Continuum Model Simulations Research Articles

Ionic solvation and association in LiCl aqueous solution: a density functional theory, polarised continuum model and molecular dynamics investigation

In this work, the ionic solvation and association behaviours in the LiCl aqueous solution were investigated using density functional theory (DFT), a polarised continuum model and classical molecular dynamics simulations. DFT calculations of LiCl(H2O)1–6,8 clusters show that contact ion pair (CIP) and solvent-shared ion pair (SSIP) conformers of LiCl(H2O)n (n ≥ 4) clusters are generally energetic both in the gas phase and in the aqueous solution. Some SSIP conformers may be slightly more stable than their CIP isomers when at least eight water molecules are incorporated in the inner hydration shells of LiCl hydrates. The transformation between CIP and SSIP conformers is easy by overcoming a small energy barrier, which mainly results from the hydration shell reorganisation of Li+. Molecular dynamics simulations show that ion pairs or ion clusters can be found in the LiCl aqueous solution, and the probability of CIP conformers or ion clusters presented in the LiCl solution generally increases with rise in temperature. However, the presentation of ion pairs or ion clusters in the LiCl aqueous solution does not inevitably lead to the nucleation of LiCl crystallisation.

Shock attenuation of PMMA sandwich panels filled with soda-lime glass beads: A fluid-structure interaction continuum model simulation

The dramatic increase of Improvised Explosive Device (IED) related injuries has stimulated many studies to reconsider the design of the current state-of-the-art vehicle and body protective equipment. Materials now need to be chosen not only to stop solid projectiles such as shrapnel or bullets but also to attenuate the injurious effects of incoming blast waves. New advanced computational models of such events have been proved to facilitate the access to information currently inaccessible to experiments. To this end, we developed a fluid–structure interaction computational continuum model to investigate the attenuation properties of foam specimens containing filler materials under shock loading. Three test specimens were examined: a solid foam sample, and two other foam samples incorporating an intermediate layer of filler material: SiO2 aerogel and soda-lime glass beads. The model was then calibrated and the results compared to the corresponding shock tube experimental results [M.D. Alley, S.F. Son, G. Christou, R. Goel, L. Young, 2009]. In conclusion, the model shows good agreement with experiment values for the peak pressure of the transmitted wave as well as its propagation time. Complementing the existing experimental results, high density soda-lime glass beads filler material is shown to substantially decrease the peak magnitude of the transmitted wave and to decrease the spatial gradient of the pressure compared to the other lower density filler samples. However, the history of the sample reaction force suggests that the frame constraining the test specimen is being subjected to a higher impulse using the high density filler. Such a model paves the road to a new series of complex numerical models designed to accompany experimental testing by providing new insights on the mechanisms of fluid–structure interaction.

Theoretical studies on the chemical decomposition of 5-aza-2′-deoxycytidine: DFT study and Monte Carlo simulation

The decomposition mechanism of 5-Aza-2′-deoxycytidine has been studied by the use of computational techniques. Optimized structures for all of the stationary points in the gas phase were investigated at B3LYP/6-31+G(d,p) level of theory. Single-point energies were determined employing the ab initio MP2 method in conjunction with the 6-311++G(d,p) basis set. Five possible pathways, paths 1–5, were evaluated. In each pathway, the direct (A-paths 1–5) and water-assisted (B-paths 1–5) processes were considered. Meanwhile, the local microhydration model with the direct participation of three water molecules around the reaction centers was adopted to mimic the system for the water-assisted decomposition mechanisms above, where one water molecule is the nucleophilic reactant and the other two are the auxiliary molecules located on each side of the nucleophilic water. The results in the gas phase exhibit that the energy barriers of the water-assisted pathways based on the local microhydration model decrease dramatically by about 15–20 kcal/mol as compared with those of the direct pathways because of the contribution of the auxiliary water molecules. In addition, bulk solvent effects of water were determined by means of the self-consistent reaction field based on the conductor-like polarized continuum model and Monte Carlo simulation with free energy perturbation (MC-FEP) technique, respectively. Our computational results indicate that B-path 3 in the decomposition reaction of 5-azadC is the most favorable, where the calculated rate constant (1.68 × 10−3 min−1) using the MC-FEP method is within the range of the experimentally determined values [(5.89 ± 0.54) × 10−3 min−1 by UV and (1.46 ± 0.08) × 10−3 min−1 by NMR].

