Related papers: Simple models for charge and salt effects in prote…
We have studied the dependence of metal oxide properties in molecular dynamics (MD) simulations on the polarizability of oxygen ions. We present studies of both liquid and crystalline structures of silica (SiO2), magnesia (MgO) and alumina…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
Salts are an integral part of the environment for living systems and, therefore, understanding their effects on proteins and other biomolecules is of fundamental interest. Small-angle X-ray scattering (SAXS) of protein solutions can provide…
Almost all the polymer crystals have several polymorphic modifications. Their structure and existence conditions, as well as transitions between them are not understood even in the case of the 'model' polymer polyethylene (PE). For analysis…
We investigate one-dimensional periodic chains of alternate type of particles interacting through mirror symmetric potentials. The optimality of the equidistant configuration at fixed density -- also called crystallization -- is shown in…
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…
We study the trapping of charged particles and macromolecules (such as DNA) in salt gradients in aqueous solutions. The source for the salt gradient can be as simple as a dissolving ionic crystal, as shown by McDermott et al. [Langmuir 28,…
Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex…
The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory. This provides effective methods to…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
Ionic crystals play a central role in functional applications. Mesoscale descriptions of these crystals are based on the continuum polarization density field to represent the effective physics of charge distribution at the scale of the…
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…
The effects of static electric field on the dynamics of lysozyme and its hydration water have been investigated by means of incoherent quasi-elastic neutron scattering (QENS). Measurements were performed on lysozyme samples, hydrated…
The study of the electrical double layer lies at the heart of colloidal and interfacial science. The standard mean-field Poisson-Boltzmann (PB) theory is incapable of modeling many phenomena originated from ion correlation. An important…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a…
A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…
We provide a systematic derivation of the scaling behaviour of various quantities and establish in particular the scale invariance of the ionization probability. We discuss the gauge invariance of the scaling properties and the manner in…
We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…
The dependence of the lower critical solution temperature (LCST) of charged, thermosensitive copolymers on their charge fraction and the salt concentration is investigated by employing systematic cloud-point experiments and analytical…