Molecular Dynamics Study Of The Mechanical Behavior Of Nickel Nanowire: Strain Rate Effects

We present the analysis of uniaxial deformation of nickel nanowires using molecular dynamics simulations, and address the strain rate effects on mechanical responses and deformation behavior. The applied strain rate is ranging from 1 x 10(8) s(-1) to 1.4 x 10(11) s(-1). The results show that two critical strain rates, i.e., 5 x 10(9) s(-1) and 8 x 10(10) s(-1), are observed to play a pivotal role in switching between plastic deformation modes. At strain rate below 5 x 10(9) s(-1), Ni nanowire maintains its crystalline structure with neck occurring at the end of loading, and the plastic deformation is characterized by {111} slippages associated with Shockley partial dislocations and rearrangements of atoms close to necking region. At strain rate above 8x10(10) s(-1), Ni nanowire transforms from a fcc crystal into a completely amorphous state once beyond the yield point, and hereafter it deforms uniformly without obvious necking until the end of simulation. For strain rate between 5 x 10(9) s(-1) and 8 x 10(10) s(-1), only part of the nanowire exhibits amorphous state after yielding while the other part remains crystalline state. Both the {111} slippages in ordered region and homogenous deformation in amorphous region contribute to the plastic deformation. (C) 2007 Published by Elsevier B.V.

Molecular dynamics studies on dislocations in crystallites of nanocrystalline alpha-iron

Molecular dynamics simulations have been carried our to study the atomic structure of the crystalline component of nanocrystalline alpha-iron. A two-dimensional computational block is used to simulate the consolidation process. It is found that dislocations are generated in the crystallites during consolidation when the grain size is large enough. The critical value of the grain size for dislocation generation appears to be about 9 nm. This result agrees with experiment qualitatively. AN dislocations that are preset in the original grains glide out during consolidation. It shows that dislocations in the crystallites we generated in consolidation process, but not in the original grains. Higher consolidation pressure results in more dislocations. Furthermore, new interfaces are found within crystallites. These interfaces might result from the special environment of nanomaterial. (C) 1998 Acta Metallurgica Inc.

Molecular dynamics simulation of plastic deformation of nanotwinned copper

The plastic deformation of polycrystalline Cu with ultrathin lamella twins has been studied using molecular dynamics simulations. The results of uniaxial tensile deformation simulation show that the abundance of twin boundaries provides obstacles to dislocation motion, which in consequence leads to a high strain hardening rate in the nanotwinned Cu. We also show that the twin lamellar spacing plays a vital role in controlling the strengthening effects, i.e., the thinner the thickness of the twin lamella, the harder the material. Additionally, twin boundaries can act as dislocation nucleation sites as they gradually lose coherency at large strain. These results indicate that controlled introduction of nanosized twins into metals can be an effective way of improving strength without suppression tensile ductility. (C) 2007 American Institute of Physics.

Dislocations in the crystallites of nanocrystalline alpha-Fe - A molecular dynamics study

Molecular dynamics simulations are carried out in order to study the atomic structure of crystalline component, of nanocrystalline alpha-Fe when it is consolidated from small grains. A two-dimensional computational block is used to simulate the consolidation process. All the preset dislocations in the original grains glide out of them in the consolidation process, but new dislocations can generate when the grain size is large enough. It shows that dislocations exist in the consolidated material rather than in the original grains. Whether dislocations exist in the crystalline component of the resultant model nana-material depends upon grain size. The critical value of grain size for dislocation generation appears to be about 9 nm. This result agrees with experiments qualitatively.

Controlling electronic structures by irradiation in single-walled SiC nanotubes: a first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects and antisite defects) are formed with threshold energies from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.

Molecular Dynamics Simulation of Methane Hydrate Dissociation Process in the Presence of Thermodynamic Inhibitor

The dissociation of methane hydrate in the presence of ethylene glycol (11.45 mol.L-1) at 277.0 K was studied using canonical ensemble (NVT) molecular dynamics simulations. Results show that hydrate dissociation starts from the surface layer of the solid hydrate and then gradually expands to the internal layer. Thus, the solid structure gradually shrinks until it disappears. A distortion of the hydrate lattice structure occurs first and then the hydrate evolves from a fractured frame to a fractional fragment. Finally, water molecules in the hydrate construction exist in the liquid state. The inner dissociating layer is, additionally, coated by a liquid film formed from outer dissociated water molecules outside. This film inhibits the mass transfer performance of the inner molecules during the hydrate dissociation process.

