Direct MD Simulations Research Articles

Self-assembly with colloidal clusters: facile crystal design using connectivity landscape analysis.

Recent experimental and theoretical studies demonstrate that prefabricated micron-scale colloidal clusters functionalized with DNA oligomers offer a practical way for introducing anisotropic interactions, significantly extending the scope of DNA-mediated colloidal assembly, and enabling the formation of interesting crystalline superstructures that are otherwise inaccessible with short-ranged, spherically symmetric interactions. However, it is apparent that the high-dimensional parameter space that defines the geometric and interaction properties of such systems poses an obstacle to assembly design and optimization. Here, we present a geometrical analysis that generates connectivity landscapes for target superstructures, greatly reducing the space over which subsequent experimental trials must search. We focus on several superstructures that are assembled from binary systems comprised of 'merged' or 'sintered' tetrahedral clusters and single spheres. We also validate and extend the analytical constraint approach with direct MD simulations of superstructure nucleation and growth.

Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides.

One of the approaches to improve our ability to characterize biologically important processes and to map out an underlying free energy landscape is to direct MD simulations to explore molecular conformational phase space faster. Intrinsically disordered systems with shallow free energy landscapes of a huge number of metastable minima pose a particular challenge in this regard. Both characterization of the often ill-defined conformational states as well as the assessment of the degree of convergence of phase space exploration are problematic. We have used a multidimensional scaling-like embedding (sketch-map) to describe the energetically accessible regions of phase space for a peptide fragment of the intrinsically disordered protein α-synuclein. Using sketch-map coordinates from a short initial simulation, we guided additional MD simulations to efficiently expand sampling of the conformational space. The sketch-map projections are very well suited to detect rare but possibly functionally relevant events, metastable intermediates, and transition states in the vast amount of data.

Thermal transport across carbon nanotube-graphene covalent and van der Waals junctions

Carbon nanotubes and graphene are promising materials for thermal management applications due to their high thermal conductivities. However, their thermal properties are anisotropic, and the radial or cross-plane direction thermal conductivity is low. A 3D Carbon nanotube (CNT)-graphene structure has previously been proposed to address this limitation, and direct molecular dynamics simulations have been used to predict the associated thermal conductivity. In this work, by recognizing that thermal resistance primarily comes from CNT-graphene junctions, a simple network model of thermal transport in pillared graphene structure is developed. Using non-equilibrium molecular dynamics, the resistance across an individual CNT-graphene junction with sp2 covalent bonds is found to be around 6×10−11 m2K/W, which is significantly lower than typical values reported for planar interfaces between dissimilar materials. In contrast, the resistance across a van der Waals junction is about 4×10−8 m2K/W. Interestingly, when the CNT pillar length is small, the interfacial resistance of the sp2 covalent junction is found to decrease as the CNT pillar length decreases, suggesting the presence of coherence effects. To explain this intriguing trend, the junction thermal resistance is decomposed into interfacial region and boundary components, and it is found that while the boundary resistance has little dependence on the pillar length, the interfacial region resistance decreases as the pillar length decreases. This is explained by calculating the local phonon density of states (LDOS) of different regions near the boundary. The LDOS overlap between the interfacial region and the center region of CNT increases as the pillar length decreases, leading to the decrease of interfacial region resistance. The junction resistance Rj is eventually used in the network model to estimate the effective thermal conductivity, and the results agree well with direct MD simulation data, demonstrating the effectiveness of our model.

Efficient Calculation of Gas Diffusivity in Single-Component and Binary Mixtures of Spherical Adsorbates in Flexible 8MR Zeolites

We use two methods, the changing snapshot method and transition state theory (TST)/snapshot method, to characterize the effects of zeolite framework flexibility on diffusion of spherical molecules in 8MR zeolites. These methods are applied to noble gases (Ne, Ar, Kr, Xe, and Rn) and CF4. We demonstrate the effect of the zeolite framework flexibility on diffusion by considering the size and loading of adsorbates and temperature. In both the methods, we approximate flexible structures as a set of discrete rigid snapshots obtained from molecular dynamics simulations of an empty framework. We show that the diffusivities predicted with these two efficient methods agree with direct MD simulations in the fully flexible structures. We studied in detail how the framework flexibility affects the loading dependence of diffusion. By looking at the computational costs, we demonstrated that both the methods are orders of magnitude more efficient than the fully flexible simulations. We then apply the changing snapshot m...

