A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between t...

The authors study the van der Waals force FvdW, between the gripper jaw and an object – cubical, spherical and conical in shape, situated at a distance L of closest approach from it. The generic and most general case is considered, when the materials of the working jaw of the gripper and the particle are made of different materials strongly preferring the liquid phase of the fluid being at temp...

The mechanism and geometry of force measurement with the atomic force microscope are analyzed in detail. The effective spring constant to be used in force measurement is given in terms of the cantilever spring constant. Particular attention is paid to possible dynamic effects. Theoretical calculations show that inertial effects may be neglected in most regimes, the exception being when relative...

Relaxation of the thermal Casimir or van der Waals force (the high temperature limit of the Casimir force) for a model dielectric medium is investigated. We start with a model of interacting polarization fields with a dynamics that leads to a frequency dependent dielectric constant of the Debye form. In the static limit, the usual zero frequency Matsubara mode component of the Casimir force is ...

in this research, modeling of limiting flux in membrane filtration of skimmed milk as well as the results of simulation by matlab is presented. the presented model is actually a force balance approach and consists of drag, gravitational and lift forces, and forces between colloidal particles (electrostatic repulsive and van der waals attractive forces). to consider the back diffusion phenomenon...

By applying a voltage pulse to a scanning tunneling microscope tip the surface under the tip will be modified. We have in this paper taken a closer look at the model of electric field induced surface diffusion of adatoms including the van der Waals force as a contribution in formations of a mound on a surface. The dipole moment of an adatom is the sum of the surface induced dipole moment (which...

We consider a single slight protuberance in perfectly conducting plane and investigate the van der Waals (vdW) interaction between this surface neutral polarizable particle. When is sufficiently smooth that proximity force approximation (PFA) well applicable, for fixed distance of particle from plane, lateral vdW always points to protuberance. On other hand, by making calculations valid beyond ...

We derive the van der Waals energy and pressure in a planar multilayer system with arbitrary number of dissipative films between two half-spaces. A unique feature of this work is that the entire analysis is performed on the real frequency axis instead of summation over Matsubara frequencies on the imaginary frequency axis. The expression we obtain for van der Waals energy is a generalization of...

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims a...

the ultrasonic velocity, density and viscosity of some schiff bases of 4-amino benzoic acid  were measured in 1,4-dioxane and dimethylformamide at 308.15 k. various acoustical properties such as isentropic compressibility (ks), rao’s molar sound function (rm), the van der waals constant (b), molar compressibility (w), inter molecular free length (lf), relaxation strength (r), internal pressure ...