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We study the shock-induced hot spot formation mechanism of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine-based explosives by molecular dynamics, compare different kinds of desensitizers and different shock velocities. A set of programs is written to calculate the physical picture of shock loading. Based on the simulations and analyses, the hot spots are found at the interface and are heated by plastic work in three ways: the interface intrinsic dissipation, the pore collapse, and the coating layer deformation. The work/heat transition rate is proved to be increasing with a loading speed. [ABSTRACT FROM AUTHOR]

In this paper, we employ first-principle calculation to investigate the Ge1–xSnx/HfO2 interface, and then evaluate its impacts on Ge1–xSnx tunneling field-effect transistor (TFET). First-principle calculations of Ge1–xSnx/HfO2 interfaces in the oxygen-rich process atmosphere indicate that the interface states originate from the Ge and Sn dangling bond, rather than Hf-bond. The total density of state shows that there are more interface states in the semiconductor bandgap with increasing Sn fraction. By further incorporating the material and interface parameters from density functional theory calculation into advanced device simulation, the electrical characteristics of Ge1–xSnx TFET are investigated. Removing the Sn atom from the first atom layer of Ge1–xSnx in device processes is found to be beneficial to reduce the degradations. For the degradation mechanisms, the trap-assisted-tunneling is the dominant mechanism at the low Sn fraction, and enhanced Shockley-Read-Hall recombination induced by traps becomes the dominant mechanism with increasing Sn fraction. The results are helpful for the interface optimization of Ge1–xSnx TFET. [ABSTRACT FROM AUTHOR]

Theoretical studies of organic solar cells are mostly based on one dimensional models. Despite their accuracy to reproduce most of the experimental trends, they intrinsically cannot correctly integrate the effects of morphology in cells based on a bulk heterojunction structure. Therefore, accounting for these effects requires the development of two dimensional models, in which donor and acceptor domains are explicitly distinct. In this context, we propose an analytical approach, which focuses on the description of the interface between the two domains. Assuming pinned charge transfer states, we rigorously derive the corresponding boundary conditions and explore the differences between this model and other existing models in the literature for various morphologies of the active layer. On one hand, all tested models are equivalent for an ideal interdigitated bulk heterojunction solar cell with a planar donor-acceptor interface, but divergences between the models rise for small sizes of the donor domain. On the other hand, we carried out a comparison on a less ideal case of cell, with a rough interface between the two domains. Simulations with such cells exhibit distinct behaviors for each model. We conclude that the boundary condition for the interface between the materials is of great importance for the study of solar cells with a non-planar interface. The model must account initially for the roughness of the interface. [ABSTRACT FROM AUTHOR]

We report a numerical study that demonstrates the interface layer between a soft and hard magnetic phase, the exchange transition layer, is the dominant factor that influences the magnetization reversal process at room temperature and long measurement times. It is found that the exchange transition layer thickness affects the magnetization reversal and the coupling of a bi-layer system by lowering the switching field and changing the angle dependent magnetization reversal. We show that the change in angle dependence of reversal is due to an increased incoherency in the lateral spin behavior. Changing the value of exchange coupling in the exchange transition layer affects only the angle dependent behavior and does not lower the switching field. [ABSTRACT FROM AUTHOR]

In the field of surface-specific vibrational sum frequency generation spectroscopy (VSFG) on organic thin films, optical interferences combined with the two-interface problem presents a challenge in terms of qualitative assessment of the data and quantitative modeling. The difficulty is amplified when considering systems comprised of more than a single material thin film layer. Recently, in our lab we have developed a generalized model that describes thin film interference in interface-specific nonlinear optical spectroscopies from arbitrary multilayer systems. Here, we apply the model to simulate VSFG spectra from the simplest multilayer: a system of two thin films, one of which is an organic small molecule and the other is a dielectric layer on a semiconductor substrate system where we idealize that the organic interfaces are equally VSFG active. Specifically, we consider the molecule N,N′-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) deposited on a silicon wafer with a thermally grown oxide dielectric. We present results for the four polarization experiments that sample the nonzero nonlinear susceptibility elements of macroscopically centrosymmetric materials (ssp, sps, pss, and ppp) and in two mIR frequency windows (the imide carbonyl stretches around 1680 cm-1 and the alkyl stretches around 2900 cm-1) as a function of both thin film thicknesses with fixed input beam angles. We use frequency dependent refractive indices for all materials. The goal is to illustrate some of the intricacies contained in the intensity data of such systems. Of particular interest is the effect of the relative polar orientation of modes at the interfaces and the possibility of designing a system where the collected signal is exclusively attributable to a single interface. Our calculations indicate that in order to unambiguously identify the relative polar orientation one must experimentally vary an additional system parameter such as thin film thickness or input beam angle and for quantitative modeling one cannot ignore either interfacial contribution. The results show that proper modeling of thin film interference effects is essential for accurate data analysis and should include the frequency dependent refractive indices, especially for modes with larger mIR absorption cross sections, even when absorptive losses are small. [ABSTRACT FROM AUTHOR]

