Related papers: Potential for modulation of the hydrophobic effect…
Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling and particle-based simulations to investigate…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
We present a numerical study of polyelectrolytes electrophoresing in free solution while squeezed by an axisymmetric confinement force transverse to their net displacement. Hybrid multi-particle collision dynamics and molecular dynamics…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
It is well stablished that confinement of supercooled liquids in nano-pores induces various effects as a strong modification of the dynamics and a layering of the local structure. In this work we raise the issue as how these confinement…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first order phase transition. The evaporation of water in the vicinity of the polymer…
We recast the problem of hydrogel swelling under physical constraints as an energy optimization problem. We apply this approach to compute equilibrium shapes of hydrogel spheres confined within a jammed matrix of rigid beads, and interpret…
Water mediates electrostatic interactions via the orientation of its dipoles around ions, molecules, and interfaces. This induced water polarization consequently influences multiple phenomena. In particular, water polarization modulated by…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
The genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of…
We study how confining the equilibrium hard-sphere fluid to restrictive one- and two-dimensional channels with smooth interacting walls modifies its structure, dynamics, and entropy using molecular dynamics and transition-matrix Monte Carlo…
Phoretic particles self-propel using self-generated physico-chemical gradients at their surface. Within a suspension, they interact hydrodynamically by setting the fluid around them into motion, and chemically by modifying the chemical…
We analyze thermodynamics of water samples confined in nanopores and prove that although the freezing temperature can be dramatically lower, the suppression of the ice nucleation leading to the freezing temperature depression is a truly…
Liquid water is reluctant to lose hydrogen-bond coordination. Here we reveal that it also demands contraction and reorientation of the second molecular shell to compensate for coordination defects. Such molecular principle will be shown to…
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…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Hydrophobic force, interfacial tension, transverse density profile in confined water system are addressed from first principles of statistical mechanics in a lattice model for water. Using molecular mean field theory technique we deduce…