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We reproduce the Debye process in the dielectric response of liquid 1-propanol by all-atom molecular dynamics simulations between 340 K and 200 K. The analysis of dipolar correlations reveals that the $\alpha$ relaxation originates from…
The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a…
We analyze the electronic structure of molecules which may exist in gas phase of chemical vapor deposition process for GeSbTe alloy using the electronic stress tensor, with special focus on the chemical bonds between Ge, Sb and Te atoms. We…
Glycerol titration distinguished from free water the local hydration shell involved in ATPase transition from active to inactive, with cooperativity for water n=16. Rat brain cortex: NE-stimulated and its basal AC in the absence of free…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…
Folding and unfolding of biopolymers are often manipulated in experiment by tuning pH, temperature, single-molecule force or shear field. Here we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting…
Protein RNA-binding domains selectively interact with specific RNA sites, a key interaction that determines the emergent cooperative behaviors in RNA-protein mixtures. Through molecular dynamics simulations, we investigate the impact of the…
Hydrogen compounds are peculiar as the quantum nature of the proton can crucially affect their structural and physical properties. A remarkable example are the high-pressure phases of H$_2$O, where quantum proton fluctuations favor the…
Most of the ongoing projects aimed at the development of specific therapies and vaccines against COVID-19 use the SARS-CoV-2 spike (S) protein as the main target [1-3]. The binding of the spike protein with the ACE2 receptor (ACE2) of the…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
We applied coherence analysis to molecular dynamics simulations of the plant protein crambin, a thionin storage protein found in Abyssinian cabbage. Coherence analysis was developed by engineers to identify linear interactions, without…
In spin crossover materials, an abrupt phase transition between a low spin state and a high spin state can be driven by temperature, pressure or by light irradiation. Of a special relevance are Fe(II) based coordination polymers where, in…
The cross section and rate constants for the title reaction are calculated for all the spin-orbit states of N$^+$($^3P_{J_A}$) using two statistical approaches, one purely adiabatic and the other one mixing quantum capture for the entrance…
For the first time, an ab initio molecular dynamics simulation was performed to describe the C$_3$S/water interface. The simulation shows that oxides with favorable environment are protonated at first, creating very stable hydroxide groups.…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…
Non-adiabatic molecular dynamics simulations are used to analyze the role of different solvent degrees of freedom in the non-radiative relaxation of the first excited state of the hydrated electron. The relaxation occurs through a…