Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.

Nonlocal continuum mechanics based ultrasonic flexural wave dispersion characteristics of a monolayer graphene embedded in polymer matrix

Wave propagation in graphene sheet embedded in elastic medium (polymer matrix) has been a topic of great interest in nanomechanics of graphene sheets, where the equivalent continuum models are widely used. In this manuscript, we examined this issue by incorporating the nonlocal theory into the classical plate model. The influence of the nonlocal scale effects has been investigated in detail. The results are qualitatively different from those obtained based on the local/classical plate theory and thus, are important for the development of monolayer graphene-based nanodevices. In the present work, the graphene sheet is modeled as an isotropic plate of one-atom thick. The chemical bonds are assumed to be formed between the graphene sheet and the elastic medium. The polymer matrix is described by a Pasternak foundation model, which accounts for both normal pressure and the transverse shear deformation of the surrounding elastic medium. When the shear effects are neglected, the model reduces to Winkler foundation model. The normal pressure or Winkler elastic foundation parameter is approximated as a series of closely spaced, mutually independent, vertical linear elastic springs where the foundation modulus is assumed equivalent to stiffness of the springs. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of flexural wave propagation model is also derived and the results of the wave dispersion analysis are shown for both local and nonlocal elasticity calculations. From this analysis we show that the elastic matrix highly affects the flexural wave mode and it rapidly increases the frequency band gap of flexural mode. The flexural wavenumbers obtained from nonlocal elasticity calculations are higher than the local elasticity calculations. The corresponding wave group speeds are smaller in nonlocal calculation as compared to local elasticity calculation. The effect of y-directional wavenumber (eta(q)) on the spectrum and dispersion relations of the graphene embedded in polymer matrix is also observed. We also show that the cut-off frequencies of flexural wave mode depends not only on the y-direction wavenumber but also on nonlocal scaling parameter (e(0)a). The effect of eta(q) and e(0)a on the cut-off frequency variation is also captured for the cases of with and without elastic matrix effect. For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(0)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this article. (c) 2012 Elsevier Ltd. All rights reserved.

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Kinetics of phase separation in polymer mixtures: A molecular dynamics study

We present detailed results from a molecular dynamics (MD) simulation of phase-separation kinetics in polymer mixtures. Our MD simulations naturally incorporate hydrodynamic effects. We find that polymeric phase separation (with dynamically symmetric components) is in the same universality class as segregation of simple fluids: the degree of polymerization only slows down the segregation kinetics. For d = 2 polymeric fluids, the domain growth law is L(t) similar to t(phi) with phi showing a crossover from 1/3 -> 1/2 -> 2/3. For d = 3 polymeric fluids, we see the crossover phi = 1/3 -> 1. Our MD simulations do not yet access the inertial hydrodynamic regime (with L similar to t(2/3)) of phase separation in 3-d fluids. (C) 2014 AIP Publishing LLC.

A dynamic coupling model for hybrid atomistic-continuum computations

A dynamic coupling model is developed for a hybrid atomistic-continuum computation in micro- and nano-fluidics. In the hybrid atomistic-continuum computation, a molecular dynamics (MD) simulation is utilized in one region where the continuum assumption breaks down and the Navier-Stokes (NS) equations are used in another region where the continuum assumption holds. In the overlapping part of these two regions, a constrained particle dynamics is needed to couple the MD simulation and the NS equations. The currently existing coupling models for the constrained particle dynamics have a coupling parameter, which has to be empirically determined. In the present work, a novel dynamic coupling model is introduced where the coupling parameter can be calculated as the computation progresses rather than inputing a priori. The dynamic coupling model is based on the momentum constraint and exhibits a correct relaxation rate. The results from the hybrid simulation on the Couette flow and the Stokes flow are in good agreement with the data from the full MD simulation and the solutions of the NS equations, respectively. (c) 2007 Elsevier Ltd. All rights reserved.

