horenko, Illia and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Sch{\"u}tte, Christof}, title = {Macroscopic Dynamics of Complex Metastable Systems}, volume = {7}, journal = {J. Appl. Dyn. Syst.}, number = {2}, doi = {10.1137/050630064}, pages = {532 -- 560}, year = {2008}, language = {en} } @article{MeerbachSchuette2008, author = {Meerbach, E. and Sch{\"u}tte, Christof}, title = {Sequential Change Point Detection in Molecular Dynamics Trajectories}, journal = {Journal of Multivariate Analysis, submitted}, year = {2008}, language = {en} } @article{DiederichsJuditskiSpokoinyetal.2008, author = {Diederichs, Elmar and Juditski, A. and Spokoiny, V. and Sch{\"u}tte, Christof}, title = {Sparse Non-Gaussian Component Analysis}, journal = {IEEE Transactions on Information Theory, submitted}, year = {2008}, language = {en} } @incollection{GraefeSchuetteNordmeier2008, author = {Gr{\"a}fe, Ch. and Sch{\"u}tte, Christof and Nordmeier, V.}, title = {Spielend lernen - ein Online-Computerspiel zur Molek{\"u}ldynamik}, booktitle = {Didaktik der Physik ?}, publisher = {Lehmanns Media}, address = {Berlin}, year = {2008}, language = {en} } @article{MetznerHorenkoSchuette2007, author = {Metzner, Ph. and Horenko, Illia and Sch{\"u}tte, Christof}, title = {Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time}, volume = {76}, journal = {Phys. Rev. E}, number = {06}, doi = {10.1103/PhysRevE.76.066702}, pages = {066702}, year = {2007}, language = {en} } @article{BornemannNettesheimSchuette1996, author = {Bornemann, Folkmar A. and Nettesheim, Peter and Sch{\"u}tte, Christof}, title = {Quantum-classical molecular dynamics as an approximation to full quantum dynamics}, volume = {105}, journal = {J. Chem. Phys.}, number = {3}, doi = {10.1063/1.471952}, pages = {1074 -- 1083}, year = {1996}, language = {en} } @article{SchuetteZumbuschBrinkmann1995, author = {Sch{\"u}tte, Christof and Zumbusch, Gerhard and Brinkmann, Ralf}, title = {Dynamics of Erbium-doped Waveguide Lasers}, journal = {preprint}, year = {1995}, language = {en} } @misc{Schuette1995, author = {Sch{\"u}tte, Christof}, title = {Smoothed Molecular Dynamics for Thermally Embedded Systems}, year = {1995}, language = {en} } @article{SchuetteDinand1995, author = {Sch{\"u}tte, Christof and Dinand, Manfred}, title = {Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers}, volume = {13}, journal = {J. Lightw. Techn.}, number = {1}, pages = {14 -- 23}, year = {1995}, language = {en} } @article{ManzParamonovPolaseketal.1994, author = {Manz, J{\"o}rn and Paramonov, G. and Polasek, M. and Sch{\"u}tte, Christof}, title = {Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D}, volume = {34}, journal = {Isr. J. Chem.}, number = {1}, pages = {115 -- 125}, year = {1994}, language = {en} } @article{Schuette1993, author = {Sch{\"u}tte, Christof}, title = {A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation}, volume = {5}, journal = {Impact of Computing in Sci. Eng.}, number = {3}, doi = {10.1006/icse.1993.1008}, pages = {176 -- 200}, year = {1993}, language = {en} } @article{SchuetteWulkow1992, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy.}, journal = {preprint}, year = {1992}, language = {en} } @article{DeuflhardHuisingaFischeretal.2000, author = {Deuflhard, Peter and Huisinga, Wilhelm and Fischer, Alexander and Sch{\"u}tte, Christof}, title = {Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains}, volume = {315}, journal = {Lin. Alg. Appl.}, number = {1-3}, doi = {10.1016/S0024-3795(00)00095-1}, pages = {39 -- 59}, year = {2000}, language = {en} } @inproceedings{SchuetteHuisinga2000, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {On Conformational Dynamics induced by Langevin Processes}, volume = {2}, booktitle = {Equadiff 99}, editor = {Fiedler, B. and Grger, K. and Sprekels, J{\"u}rgen}, publisher = {World Scientific}, doi = {10.1142/9789812792617_0234}, pages = {1247 -- 1262}, year = {2000}, language = {en} } @inproceedings{SchuetteCordes2000, author = {Sch{\"u}tte, Christof and Cordes, Frank}, title = {On Dynamical Transitions between Conformational Ensembles}, booktitle = {Molecular Dynamics on Parallel Computers}, editor = {Esser, R. and Grassberger, P. and Grotendorst, J. and Lewerenz, M.}, publisher = {World Scientific}, doi = {10.1142/9789812793768_0002}, pages = {32 -- 45}, year = {2000}, language = {en} } @article{BornemannSchuette1999, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {Adaptive Accuracy Control for Car-Parrinello Simulations}, volume = {83}, journal = {Num. Math.}, number = {2}, doi = {10.1007/s002110050445}, pages = {179 -- 186}, year = {1999}, language = {en} } @inproceedings{SchuetteBornemann1999, author = {Sch{\"u}tte, Christof and Bornemann, Folkmar A.}, title = {Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {380 -- 395}, year = {1999}, language = {en} } @inproceedings{DeuflhardDellnitzJungeetal.1999, author = {Deuflhard, Peter and Dellnitz, M. and Junge, Oliver and Sch{\"u}tte, Christof}, title = {Computation of Essential Molecular Dynamics by Subdivision Techniques}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {98 -- 115}, year = {1999}, language = {en} } @article{Schuette1999, author = {Sch{\"u}tte, Christof}, title = {Conformational Dynamics}, journal = {preprint}, year = {1999}, language = {en} } @article{SchuetteFischerHuisingaetal.1999, author = {Sch{\"u}tte, Christof and Fischer, Alexander and Huisinga, Wilhelm and Deuflhard, Peter}, title = {A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo}, volume = {151}, journal = {J. Comp. Phys}, number = {1}, doi = {10.1006/jcph.1999.6231}, pages = {146 -- 168}, year = {1999}, language = {en} }