Modeling of vibrations of carbon nanotubes

The continuum model and molecular dynamic (MD) simulation are effective in the modeling of mechanic behaviors of nano-materials. This paper presents a brief review of vibrations of single-walled carbon nanotubes (SWCNTs) investigated using the nonlocal beam model and nonlocal rod model and MD simulation. The nonlocal continuum models play an important role in studying vibration of CNTs. The applicability of the nonlocal continuum models based on the MD simulation results is summarized.

Vacancy behavior in Czochralski silicon growth

The vacancy defect behavior in silicon crystal growth has been investigated by kinetic Monte Carlo and continuum simulations. The vacancy concentration distributions in silicon crystal were obtained from continuum model simulations corresponding to experimental conditions and then the vacancy clusters distribution obtained from kinetic lattice Monte Carlo simulations. At the temperature above 1470 K, the diffusivity was almost constant because the clusters were not formed. In the clustering temperature region (1370–1270 K), the larger clusters were generated at the higher temperature, the smaller clusters were generated at the lower temperature. While the vacancy concentration led to increase in the number of clusters, the mean size of clusters was irrespective of the vacancy concentrations. Clustering phenomena were very susceptible to temperature and vacancy concentrations. The total number of vacancy clusters was linearly proportion to the crystal pull rate. The radial distribution of clusters obtained from multi-scale simulations was in good agreement with the distribution of voids in the experimental data.

Ion specific effects on phase transitions in protein solutions

A recent Monte Carlo simulation determined the potential of mean force between two lysozyme molecules in various aqueous solutions [M. Lund, Phys. Rev. Lett. 100, 258105 (2008)]. The study involved a combination of explicit solvent and continuum model simulations and showed that there are significant ion-specific protein-protein interactions due to hydrophobic patches on the protein surfaces. In this paper we use the results of their study to determine the phase diagram for lysozyme for aqueous solutions of NaCl and NaI. Two of the three phase diagrams have a stable fluid-fluid critical point, while the third has a slightly metastable critical point. This results from a secondary extremum in the potential associated with a repulsive interaction. This repulsive interaction reduces the effective range of the attractive interaction and produces a metastable critical point. We compare the results of one of these phase diagrams with that for a model that includes ion-dispersion forces, but does not contain solvent structural effects.

Ion Specific Protein Assembly and Hydrophobic Surface Forces

Large anions are attracted to hydrophobic surfaces while smaller, well solvated ions are repelled. Using a combination of explicit solvent and continuum model simulations we show that this leads to significant ion-specific protein-protein interactions due to hydrophobic patches on the protein surfaces. In solutions of NaI and NaCl we calculate the potentials of mean force and find that the resulting second virial coefficients for lysozyme correspond well with experiment. We argue that ionic interactions with nonpolar surface groups may play an important role for biomolecular assembly and Hofmeister-type effects.

Piezoelectricity enhancement in ferroelectric ceramics due to orientation

A continuum model simulation, explicitly incorporating anisotropic grain-level features, based on homogenization of materials predicts an enhancement of piezoelectricity in ferroelectric ceramics better than oriented single crystals. Incorporation of randomness in the orientation of polarization associated with the grains is demonstrated to offer great prospect in the design of ceramic ferroelectric materials such as BaTiO3.

Vibrational characteristics of single-walled carbon-nanotube: Time and frequency domain analysis

In this paper, the vibrational characteristics of higher modes of single-walled carbon-nanotube (SWNT) modeled as the continuum axisymmetric cylinder are studied in both time and frequency domains. The modeling of SWNT for the high frequency dynamic analysis is done using the wavelet based spectral element method and this numerical technique involves the Daubechies scaling function approximation in time and one spatial (axial) dimension. This model is capable of capturing the coupled longitudinal-radial vibration arising due to the finiteness of SWNT. Here, first the phonon dispersion relation is obtained and validated with the atomistic and other continuum model simulations available. The effects of dimensional parameters on higher radial, longitudinal, and coupled radial-longitudinal vibrational modes are studied. Dependence of the higher mode frequencies on these parameters are much different from that of the first mode frequencies. Further time domain responses for broadband excitations are simulated and effects of the radius and thickness of the SWNT are studied. The prominent influence of the above geometrical parameters are observed in the time domain results.

