Related papers: A Rational Approach to Ring Flexibility in Interna…
Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…
As neural networks grow in scale, their training becomes both computationally demanding and rich in dynamics. Amidst the flourishing interest in these training dynamics, we present a novel observation: Parameters during training exhibit…
Dynamic compression of iron to Earth-core conditions is one of the few ways to gather important elastic and transport properties needed to uncover key mechanisms surrounding the geodynamo effect. Herein a new machine-learned ab-initio…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Dynamic perturbation equations are derived for a generic stationary state of an elastic string model -- of the kind appropriate for representing a superconducting cosmic string -- in a flat background. In the case of a circular equilibrium…
The dynamical spin susceptibility is studied in the magnetically-disordered phase of heavy-Fermion systems near the antiferromagnetic quantum phase transition. In the framework of the $S=1/2$ Kondo lattice model, we introduce a perturbative…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
Using molecular dynamics simulations we study the static and dynamic properties of spherical nanoparticles (NPs) embedded in a disordered and polydisperse polymer network. Purely repulsive (RNP) as well as weakly attractive (ANP) polymer-NP…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Ionic Polymer Metal Composites (IPMCs) are one of the most preferred choices among biocompatible materials for industrial and biomedical applications. Despite their advantages, some of their drawbacks include non-linear and hysteretic…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Unconcatenated, unknotted polymer rings in the melt are subject to strong interactions with neighboring chains due to the presence of topological constraints. We study this by computer simulation using the bond-fluctuation algorithm for…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
We have studied the mobility of the folding catalyst, protein disulphide-isomerase (PDI), by molecular dynamics and by a rapid approach based on flexibility. We analysed our simulations using measures of backbone movement, relative…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
Fracture phenomena in soft materials span multiple length- and timescales. This poses a major challenge in computational modeling and predictive materials design. To pass quantitatively from molecular- to continuum scales, a precise…
Recent experiments have demonstrated that the nonlinear elasticity of in vitro networks of the biopolymer actin is dramatically altered in the presence of a flexible cross-linker such as the abundant cytoskeletal protein filamin. The basic…
We analyze the universal size characteristics of flexible ring polymers in solutions in presence of structural obstacles (impurities) in d dimensions. One encounters such situations when considering polymers in gels, colloidal solutions,…