Related papers: The atomic-level mechanism underlying the function…
We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the…
Hydrodynamic interactions are important for diverse fluids especially those with low Reynold's number such as microbial and particle-laden suspensions, and proteins diffusing in membranes. Unfortunately, while far-field (asymptotic)…
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Nanoporosity in silicon results in an interface-dominated mechanics, fluidics and photonics that are often superior to the ones of the bulk material. However, their active control, e.g. as a response to electronic stimuli, is challenging…
Hydrophobic solid-water interfaces underpin processes in nanofluidics, electrochemistry, and energy technologies. Microscopic insights into these systems are often inferred from our understanding of the air-water interface, which is assumed…
Active materials are capable of converting free energy into directional motion, giving rise to striking dynamical phenomena. Developing a general understanding of their structure in relation to the underlying non-equilibrium physics would…
Protein-surface interactions cause the desirable effect of controlled protein adsorption onto biodevices as well as the undesirable effect of protein fouling. The key to controlling protein-surface adsorptions is to identify and quantify…
In the present study, water is considered as a dynamic network between molecules at distances not exceeding 3.2 angstroms. The instantaneous configurations obtained by using the molecular dynamics method have been sequentially analyzed, the…
Motile bacteria play essential roles in biology that rely on their dynamic behaviors, including their ability to navigate, interact, and self-organize. However, bacteria dynamics on fluid interfaces are not well understood. Swimmers…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
We present experimental and theoretical results on intrusion-extrusion cycles of water in hydrophobic mesoporous materials, characterized by independent cylindrical pores. The intrusion, which takes place above the bulk saturation pressure,…
Interfacial interactions significantly alter the fundamental properties of water confined in mesoporous structures, with crucial implications for geological, physicochemical, and biological processes. Herein, we focused on the effect of…
Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the…
For a wide range of modern soft functional materials the selective transport of sub-nanometer-sized molecules (`penetrants') through a stimuli-responsive polymeric membrane is key to the desired function. In this study, we investigate the…
The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their function in bacteria, which in general lack membrane-bound…