Related papers: Coarse-grained molecular dynamics: Nonlinear finit…
Computer-aided molecular design (CAMD) studies quantitative structure-property relationships and discovers desired molecules using optimization algorithms. With the emergence of machine learning models, CAMD score functions may be replaced…
Quasicentroid molecular dynamics (QCMD) is a path-integral method for approximating nuclear quantum effects in dynamics simulations, which has given promising results for gas- and condensed-phase water. Here, by simulating the infrared…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…
Multimodal deep learning has substantially improved electrocardiogram (ECG) classification by jointly leveraging time, frequency, and time-frequency representations. However, existing generative models typically synthesize these modalities…
The MHD version of the adaptive mesh refinement (AMR) code, MG, has been employed to study the interaction of thermal instability, magnetic fields and gravity through 3D simulations of the formation of collapsing cold clumps on the scale of…
A discontinuous Galerkin time-domain (DGTD) method based on dynamically adaptive Cartesian meshes (ACM) is developed for a full-wave analysis of electromagnetic fields in dispersive media. Hierarchical Cartesian grids offer simplicity close…
We introduce a machine-learning framework termed coarse-grained all-atom force field (CGAA-FF), which incorporates coarse-grained message passing within an all-atom force field using equivariant nature of graph models. The CGAA-FF model…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However,…
The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the…
In this paper, we present a Constraint Energy Minimizing Generalized Multiscale Finite Element Method (CEM-GMsFEM) for parabolic equations with multiscale coefficients, arising from applications in porous media. We will present the…
The gradient discretisation method (GDM) is a generic framework for designing and analysing numerical schemes for diffusion models. In this paper, we study the GDM for the porous medium equation, including fast diffusion and slow diffusion…
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…
Computational fluid dynamics and discrete element method (CFD-DEM) coupling is an efficient and powerful tool to simulate particle-fluid systems. However, current volume-averaged CFD-DEM relying on direct grid-based mapping between the…
In this paper, equilibrium and stability equations of functionally graded material (FGM) plate under thermal environment are formulated based on isogeometric analysis (IGA) in combination with higher-order shear deformation theory (HSDT).…
Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a…
Work presented in this paper describes a general algorithm and its finite element implementation for performing concurrent multiple sub-domain simulations in linear structural dynamics. Using this approach one can solve problems in which…