The growing resistive switching database is accompanied by many detailed mechanisms which often are pure hypotheses. Some of these suggested models can be verified by checking their predictions with the benchmarks of future memory cells. The valence change memory model assumes that the different resistances in ON and OFF states are made by changing the defect density profiles in a sheet near one working electrode during switching. The resulting different READ current densities in ON and OFF states were calculated by using an appropriate simulation model with variation of several important defect and material parameters of the metal/insulator (oxide)/metal thin film stack such as defect density and its profile change in density and thickness, height of the interface barrier, dielectric permittivity, applied voltage. The results were compared to the benchmarks and some memory windows of the varied parameters can be defined: The required ON state READ current density of 105 A/cm2 can only be achieved for barriers smaller than 0.7 eV and defect densities larger than 3 × 1020 cm-3. The required current ratio between ON and OFF states of at least 10 requests defect density reduction of approximately an order of magnitude in a sheet of several nanometers near the working electrode. [ABSTRACT FROM AUTHOR]

This paper demonstrates a method for calculating the tension of a system with a curved interface from a molecular dynamics simulation. To do so, the pressure of a subset of the system is determined by applying a local (virtual) mechanical deformation, fitting the response to that of a bulk fluid, and then using the Young-Laplace equation to infer the tension of the interface. The accuracy of the method is tested by calculating the local pressure of a series of water simulations at various external pressures. The tension of a simulated curved octane-water interface is computed with the method and compares well with the planar tension (≈ 46.7 dyn/cm). Finally, an ambiguity is resolved between the Harasima and Irving-Kirkwood methods of calculating the local pressure as a means for computing the tension. [ABSTRACT FROM AUTHOR]

We propose a modified polymer reference interaction site model (PRISM) to describe the interfacial density profiles of polymers in contact with planar and curved solid surfaces. In the theoretical approach, a bridge function derived from density functional method is included. In description of hard-sphere polymer at planar and curved surfaces with an arbitrary external field, the effect of modification has been validated by the available simulation data, except for low density system. When extended to confined real systems, the modified theoretical model also shows an encouraging prospect in description of the interfacial structure and properties. [ABSTRACT FROM AUTHOR]

We have obtained the interfacial properties of short rigid-linear chains formed from tangentially bonded Lennard-Jones monomeric units from direct simulation of the vapour-liquid interface. The full long-range tails of the potential are accounted for by means of an improved version of the inhomogeneous long-range corrections of Janecˇek [J. Phys. Chem. B 110, 6264-6269 (2006)] proposed recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] valid for spherical as well as for rigid and flexible molecular systems. Three different model systems comprising of 3, 4, and 5 monomers per molecule are considered. The simulations are performed in the canonical ensemble, and the vapor-liquid interfacial tension is evaluated using the test-area method. In addition to the surface tension, we also obtain density profiles, coexistence densities, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the chain length and rigidity on these properties. According to our results, the main effect of increasing the chain length (at fixed temperature) is to sharpen the vapor-liquid interface and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness decreases and the surface tension increases as the molecular chains get longer. The surface tension has been scaled by critical properties and represented as a function of the difference between coexistence densities relative to the critical density. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been carried out to obtain the interfacial and coexistence properties of soft-sphere attractive Yukawa (SAY) fluids with short attraction range, κ = 10, 9, 8, 7, 6, and 5. All our simulation results are new. These data are also compared with the recently reported results in the literature of hard-core attractive Yukawa (HAY) fluids. We show that the interfacial and coexistence properties of both potentials are different. For the surveyed systems, here we show that all coexistence curves collapse into a master curve when we rescale with their respective critical points and the surface tension curves form a single master curve when we plot γ* vs. T/Tc. [ABSTRACT FROM AUTHOR]

We present a scattering model based on the scalar scattering theory that allows estimating far field scattering properties in both transmission and reflection for nano-textured interfaces. We first discuss the theoretical formulation of the scattering model and validate it for nano-textures with different morphologies. Second, we combine the scattering model with the opto-electric asa simulation software and evaluate this combination by simulating and measuring the external parameters and the external quantum efficiency of solar cells with different interface morphologies. This validation shows that the scattering model is able to predict the influence of nano-textured interfaces on the solar cell performance. The scattering model presented in this manuscript can support designing nano-textured interfaces with optimized morphologies. [ABSTRACT FROM AUTHOR]

