Microscopic Molecular Dynamics Research Articles

Complex fields in heterogeneous materials under shock: modeling, simulation and analysis

In this mini-review we summarize the progress of modeling, simulation and analysis of shock responses of heterogeneous materials in our group in recent years. The basic methodology is as below. We first decompose the problem into different scales. Construct/ Choose a model according to the scale and main mechanisms working at that scale. Perform numerical simulations using the relatively mature schemes. The physical information is transferred between neighboring scales in such a way: The statistical information of results in smaller scale contributes to establishing the constitutive equation in larger one. Except for the microscopic Molecular Dynamics (MD) model, both the mesoscopic and macroscopic models can be further classified into two categories, solidic and fluidic models, respectively. The basic ideas and key techniques of the MD, material point method and discrete Boltzmann method are briefly reviewed. Among various schemes used in analyzing the complex fields and structures, the morphological analysis and the home-built software, GISO, are briefly introduced. New observations are summarized for scales from the larger to the smaller.

Molecular dynamics simulations of Oxprenolol and Propranolol in a DPPC lipid bilayer

Extensive microscopic molecular dynamics simulations have been performed to study the effects of tow β-blocker drugs (Propranolol, Oxprenolol) on fully hydrated dipalmitoylphosphatidylcholine (DPPC) in the fluid phase at 323K. Simulation of 4 systems containing varying concentrations of drugs was carried out. For the purpose of comparison, a fully hydrated DPPC bilayer without drugs was also studied at the same level of simulation technique which has been done on 4 other systems. The length of each simulation was 100ns. The effects of concentrations of both drugs were analyzed on lipid bilayer properties, such as electrostatic potential, order parameter, diffusion coefficients, and hydrogen bond formation, etc. Penetration of water in the bilayer system was also investigated using radial distribution function analysis. Efficacy of varying concentrations of both drugs has no significant effect on P–N vector. Consistent with experimental results, by increasing the concentration of Propranolol, the thickness of the bilayer was increased.

Confined Molecular Dynamics for Suppressing Kinetic Loss in Sugar Fuel Cell

We corroborated substantial suppression of kinetic loss in sugar fuel cell owing to microscopic molecular dynamics at nanoporous electrodes. When electrochemical reaction is sluggish, exchange current density (j0) is governed by how often the reactants encounter the surface of catalyst. This highly frequent interaction between reactant and electrode surface can be achieved by confined molecular dynamics in nanoporous electrode. Using sucrose molecule as an oxidant fuel, the performance of nanoporous Pt (L2-ePt) with pore size of 1 to 2nm was compared with that of thin layer of Pt nanoparticles (Pt NPs) that was electrodeposited on a polished Pt surface to exclude the effects of crystalline facets and defects. As sucrose is bulkier and less adsorptive than glucose and undergoes sluggish electrochemical oxidation, sucrose oxidation substantially benefits from the confined molecular dynamics at nanoporous electrode. The current density (JRSA) normalized by real surface area (RSA) of sucrose oxidation at L2-ePt was higher than Pt NPs. In fuel cell operation, open circuit voltage of L2-ePt was measured to be 0.593V, 4.4 times higher than Pt NPs and j0 significantly increased at L2-ePt. Moreover, maximum power density (PRSA) of L2-ePt was much higher by a factor of 15.7 than Pt NPs.

Progess of discrete Boltzmann modeling and simulation of combustion system

Progess of discrete Boltzmann modeling and simulation of combustion system

Molecular Dynamics of Polymer Composites Using Rheology and Combined RheoNMR on the Example of TiO2-Filled Poly(n-Alkyl Methacrylates) and Trans-1,4-Polyisoprene

The determination of the interplay between polymeric matrices and filler particles in composites is of great interest to understand structure-property relationships and develop predictive theories. To study the molecular dynamics of polymers in composites, model systems based on poly(n-alkyl methacrylates), trans-1,4-polyisoprene (gutta percha), and titania (TiO2) were prepared and characterized using rheometry and a combined RheoNMR technique. Apparent entanglement molecular weights were obtained from small amplitude oscillatory shear (SAOS) experiments, which are related to the increasing physical cross-link density as a function of the filler content. Large amplitude oscillatory shear (LAOS) experiments were performed and analyzed within the FT-rheometry framework. The filler had a strong impact on the scaling behavior of the normalized third harmonic. A combined RheoNMR technique was used to simultaneously study the molecular dynamics via NMR and the corresponding mechanical response via rheometry. A strong correlation between the macroscopic mechanical properties and microscopic molecular dynamics was found, which might lead to a new understanding of polymer melt dynamics.

