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The effect of fluctuations on the stability of the zero-voltage state in the Josephson junction has been extensively investigated in the last four decades, due to the fundamental interest in this macroscopic quantum system and in view of possible application as a detector and, more recently, as base for quantum logic. Thermal induced escape from the zero-voltage state is well explained by consolidated theories based on the standard junction electrical model. However, at very low temperatures, significant deviations have been experimentally observed, which have triggered additional theories based on quantization of the Josephson junction effective potential and on macroscopic quantum tunneling. By looking at experiments carried out in the last forty years, we show here that the reported experimental data can be well described by standard theories down to zero temperature, provided that the Josephson potential is shifted by a constant amount, related to the junction plasma frequency. An explanation of this shift is given in terms of Anderson equations, relating chemical potential to phases, energies, and particle numbers in a superfluid flow.

In light of recent advances in time-step independent stochastic integrators for Langevin equations, we revisit the considerations for using non-Gaussian distributions for the thermal noise term in discrete-time thermostats. We find that the desirable time-step invariance of the modern methods is rooted in the Gaussian noise, and that deviations from this distribution will distort the Boltzmann statistics arising from the fluctuation-dissipation balance of the integrators. We use the GJ stochastic Verlet methods as the focus of our investigation since these methods are the ones that contain the most accurate thermodynamic measures of existing methods. Within this set of methods we find that any distribution of applied noise, which satisfies the two first moments given by the fluctuation-dissipation theorem, will result in correct, time-step independent results that are generated by the first two moments of the system coordinates. However, if non-Gaussian noise is applied, undesired deviations in higher moments of the system coordinates will appear to the detriment of several important thermodynamic measures that depend especially on the fourth moments. The deviations, induced by non-Gaussian noise, become significant with the one-time-step velocity attenuation, thereby inhibiting the benefits of the methods. Thus, we conclude that the application of Gaussian noise is necessary for reliable thermodynamic results when using modern stochastic thermostats with large time steps., Key revision from v.1 is the inclusion of the GJ methods in splitting form (Eq. (11)) with explicit half-step velocity

Langevin simulations are conducted to investigate the Josephson escape statistics over a large set of parameter values for damping and temperature. The results are compared to both Kramers and Büttiker–Harris–Landauer (BHL) models, and good agreement is found with the Kramers model for high to moderate damping, while the BHL model provides further good agreement down to lower damping values. However, for extremely low damping, even the BHL model fails to reproduce the progression of the escape statistics. In order to explain this discrepancy, we develop a new model which shows that the bias sweep effectively cools the system below the thermodynamic value as the potential well broadens due to the increasing bias. A simple expression for the temperature is derived, and the model is validated against direct Langevin simulations for extremely low damping values.

In light of the recently published complete set of statistically correct Gronbech-Jensen (GJ) methods for discrete-time thermodynamics, we revise a differential operator splitting method for the Langevin equation in order to comply with the basic GJ thermodynamic sampling features, namely the Boltzmann distribution and Einstein diffusion, in linear systems. This revision, which is based on the introduction of time scaling along with flexibility of a discrete-time velocity attenuation parameter, provides a direct link between the ABO splitting formalism and the GJ methods. This link brings about the conclusion that any GJ method has at least weak second order accuracy in the applied time step. It further helps identify a novel half-step velocity, which simultaneously produces both correct kinetic statistics and correct transport measures for any of the statistically sound GJ methods. Explicit algorithmic expressions are given for the integration of the new half-step velocity into the GJ set of methods. Numerical simulations, including quantum-based molecular dynamics (QMD) using the QMD suite LATTE, highlight the discussed properties of the algorithms as well as exhibit the direct application of robust, time step independent stochastic integrators to quantum-based molecular dynamics., Accepted for publication in Journal of Chemical Physics

We expand on two previous developments in the modeling of discrete-time Langevin systems. One is the well-documented Grønbech-Jensen Farago (GJF) thermostat, which has been demonstrated to give robust and accurate configurational sampling of the phase space. Another is the recent discovery that also kinetics can be accurately sampled for the GJF method. Through a complete investigation of all possible finite-difference approximations to the velocity, we arrive at two main conclusions: (1) It is not possible to define a so-called on-site velocity such that kinetic temperature will be correct and independent of the time step, and (2) there exists a set of infinitely many possibilities for defining a two-point (leap-frog) velocity that measures kinetic energy correctly for linear systems in addition to the correct configurational statistics obtained from the GJF algorithm. We give explicit expressions for the possible definitions, and we incorporate these into convenient and practical algorithmic forms of the normal Verlet-type algorithms along with a set of suggested criteria for selecting a useful definition of velocity.