Numerical Simulation of Constitution Relationship between Stress and Strain of Particulate Matters [Translated]<sup>†</sup>

The relations between normal stress and normal strain and that between shear stress and shear strain, which are the constitution relationships, have been obtained in a simple and general particulate field by the numerical simulation using Distinct Element Method. We calculate the dynamics of particulate matters using the continuum model based on these relations. Furthermore, the numerically calculated constitutive relations are formulated in order to use them for the continuum model simulation. The constitution relationships presented in this work confirm the following.1.Stresses are functions of strains and packing ratios.2.The constitution relationship of particulate matters has a hysteresis because of the change in the internal state of the particulate matters.3.Particulate matters are deformed more easily by the shear stress than the normal stress.† This paper, published originally in Japanese in J. Soc. Powder Technology, Japan, 42, 116-124 (2005), is published in KONA with the permission of the editorial committee of the Soc. Powder Technology, Japan.

Aggregation and Caking Processes of Granular Materials: Continuum Model and Numerical Simulation with Application to Sugar

Aggregation and caking of particles are common severe problems in many operations and processing of granular materials, where granulated sugar is an important example. Prevention of aggregation and caking of granular materials requires a good understanding of moisture migration and caking mechanisms. In this paper, the modeling of solid bridge formation between particles is introduced, based on moisture migration of atmospheric moisture into containers packed with granular materials through vapor evaporation and condensation. A model for the caking process is then developed, based on the growth of liquid bridges (during condensation), and their hardening and subsequent creation of solid bridges (during evaporation). The predicted caking strengths agree well with some available experimental data on granulated sugar under storage conditions.

Aggregation and caking processes of granular materials: continuum model and numerical simulation with application to sugar

AbstractAggregation and caking of particles are common severe problems in many operations and processing of granular materials, where granulated sugar is an important example. Prevention of aggregation and caking of granular materials requires a good understanding of moisture migration and caking mechanisms. In this paper, the modeling of solid bridge formation between particles is introduced, based on moisture migration of atmospheric moisture into containers packed with granular materials through vapor evaporation and condensation. A model for the caking process is then developed, based on the growth of liquid bridges (during condensation), and their hardening and subsequent creation of solid bridges (during evaporation). The predicted caking strengths agree well with some available experimental data on granulated sugar under storage conditions.

離散要素法を用いた粉粒体の構成関係の計算と数式化

The relations between normal stress and normal strain and that between shear stress and shear strain, which are the constitution relationships, have been obtained in a simple and general particulate field by the numerical simulation using Distinct Element Method. We calculate the dynamics of particulate matters using the continuum model based on these relations. Furthermore, the numerically calculated constitutive relations are formulated in order to use them for the continuum model simulation. The constitution relationships presented in this work confirm the following:(1) Stresses are functions of strains and packing ratios.(2) The constitution relationship of particulate matters has a hysteresis because of the change in the internal state of the particulate matters.(3) Particulate matters are deformed more easily by the shear stress than the normal stress.

Continuum modelling of hybrid-aligned nematic liquid crystal cells: optical response and flexoelectricity-induced voltage shift

A continuum model is employed to study systematically the optical response of hybrid-aligned nematic (HAN) liquid crystal cells under the application of an external electric field. The influence of the flexoelectric effect is discussed for a large range of anchoring strengths at the homeotropic alignment layer. It is shown that the optical response of HAN cells is governed by a complicated interplay between the flexoelectric coefficient and homeotropic anchoring strength. In particular, the calculations reveal that, for weak homeotropic anchoring, the flexoelectric effect leads to a non-linear voltage shift of the optical transmittance as a function of flexoelectric coefficient, and gives rise to an asymmetry in the transmittance–voltage curve. Finally, a comparison of the continuum-model simulations with recent experimental observations indicates that both the flexoelectric coefficient and the anchoring strength of the nematic liquid crystal MBBA on a homeotropic polyimide alignment layer are significantly lower than previously reported.