Direct MD Simulations of Terahertz Absorption and 2D Spectroscopy Applied to Explosive Crystals.

A direct molecular dynamics simulation of the THz spectrum of a molecular crystal is presented. A time-dependent electric field is added to a molecular dynamics simulation of a crystal slab. The absorption spectrum is composed from the energy dissipated calculated from a series of applied pulses characterized by a carrier frequency. The spectrum of crystalline cyclotrimethylenetrinitramine (RDX) and triacetone triperoxide (TATP) were simulated with the ReaxFF force field. The proposed direct method avoids the linear response and harmonic approximations. A multidimensional extension of the spectroscopy is suggested and simulated based on the nonlinear response to a single polarized pulse of radiation in the perpendicular polarization direction.

Molecular dynamics based study and characterization of deformation mechanisms near a crack in a crystalline material

Modeling crack propagation in crystalline materials is a challenging enterprise due to complexities induced by the interaction of the crack with various deformation mechanisms such as dislocation, micro twin, stacking faults etc.. As a first step toward the development of physics-based models of deformation in the presence of a crack, this paper proposes a comprehensive approach based on molecular dynamics simulations of a crystalline material with an embedded crack. The MD-based framework invokes a sequence of four tasks to accomplish the overall goal, viz. (i) MD simulation, (ii) characterization of atomic-level crack and deformation mechanisms, (iii) quantification of atomic-level deformation mechanisms and crack, and (iv) response analysis. Effective characterization methods like CNA, DXA and deformation gradient analysis followed by quantification are able to delineate the crack length/opening, dislocation structure and microtwins at a high resolution. Interactions of the crack with the dislocation networks and microtwins under mode I loading conditions are investigated for different lattice orientations. Crystal orientation has significant effect on the mechanisms activation and evolution. An important study is made through partitioning of the total energy into recoverable elastic energy, defect energy and inelastic dissipation, and correlating them with deformation characteristics such as dislocation density and twin volume fraction. Finally, a simple mechanistic model of deformation is developed, which associates dislocation density evolution with the stress–strain response in a crystalline material in the presence of a crack. Results show good quantitative agreement of material softening and hardening behavior with direct MD simulation results. The model can be further used to estimate the range of strain-rates that may be applied for physically meaningful MD simulations.

An elegant access to formation and vaporization enthalpies of ionic liquids by indirect DSC experiment and “in silico” calculations

We used DSC for determination of the reaction enthalpy of the synthesis of the ionic liquid [C(4)mim][Cl]. A combination of DSC and quantum chemical calculations presents a new, indirect way to study thermodynamics of ionic liquids. The new procedure was validated with two direct experimental measurements and MD simulations.

Temperature dependence and anisotropy of self- and mono-vacancy diffusion in α-Zr

Temperature dependence and anisotropy of self- and mono-vacancy diffusion is important for modeling irradiation-induced microstructure evolution and the concomitant macroscopic deformation in Zr and its alloys. For self-interstitials, direct MD simulation of the diffusion has yielded useful data. Vacancy and self-diffusion, however, proceeds at a much slower rate, so that a direct simulation is not always practicable, particularly in the reactor-operating temperature regime. In this paper, we follow an alternate route based on thermodynamic integration and calculate the enthalpy, entropy and attempt jump frequencies of vacancy migration and formation in α-Zr for various temperatures ranging from 100 K to 1100 K. Their jump-direction and temperature dependencies are examined. The diffusivities so derived compare very well with other calculated results. Comparison with experimental self-diffusion data shows good general agreement except in the temperature regime near the α– β transformation. In this regime, the curvature in the Arrhenius plot of the self-diffusivity obtained is substantially smaller than the corresponding experimental results. Possible reasons are discussed.

Investigation of argon nanocrystalline thermal conductivity by molecular dynamics simulation

The molecular dynamics simulation (MD) method has been widely applied to the investigation of the thermal conductivity of single crystalline materials during last decade but no report on the thermal conductivity of polycrystalline solids by direct MD simulation with three-dimensional polycrystalline structure is found so far. In this paper, the periodic configuration of nanocrystalline argon for MD simulation is constructed based on the Voronoi tessellation method. The thermal conductivity of both perfect single crystal and nanocrystalline bulk argon are calculated by the Green–Kubo method. The results are compared with experiments as well as MD simulation results reported by others. The thermal conductivity of nanocrystalline argon with the average grain size of 5 nm is much lower than that of the corresponding perfect single crystal at temperatures between 10 and 70 K. The reduction can be attributed to grain boundary thermal resistance due to large number of grain interfaces in polycrystalline argon, as well as their limitation on the phonon mean free path. The magnitude of estimated grain boundary thermal resistance at different temperatures is on the scale of 10−9 m2 K/W. The grain boundary thermal resistance is larger at lower temperature. This report demonstrates that the thermal property of polycrystalline materials can be investigated by MD simulation.

