nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides theory meets experiment
molecular dynamics simulation of thermal and thermomechanical phenomena in picosecond laser material interaction
... College 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 ... Silvestrelli, M Parrinello, Ab initio molecular dynamics simulation of laser melting of graphite, J Appl Phys 83 (1998) 2478–2483 [7] H.O Jeschke, M.E Garcia, K.H Bennemann, Theory for laser-induced ultrafast ... i index of the atom In this work, MD simulations are conducted to study the thermal and thermomechanical phenomena in laser argon interaction using the laser absorption model in which laser energy...
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molecular dynamics simulation of ultrafast laser ablation of fused silica film
... 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 obtained fused ... 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 between ... defined 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...
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molecular dynamics simulation of heat transfer and phase change during
... metal interaction in two steps including photon energy absorption in electrons and lattice heating through interaction with electrons A large body of the MD simulation of laser material interaction ... 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 ... an ensemble average of a domain with thickness of 2.5σ in the z direction In the calculation using the finite difference method, properties of the target obtained with the MD simulation are used...
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molecular dynamics simulation of heat transfer and phase change during
... metal interaction in two steps including photon energy absorption in electrons and lattice heating through interaction with electrons A large body of the MD simulation of laser material interaction ... 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 ... an ensemble average of a domain with thickness of 2.5σ in the z direction In the calculation using the finite difference method, properties of the target obtained with the MD simulation are used...
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molecular dynamics simulation of heat transfer and phase change during
... metal interaction in two steps including photon energy absorption in electrons and lattice heating through interaction with electrons A large body of the MD simulation of laser material interaction ... 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 ... an ensemble average of a domain with thickness of 2.5σ in the z direction In the calculation using the finite difference method, properties of the target obtained with the MD simulation are used...
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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 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 ... 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...
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Molecular dynamics simulation of nano indentation
... Three kinds of simulations of nano-indentation on copper were carried out: Molecular Dynamics simulation (MD), Finite Element (FE) simulation and hybrid simulation of Molecular dynamics and Finite ... 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 ... 15 2.4 Hybrid Simulation of Molecular Dynamics Chapter and Finite Element 20 Molecular Dynamics Simulations 27 3.1 Potential Functions 27 3.2 Nano-indentation Simulation 31 3.2.1 Initialization...
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Báo cáo khoa học: Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach ppt
... and ligand binding of other members of the lipocalin superfamily This is of particular interest in the light of the development of engineered lipocalins for carrying novel ligands in therapeutic ... retinolbinding protein to the epididymal retinoic acid-binding protein Biochem J 362, 265–271 Calderone V, Berni R & Zanotti G (2003) High-resolution structures of retinol-binding protein in complex ... structure of RBP [35], and so were excluded from the simulations reported here The binding of TTR to RBP has been shown to stabilize the binding of retinol to RBP Studies of the interactions of chimaera...
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Báo cáo y học: " High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study" potx
... starting structure Dagget, molecular dynamics simulations are capable of unraveling whole protein folding / unfolding pathways [1] Indeed, simulation techniques have been widely used for studying ... McLachlan AD: Solvation energy in protein folding and binding Nature 1986, 319:199-203 Hess B, Bekker H, Berendsen HJC, Fraaije JGEM: LINCS: A linear constraint solver for molecular simulations J Comp ... determined [3] 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...
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Study of nanoscale ductile mode cutting of silicon using molecular dynamics simulation
... are actively involved in investigating these processes 1.2.3.2 MD Simulation of Machining of Metals In LRL, Hoover et al (1989) studied the interface tribology using MD simulation of fabrication ... 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...
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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
... illustrated in Table Evidently, there is a preference for serine or threonine as an anchor point for position P9 of the MBP peptide-binding grooves Interestingly, truncation of the C-terminus of the ... solution based on the intermolecular energy was kept, bringing the total effective docking trials to 10 000 The best 500 solutions sorted according to the intermolecular energy (sum of van der Waals, ... importance of the nature of the amino acid at position 81 of the encephalitogenic sequence 74–85 of guinea MBP: replacement of Asp81 with an alanine seems to break a chain of electrostatic interactions,...
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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
... 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 ... 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 ... interactions surrounding the mismatch Water interaction in the vicinity of A C mismatch Figure 7A–L depicts the nature of water interaction in the neighbourhood of A24 C7 mismatch in PDwt Water interaction...
