List of works - Christof Schütte

A kernel-based approach to molecular conformation analysis

scientific article published on 01 December 2018

Ab initio molecular dynamics simulation of a medium-sized water cluster anion: from an interior to a surface-located excess electron via a delocalized state.

scientific article published on 12 June 2008

Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion

scientific article published on 24 July 2012

Adaptive approach for nonlinear sensitivity analysis of reaction kinetics.

scientific article published in July 2005

Agent-based modeling: Population limits and large timescales

scientific article published in March 2021

Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections

scientific article published in Scientific Reports

Building Markov State Models for Periodically Driven Non-Equilibrium Systems

scientific article published on 01 April 2015

Chemical potential of liquids and mixtures via adaptive resolution simulation

scientific article published in July 2014

Communications: On the linear response of mechanical systems with constraints

scientific article published in March 2010

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

scientific article

Correction: Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir and Prophylactic Efficacy against HIV-1 Infection

Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs

scientific article published in 2021

Data-based parameter estimation of generalized multidimensional Langevin processes

scientific article

Data-driven computation of molecular reaction coordinates

article

Dimension reduction by balanced truncation: application to light-induced control of open quantum systems.

scientific article published in July 2011

Discrimination of dynamical system models for biological and chemical processes.

scientific article published in June 2007

EMMA: A Software Package for Markov Model Building and Analysis.

scientific article published on 18 June 2012

EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma

scientific article published in PLoS ONE

Effective dynamics along given reaction coordinates, and reaction rate theory

scientific article published on 10 October 2016

Error estimate of short-range force calculation in inhomogeneous molecular systems

scientific article published on 8 August 2012

Estimating the sampling error: distribution of transition matrices and functions of transition matrices for given trajectory data

scientific article

Exploring the Conformational Dynamics of Alanine Dipeptide in Solution Subjected to an External Electric Field: A Nonequilibrium Molecular Dynamics Simulation

scientific article published on 24 March 2014

Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics

scientific article published on 10 September 2020

Fast simulation of polymer chains.

scientific article published in April 2009

From interacting agents to density-based modeling with stochastic PDEs

scientific article published in 2021

Fully adaptive propagation of the quantum-classical Liouville equation.

scientific article published in May 2004

Generator estimation of Markov jump processes based on incomplete observations nonequidistant in time.

scientific article published on 6 December 2007

HIV quasispecies dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs

scientific article

HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection

scientific article

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

scientific article published in April 2007

Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach

scientific article published in 2018

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems.

scientific article

Hydrogen Forms in Water by Proton Transfer to a Distorted Electron

scientific article published on 01 January 2010

Identification of biomolecular conformations from incomplete torsion angle observations by hidden Markov models.

scientific article published in November 2007

Illustration of transition path theory on a collection of simple examples.

scientific article published in August 2006

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis

scientific article

Inferring proteolytic processes from mass spectrometry time series data using degradation graphs

scientific article

Influence of pH and sequence in peptide aggregation via molecular simulation.

scientific article published in December 2015

Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli.

scientific article published on 23 July 2015

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

scientific article published on 01 June 2018

Markov model theory

scientific article published on January 2014

Markov models of molecular kinetics: generation and validation

scientific article published in May 2011

Markov state models based on milestoning.

scientific article published in May 2011

Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin

scientific article published on 24 July 2019

Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere?

scientific article published on 07 May 2018

New methods: general discussion.

scientific article published on 8 December 2016

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes.

scientific article published in January 2005

Observation uncertainty in reversible Markov chains.

scientific article published on 9 September 2010

On metastability and Markov state models for non-stationary molecular dynamics.

scientific article published in November 2016

On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems

scientific article published on 13 August 2012

Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV-1 in Resource-Poor Settings

scientific article (publication date: April 2015)