Sequence Context Dependence of Tandem Guanine:Adenine Mismatch Conformations in RNA: A Continuum Solvent Analysis

Guanine:adenine (G:A) mismatches and in particular tandem G:A (tG:A) mismatches are frequently observed in biological RNA molecules and can serve as sites for tertiary interaction, metal binding and protein recognition. Depending on the surrounding sequence tG:A mismatches can adopt different basepairing topologies. In the sequence context (5′-) G GAC (tandem G:A in bold) a face-to-face (imino or Watson-Crick-like) pairing is preferred whereas in the C GAG context, G and A adopt a sheared arrangement. Systematic conformational searches with a generalized Born continuum model and molecular dynamics simulations including explicit water molecules and ions have been used to generate face-to-face and sheared tG:A mismatches in both C GAG and G GAC sequence contexts. Conformations from both approaches were evaluated using the same force field and a Poisson-Boltzmann continuum solvent model. Although the substate analysis predicted the sheared arrangement to be energetically preferred in both sequence contexts, a significantly greater preference of the sheared form was found for the C GAG context. In agreement with the experimental observation, the analysis of molecular dynamics trajectories indicated a preference of the sheared form in the case of the C GAG-context and a favorization of the face-to-face form in the case of the G GAC context. The computational studies allowed to identify energetic contributions that stabilize or destabilize the face-to-face and sheared tandem mismatch topologies. The calculated nonpolar solvation and Lennard-Jones packing interaction were found to stabilize the sheared topology independent of the sequence context. Electrostatic contributions are predicted to make the most significant contribution to the sequence context dependence on the structural preference of tG:A mismatches.

Budding and fission dynamics of two-component vesicles

We studied the shape deformation induced by the phase separation of two-component vesicles using a dissipative particle dynamics simulation. Two types of amphiphiles, which have the same architecture but segregate from each other, are modeled by connecting particles representing the hydrophilic head and hydrophobic tail groups. After vesicle formation using a single component system, some of the amphiphiles are replaced by a second component, and then phase separation on the vesicle is simulated. Under appropriate conditions, typical shape deformations of a vesicle, such as crenated and invaginated shapes, are observed. We demonstrate that the budding and the fission are facilitated by lateral phase separation upon vesicle coupling to an asymmetric transversal distribution of amphiphiles in the bilayer. Moreover, simulations show a possible new pathway for the fission process triggered by cleavage along the domain boundary. Mesoscopic simulation based on a simple coarse-graining model reveals the dynamics of amphiphiles in vesicles that is essentially unpredictable using a conventional continuum model or full atomistic simulation.

A new simulated annealing method combined with a polarizable continuum model based on the boundary element method

We propose a novel combined method of a polarizable continuum model and molecular dynamics simulation. In this method, a solute–solvent interaction force is obtained by solving the Poisson equation of a system with the aid of the so-called boundary element method. From a 4 ns simulation for the aqueous solution of alanine dipeptide (N-acetylalanyl-N′-methylamide), it is confirmed that the calculation can provide the thermodynamically correct picture about the conformational distributions of the ϕ and ψ angles. The results of several simulated annealing runs indicate that the method is available for finding the global minimum conformation of molecules in water.

Theoretical study of electron transfer reactions in molecular clusters

Electron transfer reactions between donor and acceptor centers immersed in acetonitrile clusters are studied theoretically by using the dielectric continuum model and molecular dynamics simulations. The distribution of the electrostatic potential energy difference eΔV, between donor and acceptor sites, the solvent reorganization energy and the first-order electron transfer rate constants are estimated as functions of the cluster size. The results of both models for the clusters are compared with the corresponding results obtained for the bulk system.

Continuum model simulation program having an improved fit to actual propagation patterns

A continuum model for analyzing a Permalloy pattern in magnetic bubble field access devices is presented. The model modifys Matsutera's model [1] by expanding discretization method to making use of triangular prism elements or arbitrary quadrangular prism elements. Potential well of an asymmetric chevron pattern calculated by this model is more similar to the collapse field change value than that by the model that uses only square prism elements. The potential well contour maps for corner part of a minor loop are also shown. The detector signals calculated by this model agree qualitatively with the values measured.