Related papers: Coarse-graining molecular dynamics models using an…
Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output, while removing the degrees of…
In this work, we propose a local multiscale model reduction approach for the time-domain scalar wave equation in a heterogenous media. A fine mesh is used to capture the heterogeneities of the coefficient field, and the equation is solved…
The complexity of molecular dynamics simulations necessitates dimension reduction and coarse-graining techniques to enable tractable computation. The generalized Langevin equation (GLE) describes coarse-grained dynamics in reduced…
Predicting the molecular friction and energy landscapes under nonequilibrium conditions is key to coarse-graining the dynamics of selective solute transport through complex, fluctuating and responsive media, e.g., polymeric materials such…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
In recent years, it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the…
We present an algebraic method for constructing a highly effective coarse grid correction to accelerate domain decomposition. The coarse problem is constructed from the original matrix and a small set of input vectors that span a low-degree…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
Coarse-graining techniques play a central role in reducing the complexity of stochastic models, and are typically characterised by a mapping which projects the full state of the system onto a smaller set of variables which captures the…
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…
We introduce the spatial disorder-generalized Langevin equation (SD-GLE), a data-driven method for constructing coarse-grained (CG) dynamics in heterogeneous systems. Unlike conventional CG approaches that rely on a mean-field potential,…
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising…
We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…
Multiscale simulations facilitate the efficient exploration of large spatiotemporal scales in chemical and physical systems, yet particle-based simulations become prohibitively expensive at time and length scales beyond the molecular level.…
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…
We present a computer-assisted approach to coarse-graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph…
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…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…