Related papers: Absolute FKBP binding affinities obtained via non-…
Equilibrium molecular dynamics simulations are used to calculate the thermal conductivity of the one component plasma (OCP) via the Green-Kubo formalism over a broad range of Coulomb coupling strength, $0.1\le\Gamma\le180$. These…
Affine Body Dynamics (ABD) within the Incremental Potential Contact (IPC) framework provides accurate simulation of extremely stiff solids exhibiting near-rigid behavior, with strict non-penetration guarantees. However, IPC's globally…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
Gaining insights from realistic dynamical models of biochemical systems can be challenging given their large number of state variables. Model reduction techniques can mitigate this by decreasing complexity by mapping the model onto a…
Optimization of the intermetallic layer thickness and the suppression of interfacial defects are key elements to improve the load bearing capacity of dissimilar joints. However, till date we do not have a systematic tool to investigate the…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments…
Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling…
Silicon Dangling Bonds have established themselves as a promising competitor in the field of beyond-CMOS technologies. Their integration density and potential for energy dissipation advantages of several orders of magnitude over…
We provide a tight-binding model parametrization for black phosphorus (BP) with an arbitrary number of layers. The model is derived from partially self-consistent $GW_0$ approach, where the screened Coulomb interaction $W_0$ is calculated…
We devise a method for predicting certain receptor-ligand binding behaviors, based on stochastic dynamical modelling. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform…
We propose two semi-device-independent approaches that are able to quantify unknown multipartite quantum entanglement experimentally, where the only information that has to be known beforehand is quantum dimension, and the concept that…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…
We illustrate how to apply modern effective field theory techniques and dimensional regularization to factorize the various scales which appear in non-relativistic bound states at finite temperature. We focus here on the simplest case: the…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Ultracold fermionic atoms in optical lattices offer pristine realizations of Hubbard models, which are fundamental to modern condensed matter physics. Despite significant advancements, the accessible temperatures in these optical lattice…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…
For a paradigmatic model of chemotaxis, we analyze the effect how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve ATP hydrolysis. The…