Molecular-dynamics investigation on polarization retention of barium titanate nanofilm arising from ordered oxygen vacancy

Molecular-dynamics simulations have been carried out to investigate the electric hysteresis of barium titanate nanofilm containing oxygen vacancy ordering array parallel to the {101} crystal plane. The results obtained show a significant weakening of polarization retention from non-zero value to zero as the size of the array was reduced to a critical level, which was attributed to the formation and motion of head-to-head domain wall structure under external field loading process. By comparing with materials containing isolated oxygen vacancies, it was found that the zero retention was due to the oxygen vacancy ordering array rather than to the concentration of oxygen vacancy. Copyright (C) EPLA, 2010

Ab initio molecular dynamics simulation of a room temperature ionic liquid

Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.

Neutron diffraction, NMR and molecular dynamics study of glucose dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate

beta-D-glucose dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate in a 6 : 1 molar ratio (ionic liquid : glucose) has been studied by neutron scattering, NMR and molecular dynamics simulations. Good agreement was found between simulated neutron scattering profiles generated for isotopically substituted liquid systems and those experimentally determined as well as between simulated and experimental diffusion coefficients obtained by Pulsed Field Gradient NMR spectroscopy. The overriding glucose-ionic liquid interactions in the liquid are hydrogen-bonding between acetate oxygens and sugar hydroxyl groups. The ionic liquid cation was found to play only a minor role in the solvation of the sugar and does not participate in hydrogen-bonding with the sugar to any significant degree. NOESY experiments lend further evidence that there is no direct interaction between sugar hydroxyl groups and acidic hydrogens on the ionic liquid cation.

Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study

HIV-1 integrase (IN) has become an attractive target since drug resistance against HIV-1 reverse transcriptase (RT) and protease (PR) has appeared. Diketo acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN: however the action mechanism is not well understood. Here, to study the inhibition mechanism of DKAs we performed 10 ns comparative molecular dynamics simulations on HIV-1 IN bound with three most representative DMA inhibitors: Shionogi inhibitor, S-1360 and two Merck inhibitors L-731,988 and L-708,906. Our simulations show that the acidic part of S-1360 formed salt bridge and cation-pi interactions with Lys159. In addition, the catalytic Glu152 in S-1360 was pushed away from the active site to form an ion-pair interaction with Arg199. The Merck inhibitors can maintain either one or both of these ion-pair interaction features. The difference in potencies of the DMA inhibitors is thus attributed to the different binding modes at the catalytic site. Such structural information at atomic level, not only demonstrates the action modes of DMA inhibitors but also provides a novel starting point for structural-based design of HIV-1 IN inhibitors.

The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase:a drug target for African sleeping sickness

During the past century, several epidemics of human African trypanosomiasis, a deadly disease caused by the protist Trypanosoma brucei, have afflicted sub-Saharan Africa. Over 10 000 new victims are reported each year, with hundreds of thousands more at risk. As current drug treatments are either highly toxic or ineffective, novel trypanocides are urgently needed. The T. brucei galactose synthesis pathway is one potential therapeutic target. Although galactose is essential for T. brucei survival, the parasite lacks the transporters required to intake galactose from the environment. UDP-galactose 4'-epimerase (TbGalE) is responsible for the epimerization of UDP-glucose to UDP-galactose and is therefore of great interest to medicinal chemists. Using molecular dynamics simulations, we investigate the atomistic motions of TbGalE in both the apo and holo states. The sampled conformations and protein dynamics depend not only on the presence of a UDP-sugar ligand, but also on the chirality of the UDP-sugar C4 atom. This dependence provides important insights into TbGalE function and may help guide future computer-aided drug discovery efforts targeting this protein.

A Neutron Diffraction and Molecular Dynamics Investigation of Acetate-based Ionic Liquids as Solvents for Glucose

The liquid state structure of the ionic liquid, 1-ethyl-3-methylimidazolium acetate, and the solute/solvent structure of glucose dissolved in the ionic liquid at a 1: 6 molar ratio have been investigated at 323 K by molecular dynamics simulations and neutron diffraction experiments using H/D isotopically substituted materials. Interactions between hydrogen-bond donating cation sites and polar, directional hydrogen-bond accepting acetate anions are examined. Ion-ion radial distribution functions for the neat ionic liquid, calculated from both MD and derived from the empirical potential structure refinement model to the experimental data, show the alternating shell-structure of anions around the cation, as anticipated. Spatial probability distributions reveal the main anion-to-cation features as in-plane interactions of anions with imidazolium ring hydrogens and cation-cation planar stacking. Interestingly, the presence of the polarised hydrogen-bond acceptor anion leads to increased anion-anion tail-tail structuring within each anion shell, indicating the onset of hydrophobic regions within the anion regions of the liquid.

Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e. g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

Protection of DNA against low-energy electrons by amino acids: A first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.

The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

In this seminar, I will talk about the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscopy (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.