collisions and molecular dynamics
Báo cáo khoa học: NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist Structural implications for the MHC II (I-Au)–peptide complex from docking calculations ppt
... various systems comprised 3899 and 4516 SPC molecules for the agonist and the antagonist in water, respectively, and 817 and 927 Me2SO molecules for the agonist and the antagonist, respectively, ... [82] and (B) sequence alignment of the Vb chain TCR(79–83), MBP(74–85) and MBP(95–103) P5 and P8 are prominent, solvent-exposed TCR contact residues of the MBP(86–105) peptide, and P4, P6 and ... conformation of active and nonactive backbone cyclic analogs of substance P as a tool to elucidate features of the bioactive conformation: NMR and molecular dynamics in DMSO and water J Med Chem...
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Báo cáo khoa học: Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics pdf
... PAH_2 (2pu0) and FPAH (2pu1) Molecular dynamics Molecular dynamics simulations of 10 ns duration each were performed on the PEP complex structure, and also a structure in which the PEP and site II ... sulfate_1 and sulfate_2 structures, respectively Fig (A) Projections of the six new crystal structures and molecular dynamics trajectories on to EVs and resulting from the essential dynamics analysis ... 20 mm of ligand (PEP, PAH or FPAH) for and flash-cooled X-ray diffraction data were collected from two native crystals (referred to as sulfate_2 and sulfate_3 in Table 1) and four ligand-cocrystallised...
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A modeling study of ion implantation in crystalline silicon involving monte carlo and molecular dynamics methods
... METHODOLOGY II: MOLECULAR DYNAMICS METHODS 99 Theory of Molecular Dynamics (MD) 99 5.1.1 Integration algorithm 101 5.1.2 Interatomic potentials and force calculations 103 5.1.3 Boundary and initial ... tilt and 0° rotation and 2keV 1×1014 atoms/cm2 45° tilt and 45° rotation 82 4.10 Comparison of experimental SIMS data and simulation for N 3keV 1×1014 atoms/cm2 7° tilt and 22° rotation and 15keV ... tilt and 45° rotation and 30keV 5×1013 atoms/cm2 5.2° tilt and 17° rotation 84 4.14 Comparison of experimental SIMS data and simulation for As 5keV 1×1015 atoms/cm2 0° tilt and 0° rotation and...
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Tài liệu Báo cáo khoa học: Analysis of the molecular dynamics of medaka nuage proteins by fluorescence correlation spectroscopy and fluorescence recovery after photobleaching doc
... time point t, T0 and Tt represent the uorescence in the whole cell at time points and t, respectively, and B0 and Bt represent the uorescence in the bleached region at time points and t Diffusion ... or olvasRFP fusion gene, and diffusion analysis by FCS and FRAP was performed As shown in Fig 4A, OlvasGFP and NanosRFP colocalized on the granules in the cytoplasm, and similarly, Olvas RFP ... nuage in the PGC 344 Merge Fig Olvas, Nanos and Tudor fusion proteins expressed in the HeLa cell form granules olvasGFP and nanosRFP (A), and olvas RFP and tudorGFP (B), were cotransfected into...
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Tài liệu Báo cáo khoa học: Influence of modulated structural dynamics on the kinetics of a-chymotrypsin catalysis Insights through chemical glycosylation, molecular dynamics and domain motion analysis pptx
... the p-nitroanilide (pNA) substrate Glycoconjugate modelling and molecular dynamics simulations For all molecular modelling and molecular dynamics (MD) simulation experiments the yasara suite of ... structure and 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 ... and K Griebenow Structural dynamics and serine protease catalysis Table Kinetic and thermodynamic parameters derived from amide H D exchange rates for a-CT and for the various lactose-a-CT and...
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Báo cáo khoa học: Molecular dynamics structures of peptide nucleic acidÆDNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene ppt
... strand, and GA(23–24) (Fig 2C) and AT(24–25) (Fig 2D) steps of the PNA strand, flanking the A24 C7 mismatch in PDwt (Scheme 1), and the corresponding AT(6–7) & TC(7–8) steps of the DNA strand ... bond distances (C and E) and angles (D and F) over ns dynamics Note the strong preference for N1(A24) .N4(C7) hydrogen bond beyond 220 ps (C and D) Conformation of the PNA strand in PNAÆDNA duplexes ... cis) (A and B) and (a,e) (gauche+, trans) (C and D) conformations O6¢(G) .N2(G) hydrogen bond (C and D) is shown in dotted line (see also Fig 10 and text) Hydrogens at C2¢, C3¢, C5¢ and C8¢...