Bulk and surface properties of the ionic liquids 1-alkyl-3-methyl-imidazolium iodides ([Cnmim]I) were simulated by classical molecular dynamics using all atom non-polarizable force field (n = 4, butyl; 6, hexyl; 8, octyl). The structure of ionic liquids were initially optimized by density functional theory and atomic charges obtained by CHELPG method. Reduction of partial atomic charges (by 20% for simulation of density and surface tension, and by 10% for viscosity) found to improve the accuracy, while a non-polarizable force field was applied. Additionally, the simulation ensembles approach the equilibrium faster when the charge reduction is applied. By these refined force field parameters, simulated surface tensions in the range of 323-393 k are quite in agreement with the experiments. Simulation of temperature dependent surface tension of [C4mim]I well beyond room temperature (up to 700 K) permits prediction of the critical temperature in agreement with that predicted from experimental surface tension data. Simulated densities in the range of 298-450 K for the three ionic liquids are within 0.8% of the experimental data. Structural properties for [C4mim]I were found to be in agreement with the results of Car-Parrinello molecular dynamics simulation we performed, which indicates a rather well-structured cation-anion interaction and occurs essentially through the imidazolium ring cation. Diffusion coefficient changes with alkyl chain length in the order of [C8mim]I > [C6mim]I > [C4mim]I for the cation and the anion. Formation of a dense domain in subsurface region is quite evident, and progressively becomes denser as the alkyl chain length increases. Bivariate orientational analysis was used to determine the average orientation of molecule in ionic liquids surface, subsurface, and bulk regions. Dynamic bisector-wise and side-wise movement of the imodazolium ring cation in the surface region can be deduced from the bivariate maps. Atom-atom density profile and bivariate analysis indicate that the imidazolium cation takes a spoon like configuration in the surface region and the tilt of alkyl group is a function length of alkyl chain exposing as linear as possible to the vapor phase. [ABSTRACT FROM AUTHOR]

Complex coacervation, a liquid-liquid phase separation that occurs when two oppositely charged polyelectrolytes are mixed in a solution, has the potential to be exploited for many emerging applications including wet adhesives and drug delivery vehicles. The ultra-low interfacial tension of coacervate systems against water is critical for such applications, and it would be advantageous if molecular models could be used to characterize how various system properties (e.g., salt concentration) affect the interfacial tension. In this article we use field-theoretic simulations to characterize the interfacial tension between a complex coacervate and its supernatant. After demonstrating that our model is free of ultraviolet divergences (calculated properties converge as the collocation grid is refined), we develop two methods for calculating the interfacial tension from field-theoretic simulations. One method relies on the mechanical interpretation of the interfacial tension as the interfacial pressure, and the second method estimates the change in free energy as the area between the two phases is changed. These are the first calculations of the interfacial tension from full field-theoretic simulation of which we are aware, and both the magnitude and scaling behaviors of our calculated interfacial tension agree with recent experiments. [ABSTRACT FROM AUTHOR]

Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is 'not practical, if not impossible' based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition. [ABSTRACT FROM AUTHOR]

First-principles molecular dynamics (FPMD) simulations and static quantum chemical (QC) calculations are used to evaluate the tensile strengths, σc, of interfaces consisting of (0001) surfaces of α-Al2O3 separated by small organic species. The evaluation of σc with FPMD was achieved by performing simulations in which the simulation cell was extending in a direction normal to the fracture plane until rupture of the interface occurred. The static QC calculations employed an approach which treated fracture of the interface as a competition between uniform extension of the simulation cell and crack formation at the rupture site, which is analogous to that used in the construction of universal binding energy relationships. The results showed that the static QC calculations accurately reproduced the FPMD simulations with respect to tensile strength and the cell extension at which rupture occurred, provided that the rupture site employed in the static calculations matched the site at which rupture occurred during the FPMD simulations. A simple strategy for identifying the rupture site, even in complex systems containing many potential rupture sites, is proposed. Overall, the work extends the calculation of tensile strengths with static QC methods to highly heterogeneous interfaces, thus providing a computationally efficient alternative to demanding FPMD simulations for this purpose. [ABSTRACT FROM AUTHOR]

Electric field produced inside a solute by a uniformly polarized liquid is strongly affected by dipolar polarization of the liquid at the interface. We show, by numerical simulations, that the electric 'cavity' field inside a hydrated non-polar solute does not follow the predictions of standard Maxwell's electrostatics of dielectrics. Instead, the field inside the solute tends, with increasing solute size, to the limit predicted by the Lorentz virtual cavity. The standard paradigm fails because of its reliance on the surface charge density at the dielectric interface determined by the boundary conditions of the Maxwell dielectric. The interface of a polar liquid instead carries a preferential in-plane orientation of the surface dipoles thus producing virtually no surface charge. The resulting boundary conditions for electrostatic problems differ from the traditional recipes, affecting the microscopic and macroscopic fields based on them. We show that relatively small differences in cavity fields propagate into significant differences in the dielectric constant of an ideal mixture. The slope of the dielectric increment of the mixture versus the solute concentration depends strongly on which polarization scenario at the interface is realized. A much steeper slope found in the case of Lorentz interfacial polarization also implies a higher free energy penalty for polarizing such mixtures. [ABSTRACT FROM AUTHOR]