© 2017 American Chemical Society. Organic ligand complexes of lanthanide/actinide ions have been studied extensively for applications in nuclear fuel storage and recycling. Several complexes of 2,6-bis(2-benzimidazyl)pyridine (H2BBP) featuring the uranyl moiety have been reported recently, and the present study investigates the coordination characteristics of these complexes using density functional theory-based electronic structure analysis. In particular, with the aid of several computational models, the nonplanar equatorial coordination about uranyl, observed in some of the compounds, is studied and its origin traced to steric effects.

We expand on the previously published Gr{\o}nbech-Jensen Farago (GJF) thermostat, which is a thermodynamically sound variation on the St{\o}rmer-Verlet algorithm for simulating discrete-time Langevin equations. The GJF method has been demonstrated to give robust and accurate configurational sampling of the phase space, and its applications to, e.g., Molecular Dynamics is well established. A new definition of the discrete-time velocity variable is proposed based on analytical calculations of the kinetic response of a harmonic oscillator subjected to friction and noise. The new companion velocity to the GJF method is demonstrated to yield correct and time-step-independent kinetic responses for, e.g., kinetic energy, its fluctuations, and Green-Kubo diffusion based on velocity autocorrelations. This observation allows for a new and convenient Leap-Frog algorithm, which efficiently and precisely represents statistical measures of both kinetic and configurational properties at any time step within the stability limit for the harmonic oscillator. We outline the simplicity of the algorithm and demonstrate its attractive time-step-independent features for nonlinear and complex systems through applications to a one-dimensional nonlinear oscillator and three-dimensional Molecular Dynamics., Comment: 12 pages, 8 figures. Submitted for publication in Molecular Physics on November 1, 2018; slightly revised on December 13; accepted for publication on January 7, 2019

We present the complete set of stochastic Verlet-type algorithms that can provide correct statistical measures for both configurational and kinetic sampling in discrete-time Langevin systems. The approach is a brute-force general representation of the Verlet-algorithm with free parameter coefficients that are determined by requiring correct Boltzmann sampling for linear systems, regardless of time step. The result is a set of statistically correct methods given by one free functional parameter, which can be interpreted as the one-time-step velocity attenuation factor. We define the statistical characteristics of both true on-site $v^n$ and true half-step $u^{n+\frac{1}{2}}$ velocities, and use these definitions for each statistically correct Stormer-Verlet method to find a unique associated half-step velocity expression, which yields correct kinetic Maxwell-Boltzmann statistics for linear systems. It is shown that no other similar, statistically correct on-site velocity exists. We further discuss the use and features of finite-difference velocity definitions that are neither true on-site, nor true half-step. The set of methods is written in convenient and conventional stochastic Verlet forms that lend themselves to direct implementation for, e.g., Molecular Dynamics applications. We highlight a few specific examples, and validate the algorithms through comprehensive Langevin simulations of both simple nonlinear oscillators and complex Molecular Dynamics., Comment: To Appear in Molecular Physics

Using the recently published GJF-2GJ Langevin thermostat, which can produce time-step-independent statistical measures even for large time steps, we analyze and discuss the causes for abrupt deviations in statistical data as the time step is increased for some simulations of nonlinear oscillators. Exemplified by the pendulum, we identify a couple of discrete-time dynamical modes in the purely damped pendulum equation as the cause of the observed discrepancies in statistics. The existence, stability and kinetics of the modes are consistent with the acquired velocity distribution functions from Langevin simulations, and we conclude that the simulation deviations from physical expectations are not due to normal, systematic algorithmic time-step errors, but instead due to the inherent properties of discrete time in nonlinear dynamics., Comment: 18 pages, six figures

The dimensionality of defects in high explosives controls their heat generation and the expansion of deflagrations from them. We compare the behaviour of spherical voids in three dimensions to that of circular voids in two dimensions. The behaviour is qualitatively similar, but the additional focusing along the extra transverse dimension significantly reduces the piston velocity needed to initiate reactions. However, the reactions do not grow as well in three dimensions, so detonations require larger piston velocities. Pressure exponents are seen to be similar to those for the two-dimensional system.

High temperature mechanical measurements were conducted to study the effect of the dynamic precipitation process of PH 13-8 Mo maraging steel. Yield stress, ultimate tensile strength, total elongation, hardness, strain rate sensitivity and activation volume were evaluated as a function of the temperature. The dynamic changes in the mechanical properties at different temperatures were evaluated and a balance between precipitation hardening and annealed softening is discussed. A comparison between hardness and yield stress and ultimate tensile strength over a temperature range from 300 to 600 °C is made. The behavior of the strain rate sensitivity was correlated with the intermetallic precipitates formed during the experiments.

