Dimensional Molecular Dynamics Simulations Research Articles

Effect of porosity on shock propagation behaviour of single crystal aluminium: A molecular dynamics investigation

Materials' response to shock waves is largely affected not only by their inherent atomic structure but also by their physical structure. Current study involves analysis of shock propagation behaviour of single crystal aluminium (Al) specimens with different levels of porosities at nanoscale under a compressive shock loading using three dimensional molecular dynamics (MD) simulations. Solid, two dimensional array of pores, and three dimensional array of pores in the single crystal Al specimen were considered for detailed analysis of the shock response. It is observed that the porosity causes time delay in the travel of shock wave from front end of the surface to the rear end. The computational results indicate that the porosity results into increase in time of shock wave travel and it is found that the maximum porosity (47% in this simulation) causes 4 times the time of travel taken in solid Al specimen. The shock wave causes various sequential phenomenon in the Al specimen from compression to rarefaction which further leads to spalling of the material. The study also reveals that the pore walls act as a reflecting wall to the shock wave which causes secondary rarefactions and spalling phenomenon. Analyses show that the deformation in the material during shock loading is largely dominated by Shockley partial dislocations.

Nanoscale friction and adhesion mechanisms in articular cartilage top layer hydrated interfaces: Insights from atomistic simulations

This study investigates nanoscale adhesion and frictional behavior of an idealized cartilage-cartilage top layer atomistic contact model with nanoconfined water at the interface under range of load using three dimensional molecular dynamics (MD) simulations. Analysis reveals that water significantly replaces the cohesive interactions with adhesive at regions of unhydrated cartilage-cartilage contact by engulfing water molecules. These water molecules improve the load-bearing capacity and reduces frictional forces at the interface. Interfacial water also inhibits debonding at the interface during pull-off test at higher loads. Sliding tests reveal that at higher load-induced confined geometries there is a significant reduction in the frictional forces up to five times in comparison to dry collagen-collagen contact. Interaction energy curves predict that water molecules completely wet the collagen and thus provide an in-situ interfacial lubrication. Finally, the intermolecular interactions unveil the presence of substantial amount of water molecules at the interfaces to reduce friction drastically at the interface employing water-water interactions. Overall, a hydrated atomistic model for top layer cartilage-cartilage lubricated contact is developed and studied for adhesion and friction behavior and underlying mechanisms which is useful for understanding in-vivo boundary lubricated interfaces and design enhanced implant solutions.

Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene

In SCF (Skp, Cullin, F-box) ubiquitin-protein ligase complexes, S-phase kinase 2 (SKP2) is one of the major players of F-box family, that is responsible for the degradation of several important cell regulators and tumor suppressor proteins. Despite of having significant evidence for the role of SKP2 on tumorgenesis, there is a lack of available data regarding the effect of non-synonymous polymorphisms. In this communication, the structural and functional consequences of non-synonymous single nucleotide polymorphisms (nsSNPs) of SKP2 have been reported by employing various computational approaches and molecular dynamics simulation. Initially, several computational tools like SIFT, PolyPhen-2, PredictSNP, I-Mutant 2.0 and ConSurf have been implicated in this study to explore the damaging SNPs. In total of 172 nsSNPs, 5 nsSNPs were identified as deleterious and 3 of them were predicted to be decreased the stability of protein. Guided from ConSurf analysis, P101L (rs761253702) and Y346C (rs755010517) were categorized as the highly conserved and functional disrupting mutations. Therefore, these mutations were subjected to three dimensional model building and molecular dynamics simulation study for the detailed structural consequences upon the mutations. The study revealed that P101L and Y346C mutations increased the flexibility and changed the structural dynamics. As both these mutations are located in the most functional regions of SKP2 protein, these computational insights might be helpful to consider these nsSNPs for wet-lab confirmatory analysis as well as in rationalizing future population based studies and structure based drug design against SKP2.

