The effect of lipid oxidation on water permeability of phosphatidylcholine membranes was investigated by means of both scattering stopped flow experiments and atomistic molecular dynamics simulations. Formation of water pores followed by a significant enhancement of water permeability was observed. The molecules of oxidized phospholipids facilitate pore formation and subsequently stabilize wate...

Autoionization of water which gives rise to its pH is one of the key properties of aqueous systems. Surfaces of water and aqueous electrolyte solutions are traditionally viewed as devoid of inorganic ions; however, recent molecular simulations and spectroscopic experiments show the presence of certain ions including hydronium in the topmost layer. This raises the question of what is the pH (def...

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides remains elusive. Here, we use a multistage atomistic-coarse-grained approach, complemented by circular dichroism/infrared spectroscopy and dynamic light scattering experiments to highlight the dual nature of water in driving the self-assembly of peptide amphiphiles (PAs). We show com...

We used microsecond time scale atomistic simulations to study the relaxation dynamics of the microemulsion water/octane/C(9)E(3) system. In order to determine what transport mechanism occurs under the conditions of surfactant excess, we studied the system under a wide range of temperatures (7-88 °C) and showed that the surfactant acts as an effective solvent for water and carries out passive wa...

Globular proteins contain cavities/voids that play specific roles in controlling protein function. Elongated cavities provide migration channels for the transport of ions and small molecules to the active center of a protein or enzyme. Using Monte Carlo and Molecular Dynamics on fully atomistic protein/water models, a new computational methodology is introduced that takes into account the prote...

We discuss the concept of structural uniformity as a tool for model construction, and employ the recently proposed reverse Monte Carlo + invariant environment refinement technique (RMC+INVERT) method to create computer models of amorphous materials. We further develop the RMC+INVERT method, and apply it to model glassy GeO2, by jointly fitting partial pair-correlation functions rather than the ...

By treating both the short-range (solvation) and long-range (image force) electrostatic forces as well as charge polarization induced by these forces in a consistent manner, we obtain a simple theory for the self-energy of an ion that is continuous across the interface. Along with nonelectrostatic contributions, our theory enables a unified description of ions on both sides of the interface. Us...

How nature uses water molecules to create fascinating patterns ranging from snowflakes to ice cubes has intrigued mankind for centuries. Here we use ZnO to mimic nature's versatility in creating microscopic patterns with tunable morphology. During growth of ZnO on Zn-dominant spheres via chemical vapor deposition, highly regular and symmetric dendritic snowflake patterns and smooth compact isla...

A method is presented for incorporating a solid into a coarse grain liquid model. From the fully atomistic solid-liquid site-site description the solid is replaced by an implicit potential. The liquid particles are then coarse grained by appealing to statistical mechanics and probability theory. The dimensionality problem which arises is overcome with an approximate treatment and a force field ...

The fracture of carbon nanotubes is studied by atomistic simulations. In these simulations, the fracture behavior is found to be almost independent of the separation energy and to depend primarily on the inflection point in the interatomic potential. The results show moderate dependence of fracture strength on chirality. The range of fracture strains compares well with experimental results, but...