molecular dynamics simulation of proteins two models of anharmonic dynamics

... (FRAP) are often used to assess the dynamics and kinetic properties of proteins in living cells [1219] FCS detects the uctuations of uorescent intensity derived from the movement of a single ... in the part of the cytoplasm outside of the granules FRAP analysis in the granules provided typical recovery curves of these fusion proteins: a diffusion constant with two components of 0.9 and ... 0.8 0.6 0.4 0.2 min Fig Time-lapse LSM analysis of OlvasGFP reveals the dynamic nature of the nuage Schematic diagram of the preparation of PGCs of medaka specimen (A) OlvasGFP was expressed in...

Ngày tải lên: 18/02/2014, 16:20

... simulations of the RBP molten globule state understanding of the molten globule state of RBP, in vitro and in vivo experimental studies have been complemented with a molecular dynamics (MD) simulation ... Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation J Mol Biol 306, 329–347 Marchi M & Ballone P (1999) Adiabatic bias molecular dynamics: a method ... The networks were analyzed using a network principle termed ‘betweenness-centrality’ [37,38] This measure allows the identification of key nodes governing the network of interactions in proteins...

Ngày tải lên: 16/03/2014, 23:20

... Applications of Lasers and Electro-Optics, Laser Institute of America, Orlando, 1999, pp 219–228 [11] J.I Etcheverry, M Mesaros, Molecular dynamics simulation of the production of acoustic waves ... laser ablation of silicon: An MD simulation study, Appl Phys A 66 (1998) 35–42 [10] E Ohmura, I Fukumoto, I Miyamoto, Modified molecular dynamics simulation on ultrafast laser ablation of metal, in: ... Measurements of X-ray lattice constant, thermal expansivity, and isothermal compressibility of argon crystals, Phys Rev 150 (1996) 703–711 53 [24] X Wang, X Xu, Molecular Dynamics Simulation of Heat...

Ngày tải lên: 06/05/2014, 08:54

... amorphous structure of fused silica at 300 K through a so-called “quenching” procedure [10] The structure of the Molecular dynamics simulation of ultrafast laser ablation of fused silica film ... as in (1), qA is the charge of the ion, k is the index of structure layer, rk is the distance between the ion and the center of layer k, and nk is the number density of free electrons in layer ... laser ablation of fused silica is simulated using the molecular dynamics technique Ionization and generation of free electrons, absorption of the laser energy by free electrons, and energy coupling...

Ngày tải lên: 06/05/2014, 08:54

... results are summarized in section III II THEORY OF MD SIMULATION Molecular dynamics simulation is a computational method to investigate the behavior of materials by simulating the atomic motion ... "Application of the Morse Potential Function to Cubic Metals," Physical Review, 114, pp 687-690 11 Etcheverry, J I., and Mesaros, M., 1999, "Molecular Dynamics Simulation of the Production of Acoustic ... Computer Simulation of Liquids, Clarendon Press, Oxford 13 Broughton, J Q and Gilmer, G H., 1983, "Molecular Dynamics Investigation of the Crystal-fluid Interface I Bulk Properties," Journal of Chemical...

Ngày tải lên: 06/05/2014, 08:55

... results are summarized in section III II THEORY OF MD SIMULATION Molecular dynamics simulation is a computational method to investigate the behavior of materials by simulating the atomic motion ... "Application of the Morse Potential Function to Cubic Metals," Physical Review, 114, pp 687-690 11 Etcheverry, J I., and Mesaros, M., 1999, "Molecular Dynamics Simulation of the Production of Acoustic ... Computer Simulation of Liquids, Clarendon Press, Oxford 13 Broughton, J Q and Gilmer, G H., 1983, "Molecular Dynamics Investigation of the Crystal-fluid Interface I Bulk Properties," Journal of Chemical...