Equilibrium configuration of self-gravitating charged dust clouds: Particle approach

A three dimensional Molecular Dynamics (MD) simulation is carried out to explore the equilibrium configurations of charged dust particles. These equilibrium configurations are of astrophysical significance for the conditions of molecular clouds and the interstellar medium. The interaction among the dust grains is modeled by Yukawa repulsion and gravitational attraction. The spherically symmetric equilibria are constructed which are characterized by three parameters: (i) the number of particles in the cloud, (ii) Γg (defined in the text) where Γg−1 is the short range cutoff of the interparticle potential, and (iii) the temperature of the grains. The effects of these parameters on dust cloud are investigated using a radial density profile. The problem of equilibrium is also formulated in the mean field limit where total dust pressure, which is the sum of kinetic pressure and the electrostatic pressure, balances the self-gravity. The mean field solutions agree well with the results of MD simulations. The astrophysical significance of the results is briefly discussed.

Theory and simulation of coupled grain boundary migration and grain rotation in low angle grain boundaries

Microstructure evolution due to coupled grain boundary migration and grain rotation in low angle grain boundaries is studied through a combination of molecular dynamics and phase field modeling. We have performed two dimensional molecular dynamics simulations on a bicrystal with a circular grain embedded in a larger grain. Both size and orientation of the embedded grain are observed to evolve with time. The shrinking embedded grain is observed to have two regimes: constant dislocation density on the grain boundary followed by constant rate of increase in dislocation density. Based on these observations from the molecular dynamics simulations, a theoretical formulation of the kinetics of coupled grain rotation is developed. The grain rotation rate is derived for the two regimes of constant dislocation density and constant rate of change of dislocation density on the grain boundary during evolution. The theoretical calculation of the grain rotation rate shows strong dependence on the grain size and compares very well with the molecular dynamics simulations. A multi-order parameter based phase field model with coupled grain rotation is developed using the theoretical formulation to model polycrystalline microstructure evolution.

Multielectron dissociative ionization of methane and formaldehyde molecules with optimally tailored intense femtosecond laser pulses

The multielectron dissociative ionization of CH4 and CH2O molecules has been investigated using optimum convolution of different dual tailored short laser pulses. Based on three dimensional molecular dynamics simulations and TDDFT approach, the dissociation probability is enhanced by designing the dual chirped-chirped laser pulses and chirped-ordinary laser pulses for formaldehyde molecule. However, it is interesting to notice that the sensitivity of enhanced dissociation probability into different tailored laser pulses is not significant for methane molecule. In this presented modifications, time variation of bond length, velocity, time dependent electron localization function and evolution of the efficient occupation states are presented to analyze the time evolution of molecular dynamics. This work is proved to be a potential way to reduce the controlling costs with a currently available pulse shaping technology.

Deformation and Fracture of Metallic Nanowires

A many-body interatomic potential for metallic nanowires within the second-moment approximation of the tight-binding model (the Cleri-Rosato potential) was employed to carry out three dimensional molecular dynamics simulations. Molecular dynamics simulation results for metallic nanowires at various temperature are presented. The stress–time and stress length curves for nanowires are simulated. The breaking and yield stress of nanowires are dependent on the Volume and temperature. The necking, Plastic deformation, slipping domain, twins, clusters, microspores and break-up phenomena of nanowire are demonstrated. Stress decreases with increasing nanowire volume and temperature. The final breaking position occurs at the central part of the nanowire when it is short, as the nanowire length increases the breaking position gradually shifts to the ends.

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

The weighted histogram analysis method (WHAM) including its binless extension has been developed independently in several different contexts, and widely used in chemistry, physics, and statistics, for computing free energies and expectations from multiple ensembles. However, this method, while statistically efficient, is computationally costly or even infeasible when a large number, hundreds or more, of distributions are studied. We develop a locally WHAM (local WHAM) from the perspective of simulations of simulations (SOS), using generalized serial tempering (GST) to resample simulated data from multiple ensembles. The local WHAM equations based on one jump attempt per GST cycle can be solved by optimization algorithms orders of magnitude faster than standard implementations of global WHAM, but yield similarly accurate estimates of free energies to global WHAM estimates. Moreover, we propose an adaptive SOS procedure for solving local WHAM equations stochastically when multiple jump attempts are performed per GST cycle. Such a stochastic procedure can lead to more accurate estimates of equilibrium distributions than local WHAM with one jump attempt per cycle. The proposed methods are broadly applicable when the original data to be "WHAMMED" are obtained properly by any sampling algorithm including serial tempering and parallel tempering (replica exchange). To illustrate the methods, we estimated absolute binding free energies and binding energy distributions using the binding energy distribution analysis method from one and two dimensional replica exchange molecular dynamics simulations for the beta-cyclodextrin-heptanoate host-guest system. In addition to the computational advantage of handling large datasets, our two dimensional WHAM analysis also demonstrates that accurate results similar to those from well-converged data can be obtained from simulations for which sampling is limited and not fully equilibrated.

