Related papers: Multiscale perturbative approach to active matter …
We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…
In this paper we focus on the development of new methods suitable for efficient and reliable coarse-graining of {\it non-equilibrium} molecular systems. In this context, we propose error estimation and controlled-fidelity model reduction…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
In this work we derive and analyze coarse-grained descriptions of self-propelled particles with selective attraction-repulsion interaction, where individuals may respond differently to their neighbours depending on their relative state of…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…
Mesoscopic particle based fluid models, such as dissipative particle dynamics, are usually assumed to be coarse-grained representations of an underlying microscopic fluid. A fundamental question is whether there exists a map from…
The coarse-graining approach to deriving the quantum Markovian master equation is revisited, with close attention given to the underlying approximations. It is further argued that the time interval over which the coarse-graining is…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
The construction of coarse-grained descriptions of a system's kinetics is well established in biophysics. One prominent example is Markov state models in protein folding dynamics. In this paper, we develop a coarse-grained, discrete state…
Active matter, responsive ("smart") materials and materials under time-dependent load are systems out of thermal equilibrium. To construct coarse-grained models for such systems, one needs to integrate out a distribution of microstates that…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
The dynamics of real magnets is often governed by several interacting processes taking place simultaneously at different length scales. For dynamical simulations the relevant length scales should be coupled, and the energy transfer…
An expression for the stress tensor near an external boundary of a discrete mechanical system is derived explicitly in terms of the constituents' degrees of freedom and interaction forces. Starting point is the exact and general coarse…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…