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.

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

Molecular Dynamics Simulation of Thermal and Mechanical Properties of Polyimide-Carbon-Nanotube Composites

An aromatic polyimide and its mixture with randomly distributed carbon nanotubes (NTs) are simulated by using molecular dynamics, repeated energy minimization and cooling processes. The glass transition temperatures are identified through volume-temperature curves. Stress-strain curves, Young's moduli, densities and Poisson ratios are computed at different temperatures. It is demonstrated that the carbon NT reduces the softening effects of temperature on mechanical properties and increases the ability to resist deformation.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Forced extension of P-selectin construct using steered molecular dynamics

P-selectin, a 70-nm-long cellular adhesive molecule, possesses elastic and extensible properties when neutrophils roll over the activated endotheliam of blood vessel in inflammatory reaction. Transient formation and dissociation of P-selectin/ligand bond on applied force of blood flow induces the extension of P-selectin and relevant ligands. Steered molecular dynamics simulations were performed to stretch a single P-selectin construct consisting of a lectin (Lec) domain and an epithelial growth factor (EGF)-like domain, where P-selectin construct was forced to extend in water with pulling velocities of 0.005-0.05 nm/ps and with constant forces of 1000-2500 pN respectively. Resulting force-extension profiles exhibited a dual-peak pattern on various velocities, while both plateaus and shoulders appeared in the extension-time profiles on various forces. The force or extension profiles along stretching pathways were correlated to the conformational changes, suggesting that the structural collapses of P-selectin Lec/EGF domains were mainly attributed to the burst of hydrogen bonds within the major beta sheet of EGF domain and the disruptions of two hydrophobic cores of Lee domain. This work furthers the understanding of forced dissociation of P-selectin/ligand bond.

A Molecular Dynamics Simulation: the Effect of Finite Size on the Thermal Conductivity in a Single Crystal Silicon

Non-equilibrium molecular dynamics (NEMD) simulations are performed to calculate thermal conductivity. The environment-dependent interatomic potential (EDIP) potential on crystal silicon is adopted as a model system. The issues are related to nonlinear response, local thermal equilibrium and statistical averaging. The simulation results by non-equilibrium molecular dynamics show that the calculated thermal conductivity decreases almost linearly as the film thickness reduced at the nanometre scale. The effect of size on the thermal conductivity is also obtained by a theoretic analysis of the kinetic theory and formulas of the heat capacity. The analysis reveals that the contributions of phonon mean free path (MFP) and phonon number in a finite cell to thermal conductivity are very important.

Molecular Dynamics And Density Functional Studies Of A Body-Centered-Tetragonal Polymorph Of Zno

We report a previously unknown body-centered-tetragonal structure for ZnO. This structure results from a phase transformation from wurtzite in [0001]-oriented nanorods during uniaxial tensile loading and is the most stable phase for ZnO when stress is above 7 GPa. The stress-induced phase transformation has important implications for the electronic, piezoelectric, mechanical, and thermal responses of ZnO. The discovery of this polymorph brings about a more complete understanding of the extent and nature of polymorphism in ZnO. A crystalline structure-load triaxiality map is developed to summarize the relationship between structure and loading.

Size-Dependent Elastic Properties Of Ni Nanofilms By Molecular Dynamics Simulation

Size-dependent elastic properties of Ni nanofilms are investigated by molecular dynamics ( MD) simulations with embedded atom method (EAM). The surface effects are considered by calculating the surface relaxation, surface energy, and surface stress. The Young's modulus and yield stress are obtained as functions of thickness and crystallographic orientation. It is shown that the surface relaxation has important effects on the the elastic properties at nanoscale. When the surface relaxation is outward, the Young's modulus decreases with the film thickness decreasing, and vice versa. The results also show that the yield stresses of the films increase with the films becoming thinner. With the thickness of the nanofilms decreasing, the surface effects on the elastic properties become dominant.

Molecular Dynamics Simulation Of Adhesion Forces In A Dipalmitoylphosphatidylcholine Membrane

Adhesion forces of Dipalmitoylphosphatidylcholine ( DPPC) membrane in the gel phase are investigated by molecular dynamics ( MD) simulation. In the simulations, individual DPPC molecules are pulled out of DPPC membranes with different rates and we get the maximum adhesion forces of DPPC membrane. We find that the maximum adhesion forces increase with pull rate, from about 400 to 700 pN when pull rates are from 0.001 to 0.03 nm/ps. We analyze the relationship between pull rate and adhesion forces of different origins using Brownian dynamics and notice that viscosity of solvent plays an important role in adhesion forces. Then we simulate the motion of a single DPPC molecule in solvent and it elucidates that the maximum drag force is almost linear with respect to the pull rate. We use Stokes' relation to describe the motion of a single DPPC molecule and deduce the effective length of a DPPC molecule. Conformational analyses indicate that the free energy variation of a DPPC molecule inside and outside of the DPPC membrane is an essential part of adhesion energy.

Molecular Dynamics Study Of Mechanical Behaviour Of Screw Dislocation During Cutting With Diamond Tip On Silicon

By means of Tersoff and Morse potentials, a three-dimensional molecular dynamics simulation is performed to study atomic force microscopy cutting on silicon monocrystal surface. The interatomic forces between the workpiece and the pin tool and the atoms of workpiece themselves are calculated. A screw dislocation is introduced into workpiece Si. It is found that motion of dislocations does not occur during the atomic force microscopy cutting processing. Simulation results show that the shear stress acting on dislocation is far below the yield strength of Si.

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 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.

Study Of Mechanical Properties Of Amorphous Copper With Molecular Dynamics Simulation

The formation and mechanical properties of amorphous copper are studied using molecular dynamics simulation. The simulations of tension and shearing show that more pronounced plasticity is found under shearing, compared to tension. Apparent strain hardening and strain rate effect are observed. Interestingly, the variations of number density of atoms during deformation indicate free volume creation, especially under higher strain rate. In particular, it is found that shear induced dilatation does appear in the amorphous metal.

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.

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.