In light of the recently developed complete GJ set of single random variable stochastic, discrete-time St{\o}rmer-Verlet algorithms for statistically accurate simulations of Langevin equations, we investigate two outstanding questions: 1) Are there any algorithmic or statistical benefits from including multiple random variables per time-step, and 2) are there objective reasons for using one or more methods from the available set of statistically correct algorithms? To address the first question, we assume a general form for the discrete-time equations with two random variables and then follow the systematic, brute-force GJ methodology by enforcing correct thermodynamics in linear systems. It is concluded that correct configurational Boltzmann sampling of a particle in a harmonic potential implies correct configurational free-particle diffusion, and that these requirements only can be accomplished if the two random variables per time step are identical. We consequently submit that the GJ set represents all possible stochastic St{\o}rmer-Verlet methods that can reproduce time-step-independent statistics of linear systems. The second question is thus addressed within the GJ set. Based in part on numerical simulations of complex molecular systems, and in part on analytic scaling of time, we analyze the apparent difference in stability between different methods. We attribute this difference to the inherent time scaling in each method, and suggest that this scaling may lead to inconsistencies in the interpretation of dynamical and statistical simulation results. We therefore suggest that the method with the least inherent time-scaling, the GJ-I/GJF-2GJ method, be preferred for statistical applications where spurious rescaling of time is undesirable., Comment: 25 pages, 8 figures

The process of activation out a one-dimensional potential is investigated systematically in zero and nonzero temperature conditions. The features of the potential are traced through statistical escape out of its wells whose depths are tuned in time by a forcing term. The process is carried out on the damped pendulum system imposing specific initial conditions on the potential variable. While for relatively high values of the dissipation the statistical properties follow a behavior that can be derived from the standard Kramers model, decreasing the dissipation we observe responses/deviations which have regular dependencies on initial conditions, temperature, and loss parameter itself. It is shown that failures of the thermal activation model are originated at low temperatures, and very low dissipation, by the initial conditions and intrinsic, namely T=0, characteristic oscillations of the potential-generated dynamical equation., Comment: 25 pages and 13 Figures

Transient properties of the one-dimensional washboard potential are investigated in order to understand observed modulations in the statistics of escape events. Specifically, we analyze the effects of different kinds of initial conditions on the escape distribution obtained by linearly increasing the tilt of the potential. Despite the complexity of the dynamics leading up to the eventual escape, we find that the overall statistics can be interpreted in terms of the system parameters, which offers illuminating perspectives for driven one-dimensional systems with washboard potentials. We choose parameters sets relevant for Josephson junctions, a commonly studied system due to both its applications and its use as a model system in condensed matter physics.

Radiation damage in body-centered cubic (BCC) Fe has been extensively studied by computer simulations to quantify effects of temperature, impinging particle energy, and the presence of extrinsic particles. However, limited investigation has been conducted into the effects of mechanical stresses and strain. In a reactor environment, structural materials are often mechanically strained, and an expanded understanding of how this strain affects the generation of defects may be important for predicting microstructural evolution and damage accumulation under such conditions. In this study, we have performed molecular dynamics simulations in which various types of homogeneous strains are applied to BCC Fe and the effect on defect generation is examined. It is found that volume-conserving shear strains yield no statistically significant variations in the stable number of defects created via cascades in BCC Fe. However, strains that result in volume changes are found to produce significant effects on defect generation., 14 pages, eight figures

When a particle diffuses in a medium with spatially dependent friction coefficient $\alpha(r)$ at constant temperature $T$, it drifts toward the low friction end of the system even in the absence of any real physical force $f$. This phenomenon, which has been previously studied in the context of non-inertial Brownian dynamics, is termed "spurious drift", although the drift is real and stems from an inertial effect taking place at the short temporal scales. Here, we study the diffusion of particles in inhomogeneous media within the framework of the inertial Langevin equation. We demonstrate that the quantity which characterizes the dynamics with non-uniform $\alpha(r)$ is not the displacement of the particle $\Delta r=r-r^0$ (where $r^0$ is the initial position), but rather $\Delta A(r)=A(r)-A(r^0)$, where $A(r)$ is the primitive function of $\alpha(r)$. We derive expressions relating the mean and variance of $\Delta A$ to $f$, $T$, and the duration of the dynamics $\Delta t$. For a constant friction coefficient $\alpha(r)=\alpha$, these expressions reduce to the well known forms of the force-drift and fluctuation-dissipation relations. We introduce a very accurate method for Langevin dynamics simulations in systems with spatially varying $\alpha(r)$, and use the method to validate the newly derived expressions., Comment: 11 pages, 6 figures. Minor revisions to previous version. Accepted for publication in J. Stat. Phys