Pharmacokinetics and pharmacodynamics of the reverse transcriptase inhibitor tenofovir and prophylactic efficacy against HIV-1 infection

scientific article

Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence

scientific article published on 21 July 2017

Serum peptidome profiling revealed platelet factor 4 as a potential discriminating Peptide associated with pancreatic cancer

scientific article

Set-free Markov state model building

scientific article published on March 2017

Simulation, identification and statistical variation in cardiovascular analysis (SISCA) - A software framework for multi-compartment lumped modeling

scientific article published on 20 May 2017

Single-molecule analysis reveals agonist-specific dimer formation of µ-opioid receptors

scientific article published on 15 June 2020

Solution of the chemical master equation by radial basis functions approximation with interface tracking

scientific article

Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks

scientific article published in 2022

Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data

scientific article

Statistical analysis of tipping pathways in agent-based models

scientific article published in 2021

The furnace and the goat-A spatio-temporal model of the fuelwood requirement for iron metallurgy on Elba Island, 4th century BCE to 2nd century ce

scientific article published on 12 November 2020

The spatiotemporal master equation: Approximation of reaction-diffusion dynamics via Markov state modeling

scientific article published in December 2016

Transition Manifolds of Complex Metastable Systems: Theory and Data-Driven Computation of Effective Dynamics.

scientific article

Understanding the romanization spreading on historical interregional networks in Northern Tunisia

scientific article published on 2 August 2022

List of works by Christof Schütte

A kernel-based approach to molecular conformation analysis

Ab initio molecular dynamics simulation of a medium-sized water cluster anion: from an interior to a surface-located excess electron via a delocalized state.

Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion

Adaptive approach for nonlinear sensitivity analysis of reaction kinetics.

Agent-based modeling: Population limits and large timescales

Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections

Building Markov State Models for Periodically Driven Non-Equilibrium Systems

Chemical potential of liquids and mixtures via adaptive resolution simulation

Communications: On the linear response of mechanical systems with constraints

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

Correction: Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir and Prophylactic Efficacy against HIV-1 Infection

Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs

Data-based parameter estimation of generalized multidimensional Langevin processes

Data-driven computation of molecular reaction coordinates

Dimension reduction by balanced truncation: application to light-induced control of open quantum systems.

Discrimination of dynamical system models for biological and chemical processes.

EMMA: A Software Package for Markov Model Building and Analysis.

EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma

Effective dynamics along given reaction coordinates, and reaction rate theory

Error estimate of short-range force calculation in inhomogeneous molecular systems

Estimating the sampling error: distribution of transition matrices and functions of transition matrices for given trajectory data

Exploring the Conformational Dynamics of Alanine Dipeptide in Solution Subjected to an External Electric Field: A Nonequilibrium Molecular Dynamics Simulation

Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics

Fast simulation of polymer chains.

From interacting agents to density-based modeling with stochastic PDEs

Fully adaptive propagation of the quantum-classical Liouville equation.

Generator estimation of Markov jump processes based on incomplete observations nonequidistant in time.

HIV quasispecies dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs

HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems.

Hydrogen Forms in Water by Proton Transfer to a Distorted Electron

Identification of biomolecular conformations from incomplete torsion angle observations by hidden Markov models.

Illustration of transition path theory on a collection of simple examples.

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis

Inferring proteolytic processes from mass spectrometry time series data using degradation graphs

Influence of pH and sequence in peptide aggregation via molecular simulation.

Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli.

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

Markov model theory

Markov models of molecular kinetics: generation and validation

Markov state models based on milestoning.

Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin

Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere?

New methods: general discussion.

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes.

Observation uncertainty in reversible Markov chains.

On metastability and Markov state models for non-stationary molecular dynamics.

On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems

Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV-1 in Resource-Poor Settings

Pharmacokinetics and pharmacodynamics of the reverse transcriptase inhibitor tenofovir and prophylactic efficacy against HIV-1 infection

Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence

Serum peptidome profiling revealed platelet factor 4 as a potential discriminating Peptide associated with pancreatic cancer

Set-free Markov state model building

Simulation, identification and statistical variation in cardiovascular analysis (SISCA) - A software framework for multi-compartment lumped modeling

Single-molecule analysis reveals agonist-specific dimer formation of µ-opioid receptors

Solution of the chemical master equation by radial basis functions approximation with interface tracking

Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks

Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data

Statistical analysis of tipping pathways in agent-based models

The furnace and the goat-A spatio-temporal model of the fuelwood requirement for iron metallurgy on Elba Island, 4th century BCE to 2nd century ce

The spatiotemporal master equation: Approximation of reaction-diffusion dynamics via Markov state modeling

Transition Manifolds of Complex Metastable Systems: Theory and Data-Driven Computation of Effective Dynamics.

Understanding the romanization spreading on historical interregional networks in Northern Tunisia