Theory and molecular dynamics modeling of spall fracture in liquids

The model of fracture of liquid under tension is developed. It is based on the “nucleation-and-growth” approach introduced initially by D. R. Curran et al. Phys. Rep. 147, 253 1987. The model derives the kinetics of fracture at mesoscale from the kinetics of elementary processes of void nucleation and growth in metastable liquid. The kinetics of nucleation and growth of voids in highly metastable liquid is studied in molecular dynamics MD simulations with the Lennard-Jones interatomic potential. The fracture under dynamic loading is considered, when the homogeneous void nucleation is relevant. The model is applied to the estimation of the spall strength of liquid. The growth of nanometer-size voids is shown to be well described by the Rayleigh-Plesset equation. The calculations of the void size distribution by the proposed kinetic model are in agreement with the distributions obtained in the direct large-scale MD simulations. The spall strength evaluated by the model is in a good agreement with the experimental data the shock wave tests on hexane and the direct MD simulations. The correspondence between our results on nucleation rate and the predictions of the classical nucleation theory is discussed.

Coriolis coupling as a source of non-RRKM effects in ozone molecule: Lifetime statistics of vibrationally excited ozone molecules

A theory that describes the non-RRKM (non-Rice-Ramsperger-Kassel-Marcus) effects in the lifetime statistics of activated ozone molecules is derived. The non-RRKM effects are shown to originate due to the diffusive energy exchange between vibrational and rotational degrees of freedom in ozone molecule. The lifetime statistics is found to be intramolecular diffusion controlled at long times. The theoretical results are in good agreement with the direct MD simulations of lifetime statistics.

Grand canonical steady-state simulation of nucleation

Grand canonical molecular dynamics (GCMD) is applied to the nucleation process in a metastable phase near the spinodal, where nucleation occurs almost instantaneously and is limited to a very short time interval. With a variant of Maxwell's demon, proposed by McDonald [Am. J. Phys. 31, 31 (1963)], all nuclei exceeding a specified size are removed. In such a steady-state simulation, the nucleation process is sampled over an arbitrary time span and all properties of the metastable state, including the nucleation rate, can be obtained with an increased precision. As an example, a series of GCMD simulations with McDonald's demon is carried out for homogeneous vapor to liquid nucleation of the truncated-shifted Lennard-Jones (tsLJ) fluid, covering the entire relevant temperature range. The results are in agreement with direct nonequilibrium MD simulation in the canonical ensemble. It is confirmed for supersaturated vapors of the tsLJ fluid that the classical nucleation theory underpredicts the nucleation rate by two orders of magnitude.

Conformation of Ultrathin PFPE Lubricants With Different Structure on Magnetic Disks—Direct Observation and MD Simulation

Three types of PFPE lubricants (Z-tetraol, TA-30, and D-4OH) with different molecular structures were coated on magnetic disks and the conformations of these films were studied by atomic force microscopy using a fluoride-coated probe. The molecular conformations of these lubricant films were found to be different from each other. The Z-tetraol film showed the highest molecular height and lowest coverage among these lubricants. The TA-30 film showed a double-layer structure and the highest coverage among the lubricant films. The D-4OH film showed a monolayer structure and higher coverage than the Z-tetraol film. These observed were in agreement with the results of molecular dynamics simulations. In these simulations, the TA-30 film showed the highest coverage and lowest molecular height among the three lubricant films because the TA-30 molecules did not form a random coil shape and were adsorbed rigidly on the disk surface. The Z-tetraol molecules were adsorbed and formed a random coil shape. The D-4OH molecules were also adsorbed and formed a spiral shape.