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Molecular dynamics simulations of the tensile and melting behaviours of silicon nanowires
... increasing temperature and with decreasing strain rate, and increases with increasing diameter Additionally, it is observed that the melting temperature of the SiNWs increases with increasing diameter, ... with decreasing diameter of SiNWs at a given temperature, which indicates that surface energy increases with decreasing diameter The potential energies also increase linearly with increasing temperature ... which indicates the melting of the nanowire Conclusions In this paper, molecular dynamics simulations with Stillinger–Weber potentials are used to simulate the tensile and melting behaviours of...
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Simulation of Ground-Water Flow and Evaluation of Water-Management Alternatives in the Assabet River Basin, Eastern Massachusetts pptx
... conditions, in average annual inflows to and outflows from the surficial layer of the simulated groundwater -flow system in subbasins of the A, Assabet River Main Stem; and B, tributary subbasins, in a ... conditions, in average annual inflows to and outflows from the surficial layer of the simulated ground-water -flow system in subbasins of the A, Assabet River Main Stem; and B, tributary subbasins, in ... Brooks Increases in Assabet River flows were small, with reductions in the wastewater component of flow in September of percent or less 2 Simulation of Ground-Water Flow and Evaluation of Water-Management...
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molecular dynamics calculation of critical point
... functions determining interatomic interactions are known NUMERICAL APPROACH In molecular dynamics (MD) simulations, interactions between molecules or atoms in a material are determined by a prescribed ... Calculation of Critical Point of Nickel 13 liquid–gas saturation lines (binodes), as will be seen in the next section The peak of the two saturation lines is the critical point, and its parameters of ... and is applied in this work to describe interactions among nickel atoms, rij = D e−2b(rij −rε ) − e−b(rij −rε ) (1) Molecular Dynamics Calculation of Critical Point of Nickel 11 In Eq (1), D is...
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molecular dynamics studies of ultrafast laser induced nonthermal melting
... structure, since part of the energy deposited into the coherent phonons is converted to the kinetic energy of atoms However, we call this phenomena “nonthermal” melting in order to distinguish it ... 2.876 4.312 5.0 Molecular dynamics studies of ultrafast laser-induced nonthermal melting Fig Snapshots of atomic distributions of (a) laser heating with absorbed laser fluence of 13.1 J/m2 and ... in the ultrafast laser melting of silver [22] It Y Wang, X Xu Fig Temperature distribution in Bi2 Te3 thin film (a) Laser heating with absorbed laser fluence of 13 J/m2 and (b) nonthermal melting...
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molecular dynamics studies of ultrafast laser induced phase and structural change in crystalline silicon
... 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 temperature interface ... 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 ... Cheng, X Xu, Molecular dynamics calculation of critical point of nickel, Int J Thermophys 28 (2007) 9–19 [35] C Cheng, X Xu, Molecular dynamics simulation of ultrafast laser ablation of fused silica,...
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molecular dynamics simulation
... increase of atomic kinetic energy in laser heating, atoms vibrate more intensely in the solid region, resulting in a lower peak of the number density of atoms and a wider distribution As laser heating ... direction In the finite difference calculation, properties of argon obtained with the MD simulation are used in order to study the validity of the continuum approach in ps laser materials interaction, ... than the melting point ͑83.8 K͒, indicating superheating at the melting front Furthermore, superheating is observed at the liquid-vapor interface (z ϳ13.5 nm) at 15 ps, which is indicated by...
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Báo cáo hóa học: "Molecular Dynamics Simulations of the Roller Nanoimprint Process: Adhesion and Other Mechanical Characteristics" pot
... imprint force in the loading period increased with imprint depth The effect of imprint depth was especially strong in the Z-component, as shown in Fig 6b The time at which the maximum imprint ... This indicates that the imprint depth dominates the magnitude of the maximum imprint force and the time when it happens In the unloading process, the adhesion increased as the imprint depth increased ... imprinted using the Ni mold The imprint force, adhesion, stress, and strain distributions of the roller imprint process were studied using MD Fig Stress distribution in the process of a nanoimprinting...
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Molecular level investigation of interface energy level alignment for organic electronics
... electron in the material orbit with energy (Ei) to the vacuum The 18 energy of the photoelectron can be detected as kinetic energy (E'k) The certain energy of the initial energy state of the electron ... higher kinetic energies The WF or IP measured in this method represents the intrinsic properties of samples, eliminating the influence of the spectrometer Owing to the higher photon energy of X-rays, ... in linear scale The inset in panel (b) showing the corresponding UPS spectra at the low-kinetic energy region with a sample bias of -7 V 72 Figure 5.3.1 UPS spectra during the deposition of...
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