Related papers: Collective Molecular Dynamics in Proteins and Memb…
We apply to the nucleon-nucleus inelastic process a fully coherent microscopic multiple scattering approach. Our study addresses the complexities inherent in characterizing inelastic scattering events, offering a comprehensive theoretical…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
The lateral diffusion of lipids within membrane is of paramount importance, serving as a central mechanism in numerous physiological processes including cell signaling, membrane trafficking, protein activity regulation, and energy…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Among the different dynamical processes that take place in polymers, methyl group rotation is perhaps the simplest one, since all the relevant interactions on the methyl group can be condensed in an effective mean-field one-dimensional…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
To study the correlation between internal protein dynamics and protein functionality of bacteriorhodopsin, we have performed time-resolved quasielastic neutron scattering (QENS) experiments combined with in situ laser activation of protein…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
We present a molecular dynamics study of the collective dynamics of a flexible model for the fragile glass-former orthoterphenyl [ S. Mossa, R. Di leonardo, G. Ruocco, and M. Sampoli, Phys. Rev. E 62, 612 (2000)]. We study the behavior of…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
The viscosity of nucleonic matter is studied both classically and in a quantum mechanical description. The collisions between particles are modeled as hard sphere scattering as a baseline for comparison and as scattering from an attractive…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristic features that can distinguish water molecules inside the…
The mobility of membrane proteins controls many biological functions. The application of the model of Saffman and Delbr\"uck to the diffusion of membrane proteins does not account for all the experimental measurements. These discrepancies…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
Using a combination of dielectric spectroscopy and solid-state deuteron NMR, the hydration water dynamics of connective tissue proteins is studied at sub-ambient temperatures. In this range, the water dynamics follows an Arrhenius law. A…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…