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.

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/Cluster Statistical Thermodynamics Methods To Simulate Quasi-Static Deformations At Finite Temperature

The rapid evolution of nanotechnology appeals for the understanding of global response of nanoscale systems based on atomic interactions, hence necessitates novel, sophisticated, and physically based approaches to bridge the gaps between various length and time scales. In this paper, we propose a group of statistical thermodynamics methods for the simulations of nanoscale systems under quasi-static loading at finite temperature, that is, molecular statistical thermodynamics (MST) method, cluster statistical thermodynamics (CST) method, and the hybrid molecular/cluster statistical thermodynamics (HMCST) method. These methods, by treating atoms as oscillators and particles simultaneously, as well as clusters, comprise different spatial and temporal scales in a unified framework. One appealing feature of these methods is their "seamlessness" or consistency in the same underlying atomistic model in all regions consisting of atoms and clusters, and hence can avoid the ghost force in the simulation. On the other hand, compared with conventional MD simulations, their high computational efficiency appears very attractive, as manifested by the simulations of uniaxial compression and nanoindenation. (C) 2008 Elsevier Ltd. All rights reserved.

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 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.

Atomistic simulations of crack nucleation and intergranular fracture in bulk nanocrystalline nickel

We report large scale molecular dynamics simulations of dynamic cyclic uniaxial tensile deformation of pure, fully dense nanocrystalline Ni, to reveal the crack initiation, and consequently intergranular fracture is the result of coalescence of nanovoids by breaking atomic bonds at grain boundaries and triple junctions. The results indicate that the brittle fracture behavior accounts for the transition from plastic deformation governed by dislocation to one that is grain-boundary dominant when the grain size reduces to the nanoscale. The grain-boundary mediated plasticity is also manifested by the new grain formation and growth induced by stress-assisted grain-boundary diffusion observed in this work. This work illustrates that grain-boundary decohesion is one of the fundamental deformation mechanisms in nanocrystalline Ni.

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

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.

Molecular dynamics studies on the local disordering of σ3 and σ11 grain boundaries in aluminium bicrystal

Molecular dynamics (MD) simulations using Morse interaction potential are performed in studies of [110] symmetrical tilt grain boundary (GB) structures with mis-orientation angles 50.5 degrees(Sigma 11), 129.5 degrees(Sigma 11), 70.5 degrees(Sigma 3) and 109.5 degrees(Sigma 3) at various tempratures. The GB structures are found to start local disordering at about 0.5T(m)(T-m is the melting point of aluminium) for 50.5 degrees(Sigma 11), 0.32T(m) for 129.5 degrees(Sigma 11) and 0.38T(m) for 70.5 degrees(Sigma 3), respectively. These results agree with conclusions deduced from the anelastic measurements. But, for twin-boundary structure 109.5 degrees(Sigma 3), this disordering has not been found even when temperature increases up to 0.9T(m).

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.