ordering of tasks in molecular dynamics problem

... all (p + 1) combinations of l and m in the range of ≤ l ≤ p and −l ≤ m ≤ l Here K is the number of pseudo particles Following Makino’s approach [14], we restrict the distribution of pseudoparticles ... potential field of the original distribution of the particles The difference is that P2 M2 uses the distribution of point charges, while the Anderson’s method uses potential values In the case of P2 M2, ... fraction of the calculation procedure in the FMM can be performed on such hardware, and the speed up gain remains rather modest An outstanding problem is how to perform a large or all fraction of FMM’s...

Ngày tải lên: 22/03/2014, 11:20

... couplings from protons whose nuclear spins are interacting only very weakly with the unpaired electron spin, e.g protons from the protein backbone within the cofactor binding pocket, protons of ... modification of the cofactorbinding site at the 8a-methyl group and at the linkage of the ribityl side chain Hence, as a first result, structural information regarding the distance and location of the ... (Fig 8), the positions of the two histidines were assigned surprisingly accurately by ENDOR His365 (the analog amino acid of His354 in X laevis) is indeed located in the binding pocket nearby the...

Ngày tải lên: 16/03/2014, 02:20

... is in agreement with the domain organization in the first line The third line shows a summary of the identified linear motifs (after filtering processing taking in account the accessibility of the ... Lys4 of histone H3 tail polyamines polyamines aromatic amines aromatic amines aromatic amines L-amino acids glycine, sarcosine sarcosine gene expression regulation polyamines metabolism vitamin ... differences in the shape of the substratebinding site, the details of the active sites of flavin amine oxidases are strikingly conserved (Fig 3B) In all enzymes listed in Table (except for glycine oxidase),...

Ngày tải lên: 16/03/2014, 02:20

... are involved in recognition of the polyubiquitinated protein substrates, unfolding of the condemned protein [24], removing ubiquitin chains for recycling [25,26] and opening an axial gate into ... presence of proteasome, supporting the direct or indirect involvement of the flavin cofactor in protein complex formation [34] Mdm2 dependent polyubiquitination Fig Proposed mechanisms of ubiquitindependent ... state of the flavin cofactor present in the active site of Lot6p Recruitment of the transcription factor occurs when the flavin is in its fully reduced form This process is independent of the mode of...

Ngày tải lên: 16/03/2014, 02:20

... (b) histogram of the distribution of pore diameters in AAO films anodized for two steps including h in both in the first and the second steps S93 of current up to the same value of the first step ... replication of honeycomb structures of anodic alumina, Science 268 (1995) 1466–1468 [4] H Masuda, K Yada, A Osaka, Self -ordering of cell configuration of anodic porous alumina with large-size pores in ... step, the variation of the anodizing current was recorded against time In addition, ordered polycrystalline domains and the diameter of the nanopores were characterized using SEM on the top and...

Ngày tải lên: 19/03/2014, 16:47

... complaints of spinal and leg bone pain, was recognized as a type of chronic toxicity induced by excess Cd contamination of drinking water and cereals (mainly rice) Since then, the contamination of ... with lines depicting the kinetics of initial arrival of Cd in the respective ROI The X-intercepts of the fitting lines were adopted as the arrival times of the theoretical “leading edge” of the ... transporter protein involved in Cd storage in root vacuoles All high-Cd indica cultivars used in this study showed a loss of function of OsHMA3, resulting in failure to sequester Cd in their root...

Ngày tải lên: 11/08/2014, 11:21

... machining of brittle materials, the machining mechanism is not yet explained clearly In this research, a realistic molecular dynamics (MD) model taking into account the effect of tool cutting ... tool in grinding of ductile metals 12 Figure 1.5 Mechanism of material removal in grinding with machining with high negative rake tools .12 Figure 1.6 A projection of machining ... machining of brittle materials 1.2.4 Diamond Tool Wear in Ductile Mode Cutting Rapid wear of single point diamond tools is a limiting factor in ductile mode cutting of silicon wafers Because of...

Ngày tải lên: 12/09/2015, 08:16

... Digital model of the stone quarry created using the Triangulation with linear interpolation method As pointed out in paragraph 1.2.1 Triangulation with linear interpolation, the domain of the triangulation ... consists of data following two keywords COORD and ZCORN, which have to be included in the input data file The keyword COORD introduces the data describing coordinate lines and the keyword ZCORN introduces ... surfaces of layers generated by SurGe The surfaces of layers must be specified (using the suffix convention) in order of increasing depth beginning from the most top layer, and the top surface of each...

Ngày tải lên: 21/01/2014, 07:20

... composed of two 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 ... class of proteins (chymotrypsin-fold proteases) is directly interlinked with the dynamics of the regions containing the His57 and Asp102 catalytic residues While the importance of this calcium binding ... b-barrel domains with the nature of its collective structural dynamics being attributed to interdomain hinge-bending motions [16,20,21] Due to the location of the active site residues at the interface...

