Related papers: The atomic-level mechanism underlying the function…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
An accurate description of the structure and dynamics of interfacial water is essential for phospholipid membranes, since it determines their function and their interaction with other molecules. Here we consider water confined in stacked…
Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
Active networks made of biopolymers and motor proteins are valuable bioinspired systems that have been used in the last decades to study the cytoskeleton and its self-organization under mechanical stimulation. Different techniques are…
Amphipathic peptides are considered promising antibiotics because of their ability to form pores in bacterial membranes. In two companion papers, we analyzed both experimentally and theoretically the mechanisms and consequences of the…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
In fluid transport across nanopores, there is a fundamental dissipation that arises from the connection between the pore and the macroscopic reservoirs. This entrance effect can hinder the whole transport in certain situations, for short…
We combine quantum-chemical calculations and molecular dynamics simulations to consider aqueous ion flow across non-axisymmetric nanopores in monolayer graphene and MoS$_2$. When the pore-containing membrane is subject to uniaxial tensile…
The formation of hydrogen-bonded organic nano-structures and the role of the substrate lattice thereby were investigated by scanning tunneling microscopy. The self-organization of 5,10,15,20-tetra(p-hydroxyphenyl)porphyrin (H2THPP)…
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
A structural transformation in water upon compression was recently observed at the temperature $T=277$~K in the vicinity of the pressure $p \approx 2\;000$~Atm [R.M. Khusnutdinoff, A.V. Mokshin, J. Non-Cryst. Solids \textbf{357}, 1677…
We use molecular dynamics simulations to investigate the displacement of a simple butterfly-like molecular motor inside nanopores of various radii filled with a viscous medium. The medium is modeled with a versatile potential that may be…
Arginine has been a mainstay in biological formulation development for decades. To date, the way arginine modulates protein stability has been widely studied and debated. Here, we employed a hydrophobic polymer to decouple hydrophobic…
Active fluid droplets are a class of soft materials exhibiting autonomous motion sustained by an energy supply. Such systems have been shown to capture motility regimes typical of biological cells and are ideal candidates as building-block…
Ionic liquids constrained at interfaces or restricted in subnanometric pores are increasingly employed in modern technologies, including energy applications. Understanding the details of their behavior in these conditions is therefore…
The behavior of fluid interfaces far from equilibrium plays central roles in nature and in industry. Active swimmers trapped at interfaces can alter transport at fluid boundaries with far reaching implications. Swimmers can become trapped…
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the…
Chaperonins are biological nanomachines that help newly translated proteins to fold by rescuing them from kinetically trapped misfolded states. Protein folding assistance by the chaperonin machinery is obligatory in vivo for a subset of…