– We present numerical and analytical results describing the effect of hydrodynamic interactions on the dynamics of a short polymer chain in solution. A molecular dynamics algorithm for the polymer is coupled to a direct simulation Monte Carlo algorithm for the solvent. We give an explicit expression for the velocity autocorrelation function of the centre of mass of the polymer which agrees wel...

The central importance of solvent interactions in stabilization of specific protein structure has long been recognized. Decades ago, Tanford and Kirkwood treated in detail the interaction of charges with solvent, and they showed how desolvation/burial of charges upon protein folding was an important factor in stability.1 The influence of their model, with further elaborations, can still be seen...

The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large-scale simulations. The current study uses the beta-hairpin from C-terminus of protein G as an example to explore the folding free energy l...

We used three-dimensional self-consistent field theory to investigate the micellization behavior of A-b(B-alt-C)n multiblock terpolymers in the presence of a solvent that is selective to the terminal A-block. In particular, we focused on the effects of the incompatibility parameter between B and C, cBC, and the composition of the solvophilic A-block, fA, on the formation of micelles from ABC tr...

Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force ⟨f⟩ vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is ...

The energy of the frontier molecular orbitals and reactivity indices such as chemical potential, hardness, and electrophilicity of neutral and charged molecules have been investigated in aqueous solution using explicit model for the solvent with the sequential Monte Carlo/quantum mechanics methodology. The supermolecular structures of the solute-solvent system were generated by Monte Carlo simu...

We develop a new, rapid method for the lattice Monte Carlo simulation of ion-containing liquids that accounts for the effects of the reorganization of solvent dipoles under external electrostatic fields. Our results are in reasonable agreement with the analytical solutions to the dielectric continuum theory of Booth for single ions, ion pairs, and ionic cross-links. We also illustrate the subst...

The ion permeation process, driven by a membrane potential through an outer membrane protein, OmpF porin of Escherichia coli, was simulated by molecular dynamics. A Na+ ion, initially placed in the solvent region at the outer side of the porin channel, moved along the electric field passing through the porin channel in a 1.3 nsec simulation; the permeation rate was consistent with the experimen...

An in-house designed membrane process suitable for subsea natural gas dehydration was studied. The use of a absorber together with thermopervaporation (TPV) unit solvent regeneration in closed loop enables the effective and clean production high-pressure close to wellhead. This avoids continuous chemical injection preventing hydrate formation pipelines. absorbent agent (triethylene glycol (TEG)...