Related papers: Grid-based state space exploration for molecular b…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
The method of McCurdy, Baertschy, and Rescigno, J. Phys. B, 37, R137 (2004) is generalized to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules.…
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of…
The one-dimensional harmonic oscillator in a box problem is used to introduce the concept of a mixed-mode shell-model scheme. The method combines low-lying ``pure mode'' states of a system to achieve a better description in situations where…
A general real-space multigrid algorithm MIKA (Multigrid Instead of the K-spAce) for the self-consistent solution of the Kohn-Sham equations appearing in the state-of-the-art electronic-structure calculations is described. The most…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
Understanding the contact dynamics of nonspherical particles beyond the microscale is crucial for accurately modeling colloidal and granular systems, where shape anisotropy dictates structural organization and transport properties. In this…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
We propose an approach to detect individual Rydberg molecules with each molecule consisting of two atoms in different Rydberg states. The scheme exploits the movement of atoms in the presence of an external force that exerts only on atoms…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
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.…
Molecular dynamics (MD) simulations provide atomistic insight into biomolecular systems but are often limited by high computational costs required to access long timescales. Coarse-grained machine learning models offer a promising avenue…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
The goal of this primer is to provide a relatively short exposition of the basics of multigrid methods, simplified by focusing on fundamental concepts in a variational setting. This is done by way of a quadratic energy minimization…