Ngày tải lên: 19/02/2014, 05:20

... 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 ... 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 presence of ... amino group of C7 with A6 (Fig 4B) or through the overlap of the six-member ring of C7 with A6 (Fig 4C) Thus, unlike in PDwt (Fig 2B), uninterrupted stacking prevails at all the steps of DDwt Interestingly,...

Ngày tải lên: 07/03/2014, 21:20

... support of the start-up fund from the College of Engineering and Technology and the Department of Mechanical Engineering at the University of Nebraska at Lincoln References [1] H H€kkinen, U ... Quantum molecular dynamics study of light-to-heat absorption mechanism in atomic systems, Int J Heat Mass Transfer 41 (1998) 839–849 [6] P.L Silvestrelli, M Parrinello, Ab initio molecular dynamics ... U Landman, Superheating, melting, and a annealing of copper surfaces, Phys Rev Lett 71 (1993) 1023–1026 [2] M.D Kluge, J.R Ray, Pulsed laser melting of silicon: A molecular dynamics study, J Chem...

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 ... Especially, the kinetics of melting and solidification of silicon have been investigated detailedly in the context of laser processing and explosive crystallization Using nonequilibrium molecular- dynamics ... to determine the interface velocity-superheating/undercooling function even for single-component materials because of the technical difficulties in measuring the interface temperature during rapid...

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 ... spherical indenter was first adopted to interpret phase transformation features in monocrystalline Si We then adopted a Berkovich indenter in the simulations to compare the difference of phases induced ... shown in Fig 3, are in general similar to the ones induced by a spherical indenter, while the phase transformation region of the former is smaller than the latter A ring surrounding Si-II of a...

Ngày tải lên: 21/06/2014, 22:20

... the start 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, ... movement, and cutting forces during the cutting processes of no-wear, adherence, plowing, and cutting regimes; Komanduri et al [5–7] carried out MD simulations of nanometric cutting of single-crystal ... cutting force in nanometric cutting can be explained by the metallic bonding The special feature of metallic bonding is that the strength of the individual bond has a 123 Fig The resultant cutting...

Ngày tải lên: 22/06/2014, 01:20

... ion in center -of- mass (CM) coordinates VC Velocity of projectile ion in center -of- mass (CM) coordinates φ Angle of recoil after impact in laboratory coordinates Φ Angle of recoil after impact in ... 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 other atoms of the ... DOCTOR OF PHILOSOPHY DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2006 ACKNOWLEDGEMENT I wish to thank my main supervisor, Associate Professor Srinivasan...

Ngày tải lên: 12/09/2015, 21:02

... version of the PES This process of simulating the reaction, choosing a configuration, performing the ab initio calculation and adding a new data point to the set is repeated again and again until ... powerful theoretical tool in the simulation of reaction dynamics In this chapter, we give a brief review of some basic concepts in molecular reaction dynamics[ 18] We first introduce the approximation ... locally define a 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...

Ngày tải lên: 13/09/2015, 19:53

... two include the substitution of methionine (M) by the amino acids isoleucine (I) or valine (V) in the YMDD motif (C domain) at position rtM204V/I In the majority of cases, these mutations in the ... no intermediate high Complexity of Labor Automatability interpretation intensiveness intermediate intermediate low intermediate intermediate high Intermediate high high low low intermediate intermediate ... its role as a ‘baseline’ indicator of HBV infectivity, the measurement of viral load is an indispensable means for monitoring and confirming resistance to lamivudine therapy Indeed, resistance...

Ngày tải lên: 03/11/2012, 09:41

... chains are shown in gray and light chains in pink Solid black lines indicate continuation of the polypeptide backbone (simple lines indicate the constant parts of the antibody, curly lines indicate ... expressed in plants Heavy-chain derivatives are shown in gray and light-chain derivatives in pink Solid black lines indicate continuation of the polypeptide backbone (simple lines indicate the ... advantages of tomato include the high biomass yields (about 68,000 kg/ha, approaching the yields possible in tobacco) and the increased containment offered by growth in greenhouses Instead of introducing...

Ngày tải lên: 25/10/2013, 05:20

... IVIg to recombinant human IFN-c (D) Increased binding of low-pH buffer-exposed IVIg to human factor H In both panels, binding of the native IVIg is indicated by a solid line, and that of the low-pH ... same antigen– antibody interaction in the presence of increasing concentrations of NaCl In both experiments, binding intensities are represented in RU, and each data point shows the mean value ... appearance of a number of novel antigen-binding specificities (Fig 1B) Enhanced binding of low-pH buffer-exposed IVIg to recombinant human interferon-c (IFN-c) and other self-antigens Interactions of...

Ngày tải lên: 16/02/2014, 15:20

... as increasing lipid order in the cytofacial leaflet Simulations of melittin in DPPC lead to an interesting comparison with the Ab-DPPC simulations reported in the present study Both melittin and ... experimentally-determined thickness of 3.7 nm [38] It is also observed that melittin can lead to a similar magnitude of bilayer thinning, in the order of 0.5–1.0 nm This thinning only occurs in regions ... lowest numbering, increasing as the lipids are further away from the peptide For clarity, running averages of the data are shown, using a window of ten data points designation In the case of simulation...

Ngày tải lên: 18/02/2014, 08:20