vibrational energy flow in proteins molecular dynamics based methods

... advances made in fragment molecular orbital based molecular dynamics, which is the ab inito molecular dynamics simulations, to treat large molecular systems with solvent molecules being treated ... the kinetic and potential energy over time at the minimum temperature of 298 K and initial kinetic energy of 0.1 eV The kinetic energy oscillates during the collision with the slower cooling rate ... stronger in cis-platin than in trans-platin As a result, the Pt-Cl bonds are easier to elongate for the cleavage in the hydrated cis-platin than in the hydrated trans-platin Thus, by using FMOMD...

Ngày tải lên: 28/06/2014, 10:20

... effect is found in a special class of proteins, so-called allosteric proteins Substrate binding to one subunit of these multimeric proteins triggers conformational changes in proteins which alters ... MAINTAINED, throughout NOT MAINTAINED; rather motions created, burying surface Motion at interface Parallel to plane of interface Perpendicular to interface (shear) Mainchain packing Constrained ... functions In a protein, the amino acids are linked together into a polypeptide chain by peptide bond, as being indicated in Fig 1.1 The peptide bond itself is rigid, because it is involved into tautomerization...

Ngày tải lên: 17/09/2015, 17:17

... properties of proteins [13] and binding interactions [14] FRAP is a conventional technique used to study the kinetic properties of proteins in a cell by measuring the uorescence recovery rate in a bleached ... photobleaching (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 ... 342 Herein we report dynamic properties of proteins in the PGC determined by FCS and FRAP A fusion protein consisting of Olvas and green uorescent protein (GFP) (OlvasGFP) expressed in the PGC...

Ngày tải lên: 18/02/2014, 16:20

... rigid domains [domain (residues 1119) and domain (residues 151245)] linked by an interdomain hinge (residues 120150) Interestingly, the connection between the two domains and the hinge appears ... reducing the kinetics of catalysis The results also suggest that the dynamics of the calcium binding site in this structural class of proteins (chymotrypsin-fold proteases) is directly interlinked ... (II) binding site in trypsin, chymotrypsin, and subtilisin Biochemistry 28, 75247531 83 Krieger E, Darden T, Nabuurs SB, Finkelstein A & Vriend G (2004) Making optimal use of empirical energy...

Ngày tải lên: 19/02/2014, 05:20

... C2¢ endo domain Discussion Base pair mismatch in duplex DNA contributes an element of instability resulting in lowering of the melting temperature and increase in free energy Surprisingly, the ... deciphering the origin of the destabilization and hence, diminution of the melting temperature (Tm) in the former Base stacking in the vicinity of A C mismatch in PNAÆDNA and DNA duplexes Intra ... hydrogen bond in PNAÆDNA than in DNA duplex As expected, these bring forth significant variableness in the water interactions surrounding the mismatch Water interaction in the vicinity of A C mismatch...

Ngày tải lên: 07/03/2014, 21:20

... performed in the same way as in the original FMM At the M2M transition stage, we compute positions and charges of pseudoparticles, instead of forming multipole expansion as in the original FMM ... MDGRAPE-2 board (16 pipelines, 48GFlops) and a host computer Pentium 2.2GHz, Intel D850 motherboard In the tests, we distributed particles uniformly within a unit cube centered at origin, and evaluated ... Rokhlin, A fast algorithm for particle simulations, Journal of Computational Physics 73 (1987) 325 [3] P Lakshminarasimhulu, J.D Madura, A cell multipole based domain decomposition algorithm for molecular...

Ngày tải lên: 22/03/2014, 11:20

... site involving a His residue at position ‘0’ (i.e immediately preceding the natural initiator Met within the tail downstream of the thrombin cleavage site in the N-terminal extension containing ... optimized inhibitors of this kind should have minimal effects on other proteins in vivo Indeed, a prodrug version of an aldolase inhibitor kills parasite cells without detectable cytotoxicity against ... residues (e.g lysines in both cases), selective inhibitors against aldolase [24] and phosphofructokinase [25] have been developed Despite bearing chemically reactive groups, by combining high affinity...

Ngày tải lên: 23/03/2014, 07:20

... of Engineering and Technology and the Department of Mechanical Engineering at the University of Nebraska at Lincoln References [1] H H€kkinen, U Landman, Superheating, melting, and a annealing ... and the linked list methods [18] In these methods, the computational domain is divided to small cells with a characteristic size of rc , and each atom is sorted into a certain cell based on its ... Only the interaction between atoms in adjacent cells is considered The laser beam absorption in the target is simulated by exciting the kinetic energy of atoms, and is fulfilled by scaling the...

Ngày tải lên: 06/05/2014, 08:54

... the interface superheating and undercooling, during which the RDF was tried to be applied in determining the interface Tint DT Vint Dz melt-solid interface temperature interfacial superheating/undercooling ... difficulties in measuring the interface temperature during rapid resolidification, however, in order to analyze interface kinetics, the interface location and the interface temperature need to be determined ... to investigate the interface kinetics, i.e., interface superheating and undercooling temperature in the phase change process induced by an ultrafast laser pulse, and its effect on the resulting...