Geometric Confinement Governs the Rupture Strength of H-bond Assemblies at a Critical Length Scale

The ultrastructure of protein materials such as spider silk, muscle tissue, or amyloid fibers consists primarily of beta-sheets structures, composed of hierarchical assemblies of H-bonds. Despite the weakness of H-bond interactions, which have intermolecular bonds 100 to 1000 times weaker than those in ceramics or metals, these materials combine exceptional strength, robustness, and resilience. We discover that the rupture strength of H-bond assemblies is governed by geometric confinement effects, suggesting that clusters of at most 3-4 H-bonds break concurrently, even under uniform shear loading of a much larger number of H-bonds. This universally valid result leads to an intrinsic strength limitation that suggests that shorter strands with less H-bonds achieve the highest shear strength at a critical length scale. The hypothesis is confirmed by direct large-scale full-atomistic MD simulation studies of beta-sheet structures in explicit solvent. Our finding explains how the intrinsic strength limitation of H-bonds can be overcome by the formation of a nanocomposite structure of H-bond clusters, thereby enabling the formation of larger and much stronger beta-sheet structures. Our results explain recent experimental proteomics data, suggesting a correlation between the shear strength and the prevalence of beta-strand lengths in biology.

Solid−Liquid Interfacial Free Energy of Water: A Molecular Dynamics Simulation Study

The superheating-undercooling hysteresis method and molecular dynamics simulation [Luo et al. Phys. Rev. B 2003, 68, 134206] were applied to estimate solid-liquid interfacial free energy (γ) of model water at ambient pressure. Two models of water were selected, the TIP4P-Ew and TIP5P-Ew, which are the improved TIP4P and TIP5P model (for the use with Ewald technique), respectively. The calculated γ at 1 bar is 37 mJ/m(2) for TIP4P-Ew and 42 mJ/m(2) for TIP5P-Ew, consistent with a previous direct MD simulation (39 mJ/m(2)), as well as within the range of measured values (25-44 mJ/m(2)).

Cu diffusion in α-Fe: determination of solute diffusivities using atomic-scale simulations

The nucleation and growth of radiation-induced Cu-rich clusters have proved an important topic in the study of microstructural and chemical evolution responsible for property changes in pressure vessel steels subjected to neutron irradiation. Small Cu clusters can act as precipitate precursors and contribute to the hardening of the material by impeding dislocation glide. Reliable Cu diffusion coefficients provide critical input to Monte Carlo and rate theory approaches to study the kinetics of diffusion and clustering that lead to the formation of such Cu-rich features. In this paper we report the results of a molecular dynamics study of Cu solute-atom diffusion in a Fe–0.9at%Cu alloy, using high-temperatures and high-vacancy concentrations to hasten the convergence of the calculation. We find a value of 0.61 eV for the migration energy of Cu in the b.c.c Fe matrix, in good agreement with available experimental results. The main diffusion mechanisms under the conditions simulated are identified and discussed, and the effect of vacancy and solute clustering on Cu migration is assessed. In addition, a rigorous computation of the solute enhancement factor, correlation factor and solute diffusivity is performed within the five-frequency theoretical framework and the harmonic approximation. The results obtained are compared with those yielded by the direct MD simulations and the observed differences discussed.

Structural and mechanical properties of well-relaxed amorphous–crystal interface in silicon: molecular dynamics study

Amorphous–crystal interface properties in silicon are key parameters for the control of the mechanical and electrical properties of polycrystalline thin film. We propose a method to calculate the interface properties of the well-relaxed amorphous–crystal interface by using structural parameters to evaluate the interface structures. The amorphous–crystal interface energies, γ I=0.29 and 0.33 J/m 2, are obtained for (0 0 1) and (1 1 1) plane, respectively. Structural relaxation greatly influences those values. It is found that the interface energies are smaller than the surface energies and depend weakly on the crystal orientation. These findings agree very well with the experiments. The interface stress is small as compared with that of metal/metal interface and involves the scattering across a broad range. A critical nucleus size estimated by the calculated interface energy is slightly smaller than that estimated by the direct MD simulation for homogeneous nucleation. That small mismatch is thought to be caused by the limit of the classical nucleation theory.

Ab Initio Direct Molecular Dynamics Simulations and QM/MM Computations in Search of Organic Reaction Mechanisms

Abstract Ab initio direct-MD simulations and combined QM/MM computations are the theoretical methods that are expected to play an important role in the study of organic reaction mechanisms in the near future. This account reviews recent achievements with these methods in mechanistic studies of organic reactions. In particular the focus is placed on proton transfer, SN1, SN2, and SN2/ET borderline reactions as illustrative examples. The direct-MD simulations revealed the importance of dynamics in controlling the reaction path, which can often be different from the minimum energy path on the potential energy surface. It was also demonstrated that the QM/MM computations could be a promising method to analyze reactions in solution.