Related papers: Improved Adaptive Resolution Molecular Dynamics Si…
We present a fully adaptive multiresolution scheme for spatially two-dimensional, possibly degenerate reaction-diffusion systems, focusing on combustion models and models of pattern formation and chemotaxis in mathematical biology.…
Quantum simulation of chemical systems is one of the most promising near-term applications of quantum computers. The variational quantum eigensolver, a leading algorithm for molecular simulations on quantum hardware, has a serious…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
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…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
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 present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Artificial Intelligence predicts drug properties by encoding drug molecules, aiding in the rapid screening of candidates. Different molecular representations, such as SMILES and molecule graphs, contain complementary information for…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used…
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…
We introduce a lattice gas implementation that is based on coarse-graining a Molecular Dynamics (MD) simulation. Such a lattice gas is similar to standard lattice gases, but its collision operator is informed by an underlying MD simulation.…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…