Ngày tải lên: 06/05/2014, 08:54

... 72 and nanoindentation-induced phase transformations during loading and unloading Both spherical and Berkovich indenters were considered Molecular Dynamics Simulation The interatomic potential ... Si(100) were investigated through MD simulations The Si-III and Si-XII were distinguished from Si-I by searching the presence of the fifth neighboring atom within a non-bonding length Crystallinity 123 ... different stress distributions induced by spherical and Berkovich indenters would result in different Si-III and Si-XII distributions within the nanoindentation-induced deformed region Boyer et...

Ngày tải lên: 21/06/2014, 22:20

... nanometric cutting The workpiece sizes are 40 20 30 nm containing 2,053,594 atoms, 40 40 30 nm containing 4,098,686 atoms, and 70 44 40 nm containing 10,137,600 atoms The diamond tool contains 8446 ... atomic interactions in the MD simulations of nanometric cutting processes: (1) the interaction in the workpiece; (2) the interaction between the workpiece and the tool; and (3) the interaction in ... of the cutting Then the cutting forces tend to remain steady during the rest of the cutting process The formation of dislocations results in the release of the accumulated cutting energy, which...

Ngày tải lên: 22/06/2014, 01:20

... efficient packet discarding policy should consider preceding nodes’ invested energy In the matter, the α coefficients could evolve based on their sink proximity or, in the same way, in their distance ... evaluated the consumed energy by transmitting reliably the whole image (16 394 bytes, including the 10-byte image header) without applying DWT In the following, we call that the original scenario The ... Comparison of resulting images by applying different prioritization strategies and packet discarding the energy savings Let us show this statement by applying different α in our model Graphics in Figure...

Ngày tải lên: 22/06/2014, 22:20

... Discussion Variations in the infecting dose As expected, increases to the constant φ resulted in an increase in a person's viral load It bears noting that, increasing the viral load incoming from a person's ... cells after single instance of re-introducing viral antigen (B) assuming antigen is eliminated (black line) or antigen persists (red line), as well as repeated re-introduction (C) assuming antigen ... modelling has enriched our understanding of the properties of infectious disease thus enabling humankind to better control its spread [2] Within an individual host, a major factor governing infectious...

Ngày tải lên: 13/08/2014, 16:21

Ngày tải lên: 13/11/2014, 10:12

... Models: Monte Carlo and Molecular Dynamics methods The atoms set in motion by interactions with incident ions dissipate their initial kinetic energies in a series of inelastic encounters with ... electronic energy loss in modified Oen-Robinson model Pd Probability that in a certain depth interval of the target a pseudo-projectile is moving in a damaged region xix Ps Saturation level of sub-linear ... for the scattering of an electron EF Fermi energy xx CHAPTER 1.1 INTRODUCTION Motivation The main driving force for performance in the semiconductor industry lies in the need to increase both...

Ngày tải lên: 12/09/2015, 21:02

... the corresponding nuclear wave function in the adiabatic representation Substituting the expression in Eq.(2.5) into Eq.(2.3), and integrating over the electron coordinates, we obtain the coupled ... many years in the accurate ab initio evaluation of the molecular energy Further information about the shape of the energy surface may be obtained from evaluating derivatives of the energy with ... set of 3N − independent internal coordinates as linear combination of the {Zn } Thus at a certain configuration, Z, let ξ denote the 3N − local internal coordinates The potential energy at a configuration,...

Ngày tải lên: 13/09/2015, 19:53

... comparing the consistency between the new design and a routine control selection design in a large case-control study that was incorporated into a nationwide mortality survey in China in 1989–1991 ... smoking-related cancer deaths in Chinese adult men We also offer specific suggestions that we believe are useful in choosing controls within the framework of the study principles SUBJECTS AND METHODS ... assessment of smoking habits in the control group,1 however, insisting on a dead control group violates the study base principle, since the base consists of living subjects In the same situation,...

Ngày tải lên: 26/10/2012, 09:48

... reported injury in spite of the installation of more than 600 mega Watts of wind energy world wide It was concluded that the risk of anything or anyone being hit by ice from a wind turbine has ... person being hit by a lightning strike in the UK c Noise: In wind turbines, the noise emitted can be due to the moving mechanical parts or due to revolution of blades Modern wind turbines are ... continue unhindered after the wind farm has been built.(ref : Greece paper) Besides this, the leasing of land for wind turbines, can bring substantial benefits to landowners in the form of increased...

Ngày tải lên: 25/04/2013, 08:20

... ACTION PLAN MAKING A CHART OF THE ENERGY CONSUMPTION IN H.C.M CITY INTRODUCTION OF GOAL • In new basic program of English 11.Unit 11 “sources of energy Part D writing: describing information from ... impossible without being applied for live society • Interactive learning is impossible without pairworks and groupworks And learning or teaching in the 21st century must always be put in the 4L situation ... Work in groups of four or five Each group works independently The teacher is the monitor and the facilitator Every member in the group has to take part in their work going to each of the family in...

Ngày tải lên: 22/07/2013, 01:27