Related papers: Coarse-grained molecular dynamics: Nonlinear finit…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Simulation of 3D low-frequency electromagnetic fields propagating in the Earth is computationally expensive. We present a fictitious wave domain high-order finite-difference time-domain (FDTD) modelling method on nonuniform grids to compute…
We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…
Generative models have the potential to accelerate key steps in the discovery of novel molecular therapeutics and materials. Diffusion models have recently emerged as a powerful approach, excelling at unconditional sample generation and,…
Absorption-line measurements of the circumgalactic medium (CGM) display a highly non-uniform distribution of lower ionization state species accompanied by more widespread higher ionization state material. This suggests that the CGM is a…
Molecular dynamics (MD) simulations are used to calculate transport coefficients in a two-component plasma interacting through a repulsive Coulomb potential. The thermal conductivity, electrical conductivity, electrothermal coefficient,…
For classical discrete systems under constant composition, canonical average provides equilibrium configuration from a set of many-body interactions, which typically acts as nonlinear map. The nonlinearity has recently been investigated in…
Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…
Advances in deep learning have enabled physics-informed neural networks to solve partial differential equations. Numerical differentiation using the finite-difference (FD) method is efficient in physics-constrained designs, even in…
We investigate the numerical implementation of functionally graded properties in the context of the finite element method. The macroscopic variation of elastic properties inherent to functionally graded materials (FGMs) is introduced at the…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
The aim of this work is the description of the chain formation phenomena observed in colloidal suspensions of superparamagnetic nanoparticles under high magnetic fields. We propose a new methodology based on an on-the-fly Coarse-Grain (CG)…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
While many diffusion models perform well when controlling particular aspects such as style, character, and interaction, they struggle with fine-grained control due to dataset limitations and intricate model architecture design. This paper…
We present a coarse molecular-dynamics (CMD) approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable),…
This study proposes a new method for predicting the crystal-melt interfacial free energy ($\gamma$) using the Ginzburg-Landau (GL) model, enhanced by atomistic simulation data for more accurate density wave profiles. The analysis focuses on…
We introduce a coarse-grained model for atomic glass formers. Its elements are physically motivated local microscopic dynamical rules parameterized by observables. Results of the model are established and used to interpret the measured…