Mathematical models of ion transport through cell membrane channels

We discuss various models of ion transport through cell membrane channels. Recent experimental data shows that sizes of some ion channels are compared to those of ions and that only few ions may be simultaneously in any single channel. Theoretical description of ion transport in such channels should therefore take into account stochastic fluctuations and interactions between ions and between ions and channel proteins. This is not satisfied by macroscopic continuum models based on the Poisson-Nernst-Planck equations. More realistic descriptions of ion transport are offered by microscopic molecular and Brownian dynamics. We present a derivation of the Poisson-Nernst-Planck equations. We also review some recent models such as single-file diffusion and Markov chains of interacting ions (boundary driven lattice gases). Such models take into account discrete and stochastic nature of ion transport and specifically interactions between ions in ion channels.

Lagrangian particle-based simulation of fluid-solid coupling on graphics processing units

Lagrangian particle method has been widely used in computer physics and graphics; however, numerically solving the partial differential physical equation on a great number of particles is a computationally complex task. In this paper, a unified particle method on graphics processing units is proposed to simulate fluid-solid interaction with large density ratio interactively. Motivated by microscopic molecular dynamics, we consider the solid object as a particular fluid limited to solid motions; therefore, fluid-solid interaction as well as solid-solid interaction could be solved directly using multiphase weakly compressible smoothed particle hydrodynamics solvers. And then, we present a momentum-conserving particle collision handling scheme to prevent fluid penetrating into solid objects. In the simulation, a measure of particle densities is used to handle density discontinuities at fluid-solid interfaces, and consequently, new formulations for density-weighted inter-particle pressure and viscous forces are derived. Moreover, to realistically simulate various small-scale interaction phenomena such as water droplets flowing on solids' surfaces, a surface tension model that uses density-weighted color gradient and can obtain a stable and accurate surface curvature is employed to capture the interfacial fluid-solid tensions. Because all of the computation is carried out on graphics processing unit and no CPU processing is needed, the proposed algorithm can exploit the massive computational power of graphics processing unit for interactive simulation with a higher particle resolution. The experiment results show that our method can simulate realistic fluid-solid couplings at interactive frame-rates even for up to 126 k particles. Copyright © 2014 John Wiley & Sons, Ltd.

SYMPLER: SYMbolic ParticLE simulatoR with grid-computing interface

We present the main design concepts of the object-oriented particle dynamics code SYMPLER. With this freely available software, simulations can be performed ranging from microscopic classical molecular dynamics up to the Lagrangian particle-based discretisation of macroscopic continuum mechanics equations. We show how the runtime definition of arbitrary degrees of freedom and of arbitrary equations of motion allows for modular and symbolic computation with high flexibility. Arbitrary symbolic expressions for inter-particle forces can be defined as well as fluxes of arbitrarily many additional scalar, vectorial or tensorial degrees of freedom. The integration in a high performance grid computing environment makes huge geographically distributed computational resources accessible to the software by an easy-to-use interface. Program summaryProgram title: SYMPLERCatalogue identifier: AERQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERQ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 221255No. of bytes in distributed program, including test data, etc.: 1805954Distribution format: tar.gzProgramming language: C++.Computer: Any system operatable with Linux.Operating system: Linux, MacOS.Has the code been vectorised or parallelised?: Experimental OpenMP parallelisation for usually up to 8 cores, the grid-version can use hundreds of cores.RAM: tens of MB to several GB, depending on problem.Classification: 7.7, 12, 16.1, 16.3, 16.13, 23.External routines: GSL, libxml2; optional: libsdl, OpenMP, libjama, libtnt, libsuperluNature of problem:A unified flexible and modular simulation tool allowing for the investigation of structural, thermodynamic, and dynamical properties of fluids and solids from microscopic over mesoscopic up to macroscopic time and length scales with suitable particle based simulation methods such as molecular dynamics, dissipative particle dynamics or smoothed particle hydrodynamics. The user should be enabled to freely define his own physical models without the need for recoding or code extensions.Solution method:SYMPLER provides flexibility to the user by 1.a modular object oriented structure that is passed to the user level and allows easy switching among different integration algorithms, particle interaction forces, boundary conditions, etc.2.an arbitrary number of particle-species for the simulation of complex multi-component systems3.an arbitrary number of additional user-defined degrees of freedom per particle-species4.symbolic definition of runtime-compiled mathematical expressions for particle interactions5.import of CAD-geometries6.a flexible choice of available computational cores through a grid-computing interface, amongst others.Restrictions:Classical deterministic and stochastic Newtonian dynamics.Unusual features:Symbolic runtime-compiled user-defined expressions.Additional comments:The current version and all future updates to the code are also found at http://sympler.org.Running time:Some benchmarks are given in the paper. The running time is problem dependent and ranges from seconds to days.

