فهرست مقالات Langevin Dynamics

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  1 - Investigation of Monte Carlo, Molecular Dynamic and Langevin dynamic simulation methods for Albumin- Methanol system and Albumin-Water system
  M. Monajjemi N. Dalili Mansour A. Kazemi Babaheydari M. Khaleghian
  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), M چکیده کامل

  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 273 to 313K), it is found thatMC method is not suitable for macromolecule simulations. Also by comparing optimizedenergy in Albumin-water system and Albumin-methanol system,it is distinguished thatbecause of existing more hydrogen bondings Albumin-water system is more stable thanAlbumin-methanol. پرونده مقاله
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  2 - Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations
  M. Monajjemi A. R. Oliaey
  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 en چکیده کامل

  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 native structure, - helix and - sheet conformation by Monte Carlo, Molecular andlangevin dynamics simulations. It was found when the temperature is increased the kinetic energyis increased too, and its diagram is linear. Monte Carlo simulation is a stochastic method andtherefore, is the best method to evaluate gyration radius. Considering the gained values fromMonte Carlo, Molecular and langeving dynamics simulations for - helix conformation and littledeviations from the experimental value, it can be understood that the second structure of thisprotein is the kind in which - helix is more. All the calculations were carried out usingHyperchem 8.0 program package. Gyration radius is calculated using VMD 1.8.6 Software. پرونده مقاله
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  3 - Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
  F. Mollaamin T. Nejadsattari I. Layali
  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 چکیده کامل

  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 computersimulation approaches. Molecular dynamics simulations may be used to probe the interactions ofmembrane proteins with lipids and with detergents at atomic resolution .Examples of such simulationsfor ion channels and for bacterial outer membrane has already been studied. In this work, to characterizeprotein behavior, we observed quantities such as gyration radius and energy average. It was studied thechanges of these factors for potassium channel Protein in gas, water, Methanol and Ethanol phases withnative conformation by Monte Carlo, Molecular and Langevin Dynamics simulations. Monte Carlosimulation is stochastic method and therefore, is the best method to evaluate the radius of gyration in gasphase. when the temperature is increased the kinetic energy is increased too, and its correlation is linear.All the calculations were carried out By Hyperchem 8.0 program. The radius of gyration for differentsolvent is calculated by VMD 1.8.7 Software. The determination of gyration radius is a spectacular forconfiguration of a Macromolecule. It also reflects molecular compactness shape. Monte Carlo simulationis the best method to evaluate gyration radius. پرونده مقاله