Related papers: A Modular and Extensible CHARMM-Compatible Model f…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
N-carbophenes are a class of two-dimensional covalent organic frameworks with potential for solid-state gas storage and as 2D topological materials. Previous studies have demonstrated that variations in their bonding, topology, and…
Recently, fictitious identical particles have provided a promising way to overcome the fermion sign problem and have been used in path integral Monte Carlo (PIMC) to accurately simulate warm dense matter with up to 1000 electrons (T.…
The accuracy and efficiency of a coarse-grained (CG) force field are pivotal for high-precision molecular simulations of large systems with complex molecules. We present an automated mapping and optimization framework for molecular…
Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…
Progress in Prognostics and Health Management (PHM) is hindered by the lack of standardized and reusable evaluation practices across tasks, datasets, and application domains. Reported results are often difficult to reproduce and compare, as…
Mixed atomistic and continuum methods offer the possibility of carrying out simulations of material properties at both larger length scales and longer times than direct atomistic calculations. The quasi-continuum method links atomistic and…
Herein, we describe new methods to produce colloidal particle chains of three stiffness regimes that can be observed on a single-particle level, that is, on the level of the monomers that make up the chain; the chains can even be observed…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an…
We present a new class of tensor network states that are specifically designed to capture the electron correlation of a molecule of arbitrary structure. In this ansatz, the electronic wave function is represented by a Complete-Graph Tensor…
Simulations have acted as a cornerstone to understand MOF/polymer interface structure, however, no molecular-level simulation has yet been performed at the nanoparticle scale. In this work, a hybrid MARTINI/Force Matching (FM) force field…
Pre-trained protein models (PTPMs) represent a protein with one fixed embedding and thus are not capable for diverse tasks. For example, protein structures can shift, namely protein folding, between several conformations in various…
We present a computational framework for the simulation of blood flow with fully resolved red blood cells (RBCs) using a modular approach that consists of a lattice Boltzmann solver for the blood plasma, a novel finite element based solver…
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles…
For nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However, calculation of the centroid effective force…