Research

Protein Folding

Understanding the nature of the interactions that stabilize protein structures and govern protein folding mechanisms is a fundamental problem of molecular biology. The extreme complexity of the problem due to the numerous numbers of interacting atoms has made the study of the problem practically impossible in the atomic scales. The simplified coarse-grained models introduce a feasible way to understand significant macroscopic characteristics of the macromolecules without any reference to the atomic details.

DNA Elasticity

Following the discovery of the double helix DNA by Watson and Crick, the structure and elasticity of DNA has been investigated on various length scales.
These long macromolecules which carry the huge amount of information of living creatures, behave very similar to classical elastic rod in macroscopic scales, but in nano scales the microscopic anisotropies can affect their structures.

Microtubular Structures

Microtubules are a filamentous assembly of protein subunits, Alpha- and Beta-tubulin, that are involved in various vital cells functions, e.g. motility, division, and transport. They are hollow cylinders with nano scale diameters and micro scale length.

RE² Potential

In molecular simulations, short-range attractive and repulsive interactions are typically represented using Lennard-Jones potentials. For large molecules, the exact evaluation of the interaction potential of this type involves a computationally expensive double summation over the respective interacting atoms. We have recently used results from colloid science to derive an approximate interaction potential based on the Hamaker theory for mixtures of ellipsoids of arbitrary size and shape. (More...)

EMD code

EMD (acronym for Ellipsoidal Molecular Dynamics ) is a free open-source software written in C++ (tested under LINUX OS) under the GPL license for molecular dynamics simulation of coarse-grained ellipsoids. This software is currently capable of simulating multiple ellipsoid particles, their interaction with surfaces and spheres through EES force field. The MD algorithm is based on "symplectic integration of quaternion rigid-body coordinates" and supports NVE, NVT and NPT ensembles . (More...)

EES Potential

The EES potential is the exact description of the surface interaction of ellipsoidal colloidal particles. Having an adjustable density function, the exact ellipsoid-substrate potential may be employed as a coarse-grained model for the surface interactions of rigid ellipsoidal molecules at nanoscale as well, with a negligible error as low as 3%. The EES potential possesses no nonphysical limits and is a reliable alternative to the expensive atomistic descriptions in molecular simulations. (More...)

Water Film Motor

In a two-dimensional cell used for electrolysis of water films, one can electrically induce a hydrodynamic rotation. It is a project in collaboration with Medical Physics Lab (Dr. Amjadi) at Physics department of Sharif University of Technology. (More...)