Related papers: A Rational Method for Probing Macromolecules Disso…
A unified framework to derive discrete time-marching schemes for coupling of immersed solid and elastic objects to the lattice Boltzmann method is presented. Based on operator splitting for the discrete Boltzmann equation, second-order…
This work introduces novel unconditionally stable operator splitting methods for solving the time dependent nonlinear Poisson-Boltzmann (NPB) equation for the electrostatic analysis of solvated biomolecules. In a pseudo-transient…
We propose a stroboscopic method to dynamically decouple the effects of two-body atom-atom interactions for ultracold atoms, and realize a system dominated by elastic three-body interactions. Using this method, we show that it is possible…
Ligand unbinding is mediated by the free energy change, which has intertwined contributions from both energy and entropy. It is important but not easy to quantify their individual contributions. We model hydrophobic ligand unbinding for two…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
A new approach to dissipative quantum systems modelled by a system plus environment Hamiltonian is presented. Using a continuous sequence of infinitesimal unitary transformations the small quantum system is decoupled from its…
We investigate a scenario where conditions for Mott dissociation of charmonium are fulfilled locally in ultrarelativistic heavy ion collisions at the short time scales before hadronization and study possible consequences to be drawn from…
We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a…
We propose an experimental protocol for using cold atoms to create and probe quantum dimer models, thereby exploring the Pauling-Anderson vision of a macroscopic collection of resonating bonds. This process can allow the study of exotic…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…
For sufficiently low reservoir temperatures, it is known that open quantum systems subject to decoherent interactions with the reservoir relax towards their ground state in the weak coupling limit. Within the framework of quantum master…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…
Thin-walled structures clamped by friction joints, such as aircraft skin panels are exposed to bending-stretching coupling and frictional contact. We propose an original sub-structuring approach, where the system is divided into thin-walled…
The recursion and path-integral methods are applied to analytically study the electronic structure of a neutral $C_{60}$ molecule. We employ a tight-binding Hamiltonian which considers both the $s$ and $p$ valence electrons of carbon. From…