Ngày tải lên: 06/05/2014, 08:57

... results are summarized in section III II THEORY OF MD SIMULATION Molecular dynamics simulation is a computational method to investigate the behavior of materials by simulating the atomic motion ... "Application of the Morse Potential Function to Cubic Metals," Physical Review, 114, pp 687-690 11 Etcheverry, J I., and Mesaros, M., 1999, "Molecular Dynamics Simulation of the Production of Acoustic ... Computer Simulation of Liquids, Clarendon Press, Oxford 13 Broughton, J Q and Gilmer, G H., 1983, "Molecular Dynamics Investigation of the Crystal-fluid Interface I Bulk Properties," Journal of Chemical...

Ngày tải lên: 06/05/2014, 08:59

... Berkovich indenters were considered Molecular Dynamics Simulation The interatomic potential function proposed by Tersoff [15–18] that considers the effect of bond angle and covalent bonds has ... Behavior of monocrystalline silicon under cyclic microindentations with a spherical indenter Appl Phys Lett 82(7), 1027–1029 (2003) 12 W.C.D Cheong, L.C Zhang, Molecular dynamics simulation of phase ... between metastable phases of silicon Phys Rev B 50(17), 13043–13046 (1994) ¨ 24 F Shimojo, I Ebbsjo, R.K Kalia, A Nakano, J.P Rino, P Vashishta, Molecular dynamics simulation of structural transformation...

Ngày tải lên: 21/06/2014, 22:20

... Figure Time evolution of the radius of gyration (nm) Time evolution of the radius of gyration (nm) of the unfolding process, at least in respect of CI2 and the homeodomain of engrailed [7] It is ... Moreover, a few folding simulations of have been carried out using implicit solvation models [4-6] In this article, the results of a high-temperature unfolding simulation of the Trp-cage mini-construct ... terms of their radii of gyration, are shown to be Gaussian ensembles Structural features representing each of these ensembles are also illustrated Results and Discussion Molecular dynamics simulations...

Ngày tải lên: 13/08/2014, 22:22

... Atomistic models of carbon nanotubes 16 1.2.2 Continuum models of CNT 19 1.3 Literature review 22 1.3.1 Atomistic simulations of compression and torsional buckling of CNT ... Computational models are broadly classified into atomistic models and continuum models In the following sections, different types of computational models for CNT are described 1.2.1 Atomistic models of ... deformation, torsion, and vibration In general, continuum models of CNT are calibrated from atomistic simulations Existing molecular dynamics (MD) simulation results for CNT under uni-axial deformation,...

Ngày tải lên: 09/09/2015, 11:19

... the MD simulation of nanoscale ductile mode cutting of silicon: (a) a schematic of the MD model, (b) an output of the MD simulation system 47 Figure 2.6 Flow chart of the MD simulation ... Chapter 2: Molecular Dynamics Simulation Method and Model Chapter Molecular Dynamics Simulation Method and Model 2.1 Introduction A simulation system for nanoscale ductile mode cutting of monocrystalline ... Dynamics Simulation Method 2.2.1 The Principles of MD Simulation In the MD simulation method, an appropriate potential energy function of the material 29 Chapter 2: Molecular Dynamics Simulation...

Ngày tải lên: 12/09/2015, 08:16

... (MD), Finite Element (FE) simulation and hybrid simulation of Molecular dynamics and Finite Element The molecular dynamics simulations predicted mechanical properties of copper: The Young’s modulus ... SUMMARY Simulation is an effective method to study the mechanical properties of materials Three kinds of simulations of nano-indentation on copper were carried out: Molecular Dynamics simulation ... curves of four simulations 88 Figure 5.5 Comparison of Von Mises stress of three simulations 90-91 VI LIST OF TABLES Table 2.1 Properties of materials used in indentation cracking measurement of...

Ngày tải lên: 26/11/2015, 12:47

... table of electromechanical analogs for inverse system [9] Fig Simulation circuit of VCS Fig Simulation scheme of power converter with phase control Simulation circuit with phase angle control of ... model of this system, we will divide the system into two subsystems, shown in Fig IV MATHEMATICAL MODEL OF THE VCS Description of one type of two- mass electromagnetic vibratory conveyor is shown ... change of vibratory width is due to change of phase angle By decrease of phase angle, the effective voltage and coil current increase This is caused by increase of the oscillation amplitude of LCE...