A new molecular dynamics simulation method, with coupling to external baths, is used to perform equilibrium simulations on polyamide-6,6 trimers nanoconfined between graphene surfaces, in equilibrium with the bulk polymer. The method is coupled with the reverse nonequilibrium molecular dynamics simulation technique to exchange heat in the direction normal to the surfaces. To be able to study the effect of confinement on the heat conductance in nanoconfined pores, in this work a number of simulations on systems with different pore sizes are done. It is concluded that the coefficient of heat conductivity depends on the degree of polymer layering between the surfaces and on the pore width. Our results further indicate a considerable temperature drop at the interface between the surfaces and polymer. The calculated Kapitza lengths depend on the intersurface distance and on the layering of the polymer nanoconfined between the surfaces. [ABSTRACT FROM AUTHOR]

While the interaction of colloidal particles (sizes in excess of 100 nm) with liquid interfaces may be understood in terms of continuum models, which are grounded in macroscopic properties such as surface and line tensions, the behaviour of nanoparticles at liquid interfaces may be more complex. Recent simulations [D. L. Cheung and S. A. F. Bon, Phys. Rev. Lett. 102, 066103 (2009)] of nanoparticles at an idealised liquid-liquid interface showed that the nanoparticle-interface interaction range was larger than expected due, in part, to the action of thermal capillary waves. In this paper, molecular dynamics simulations of a Lennard-Jones nanoparticle in a binary Lennard-Jones mixture are used to confirm that these previous results hold for more realistic models. Furthermore by including attractive interactions between the nanoparticle and the solvent, it is found that the detachment energy decreases as the nanoparticle-solvent attraction increases. Comparison between the simulation results and recent theoretical predictions [H. Lehle and M. Oettel, J. Phys. Condens. Matter 20, 404224 (2008)] shows that for small particles the incorporation of capillary waves into the predicted effective nanoparticle-interface interaction improves agreement between simulation and theory. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been used to investigate the kinetics of spontaneous cavitation and crystallization in a Lennard-Jones liquid at negative pressures in the temperature range where these processes compete with each other. The nucleation rate has been calculated in NVE and NpT ensembles by the method of mean lifetime and the transition interface sampling method with parallel path swapping. The data obtained have been used to determine in the framework of classical nucleation theory the value of the ratio of the solid-liquid and the liquid-void interfacial free energy for critical crystals and cavities and the values of their volumes at points where the cavitation rate of the liquid is equal to the rate of its crystallization. [ABSTRACT FROM AUTHOR]

We obtain an analytic expression that allows to determine the static η and high-frequency η∞ viscosities as function of the volume fraction [lowercase_phi_synonym] of a concentrated suspension of soft spherical particles in a liquid of viscosity η0. The particles consist of a hard core of radius a covered by a porous layer of thickness d. Suspensions of hard spheres and homogeneous porous particles are limiting cases of the model. The proposed expression incorporates the results for the intrinsic viscosity obtained on the basis of a cell model [H. Ohshima, Langmuir 26, 6287 (2010)] into a recently obtained relation for the effective viscosity of concentrated colloidal suspensions [C. I. Mendoza and I. Santamaría-Holek, J. Chem. Phys. 130, 044904 (2009); J. Colloid. Interface Sci. 346, 118 (2010)]. In this model, the correlations between the particles due to crowding effects are introduced through an effective volume fraction [lowercase_phi_synonym]eff which is then used as integration variable in a differential effective medium procedure. The final expression is simple, accurate, and allows to collapse all the data in a universal master curve that is independent of the parameters characterizing the system. The only difference between the static and high-frequency cases is that in the later case [lowercase_phi_synonym]eff also incorporates hydrodynamic interactions arising from the so-called relaxation term. We have tested the accuracy of our model comparing with experimental results for spherical polymeric brushes and simulations for the high-frequency viscosity of homogeneous porous particles. In all cases the agreement with the data is extremely good. [ABSTRACT FROM AUTHOR]

We demonstrate that a recently proposed adaptive optimization algorithm for forward flux sampling simulations [E. E. Borrero and F. A. Escobedo, J. Chem. Phys. 129, 024115 (2008)] can be easily applied within the framework of transition interface sampling. This optimization algorithm systematically identifies the kinetic bottlenecks along the order parameter used to partition phase space via interfaces and improves the statistical accuracy of the reaction rate constant estimate. In different versions of the algorithm, the number or the placement of the interfaces (or both) are varied in order to allocate the numerical effort in a balanced way. The algorithm is demonstrated for a simple two-dimensional model and for the dipole flip transition of icelike structures inside carbon nanotubes. For these test systems, the optimization yielded an efficiency increase by a factor of 2-15. [ABSTRACT FROM AUTHOR]