Mechanism of crack healing at room temperature revealed by atomistic simulations

Three dimensional molecular dynamics (MD) simulations are systematically carried out to reveal the mechanism of the crack healing at room temperature, in terms of the dislocation shielding and the atomic diffusion to control the crack closure, in a copper (Cu) plate suffering from a shear loading. The results show that the process of the crack healing is actualized through the dislocation emission at a crack tip accompanied with intrinsic stacking faults ribbon forming in the crack tip wake, the dislocation slipping in the matrix and the dislocation annihilation in the free surface. Dislocation included stress compressing the crack tip is examined from the MD simulations and the analytical models, and then the crack closes rapidly due to the assistance of the atomic diffusion induced by the thermal activation when the crack opening displacement is less than a threshold value. This phenomenon is very different from the previous results for the crack propagation under the external load applied because of the crack healing (advancing) largely dependent on the crystallographic orientations of crack and the directions of external loading. Furthermore, based on the energy characteristic and considering the crack size effect, a theoretical model is established to predict the relationships between the crack size and the shear stress which qualitatively agree well with that obtained in the MD simulations.

Simulation of cohesive fine powders under a plane shear.

Three-dimensional molecular-dynamics simulations of cohesive dissipative powders under a plane shear are performed. We find the various phases depending on the dimensionless shear rate and the dissipation rate as well as the density. We also find that the shape of clusters depends on the initial condition of velocities of particles when the dissipation is large. Our simple stochastic model reproduces the non-Gaussian velocity distribution function appearing in the coexistence phase of a gas and a plate.

Effect of Length and Cross-Sectional Area on Ni<sub>3</sub>Fe Alloy Plasticity

Molecular Dynamics (MD) simulations have been carried out on ultrathin Ni3Fe alloy with face-centered cubic (FCC) lattice upon application of uniaxial tension at nanolevel with a speed of 20 m/s. the deformation corresponds to the direction <001>. To the calculated block of crystal - free boundary conditions are applied in the directions <100>, <010>. Morse potential was employed to carry out three dimensional molecular dynamics simulations. A computer experiment is performed at a temperature corresponding to 300 K. MD simulation used to investigate the effect of long of ultrathin Ni3Fe alloy on the nature of deformation and fracture. The engineering stress–time diagrams obtained by the MD simulations of the tensile specimens of these ultrathin Ni3Fe alloy show a rapid increase in stress up to a maximum followed by a gradual drop to zero when the specimen fails by ductile fracture. The feature of deformation energy can be divided into four regions: quasi-elastic, plastic, flow and failure. The yield strength decreased with increasing long of alloy, but increases with increasing the cross sectional area. Plasticity disappear when the length of the allays is too large. The results showed that breaking position depended on the alloy length.

Molecular Dynamic Simulations of ultrathin Nickel nanowires at various temperatures

The mechanical properties of ultrathin Nickel nanowires have been studied at different temperatures using molecular dynamics simulations. Molecular Dynamics (MD) simulations have been carried out on pure ultrathin Nickel (Ni) crystal with face-centered cubic (FCC) lattice upon application of uniaxial tension at nanolevel with a speed of 20 m/s. The deformation corresponds to the direction . To the calculated block of crystal free boundary conditions are applied in the directions , . Morse potential was employed to carry out three dimensional molecular dynamics simulations. MD simulation used to investigate the effect of temperature of ultrathin Ni nanowire on the nature of deformation and fracture. Temperature effect on the extension property of metal nanowire is discussed in detail. The mechanical strengths and the mechanical strain of the nanowires decrease linearly with the increasing temperature. The feature of deformation energy can be divided into four regions: quasi-elastic, plastic, flow and failure. Experiments have shown that when the temperature increases the first stage of deformation was narrowed, and the second stage was widened. The results showed that breaking position depended on temperature. The simulation results at nanoscale play an important role on the mechanical behaviors of nanostructures.