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models.

Transcription factors search for specific operator sequences by alternating rounds of 3D diffusion with rounds of 1D diffusion (sliding) along the DNA. The details of such sliding have largely been beyond direct experimental observation. For this purpose we devised an analytical formulation of umbrella sampling along a helical coordinate, and from extensive and fully atomistic simulations we quantified the free-energy landscapes that underlie the sliding dynamics and dissociation kinetics for the LacI dimer. The resulting potential of mean force distributions show a fine structure with an amplitude of 1 k(B)T for sliding and 12 k(B)T for dissociation. Based on the free-energy calculations the repressor slides in close contact with DNA for 8 bp on average before making a microscopic dissociation. By combining the microscopic molecular-dynamics calculations with Brownian simulation including rotational diffusion from the microscopically dissociated state we estimate a macroscopic residence time of 48 ms at the same DNA segment and an in vitro sliding distance of 240 bp. The sliding distance is in agreement with previous in vitro sliding-length estimates. The in vitro prediction for the macroscopic residence time also compares favorably to what we measure by single-molecule imaging of nonspecifically bound fluorescently labeled LacI in living cells. The investigation adds to our understanding of transcription-factor search kinetics and connects the macro-/mesoscopic rate constants to the microscopic dynamics.

Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2

The adaptive immunity of bacteria against foreign nucleic acids, mediated by CRISPR (clustered regularly interspaced short palindromic repeats), relies on the specific incorporation of short pieces of the invading foreign DNA into a special genomic locus, termed CRISPR array. The stored sequences (spacers) are subsequently used in the form of small RNAs (crRNAs) to interfere with the target nucleic acid. We explored the DNA-binding mechanism of the immunization protein Csn2 from the human pathogen Streptococcus agalactiae using different biochemical techniques, atomic force microscopic imaging and molecular dynamics simulations. The results demonstrate that the ring-shaped Csn2 tetramer binds DNA ends through its central hole and slides inward, likely by a screw motion along the helical path of the enclosed DNA. The presented data indicate an accessory function of Csn2 during integration of exogenous DNA by end-joining.

Evaluation of Adamantane Derivatives as Inhibitors of Dengue Virus mRNA Cap Methyltransferase by Docking and Molecular Dynamics Simulations.