Though the local dielectric constant at interfaces is an important phenomenological parameter in the analysis of surface spectroscopy, its microscopic definition has been uncertain. Here, we present a full molecular theory on the local field at interfaces with the help of molecular dynamics simulation, and thereby provide microscopic basis for the local dielectric constant so as to be consistent to the phenomenological three-layer model of interface systems. To demonstrate its performance, we applied the theory to the water/vapor interface, and obtained the local field properties near the interface where the simple dielectric model breaks down. Some computational issues pertinent to Ewald calculations of the dielectric properties are also discussed. [ABSTRACT FROM AUTHOR]

A common theme of studies using molecular simulation is a necessary compromise between computational efficiency and resolution of the forcefield that is used. Significant efforts have been directed at combining multiple levels of granularity within a single simulation in order to maintain the efficiency of coarse-grained models, while using finer resolution in regions where such details are expected to play an important role. A specific example of this paradigm is the development of hybrid solvent models, which explicitly sample the solvent degrees of freedom within a specified domain while utilizing a continuum description elsewhere. Unfortunately, these models are complicated by the presence of structural artifacts at or near the explicit/implicit boundary. The presence of these artifacts significantly complicates the use of such models, both undermining the accuracy obtained and necessitating the parameterization of effective potentials to counteract the artificial interactions. In this work, we introduce a novel hybrid solvent model that employs a smoothly decoupled particle interface (SDPI), a switching region that gradually transitions from fully interacting particles to a continuum solvent. The resulting SDPI model allows for the use of an implicit solvent model based on a simple theory that needs to only reproduce the behavior of bulk solvent rather than the more complex features of local interactions. In this study, the SDPI model is tested on spherical hybrid domains using a coarse-grained representation of water that includes only Lennard-Jones interactions. The results demonstrate that this model is capable of reproducing solvent configurations absent of boundary artifacts, as if they were taken from full explicit simulations. [ABSTRACT FROM AUTHOR]

Commonly, the confinement effects are studied from the grand canonical Monte Carlo (GCMC) simulations from the computation of the density of liquid in the confined phase. The GCMC modeling and chemical potential (μ) calculations are based on the insertion/deletion of the real and ghost particle, respectively. At high density, i.e., at high pressure or low temperature, the insertions fail from the Widom insertions while the performing methods as expanded method or perturbation approach are not efficient to treat the large and complex molecules. To overcome this problem we use a simple and efficient method to compute the liquid's density in the confined medium. This method does not require the precalculation of μ and is an alternative to the GCMC simulations. From the isothermal-isosurface-isobaric statistical ensemble we consider the explicit framework/liquid external interface to model an explicit liquid's reservoir. In this procedure only the liquid molecules undergo the volume changes while the volume of the framework is kept constant. Therefore, this method is described in the NpnAVfT statistical ensemble, where N is the number of particles, pn is the normal pressure, Vf is the volume of framework, A is the surface of the solid/fluid interface, and T is the temperature. This approach is applied and validated from the computation of the density of the methanol and water confined in the mesoporous cylindrical silica nanopores and the MIL-53(Cr) metal organic framework type, respectively. [ABSTRACT FROM AUTHOR]

Density functional molecular dynamics simulations have been performed in the NVT ensemble (moles (N), volume (V) and temperature (T)) on a system formed by ten acetone molecules at a temperature of 2000 K and density ρ = 1.322 g cm-3. These conditions resemble closely those realized at the interface of an acetone vapor bubble in the early stages of supercompression experiments and result in an average pressure of 5 GPa. Two relevant reactive events occur during the simulation: the condensation of two acetone molecules to give hexane-2,5-dione and dihydrogen and the isomerization to the enolic propen-2-ol form. The mechanisms of these events are discussed in detail. [ABSTRACT FROM AUTHOR]

We present an atomistic simulation study on the size dependence of dopant distribution and the influence of nanoscale film thickness on carrier transport properties of the model oxide-ion conductor yttria stabilized zirconia (YSZ). Simulated amorphization and recrystallization approach was utilized to generate YSZ films with varying thicknesses (3-9 nm) on insulating MgO substrates. The atomic trajectories generated in the molecular dynamics simulations are used to study the structural evolution of the YSZ thin films and correlate the resulting microstructure with ionic transport properties at the nanoscale. The interfacial conductivity increases by 2 orders of magnitude as the YSZ film size decreases from 9 to 3 nm owing to a decrease in activation energy barrier from 0.54 to 0.35 eV in the 1200-2000 K temperature range. Analysis of dopant distribution indicates surface enrichment, the extent of which depends on the film thickness. The mechanisms of oxygen conductivity for the various film thicknesses at the nanoscale are discussed in detail and comparisons with experimental and other modeling studies are presented where possible. The study offers insights into mesoscopic ion conduction mechanisms in low-dimensional solid oxide electrolytes. [ABSTRACT FROM AUTHOR]