Features of deformation and breaking for Ni nanowire

Molecular Dynamics (MD) simulations have been carried out on pure Nickel (Ni) crystal with face-centered cubic (FCC) lattice upon application of uniaxial tension at nanolevel with a speed of 20 m/s. The deformation corresponds to the direction <001>. To the calculated block of crystal - free boundary condi-tions are applied in the directions <100>, <010>. A many-body interatomic potential for Ni within the sec-ond-moment approximation of the tight-binding model (the Cleri and Rosato potentials) was employed to carry out three dimensional molecular dynamics simulations. A computer experiment is performed at a tem-perature corresponding to 10K, 300Kand 1000K. MD simulation used to investigate the effect of long of Ni nanowire on the nature of deformation and fracture. The feature of deformation energy can be divided into four regions: quasi-elastic, plastic, flow and failure. The nature of deformation, slipping, twinning and neck-ing were studied. Stress decreased with increasing volume. The results showed that breaking position de-pended on the nanowire length.

Molecular Dynamics Simulations of Thermal Transport at the Nanoscale Solid-Liquid Interface

Simulation of nanoscale thermo-fluidic transport has attracted considerable attention in recent years owing to rapid advances in nanoscience and nanotechnology. The three- dimensional molecular dynamics simulations are performed for the system of a liquid layer between two parallel solid walls at different wall temperatures. The solid-solid interaction is modeled by the embedded atom method. The heat flux through the solid-liquid interface is calculated by Green-Kubo method. The effects of interface wettability and wall temperature on the interfacial thermal resistance are also analyzed. It is found that there exist the relatively immobile quasi-crystalline interfacial layers close to each solid wall surface with higher number density and thus higher local thermal conductivity than the corresponding liquid phase. The interfacial thermal resistance length is overestimated by 8.72% to 19.05% for the solid-solid interaction modeled by the Lennard-Jones potential, and underestimated based on heat fluxes calculated by Fourier equation.

IN VIVO INVESTIGATION OF AN INNOVATIVE SILK SCAFFOLD FOR PARTIAL MENISCUS REPLACEMENT

This study investigates nanoscale adhesion and frictional behavior of an idealized cartilage-cartilage top layer atomistic contact model with nanoconfined water at the interface under range of load using three dimensional molecular dynamics (MD) simulations. Analysis reveals that water significantly replaces the cohesive interactions with adhesive at regions of unhydrated cartilage-cartilage contact by engulfing water molecules. These water molecules improve the load-bearing capacity and reduces frictional forces at the interface. Interfacial water also inhibits debonding at the interface during pull-off test at higher loads. Sliding tests reveal that at higher load-induced confined geometries there is a significant reduction in the frictional forces up to five times in comparison to dry collagen-collagen contact. Interaction energy curves predict that water molecules completely wet the collagen and thus provide an in-situ interfacial lubrication. Finally, the intermolecular interactions unveil the presence of substantial amount of water molecules at the interfaces to reduce friction drastically at the interface employing water-water interactions. Overall, a hydrated atomistic model for top layer cartilage-cartilage lubricated contact is developed and studied for adhesion and friction behavior and underlying mechanisms which is useful for understanding in-vivo boundary lubricated interfaces and design enhanced implant solutions.

A Study on Nanocutting of Monocrystalline Silicon by Molecular Dynamics Simulation

Three dimensional molecular dynamics simulation on the nanocutting of monocrystalline silicon is carried out to investigate the material deformation behaviors and atomic motion characteristics of the machined workpiece. A deformation criterion is developed to determine the material deformation and phase transformation behavior in the subsurface layer based on the single-atom potential energy variations. The results show that the machined chips suffer a complex phase transformation and eventually present an amorphous structure caused by the plastic deformation behavior. A polycrystalline structure is obtained on the machined surface. Both plastic and elastic deformation simultaneously takes place on the machined surface, and elastic deformation takes place under the machined surface. In order to further unveil the mechanism of nanocutting process, the displacements of all atoms are also simulated. The simulation results shows that different atomic motions occur in different regions in the workpiece, and the chips formations occur via extrusion.