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Molecular dynamics simulations of the tensile and melting behaviours of silicon nanowires
... pentagonal and hexagonal SiNWs along the /11 0S direction Justo et al [24] reported classical molecular dynamic simulations of silicon nanowires of various shapes and orientations Menon [20] and Ponomareva ... 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 interaction ... stretched and preserve their fourfold coordination in the nanowire, and no structural defects appear at this stage For larger strains, bond breakage in the outmost layer is observed and spreads...
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molecular dynamics simulation of thermal and thermomechanical phenomena in picosecond laser material interaction
... dt2 j6¼i displacement velocity ð1Þ where mi and ri stand for the mass and position of atom i, respectively Fij is the interaction force between atoms i and j, which is calculated from the Lennard–Jones ... used, and are listed in Table [22,23] The thermal conductivity and specific heat have been adjusted based on the MD simulation results [24] Results and discussions In this work, the thermal and ... cells in both x and y directions, and 320 fcc unit cells in the z direction This target consists of 1,310,720 atoms, and measures 17.32 nm in both x and y directions, and 173.25 nm in the z direction...
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molecular dynamics studies of ultrafast laser induced phase and structural change in crystalline silicon
... of crystalline-liquid and liquid-amorphous silicon; and the second focus is to understand the resulting microstructure, i.e., crystalline vs amorphous, and the qualitative and quantitative relations ... Chowdhury, Molecular dynamics study of phase change mechanisms during femtosecond laser ablation, J Heat Transfer 126 (2004) 727–734 [10] X Wang, X Xu, Molecular dynamics simulation of thermal and thermomechanical ... kinetics of melting and solidification of silicon have been investigated detailedly in the context of laser processing and explosive crystallization Using nonequilibrium molecular- dynamics (NEMD)...
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molecular dynamics simulation of heat transfer and phase change during
... S., and Kuroki, M., 1993, "Molecular Dynamics Study of Solid Melting and Vaporization by Laser Irradiation," International Journal of Heat and Mass Transfer, 36, pp 20612067 Herrmann, R F W., and ... S., and Garrison, J., 1997, "Molecular Dynamics Model for Laser Ablation and Desorption of Organic Solids," Journal of Physical Chemistry B, 101, pp 2028-2037 Zhigilei, L V., Kodali, P B S., and ... starts, and the lattice structure is destroyed in the melted region and is replaced by a random atomic distribution After 20 ps, the solid liquid interface stops moving into the target, and vaporized...
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molecular dynamics simulation of heat transfer and phase change during
... S., and Kuroki, M., 1993, "Molecular Dynamics Study of Solid Melting and Vaporization by Laser Irradiation," International Journal of Heat and Mass Transfer, 36, pp 20612067 Herrmann, R F W., and ... S., and Garrison, J., 1997, "Molecular Dynamics Model for Laser Ablation and Desorption of Organic Solids," Journal of Physical Chemistry B, 101, pp 2028-2037 Zhigilei, L V., Kodali, P B S., and ... starts, and the lattice structure is destroyed in the melted region and is replaced by a random atomic distribution After 20 ps, the solid liquid interface stops moving into the target, and vaporized...
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molecular dynamics simulation of heat transfer and phase change during
... S., and Kuroki, M., 1993, "Molecular Dynamics Study of Solid Melting and Vaporization by Laser Irradiation," International Journal of Heat and Mass Transfer, 36, pp 20612067 Herrmann, R F W., and ... S., and Garrison, J., 1997, "Molecular Dynamics Model for Laser Ablation and Desorption of Organic Solids," Journal of Physical Chemistry B, 101, pp 2028-2037 Zhigilei, L V., Kodali, P B S., and ... starts, and the lattice structure is destroyed in the melted region and is replaced by a random atomic distribution After 20 ps, the solid liquid interface stops moving into the target, and vaporized...
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Báo cáo hóa học: "Molecular Dynamics Simulations of the Roller Nanoimprint Process: Adhesion and Other Mechanical Characteristics" pot
... the process of nanoimprinting a and roller imprinting (b and d) a and b were simulated at room temperature and c and d were simulated at a temperature of 400 K and 500 K, respectively simulations ... study are to understand the deformation behavior of imprinted film and the effect of adhesion and friction with changes of the roller tooth geometry, imprint temperature, and imprint depth using ... characteristic width and height of the roller tooth were both nm The roller was composed of 11294 atoms The width and height of the Au substrate, which was composed of 99840 atoms, were 32.6 and 21.2 nm,...