Investigations of cohesive zone properties of the interface between metal film and ceramic substrate at nano- and micro-scales

Cohesive zone characterizations of the interface between metal film and ceramic substrate at micro- and nano-scales are performed in the present research. At the nano-scale, a special potential for special material interface (Ag/MgO) is adopted to investigate the interface separation mechanism by using MD simulation, and stress-separation relationship will be obtained. At the micro-scale, peeling experiment is performed for the Al film/Al2O3 substrate system with an adhesive layer at the interface. Adhesive is a mixture of epoxy and polyimide with mass ratio 1:1, by which a brittle cohesive property is obtained. The relationships between energy release rate, the film thickness and the adhesive layer thickness are measured during the steady-state peeling. The experimental result has a similar trend as modeling result for a weak adhesion interface case.

Molecular dynamics studies of brittle fracture of SiO2

By applying for molecular dynamics (MD) simulation and Griffith fracture criterion, the brittle behavior of crack extension of mode I type is investigated. The critical stress intensity factor (SIF)K-Ic(MD) of crack extension is calculated, and the evolution of atoms near crack tip is observed. It is found that K-Ic(MD) is in good agreement with the Griffith ftacture criterion K-Ic(Griffith).

Effect Of Water On Brittle Fracture Of Sio2 By Molecular Dynamics Study

The influence of water on the brittle behavior of beta-cristobalite is studied by means of molecular dynamics (MD) simulation With the TTAM potential. Crack extension of mode 1 type is observed as the crack opening is filled LIP With water. The critical stress intensity factor K-lc(MD) is used to characterize the crack extension of MD simulation. The surface energy of SiO2 covered with layers of water is calculated at temperature of 300 K. Based oil the Griffith fracture criterion, the critical stress intensity factor K-lc(Griffith) is calculated, and it is in good agreement with that of MD simulation. (C) 2008 Elsevier B.V. All rights reserved.

A New Criterion Number for the Boundary Conditions at the Solid/Liquid Interface in Nanoscale

A simple, but important three-atom model was proposed at the solid/liquid interface, leading to a new criterion number, lambda, governing the boundary conditions (BCs) in nanoscale. The solid wall is considered as the face-centered-cubic (fcc) structure. The fluid is the liquid argon with the well-known LJ potential. Based on the concept, the two micro-systems have the same BCs if they have The same criterion number. The degree of the locking BCs is enhanced when lambda equals to 0.757. Such critical criterion number results in the substantial epitaxial ordering and one, two, or even three liquid layers are locked by the solid wall, depending on the coupling energy scale ratio of the solid and liquid atoms. With deviation from the critical criterion number, the flow approaches the slip BCs and there are little ordering structures within the liquid. Always at the same criterion number, the degree of the slip is decreased or the locking is enhanced with increasing the coupling energy scale ratio of the solid and liquid atoms. The above analysis is well confirmed by the molecular dynamics (MD) simulation. The slip length is well correlated in terms of the new criterion number. The future work is suggested to extend the present theory for other microstructures of the solid wall atoms and quasi-LJ potentials.

Mechanical Behavior of Nanometer Ni by Simulating Nanoindentation

An indentation simulation of the crystal Ni is carried out by a molecular dynamics technique (MD) to study the mechanical behavior at nanometer scales. Indenter tips with both sphere shape and conical shape with 60 cone angle are used, and simulation samples with different crystal orientations are adopted. Some defects such as dislocations and point defects are observed. It is found that nucleated defects (dislocations, amorphous atoms) are from the local region near the pin tip or the sample surface. The temperature distribution of the local region is analyzed and it can explain our MD simulation results.

