Related papers: MSM/RD: Coupling Markov state models of molecular …
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
Rate processes are often modeled using Markov-State Models (MSM). Suppose you know a prior MSM, and then learn that your prediction of some particular observable rate is wrong. What is the best way to correct the whole MSM? For example,…
Molecular Dynamics (MD) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…
Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD)…
Non-equilibrium Markov State Modeling (MSM) has recently been proposed [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
The Journal of Chemical Physics (JCP) article collection on Markov Models of Molecular Kinetics (MMMK) features recent advances developing and using Markov State Models (MSMs) in atomistic molecular simulations and related applications.…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…