the determination of gyration radius is a strong research for configuration of a macromolecule. italso reflects molecular compactness shape. in this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. we studiedthe changes of these factors as a function of temperature for acetylcholine receptor protein in gasphase with n...

serum albumin is the most aboundant protein in blood plasma. its two major roles aremaintaining osmotic pressure and depositing and transporting compounds. in this paper,albumin-methanol solution simulation is carried out by three techniques including montecarlo (mc), molecular dynamic (md) and langevin dynamic (ld) simulations. byinvestigating energy changes by time and temperature (between 27...

potassium channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. potassium channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. realistic studies of ion current in biologic channels present a major challenge for compu...

medicinal chemistry depends on many other disciplines ranging from organic chemistry andpharmacology to computational chemistry. typically medicinal chemists use the moststraightforward ways to prepare compounds. the validation of any design project comes from thebiological testing.studies of the binding site of vinblastine by a single cross—linking experiment identified it asbeing between resi...

The secondary structure of the member of the AKH/RPCH family has been studied by Molecular Dynamics and Langevin Dynamics methods. Molecular dynamics simulation were performed in vacuum, model aqueous solution and simulated membrane. Langevin dynamics simulation was performed using the friction factor y equal to 2 ps_1. Molecular dynamics as well as Langevin Dynamics simulation were conducted a...

An attempt to generalize the Langevin dynamics simulation method is presented based on the generalized Langevin theory of liquids, in which the dynamics of both solute and solvent is treated by the generalized Langevin equations, but the integration of the equation of motion of solute is made in the manner similar to the ordinary molecular dynamics simulation with discretized time steps along a...

A systematic computational approach to describe the conformational dynamics of biomolecules in reduced dimensionality is presented. The method is based on (i) the decomposition of a high-dimensional molecular dynamics trajectory into a few "system" and (many) "bath" degrees of freedom and (ii) a Langevin simulation of the resulting model. Employing principal component analysis, the dimension of...

We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the canonical distribution in a simulation of rigid molecules. We propose simple, quasisymplectic second-order numerical integrators a...