Micromechanics and statistics of slipping events in a granular seismic fault model

The stick-slip is investigated in a seismic fault model made of a confined granular system under shear stress via three dimensional Molecular Dynamics simulations. We study the statistics of slipping events and, in particular, the dependence of the distribution on model parameters. The distribution consistently exhibits two regimes: an initial power law and a bump at large slips. The initial power law decay is in agreement with the the Gutenberg-Richter law characterizing real seismic occurrence. The exponent of the initial regime is quite independent of model parameters and its value is in agreement with experimental results. Conversely, the position of the bump is solely controlled by the ratio of the drive elastic constant and the system size. Large slips also become less probable in absence of fault gouge and tend to disappear for stiff drives. A two–time force–force correlation function, and a susceptibility related to the system response to pressure changes, characterize the micromechanics of slipping events. The correlation function unveils the micromechanical changes occurring both during microslips and slips. The mechanical susceptibility encodes the magnitude of the incoming microslip. Numerical results for the cellular-automaton version of the spring block model confirm the parameter dependence observed for size distribution in the granular model.

Unjamming Dynamics: The Micromechanics of a Seismic Fault Model

The unjamming transition of granular systems is investigated in a seismic fault model via three dimensional molecular dynamics simulations. A two-time force-force correlation function, and a susceptibility related to the system response to pressure changes, allow us to characterize the stick-slip dynamics, consisting in large slips and microslips leading to creep motion. The correlation function unveils the micromechanical changes occurring both during microslips and slips. The susceptibility encodes the magnitude of the incoming microslip.

Effect of changes in tropocollagen residue sequence and hydroxyapatite mineral texture on the strength of ideal nanoscale tropocollagen-hydroxyapatite biomaterials

Changes in mineral texture (e.g. hydroxyapatite (HAP) or aragonite) and polypeptide (e.g. tropocollagen (TC)) residue sequence are characteristic features of a disease known as osteogenesis imperfecta (OI). In OI, different possibilities of changes in polypeptide residue sequence as well as changes in polypeptide helix replacement (e.g. 3 alpha1 chains instead of 2 alpha1 and 1 alpha2 chain in OI murine) exist. The cross section of the HAP crystals could be needle like or plate like. Such texture and residue sequence related changes can significantly affect the material strength at the nanoscale. In this work, a mechanistic understanding of such factors in determining strength of nanoscale TC-HAP biomaterials is presented using three dimensional molecular dynamics (MD) simulations. Analyses point out that the peak interfacial strength for failure is the highest for supercells with plate shaped HAP crystals. TC molecules with higher number of side chain functional groups impart higher strength to the TC-HAP biomaterials at the nanoscale. Overall, HAP crystal shape variation, the direction of applied loading with respect to the relative TC-HAP orientation, and the number of side chain functional groups in TC molecules are the factor that affect TC-HAP biomaterial strength in a significant manner.

Axial segregation in horizontally vibrated granular materials: A numerical study

It is known that a horizontally vibrated binary mixture in a tapered and inclined channel segregates axially, with the two species moving to the opposite ends of the channel. In general, the parameters that affect the segregation process include the forcing frequency and its amplitude, the constituents’ mass and size, and the taper and inclination of the channel. The ultimate goal here is to locate those parameters that are most significant to the segregation process, thereby providing control variables for practical applications. However, owing to the complexity of the problem, as a first step to better understand the physics behind this phenomenon, we undertake three dimensional molecular dynamics simulations of a horizontally vibrated mono-disperse granular particles in a tapered and inclined channel. Though at this stage, the immediately addressed problem is of more relevance to the granular material industry, it is envisaged that tools developed to understand this process will ultimately have wide applicability to granular systems, occurring in both natural contexts and in geotechnical engineering.