Binding of the Dengue virus S-adenosyl-L-methionine (AdoMet)-dependent mRNA cap methyltransferase (NS5MTaseDV ) with adamantane derivatives was explored using molecular modeling methods and (nucleoside-2'O)-methyltransferase bioassay. The studied compounds include urea derivatives of adamantane and the antiviral drugs amantadine and rimantadine. The urea derivatives of adamantanes had previously been identified as inhibitors of NS5MTaseDV . The docking simulations using GOLD, Glide, and Dock give consistent binding modes and binding affinities of adamantanes in the AdoMet-binding site of NS5MTaseDV and, in particular, yield similar positions for the previously found inhibitors. Combined, they perfectly correspond to the bioassay measurements of nucleoside-2'O-methyltransferase activity of NS5TaseDV , which confirmed inhibitory properties of the active urea adamantane but did not show inhibitory activity for amantadine and rimantadine. We also employed microscopic molecular dynamics (MD) simulations and a linear interaction energy (LIE) method to verify the docking results. The MD/LIE binding free energies of selected protein-inhibitor complexes agree overall with the binding affinities from docking and demonstrate that amantadine and rimantadine only weakly bind at the explored site. The MD simulations also demonstrated the flexible character of a protein loop that is located between the β2 and β3 strands and is part of the AdoMet-binding pocket of NS5MTaseDV .

New measurement of the3He(α,γ)7Be cross section at medium energies

We report on a new cross-section measurement for the ${}^{3}$He($\ensuremath{\alpha}$, $\ensuremath{\gamma}$)${}^{7}$Be reaction at three medium energies of ${E}_{\mathrm{c}.\mathrm{m}.}$ between 1 and 3 MeV. The interest stems from the significant role played by the reaction in calculating an accurate solar neutrino flux and the primordial ${}^{7}$Li abundance. The energy dependence of the astrophysical ${S}_{34}$ factor observed in the present work, especially above 1 MeV, highlights the need to constrain theories in order to obtain a precise extrapolated value for ${S}_{34}(0)$. In this context, a comparison with the recent theoretical work in a fully microscopic fermionic molecular dynamics approach and a few other representative calculations emphasize the need for further experimental as well as theoretical work to resolve the existing conflicts.

Adsorbents and columns in analytical high‐performance liquid chromatography: A perspective with regard to development and understanding

A brief historical survey is presented on the evaluation of silica adsorbents in analytical HPLC. The theory of analytical HPLC is mostly still being based on the height equivalent to a theoretical plate concept and the van Deemter equation that was derived from gas phase adsorption involving a linear adsorption isotherm and fast mass transfer kinetics. One can obviously wonder whether the use of the van Deemter equation is relevant and valid for the evaluation of the performance of HPLC systems, where most often the liquid solutes involve charged molecules in electrolytes and in very many cases the adsorbates are macromolecules having diffusion coefficients of small magnitude. Instead of the van Deemter equation, a multi-scale modelling approach that involves microscopic and macroscopic dynamic non-linear mass-transfer-rate models should be employed. Furthermore, advanced experimental methods for the characterisation of porous media and the distribution of the density of immobilised active sites (e.g., ligands) on surfaces as well as microscopic pore-network modelling and molecular dynamics modelling and simulation methods could be used for the design of novel adsorbents whose porous structures and immobilised active sites would provide effective mass transport and adsorption rates for realising efficient separations as well as high dynamic capacities when larger throughputs are required.

Collective energy absorption of ultracold plasmas through electronic edge-modes

We investigate the collective dynamics of electrons in ultracold neutral plasmas driven by an oscillating radio-frequency field. We point out the importance of a sharp density drop at the plasma boundary that arises due to unavoidable charge imbalances, and show that this plasma edge provides the major mechanism for energy absorption from the external field. Using a cold fluid theory, we derive the corresponding absorption frequency and validate our findings by microscopic molecular dynamics simulations. The proposed edge-mode is shown to provide a consistent explanation for the observed absorption spectra measured in different experiments. Understanding the response of the electronic plasma component to weak external driving is essential since it grants experimental access to the time-evolving density and temperature of ultracold plasmas.

Free-energy molecular simulations of the inclusion complex of Ne with fullerene C60 in water

Binding free energy of Ne in the endohedral fullerene Ne@C60 in water was calculated using closed thermodynamic cycle that involves annihilation in silico of Ne in the free and bound states. The underlying microscopic force field molecular dynamics simulations were performed at 300 K in the constant-volume 27.9 Å periodic box of the TIP3P water molecules. The reference binding free energy of a dummy atom to C60 was calculated from the ideal gas theory equations. The free energies of atom annihilation were computed by means of the free-energy perturbation and Bennett acceptance ratio methods. Introduction of intermediate particle of small size in the mutation scheme in C60 substantially improved free-energy convergence. The predicted binding free energies of Ne and Ne cavity to C60 at the standard state concentration are about − 5 kJ mol− 1 and +22 kJ mol− 1, respectively. The free energy of reversible annihilation of Ne is controlled by the insertion step for simulations both in water and in C60.