Ngày tải lên: 03/01/2014, 19:16

... 25 ns of simulation Peptide conformations are from the final frame of each simulation, which is representative of the final 50 ns of simulation time For perspective, the embedded region of the ... all other simulations of Ab (see Figs S10–S15), except for A2 In simulation A2, the peptide unfolded to the greatest extent of any of the simulations, thus contacting the greatest number of lipids ... Lipid-protein interactions of integral membrane proteins: a comparative simulation study Biophys J 87, 3737–3749 22 Kandasamy SK & Larson RG (2006) Molecular dynamics simulations of model Trans-membrane...

Ngày tải lên: 18/02/2014, 08:20

... rest of the kinetic method was the same as that used for the p-nitroanilide (pNA) substrate Glycoconjugate modelling and molecular dynamics simulations For all molecular modelling and molecular dynamics ... dynamics of MHC class I glycoprotein: a molecular dynamics study Biopolymers 59, 1123 Mukhopadhyay C (1998) Molecular dynamics simulation of glycoprotein-glycans of immunoglobulin G and immunoglobulin ... study of its impact on the protein fundamental biophysical properties [36] It was employed in this work to study the inuence of structural dynamics on the kinetics of a-CT catalysis Two glycans of...

Ngày tải lên: 19/02/2014, 05:20

... activity of RP mRNA for adjustment of the biosynthesis of ribosomes to the requirements of cell growth and differentiation In addition, a relevant contribution of protein turnover to the regulation of ... binding of these two proteins on the 5¢-UTRs of TOP mRNAs led Pellizzoni to propose that La may increase translation, whereas CNBP ⁄ ZNF9 could act as a translational repressor The interaction of ... Analysis of the molecular FEBS Journal 276 (2009) 3199–3210 ª 2009 The Authors Journal compilation ª 2009 FEBS S Caldarola et al mechanism of DBA in cultured cells showed that alteration of any of...

Ngày tải lên: 07/03/2014, 01:20

... elucidate the role of the positively charged residue Arg78 and the effect of the reduction of cationicity of MBP in the triggering of multiple sclerosis Flexible docking calculations of the MBP(74–85) ... comparison of the chemical-shift data of the two peptides suggests that the backbone of the two molecules should exhibit different structural features in both solvents Structure determination of MBP(74–85) ... from the side chain of Arg78 The side chain of Arg78 is less well defined, as in the case of aqueous solution, because of the absence of interactions with the side chains of Asp81 (in the agonist...

Ngày tải lên: 07/03/2014, 16:20

... Ciccotti G & Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J Comp Phys 23, 327–341 64 Simmerling C, ... program for visualization of structure and dynamics of biomolecules and STO – A program for computing stochastic paths In Modeling of Biomolecular Structure 4069 Effect of A .C mismatch in PNAÆDNA ... AC(6–7) step in the DNA strand of PDwt is retained during the entire simulation in spite of the large movement of C7 (Fig 2A) This occurs due to the coordinated movements of C7 and A6 which ensure...

Ngày tải lên: 07/03/2014, 21:20

... differences in the dynamics of these two proteins The rmsd from the starting structures of the two proteins (supplementary Fig S1) showed, in fact, good stability over all the simulation times ... Darden TA & Kolman PA (1995) Molecular dynamics simulation on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins J Am Chem Soc 117, ... Ciccotti G & Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J Comput Phys 23, 327–341 39 Berendsen HJC,...

Ngày tải lên: 16/03/2014, 10:20

... potential consists of two- and three-body interaction terms and were originally fitted to describe the crystalline and liquid silicon phases This potential consists of sums of two- and three-body ... properties of SiNWs The loading state in the present tension simulations is as follows: the relative positions of atoms within the five atomic layers at the top and bottom of NWs are fixed during simulations, ... experiment, because only very short period of time can be simulated due to the time scale of molecular dynamics set by the atomic motion One consequence of the short time scale is that very high...

Ngày tải lên: 16/03/2014, 15:18