In this paper we calculate the interfacial resistances to heat and mass transfer through a liquid-vapor interface in a binary mixture. We use two methods, the direct calculation from the actual nonequilibrium solution and integral relations, derived earlier. We verify, that integral relations, being a relatively faster and cheaper method, indeed gives the same results as the direct processing of a nonequilibrium solution. Furthermore we compare the absolute values of the interfacial resistances with the ones obtained from kinetic theory. Matching the diagonal resistances for the binary mixture we find that kinetic theory underestimates the cross coefficients. The heat of transfer is, as a consequence, correspondingly larger. [ABSTRACT FROM AUTHOR]

A one-dimensional kinetic Monte Carlo (KMC) model has been developed to simulate the chemical vapor deposition of a diamond (100) surface under conditions used to grow single-crystal diamond (SCD), microcrystalline diamond (MCD), nanocrystalline diamond (NCD), and ultrananocrystalline diamond (UNCD) films. The model considers adsorption, etching/desorption, lattice incorporation and surface migration but not defect formation or renucleation processes. Two methods have been devised for estimation of the gas phase concentrations of species at the growing diamond surface, and are used to determine adsorption rates for C1Hx hydrocarbons for the different conditions. The rate of migration of adsorbed carbon species is governed by the availability of neighboring radical sites, which, in turn, depend upon the rates of H abstraction and of surface-radical migration. The KMC model predicts growth rates and surface roughness for each of diamond types consistent with experiment. In the absence of defect formation and renucleation the average surface diffusion length, ℓ, is a key parameter controlling surface morphology. When ℓ<2, surface migration is limited by the lack of availability of surface radical sites, and the migrating surface species simply hop back and forth between two adjacent sites but do not travel far beyond their initial adsorption site. Thus, Eley-Rideal processes dominate the growth, leading to the rough surfaces seen in NCD and UNCD. The maximum or 'intrinsic' surface roughness occurs for nominally zero-migration conditions (ℓ=0) with an rms value of approximately five carbon atoms. Conversely, when migration occurs over greater distances (ℓ>2), Langmuir-Hinshelwood processes dominate the growth producing the smoother surfaces of MCD and SCD. By extrapolation, we predict that atomically smooth surfaces over large areas should occur once migrating species can travel approximately five sites (ℓ∼5). β-scission processes are found to be unimportant for MCD and SCD growth conditions, but can remove up to 5% of the adsorbing carbon for NCD and UNCD growth. C1Hx insertion reactions also contribute <1% to the growth for nearly all conditions, while C2Hx (x<2) insertion reactions are negligible due their very low concentrations at the surface. Finally, the predictions for growth rate and morphology for UNCD deposition in a microwave system were found to be anomalous compared to those for all the other growth conditions, suggesting that carbonaceous particulates created in these plasmas may significantly affect the gas chemistry. [ABSTRACT FROM AUTHOR]

We consider the computation of the interfacial properties of molecular chains from direct simulation of the vapor-liquid interface. The molecules are modeled as fully flexible chains formed from tangentially bonded monomers with truncated Lennard-Jones interactions. Four different model systems comprising of 4, 8, 12, and 16 monomers per molecule are considered. The simulations are performed in the canonical ensemble, and the vapor-liquid interfacial tension is evaluated using the test area and the wandering interface methods. In addition to the surface tension, we also obtain density profiles, coexistence densities, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the chain length on these properties. According to our results, the main effect of increasing the chain length (at fixed temperature) is to sharpen the vapor-liquid interface and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness decreases and the surface tension increases as the molecular chains get longer. The interfacial thickness and surface tension appear to exhibit an asymptotic limiting behavior for long chains. A similar behavior is also observed for the coexistence densities and critical properties. Our simulation results indicate that the asymptotic regime is reached for Lennard-Jones chains formed from eight monomer segments. We also include a preliminary study on the effect of the cutoff distance on the interfacial properties. Our results indicate that all of the properties exhibit a dependence with the distance at which the interactions are truncated, though the relative effect varies from one property to the other. The interfacial thickness and, more particularly, the interfacial tension are found to be strongly dependent on the particular choice of cutoff, whereas the density profiles and coexistence densities are, in general, less sensitive to the truncation. [ABSTRACT FROM AUTHOR]

