Sharif Digital Repository

We have proposed an efficient parametrization method for a recent variant of the Gay Berne potential for dissimilar and biaxial particles [Phys. Rev. E 67, 041710 (2003)] and demonstrated it for a set of small organic molecules. Compared with the previously proposed coarse-grained models, the new potential exhibits a superior performance in close contact and large distant interactions. The repercussions of thermal vibrations and elasticity have been studied through a statistical method. The study justifies that the potential of mean force is representable with the same functional form, extending the application of this coarse-grained description to a broader range of molecules. Moreover, the... 

An effective potential for longitudinal interactions between adjacent protofilaments in a microtubule is introduced. Our proposed interaction potential is a periodic and continuous function of the offset between two protofilaments, which also incorporates the bending energy of protofilaments. This potential produces the results of atomistic simulations. Further, using the potential, a Monte Carlo simulation gives results for the skew angles of observed structures that are in good agreement with experiments. © 2008 The American Physical Society  

In this work, the group contribution approach has been used in combination with the linear isotherm regularity (LIR) equation of state to estimate pvT properties of primary, secondary and tertiary alcohols, ketones and 1-carboxylic acid. In addition, the isothermal compressibility and thermal expansion coefficient of these compounds have been predicted. We assume each of these organic compounds as a hypothetical mixture of methyl, methylene and a functional group, in which the interaction potential of each pair is assumed to be the average effective pair potential. Then, the LIR equation of state (EOS) has been extended to such a hypothetical mixture. Three basic compounds, namely propane,... 

The concept of effective pair potential (EPP), in which medium effects and contribution of long-range interactions are added to near-neighbor pair interactions, is a useful tool to derive and calculate the thermodynamic quantities. It has been shown that the extended Lennard-Jones (12, 6, 3) potential is an accurate EPP for many systems. However, the parameters of this EPP are not known for any systems. We introduce a new approach to use experimental pvT data of a fluid to calculate its EPP parameters. Such calculation has been carried out for some fluids at some temperatures. Unlike the isolated pair potential, it has been shown that the parameters significantly vary with temperature. We... 

Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's... 

The interaction potential energy and heat of sublimation of nanoparticles of HMX crystal polymorphs are studied by using molecular dynamics methods with a previously developed force field [Bedrov, et al., J. Comput.-Aided Mol. Des. 8 (2001) 77]. Molecular dynamics simulations of nanoparticles with 10, 20, 30, 40, 50, 60, 70, 80, 90, and 100 molecules of HMX are carried out at 300 K. The intermolecular, intramolecular and total interaction energies per mole for the nanoparticles are calculated at 300 K. Then, we have calculated sublimation enthalpy of HMX crystal polymorphs with different sizes. For the all sizes, the β-HMX is found to be the most stable phase, due to having the least total... 

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the... 

Developments of sensitive, rapid, and cheap systems for identification of a wide range of biomolecules have been recognized as a critical need in the biology field. Here, we introduce a simple colorimetric sensor array for detection of biological thiols, based on aggregation of three types of surface engineered gold nanoparticles (AuNPs). The low-molecular-weight biological thiols show high affinity to the surface of AuNPs; this causes replacement of AuNPs' shells with thiol containing target molecules leading to the aggregation of the AuNPs through intermolecular electrostatic interaction or hydrogen-bonding. As a result of the predetermined aggregation, color and UV-vis spectra of AuNPs...