In this paper, the radial breathing mode (RBM) frequencies of multi-walled carbon nanotubes (MWCNTs) are  obtained based on the multiple-elastic thin shell model. For this purpose, MWCNT is considered as a multiple concentric elastic thin cylindrical shells, which are coupled through van der Waals (vdW) forces between two adjacent tubes. Lennard-Jones potential is used to calculate the vdW ...

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue – residue contact interactions are selected based on a cutoff distance, Rc, between the Cα atoms. The folding times depend on the value of Rc strongly and non-monotonically due to the interplay between frustration and the free energy barrier ...

Results from ab initio electronic structure theory calculations on model systems allow for the detailed comparison of tunneling through covalently bonded contacts, hydrogen bonds, and van der Waals contacts. Considerable geometrical sensitivity as well as an exponential distance dependence of the tunneling is observed for tunneling through various nonbonded contacts. However, the fundamental re...

We describe a novel computer system directed to evaluate protein complex formation in a liquid environment. The relevant feature of the system is a potential function expressing the main thermodynamic and kinetic factors leading to protein interaction in solution. The protein interaction model expresses the interaction energy as basically composed of three forces: electrostatic (hydrogen bond),...

Reaction mechanism among indoline-2,3-dione, pyrrolidine-2-carboxylic acid and (Z)-2-(1-(2-hydroxynaphthalen-1-yl)ethylidene)hydroxycarboxamide to form 1’-((((aminooxy)carbonyl)amino)methyl)-2’-(1-hydroxynaphthalen-2-yl)-2’-methyl-1’,2’,5’,6’,7’,7a’-hexahydrospiro[indoline-3,3’-pyrrolo[1,2-a]imidazole-2-one was investigated using density functional theory (DFT) at B3LYP basis theory. The three-...

Effect of interparticle force on the hydrodynamics of gas-solid fluidized beds was investigated using the combined method of computational fluid dynamics and discrete element method (CFD-DEM). The cohesive force between particles was considered to follow the van der Waals equation form. The model was validated by experimental results from literature in terms of bed voidage distribution and Eule...

We analyzed the thermodynamic and structural determinants of indolicidin interactions with eukaryotic and prokaryotic cell membranes using a series of atomistically detailed molecular dynamics simulations. We used quartz-supported bilayers with two different compositions of zwitterionic and anionic phospholipids as model eukaryotic and prokaryotic cell membranes. Indolicidin was preferentially ...

Stability of self-similar solutions for van der Waals driven thin film rupture.

Recent experiments have established that, at least for van der Waals glass formers, volume fluctuations contribute significantly to the slowing down of the dynamics near T(g). Accordingly, we use the Cohen-Grest (CG) free-volume model to analyze dielectric relaxation data for six van der Waals liquids. The CG equation accurately describes the structural relaxation times over broader ranges of t...

We extend the dynamic van der Waals model introduced by A. Onuki [Phys. Rev. Lett., 2005, 94, 054501] to the description of cohesive granular flows under a plane shear to study their hydrodynamic instabilities. By numerically solving the dynamic van der Waals model, we observed various heterogeneous structures of density fields in steady states, where the viscous heating is balanced with the en...