molecular dynamics and first principles calculations
IONIC LIQUIDS FOR CELLULOSE PROCESSING AND CARBON CAPTURE FROM FIRST PRINCIPLES CALCULATIONS TO ATOMISTIC SIMULATIONS
... convey my deepest gratitude and warmest thanks to my siblings - Mrs Yatri Devi, Mr S B Gupta, and Mr R.B Gupta and all other relatives and friends for their love and cherished moments I will ... 120 9.2 Models and Methods 121 9.2.1 Atomistic Models 121 9.2.2 Molecular Dynamics Simulations 122 9.2.3 Ab Initio Calculations 124 9.3 Results and Discussion ... increased energy demand and severe global warming are two major but contradictory challenges Fossil fuels (coal, oil, and gas) are supplying nearly 85% of total energy demand and their combustion...
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First principles calculations and in situ characterizations
... interface structures of β-Ge3 N4 /Ge(111) and SrZrO3 /Ge(100) interfaces 2.3 First- principles calculations First- principles or ab initio calculations refer to calculations that not rely on any adjustable ... and Ge3 N4 ), and to study, both experimentally (using XPS and TEM) and theoretically (using first -principles calculations) , the electronic, intrinsic defect, and interface properties and thermal ... bands and obtain the band offsets All-electron calculations can actually mimic this approach, and provide information about core-level lineups as well as band offsets Although pseudopotential calculations...
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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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A Guide to Molecular Mechanics and Quantum Chemical Calculations
... of molecular structure and stability and chemical reactivity and selectivity Chapter introduces Potential Energy Surfaces as the connection between structure and energetics, and shows how molecular ... models” to visualize molecular shape and quantify steric demands Quantum chemical calculations, once a mere novelty, continue to play an ever increasing role in chemical research and teaching They ... a finished book first page 3/21/03, 10:52 AM first page 3/21/03, 10:52 AM To the memory of Edward James Hehre 1912-2002 mentor and loving father first page 3/21/03, 10:52 AM first page 3/21/03,...
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Báo cáo y học: "Determining promoter location based on DNA structure first-principles calculations" ppsx
... (fprom [1], firstef [13], dpf [12] and nscan [29]), the identification of CpG islands (eponine [22], cpgprod [16] and dgsf [21]), compositional sequence biases (mcpromoter [26,33]) and other criteria ... Rise, shift, and slide; (b,d) twist, tilt, and roll Results are shown for the complete training set of promoter regions (a,b) (see Materials and methods) and for the subset with no CpG island (c,d) ... and conservation; and the existence of sequence profiles that might signal promoter region In the first case, statistical algorithms are used to find signals of genes that locate the 5'-end and...
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Lithium nitrogen based compound as lithium ionic conductor and chemical hydride for hydrogen storage experimental and first principles investigation
... Zhitao XIONG, who builds our lab in very effective and committed way with a pair of fat and unusually skillful hands, and I gradually understand and appreciate his unique “Xiong’s style” to guide ... crisis and environmental problems in the 21st century Section 1.2 and 1.3 introduce the basic concepts and knowledge to understand hydrogen storage materials and solid lithium ionic conductor, and ... terms (kBT) due to the molecular degrees of freedom In eqs (1.11) and (1.12), Eelec is the total electronic energy at T=0 K calculated by the first- principles calculations, and the term Hvib (T)...
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Investigation of properties in barium chalcogenides from first principles calculations
... is first proposed Then, the behavior of the oxygen atom on the BaTe(111) surface is studied using first- principles calculations The theory for calculating surface energy from first- principles calculations ... & Kohn (1964) and Kohn & Sham (1965), which provided the foundation for theoretical calculations DFT is one of the most important methods in first- principles calculations First- principles calculation ... (LCs), band structures, densities of state and energy gaps of all binaries, i.e., BaO, BaS, BaSe, BaTe, and BaPo, were calculated based on both the GGA and LDA methods from first- principles calculations...
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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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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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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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First principles optical properties of silicon and germanium nanowires
... Optical gaps in SiNWs and GeNWs: quantum confinement and anisotropy effects In this section, we will describe the electronic properties of hydrogen passivated, free standing silicon and germanium nanowires ... gap in SiNWs (left) and GeNWs (right) as a function of wires’ size and orientation Table DFT-LDA electronic gaps in SiNWs and GeNWs are reported, respectively, in the third and fourth column, ... (NMP4-CT-2004-500198), and by MIUR through NANOSIM and PRIN 2005 We acknowledge the CINECA CPU time granted by INFM We are grateful to Andrea Marini for useful discussions and for providing us...
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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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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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- fair use and first sale principles
- data sharing in molecular dynamics we distinguish between sharing for reads read writes and accumulations
- the molecular structure and conformational dynamics of chitosan polymers an integrated perspect
- collisions and molecular dynamics
- 4 molecular structure and dynamics
- thermodynamics protein modification and molecular dynamics in characterizing lactose repressor protein strategies for co
- unifying molecular dynamics and electronic structure
- principles of cardiovascular molecular biology and genetics
- studies of drug resistance and the dynamic behavior of hiv 1 protease through molecular dynamics simulations
- remarks concerning the partition functions the relation of vpie to condensed phase molecular properties and vibrational dynamics
- energy flow analysis in proteins via ensemble molecular dynamics simulations time resolved vibrational analysis and surficial kirkwood buff theory
- molecular dynamics simulation studies of coupled protein and water dynamics
- first principles components holism and context of the transition to adulthood
- gft method and screened hartree fock exchange potential for first principles band structure calculations
- conformation molecular dynamics and
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