Microscopic calculation of the 3He(α,γ)7Be reaction rate using realistic interactions

The radiative capture cross sections for the 3He(α,γ)7Be and the 3H(α,γ)7Li reactions are calculated in the fully microscopic fermionic molecular dynamics approach. A realistic effective interaction derived in the unitary correlation operator method is employed. The model space consists of frozen cluster configurations at large distances and polarized configurations, obtained by variation of the many-body wave functions, in the interaction region. These polarized configurations are essential for the description of the 7Be and 7Li bound states and for the S- and D-wave scattering phase shifts. The calculated capture cross section agrees with both the normalization and the energy dependence of the modern 3He(α,γ)7Be data. In case of the 3H(α,γ)7Li reaction the energy dependence of the most recent data is described well but the normalization is larger by about 15% compared to experiment.

Microscopic Calculation of theHe3(α,γ)Be7andH3(α,γ)Li7Capture Cross Sections Using Realistic Interactions

The radiative capture cross sections for the 3He(alpha,gamma)7Be and 3H(alpha,gamma)7Li reactions are calculated in the fully microscopic fermionic molecular dynamics approach using a realistic effective interaction that reproduces the nucleon-nucleon scattering data. At large distances bound and scattering states are described by antisymmetrized products of 4He and 3He/3H ground states. At short distances the many-body Hilbert space is extended with additional many-body wave functions needed to represent polarized clusters and shell-model-like configurations. Properties of the bound states are described well, as are the scattering phase shifts. The calculated S factor for the 3He(alpha,gamma)7Be reaction agrees very well with recent experimental data both in absolute normalization and energy dependence. In case of the 3H(alpha,gamma)7Li reaction the calculated S factor is larger than available experimental data by about 15%.

On relation between the free-energy perturbation and Bennett’s acceptance ratio methods: Tracing the influence of the energy gap

The "double-end" free-energy perturbation (DEFEP) expression, as the Taylor expansions show, presents an asymptotic solution for Bennett's acceptance ratio (BAR) method at large energy gaps. Iterative self-consistent calculations for solving the BAR equation oscillate between two energy values in such a case, and only using the DEFEP result as a first-guess yields formal convergence of the self-consistence procedure. The DEFEP estimate also provides a good starting point for the iterative procedure of BAR for the whole range of state overlap. Microscopic force field molecular dynamics simulations of the hydration free energies for transformation O(+)-->O(-) support these data. The simulations also prove robustness of the multistage perturbation schemes as compared with single-stage calculations. The observed difference between the BAR and DEFEP results has a maximum at intermediate values of energy gaps and is getting smaller for energy gaps less than 10-15 kT.

Vibrational wave packet induced oscillations in two-dimensional electronic spectra. I. Experiments

This is the first in a series of two papers investigating the effect of electron-phonon coupling in two-dimensional Fourier transformed electronic spectroscopy. We present a series of one- and two-dimensional nonlinear spectroscopic techniques for studying a dye molecule in solution. Ultrafast laser pulse excitation of an electronic transition coupled to vibrational modes induces a propagating vibrational wave packet that manifests itself in oscillating signal intensities and line shapes. For the two-dimensional electronic spectra we can attribute the observed modulations to periodic enhancement and decrement of the relative amplitudes of rephasing and nonrephasing contributions to the total response. Different metrics of the two-dimensional signals are shown to relate to the frequency-frequency correlation function which provides the connection between experimentally accessible observations and the underlying microscopic molecular dynamics. A detailed theory of the time-dependent two-dimensional spectral line shapes is presented in the accompanying paper [T. Mančal et al., J. Chem. Phys. 132, 184515 (2010)].

A stochastic phase-field model determined from molecular dynamics

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average.