Related papers: MSM/RD: Coupling Markov state models of molecular …
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
We present a mathematical study for the development of Multiple Sclerosis in which a spatio-temporal kinetic { theory} model describes, at the mesoscopic level, the dynamics of a high number of interacting agents. We consider both…
The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in many cases is inconsistent with a…
Simulations have played a critical role in the advancement of our knowledge of magnetic reconnection. However, due to the inherently multiscale nature of reconnection, it is impossible to simulate all physics at all scales. For this reason,…
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations provide a rigorous physical basis for studying these dynamics,…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Herein, epoxy resin is cured by coupling quantum chemical (QC) calculations with molecular dynamics (MD) simulations that enable parameter-free prediction of material characteristics. A polymer network is formed by the reaction between base…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic…
The most interesting step of condensation is the cluster formation up to the critical size. In a closed system, this is an instationary process, as the vapour is depleted by the emerging liquid phase. This imposes a limitation on direct…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…