A multi-scale atomistic-continuum modelling of crack propagation in a two-dimensional macroscopic plate

A novel multi-scale seamless model of brittle-crack propagation is proposed and applied to the simulation of fracture growth in a two-dimensional Ag plate with macroscopic dimensions. The model represents the crack propagation at the macroscopic scale as the drift-diffusion motion of the crack tip alone. The diffusive motion is associated with the crack-tip coordinates in the position space, and reflects the oscillations observed in the crack velocity following its critical value. The model couples the crack dynamics at the macroscales and nanoscales via an intermediate mesoscale continuum. The finite-element method is employed to make the transition from the macroscale to the nanoscale by computing the continuum-based displacements of the atoms at the boundary of an atomic lattice embedded within the plate and surrounding the tip. Molecular dynamics (MD) simulation then drives the crack tip forward, producing the tip critical velocity and its diffusion constant. These are then used in the Ito stochastic calculus to make the reverse transition from the nanoscale back to the macroscale. The MD-level modelling is based on the use of a many-body potential. The model successfully reproduces the crack-velocity oscillations, roughening transitions of the crack surfaces, as well as the macroscopic crack trajectory. The implications for a 3-D modelling are discussed.

Modelling the nano-scale phenomena in condensed matter physics via computer-based numerical simulations

A review of the atomistic modelling of the behaviour of nano-scale structures and processes via molecular dynamics (MD) simulation method of a canonical ensemble is presented. Three areas of application in condensed matter physics are considered. We focus on the adhesive and indentation properties of the solid surfaces in nano-contacts, the nucleation and growth of nano-phase metallic and semi-conducting atomic and molecular films on supporting substrates, and the nano- and multi-scale crack propagation properties of metallic lattices. A set of simulations selected from these fields are discussed, together with a brief introduction to the methodology of the MD simulation. The pertinent inter-atomic potentials that model the energetics of the metallic and semi-conducting systems are also given.

Surface physics at the nano-scale via scanning probe microscopy and molecular dynamics simulations

Probe-based scanning microscopes, such as the STM and the AFM, are used to obtain the topographical and electronic structure maps of material surfaces, and to modify their morphologies on nanoscopic scales. They have generated new areas of research in condensed matter physics and materials science. We will review some examples from the fields of experimental nano-mechanics, nano-electronics and nano-magnetism. These now form the basis of the emerging field of Nano-technology. A parallel development has been brought about in the field of Computational Nano-science, using quantum-mechanical techniques and computer-based numerical modelling, such as the Molecular Dynamics (MD) simulation method. We will report on the simulation of nucleation and growth of nano-phase films on supporting substrates. Furthermore, a theoretical modelling of the formation of STM images of metallic clusters on metallic substrates will also be discussed within the non-equilibrium Keldysh Green function method to study the effects of coherent tunnelling through different atomic orbitals in a tip-sample geometry.

The development of a surface defect machining method for hard turning processes

Hard turning (HT) is a material removal process employing a combination of a single point cutting tool and high speeds to machine hard ferrous alloys which exhibit hardness values over 45 HRC. In this paper, a surface defect machining (SDM) method for HT is proposed which harnesses the combined advantages of porosity machining and pulsed laser pre-treatment processing. From previous experimental work, this was shown to provide better controllability of the process and improved quality of the machined surface. While the experiments showed promising results, a comprehensive understanding of this new technique could only be achieved through a rigorous, in depth theoretical analysis. Therefore, an assessment of the SDM technique was carried out using both finite element method (FEM) and molecular dynamics (MD) simulations.
FEM modelling was used to compare the conventional HT of AISI 4340 steel (52 HRC) using an Al2O3 insert with the proposed SDM method. The simulations showed very good agreement with the previously published experimental results. Compared to conventional HT, SDM provided favourable machining outcomes, such as reduced shear plane angle, reduced average cutting forces, improved surface roughness, lower residual stresses on the machined surface, reduced tool–chip interface contact length and increased chip flow velocity. Furthermore, a scientific explanation of the improved surface finish was revealed using a state-of-the-art MD simulation model which suggested that during SDM, a combination of both the cutting action and rough polishing action help improve the machined surface finish.