The Wolf method for the calculation of electrostatic interactions is applied in a liquid phase and at the liquid-vapor interface of water and its results are compared with those from the Ewald sums method. Molecular dynamics simulations are performed to calculate the radial distribution functions at room temperature. The interface simulations are used to obtain the coexisting densities and surface tension along the coexistence curve. The water model is a flexible version of the extended simple point charge model. The Wolf method gives good structural results, fair coexistence densities, and poor surface tensions as compared with those obtained using the Ewald sums method. [ABSTRACT FROM AUTHOR]

Using classical molecular dynamics simulations, we study the dynamical properties of a single polymer chain dissolved in an explicit solvent and strongly adsorbed at solid-liquid interface. To circumvent a serious challenge posed by finite size effects due to long-range hydrodynamic effects, we developed a correction procedure that substantially limits the finite size effects. Concurrently, we provide an analysis of distinctly different size effects in the directions transverse and normal to the interface. We find that on analytically smooth interfaces, corresponding to the slip boundary condition, the motions of the polymer chain and the surrounding solvent are hydrodynamically coupled. This leads to the chain diffusion coefficient D scaling with the chain degree of polymerization N as D∼N-3/4, consistent with the Zimm dynamics for strongly adsorbed chains. Introduction of transverse forces at the interface results in loss of correlation between the motion of the polymer chain and the solvent. Consequently, D∼N-1, which is a characteristic of the Rouse dynamics. [ABSTRACT FROM AUTHOR]

Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, here methods were developed to model several important surface formulations using exact surface discretizations. Following and refining Zauhar’s work [J. Comput.-Aided Mol. Des. 9, 149 (1995)], two classes of curved elements were defined that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. Numerical integration techniques are presented that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, a set of calculations are presented that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planar-triangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute-solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved approximations with increasing discretization and associated increases in computational resources. The results clearly demonstrate that the methods for approximate integration on an exact geometry are far more accurate than exact integration on an approximate geometry. A MATLAB implementation of the presented integration methods and sample data files containing curved-element discretizations of several small molecules are available online as supplemental material. [ABSTRACT FROM AUTHOR]

Streaming transport of the two-dimensional (2D) electron gas in a model GaN-based heterostructure is investigated using the ensemble Monte Carlo simulation method. It is demonstrated that interface roughness (IFR) scattering, being, in contrast to three-dimensional (3D) transport, an additional relevant scattering mechanism, plays a crucial role in fulfilling the streaming conditions for 2D transport. For a calculation of the IFR scattering rates we use the widely adopted Gaussian and exponential autocovariance functions to quantitatively describe the interface roughness. Even neglecting the interface roughness the streaming conditions are fulfilled only at low temperatures, similar to the 3D case. Taking into account IFR scattering, the nearly quasiballistic motion of 2D electrons in the passive region (below the optical phonon energy hωLO), being one of the necessary conditions for the streaming transport, can be realized only for sufficiently smooth interfaces. [ABSTRACT FROM AUTHOR]

We report molecular dynamics simulations of three globular proteins: ubiquitin, apo-calbindin D9K, and the C-terminal SH2 domain of phospholipase C-γ1 in explicit water. The proteins differ in their overall charge and fold type and were chosen to represent to some degree the structural variability found in medium-sized proteins. The length of each simulation was at least 15 ns, and larger than usual solvent boxes were used. We computed radial distribution functions, as well as orientational correlation functions about the surface residues. Two solvent shells could be clearly discerned about charged and polar amino acids. Near apolar amino acids the water density near such residues was almost devoid of structure. The mean residence time of water molecules was determined for water shells about the full protein, as well as for water layers about individual amino acids. In the dynamic properties, two solvent shells could be characterized as well. However, by comparison to simulations of pure water it could be shown that the influence of the protein reaches beyond 6 Å, i.e., beyond the first two shells. In the first shell (r≤=3.5 Å), the structural and dynamical properties of solvent waters varied considerably and depended primarily on the physicochemical properties of the closest amino acid side chain, with which the waters interact. By contrast, the solvent properties seem not to depend on the specifics of the protein studied (such as the net charge) or on the secondary structure element in which an amino acid is located. While differing considerably from the neat liquid, the properties of waters in the second solvation shell (3.5≤r≤=6 Å) are rather uniform; a direct influence from surface amino acids are already mostly shielded. [ABSTRACT FROM AUTHOR]

