Related papers: Resolution limit of data-driven coarse-grained mod…
Bio-inspired composites are a great promise for mimicking the extraordinary and highly efficient properties of natural materials. Recent developments in voxel-by-voxel 3D printing have enabled extreme levels of control over the material…
We present the state-of-the-art theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of…
Coarse-grained (CG) force field models are extensively utilised in material simulations due to their scalability. Traditionally, these models are parameterized using hybrid strategies that integrate top-down and bottom-up approaches;…
We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
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…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…
Reticular materials, including metal-organic frameworks and covalent organic frameworks, combine relative ease of synthesis and an impressive range of applications in various fields, from gas storage to biomedicine. Diverse properties arise…
Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governing each interaction potential. While cross correlations…
We present a real-space formulation for coarse-graining Kohn-Sham Density Functional Theory that significantly speeds up the analysis of material defects without appreciable loss of accuracy. The approximation scheme consists of two steps.…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Markov state models (MSMs)---or discrete-time master equation models---are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative…
The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on…
Accurate low dimension chemical kinetic models for methane are an essential component in the design of efficient gas turbine combustors. Kinetic models coupled to computational fluid dynamics (CFD) provide quick and efficient ways to test…