Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

X-ray crystal structure and molecular mechanics calculations of (2,6-iso-dipropyl-phenylamide) dimethyl (tetra-methylcyclopenta-dienyl) silane titanium dichloride

Crystal and molecular structure of (2.6-dipropylphenylamide) dimethyl (tetra-methyl cyclopentadienyl) silane titanium dichloride (I) was fully characterized by X-ray diffraction. The crystal is obtained from a mixture of ether/hexane as orthorhombic. with a = 12.658 (3) Angstrom. b = 16.62 (3) Angstrom. c = 11.760 (2) Angstrom. V = 2474.2 (9) Angstrom(3). Z = 4, space group Pnma. R = 0.0399; Componud I compose of the pi-bounded ring with its dimethylsilyl-dipropyl phenyl amido group and the two terminal chloride atoms coordinated to central metal to form a so-called constrained geometry catalyst (CGC) structure. The result of molecular mechanics (MM) calculations on compound I shows that bond lengths and bond angles from the MM calculation are comparable to the data obtained from the X-ray diffraction study. The relation of the structure of CGCs and their catalytic activity by MM calculations is also discussed.

Formation of Fivefold Deformation Twins in Nanocrystalline Face-Centered-Cubic Copper Based on Molecular Dynamics Simulations

Fivefold deformation twins were reported recently to be observed in the experiment of the nanocrystalline face-centered-cubic metals and alloys. However, they were not predicted previously based on the molecular dynamics (MD) simulations and the reason was thought to be a uniaxial tension considered in the simulations. In the present investigation, through introducing pretwins in grain regions, using the MD simulations, the authors predict out the fivefold deformation twins in the grain regions of the nanocrystal grain cell, which undergoes a uniaxial tension. It is shown in their simulation results that series of Shockley partial dislocations emitted from grain boundaries provide sequential twining mechanism, which results in fivefold deformation twins. (c) 2006 American Institute of Physics.

Grain Boundary Effects On Plastic Deformation And Fracture Mechanisms In Cu Nanowires: Molecular Dynamics Simulations

Metallic nanowires have many attractive properties such as ultra-high yield strength and large tensile elongation. However, recent experiments show that metallic nanowires often contain grain boundaries, which are expected to significantly affect mechanical properties. By using molecular dynamics simulations, here, we demonstrate that polycrystalline Cu nanowires exhibit tensile deformation behavior distinctly different from their single-crystal counterparts. A significantly lowered yield strength was observed as a result of dislocation emission from grain boundaries rather than from free surfaces, despite of the very high surface to volume ratio. Necking starts from the grain boundary followed by fracture, resulting in reduced tensile ductility. The high stresses found in the grain boundary region clearly play a dominant role in controlling both inelastic deformation and fracture processes in nanoscale objects. These findings have implications for designing stronger and more ductile structures and devices on nanoscale.

Molecular dynamics simulations of DFZ

Dislocation emission from the crack tip in copper under mode II loading is simulated with molecular dynamics method. After 26 partial dislocations are emitted and then relaxed to reach the equilibrium under the constant displacement, the double pile-ups (including an inverse pile-up and a pile-up) are formed. i.e., the first dislocation is piled up before the obstruction, and the last dislocation is piled up ahead of the crack tip. These results conform to the TEM observations.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Molecular Mechanics Simulation of Recognition Identity of tRNA~(His/GUG)

本文选用经过实验验证的碱基序列 ,用简化的方式 ,构建了被水分子和镁离子修饰的核酸序列的分子模型 ,应用分子力学模拟方法对序列进行能量优化 ,对优化后序列的构象参数、成键状况和能量数据等进行了分析。对tRNAHHis GUG的识别特性作了初步的探索 ,得到了和实验结果相近的结论。此外 ,还从能力学的角度讨论了溶剂 -溶质 -溶剂相互作用形成的网状氢键网络对核酸结构稳定性的影响 ,探讨了非Crick_WatsonGU、UU配对的能力学特征并存在于被水分子和镁离子修饰的核酸序列中的GU、UU配对情况。

Calculating the equation of state parameters and predicting the spinodal curve of isotactic polypropylene/poly(ethylene-co-octene) blend by molecular dynamics simulations combined with Sanchez-Lacombe lattice fluid theory

Molecular dynamics simulations are adopted to calculate the equation of state characteristic parameters P*, rho*, and T* of isotactic polypropylene (iPP) and poly(ethylene-co-octene) (PEOC), which can be further used in the Sanchez-Lacombe lattice fluid theory (SLLFT) to describe the respective physical properties. The calculated T* is a function of the temperature, which was also found in the literature. To solve this problem, we propose a Boltzmann fitting of the data and obtain T* at the high-temperature limit. With these characteristic parameters, the pressure-volume-temperature (PVT) data of iPP and PEOC are predicted by the SLLFT equation of state. To justify the correctness of our results, we also obtain the PVT data for iPP and PEOC by experiments. Good agreement is found between the two sets of data. By integrating the Euler-Lagrange equation and the Cahn-Hilliard relation, we predict the density profiles and the surface tensions for iPP and PEOC, respectively. Furthermore, a recursive method is proposed to obtain the characteristic interaction energy parameter between iPP and PEOC. This method, which does not require fitting to the experimental phase equilibrium data, suggests an alternative way to predict the phase diagrams that are not easily obtained in experiments.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

A study of a molecular mechanics field used in simulating enantiorecognition

A molecular mechanics field, Alchemy II, was utilized to model the chiral recognition between S-N-acetyl-alpha-methyl-alpha-naphthylamine and (R, S)-N-(3, 5-dinitrophrnyl)-alpha-methyl-benzeneacetamide and between beta-cyclodextrin and (R, S)-fenoprofen. Some preliminary results have: been obtained to sustain the three-point action models and the induce-fit action in enantiorecognition.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.

Molecular Dynamics Modeling of Diffusion Bonding

Molecular dynamics simulations on diffusion bonding of Cu-Ag showed that the thickness of the interfacial region depended on the stress. The interfacial region became amorphous during diffusion bonding, and it would normally transform from amorphous into crystalline structure when the structure was cooled to the room temperature.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.