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Báo cáo hóa học: " Molecular Dynamics Simulation of Nanoindentation-induced Mechanical Deformation and Phase Transformation in Monocrystalline Silicon" potx
... 72 and nanoindentation-induced phase transformations during loading and unloading Both spherical and Berkovich indenters were considered Molecular Dynamics Simulation The ... effect of bond angle and covalent bonds has been shown to be particularly feasible in dealing with IV elements and those with a diamond lattice structure such as carbon, silicon, and germanium The ... metastable Si-III and Si-XII phases is strongly stress-dependent, different stress distributions induced by spherical and Berkovich indenters would result in different Si-III and Si-XII distributions...
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MOLECULAR DYNAMICS – THEORETICAL DEVELOPMENTS AND APPLICATIONS IN NANOTECHNOLOGY AND ENERGY pot
... Antisymmetrized Molecular Dynamics and Nuclear Structure 133 Gaotsiwe J Rampho and Sofianos A Sofianos VI Contents Chapter Antisymmetrized Molecular Dynamics with Bare Nuclear Interactions: Brueckner-AMD, and ... permission 10 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy The DF algorithm gracefully handles molecular systems consisting of small solute and solvent ... the 30 Molecular Dynamics – Theoretical Developments and Applications in Nanotechnology and Energy energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular...
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practical applications of molecular dynamics techniques and time correlation function theories
... the molecular dynamics techniques used to calculate molecular volumes are introduced Chapter outlines the calculation of the molecular volumes of water, the β-sheet peptide, and methane and also ... the molecular dynamics techniques employed in calculating molecular volumes are introduced In Chapter 3, the application of molecular dynamics to several simple model system is discussed, and ... TCFs A and B under the Anharmonic Approximation 101 10.6 Relating BR and BI under the Anharmonic Approximation 107 vi Practical Applications of Molecular Dynamics Techniques and Time...
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Comprehensive molecular dynamics simulations of carbon nanotubes under axial force or torsion vibration and new continuum models
... Mitra and Bharati Sengupta, and my mother Mina Roy Chowdhury for being so awesome, caring and supporting My special thanks also go to three of my very close childhood friends Sandip Saha, Sandip ... graphene lattice and CNT unit cell 40 Figure 2.2: Molecular dynamics simulation set-up for CNT under uniaxial deformation/torsion 41 Figure 2.3: Molecular dynamics simulation ... 101 Figure 4.16: Effect of θ and twist direction on cr and Mcr Filled symbols denote cr and Mcr values under clockwise torsion and open symbols denote cr and Mcr values under anticlockwise...
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Tài liệu OXFORD DICTIONARY OF Biochemistry and Molecular Biology REVISED EDITION Managing Editor Professor pdf
... cortisol and the androgens dehydroepiandrosterone and androstenedione adrenaline see epinephrine adrenal medulla see adrenal gland adrenal medullary hormone any catecholamine hormone elaborated and ... produced by the adrenal glands the adrenal gland itself adrenal androgen any of the C19 steroid hormones produced in the cortex of the adrenal gland, including androstenedione and testosterone adrenal ... where p and A are phosphoric and adenosine residues, respectively, and a and n are small integers (a = 1, 2, or and n commonly = 2, 3, or 4) Potent inhibitors of protein biosynthesis in vivo and...
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Chemical bonding and molecular geometry( liên két hóa học và hình học phân tử)
... Chemical bonding and molecular geometry from Lewis to electron densities / R.i Gillespie, P.L.A Popelier p cm -(Topics in inorganic chemistry) Includes bibliographical references and index ISBN ... function L = - VZ p for L = au (blue) and L = 0.60 au (orange) The L = 0.60 surface shows the charge concentations corresponding to the lone pairs on the sulfur atom and torodial charge concentrations ... Oxford University Press Oxford New York Athens Auckland Bangkok Bogota Buenos Aires Calcutta Cape Town Chennai Dar es Salaam Delhi Florence Hong Kong...
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Chemical bonding and molecular geometry( liên kết hóa học và hình học phân tử)
... Chemical bonding and molecular geometry from Lewis to electron densities / R.i Gillespie, P.L.A Popelier p cm -(Topics in inorganic chemistry) Includes bibliographical references and index ISBN ... function L = - VZ p for L = au (blue) and L = 0.60 au (orange) The L = 0.60 surface shows the charge concentations corresponding to the lone pairs on the sulfur atom and torodial charge concentrations ... Oxford University Press Oxford New York Athens Auckland Bangkok Bogota Buenos Aires Calcutta Cape Town Chennai Dar es Salaam Delhi Florence Hong Kong...
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