相关论文: Rupture of multiple parallel molecular bonds under…
Ab initio molecular dynamics simulations of liquid water under equilibrium ambient conditions, together with a novel energy decomposition analysis, have recently shown that a substantial fraction of water molecules exhibit a significant…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…
A time-dependent global fiber-bundle model of fracture with continuous damage is formulated in terms of a set of coupled non-linear differential equations. A first integral of this set is analytically obtained. The time evolution of the…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
The adhesion between a polymer melt and substrate is studied in the presence of chemically attached chains on the substrate surface. Extensive molecular dynamics simulations have been carried out to study the effect of temperature, tethered…
We show that in a gas of ultra cold atoms distance selective two-body loss can be engineered via the resonant laser excitation of atom pairs to interacting electronic states. In an optical lattice this leads to a dissipative Master equation…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
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…
A random fuse network, or equivalently a two-dimensional spring network with quenched disorder, is subjected to a constant load and thermal noise, and studied by means of numerical simulations. Rupture is thermally activated and the…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…
We propose a theoretical model for branching instabilities in 2-dimensional fracture, offering predictions for when crack branching occurs, how multiple cracks develop, and what is the geometry of multiple branches. The model is based on…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized…
We conduct molecular dynamics simulations of the collision of atomic clusters with a weakly-attractive surface. We focus on an intermediate regime, between soft-landing and fragmentation, where the cluster undergoes deformation on impact…
The decoupling and freeze-out of energetic nuclear collisions is analysed in terms of transparent semi-classical decoupling formulae. They provide a smooth transition and generalise frequently employed instantaneous freeze-out procedures.…