A novel method for the refinement of misfolded protein structures is proposed in which the properties of the solvent environment are oscillated in order to mimic some aspects of the role of molecular chaperones play in protein folding in vivo. Specifically, the hydrophobicity of the solvent is cycled by repetitively altering the partial charges on solvent molecules (water) during a molecular dy...

Fluorescence anisotropy measurements reveal a non-monotonic density dependence for average rotation time (τ(R)) of a polar solute, coumarin153 (C153) in polar supercritical fluoroform (CHF(3)). The conventional Stokes-Einstein-Debye model, relating τ(R) to the solvent viscosity, fails to explain the observed density dependence, because the experimental viscosity increases monotonously with dens...

Terpolymer raspberry vesicles contain domains of different chemical affinities. They are potential candidates as multi-compartment cargo carriers. Their efficacy depends on their stability and load capacity. Using a model star terpolymer system in an aqueous solution, a dissipative particle dynamic (DPD) simulation is employed to investigate how equilibrium aggregate structures are affected by ...

Diolefinic antibacterial laser dye namely 1,4-Bis[2-(4-Pyridyl) Vinyl] Benzene (4PVB)have been investigated electrochemically using cyclic voltammetry, chronoamperometry, convolution and deconvolution voltammetry combined with digital simulation techniques at a platinum electrode in 0.1 mol / L Tetra Butyl Ammonium Perchlorate (TBAP) in  solvent 1,2-dichloroethane.  The diolefinic ...

The evolution of the contact zone between pure surfactant and solvent has been studied by mesoscale simulation. It is found that mesophase formation becomes diffusion controlled and follows the equilibrium phase diagram adiabatically almost as soon as individual mesophases can be identified, corresponding to times in real systems of order 10 micros.

Asphaltenes are known as the 'cholesterol' of crude oil. They form nano-aggregates, precipitate, adhere to surfaces, block rock pores and may alter the wetting characteristics of mineral surfaces within the reservoir, hindering oil recovery efficiency. Despite a significant research effort, the structure, aggregation and deposition of asphaltenes under flowing conditions remain poorly understoo...

Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comp...

Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electro...

The absorption spectra of aminocoumarin C151 in water and n-hexane solution are investigated by an explicit quantum chemical solvent model. We improved the efficiency of the frozen-density embedding scheme, as used in a former study on solvatochromism (J. Chem. Phys. 2005, 122, 094115) to describe very large solvent shells. The computer time used in this new implementation scales approximately ...

We present and discuss data obtained by an extensive nonequilibrium molecular dynamics computer simulation study of polymer solutions under shear, where the chain consists of N beads connected by a finitely extendable nonlinear elastic (FENE) spring force and the solvent is explicitly taken into account. Various scaling laws are extracted from the data which allow one to predict the qualitative...