We report molecular dynamics (MD) simulations of three protein-water systems (ubiquitin, apo-calbindin D9K, and the C-terminal SH2 domain of phospholipase C-γ1), from which we compute the dielectric properties of the solutions. Since two of the proteins studied have a net charge, we develop the necessary theory to account for the presence of charged species in a form suitable for computer simulations. In order to ensure convergence of the time correlation functions needed for the analysis, the minimum length of the MD simulations was 20 ns. The system sizes (box length, number of waters) were chosen so that the resulting protein concentrations are comparable to experimental conditions. A dielectric component analysis was carried out to analyze the contributions from protein and water to the frequency-dependent dielectric susceptibility χ(ω) of the solutions. Additionally, an even finer decomposition into protein, two solvation shells, and the remaining water (bulk water) was carried out. The results of these dielectric decompositions were used to study protein solvation at mesoscopic resolution, i.e., in terms of protein, first and second solvation layers, and bulk water. This study, therefore, complements the structural and dynamical analyses at molecular resolution that are presented in the companion paper. The dielectric component contributions from the second shell and bulk water are very similar in all three systems. We find that the proteins influence the dielectric properties of water even beyond the second solvation shell, in agreement with what was observed for the mean residence times of water molecules in protein solutions. By contrast, the protein contributions, as well as the contributions of the first solvation shell, are system specific. Most importantly, the protein and the first water shell around ubiquitin and apo-calbindin are anticorrelated, whereas the first water shell around the SH2 domain is positively correlated. [ABSTRACT FROM AUTHOR]

We describe a novel algorithm that includes the effect of host lattice flexibility into molecular dynamics simulations that use rigid lattices. It uses a Lowe-Andersen thermostat for interface-fluid collisions to take the most important aspects of flexibility into account. The same diffusivities and other properties of the flexible framework system are reproduced at a small fraction of the computational cost of an explicit simulation. We study the influence of flexibility on the self-diffusion of simple gases inside single walled carbon nanotubes. Results are shown for different guest molecules (methane, helium, and sulfur hexafluoride), temperatures, and types of carbon nanotubes. We show, surprisingly, that at low loadings flexibility is always relevant. Notably, it has a crucial influence on the diffusive dynamics of the guest molecules. [ABSTRACT FROM AUTHOR]

The junction space-charge region (JSCR) is modeled as a separate region with carrier recombination at the surface and in the bulk. Bulk recombination is modeled according to the idealized model of C. T. Sah, R. N. Noyce, and W. Shockley [Proc. IRE45, 1228 (1957)]. JSCR surface recombination is modeled by combining at high biases the approaches of A. S. Grove [Physics and Technology of Semiconductor Devices (Wiley, New York, 1967), pp. 301–302] and of C. H. Henry, R. A. Logan, and F. R. Merrit [J. Appl. Phys. 49, 3530 (1978)]. In the treatment, it is assumed that the densities of states in the bulk and at the surface are related to each other. The transport equations are solved in JSCR at high biases and an expression for the JSCR recombination current is obtained. The model is adjusted for Si emitters and diodes, in such a way that it agrees with the numerical simulation program PC1D at all voltages. [ABSTRACT FROM AUTHOR]

Proposes a numerical method for simulating the non-normal incidence reflectance difference spectroscopy (RDS) spectra of biaxial anisotropic multilayer systems. Description on the RDS spectra of a typical ZnSe/GaAs sample; Presentation of the theory for the biaxial ZnSe/GaAs interface RDS; Overview on the numerical simulation.

The purpose of this paper is to derive a set of boundary conditions appropriate for simulating a wide variety of electrochemical and biophysical systems which are not necessarily electrically neutral. This is done by using the method of Green’s function, a generalization of the method of images, for solving the Poisson equation to provide boundary conditions for simulating electrochemical reactions involving ions confined between metal electrodes as well as ions in membranes enclosed between regions of aqueous electrolytes. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Using the molecular dynamics simulation technique, we study the effect of a highly ordered physisorbed alkyl monolayer on the surface induced liquid structure near a smooth solid–liquid interface. The system considered here is 1,12-dodecanediol adsorbed at the benzene–graphite interface. We compare the results on the graphite–1,12-dodecanediol–benzene interface to previous simulations on the bare graphite–benzene interface. We find that the surface induced liquid structure near the adsorbate covered interface differs from the structure induced by the bare interface only within the first solvation shell. Beyond the first solvation shell, there is no discernible difference, even though the surface induced structure is still pronounced. In addition, we study the structure of the hydrogen bond stabilized molecular adsorbate network. Here we find that the hydrogen bonds link the 1,12-dodecanediol molecules in a chain-like fashion across the boundaries of the herringbone structure formed by the adsorbate. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are used to study the structure of the vapor–liquid interface of three-dimensional fluids. Particles interact via a truncated Lennard-Jones pair potential in the absence of external fields. The effect of the surface area on the surface tension is investigated. It is found that the surface tension increases with the decrease of the surface area. However, this finite-size effect is pronounced only in small surface areas. In addition, our simulation results show that the finite-size correction of the surface tension is directly proportional to the reciprocal of the surface area, in accord with the prediction of the Gaussian model of capillary waves. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]