Mixing energies (Δ H mix ) for fluorite-structured (Zr 1− x Ce x )O 2 and (Th 1− x Ce x )O 2 solid solutions are computed from density functional theory (DFT), employing cluster-expansion (CE), special-quasirandom-structure (SQS), and continuum-elasticity approaches. These systems are of interest as models for actinide-dioxide mixtures, due to the availability of calorimetric data which allows a direct assessment of the accuracy of the different computational methods for calculating Δ H mix in such fluorite-structured solid solutions. The DFT-based SQS and CE results for solid solutions with random configurational disorder are in very good agreement, and are used along with the calorimetry data to test the accuracy of a linear-elasticity model which allows predictions of the Δ H mix under the assumption that the dominant contribution in these homovalent solid solutions arises from elastic strain energy. The linear-elasticity models describe the mixing energies to within an accuracy of approximately 2 and 0.1 kJ/mol for the Zr and Th based systems, respectively. The excellent accuracy for the ThO 2 -based system is interpreted to result from the smaller size mismatch, and corresponding high accuracy of the linear elasticity approximation. We thus apply elasticity theory to estimate the magnitudes of Δ H mix for (Th 1− x M x )O 2 and (U 1− x M x )O 2 actinide-dioxide solid solutions, with M = U, Th, Ce, Np, Pu and Am, for which the degree of size mismatch is comparable to that in (Th 1− x Ce x )O 2 ; the results yield elastic contributions to Δ H mix with a maximum magnitude of 3 kJ/mol.

We present a revision to the well known Stormer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate that the new algorithm correctly reproduces diffusive behavior of a particle in a flat potential. For a harmonic oscillator, our algorithm provides the exact Boltzmann distribution for any value of damping, frequency, and time step for both underdamped and over damped behavior within the usual the stability limit of the Verlet algorithm. Given the structure and simplicity of the method we conclude this approach can trivially be adapted for contemporary applications, including molecular dynamics with extensions such as molecular constraints., Comment: 10 pages, one figure. Minor typographical errors fixed; clarification on applicability included

We study the dynamics of Brownian particles in a heterogeneous one-dimensional medium with a spatially-dependent diffusion coefficient of the form $D(x)\sim |x|^c$, at constant temperature. The particle's probability distribution function (PDF) is calculated both analytically, by solving Fick's diffusion equation, and from numerical simulations of the underdamped Langevin equation. At large times, the PDFs calculated by both approaches yield identical results, corresponding to subdiffusion for $c1$, the diffusion equation predicts that the particles accelerate. Here, we show that this phenomenon, previously considered in several works as an illustration for the possible dramatic effects of spatially-dependent thermal noise, is unphysical. We argue that in an isothermal medium, the motion cannot exceed the ballistic limit ($\left\langle x^2\right\rangle \sim t^2$). The ballistic limit is reached when the friction coefficient drops sufficiently fast at large distances from the origin, and is correctly captured by Langevin's equation., Comment: 7 pages, 4 figures, accepted for publication in Phys. Rev. E

Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system particles, thus allowing them to overlap. This supposedly permits relatively large integration time steps, which is an important feature for simulations on large temporal scales. In practice, however, an increase in the integration time step leads to increasingly larger systematic errors in the sampling statistics. Here, we demonstrate that the prime origin of these systematic errors is the multiplicative nature of the thermal noise term in Langevin's equation, i.e., the fact that it depends on the instantaneous coordinates of the particles. This lead to an ambiguity in the interpretation of the stochastic differential Langevin equation, known as the It\^o-Stratonovich dilemma. Based on insights from previous studies of the dilemma, we propose a novel algorithm for DPD simulations exhibiting almost an order of magnitude improvement in accuracy, and nearly twice the efficiency of commonly used DPD Langevin thermostats., Comment: 6 pages, 3 figures, Accepted for publication in J. Chem. Phys

We implement the statistically sound G-JF thermostat for Langevin Dynamics simulations into the ESPREesSo molecular package for large-scale simulations of soft matter systems. The implemented integration method is tested against the integrator currently used by the molecular package in simulations of a fluid bilayer membrane. While the latter exhibits deviations in the sampling statistics that increase with the integration time step dt, the former reproduces near-correct configurational statistics for all dt within the stability range of the simulations. We conclude that, with very modest revisions to existing codes, one can significantly improve the performance of statistical sampling using Langevin thermostats., Six pages, seven figures. Accepted for publication in Israel Journal of Chemistry

The threshold displacement energy (TDE) is the minimum amount of kinetic energy required to displace an atom from its lattice site. The magnitude of the TDE displays significant variance as a function of the crystallographic direction, system temperature and applied strain, among a variety of other factors. It is critically important to determine an accurate value of the TDE in order to calculate the total number of displacements due to a given irradiation condition, and thus to understand the materials response to irradiation. In this study, molecular dynamics simulations have been performed to calculate the threshold displacement energy in body-centered cubic iron as a function of strain and temperature. With applied strain, a decrease of the TDE of up to approximately 14 eV was observed. A temperature increase from 300 K to 500 K can result in an increase of the TDE of up to approximately 9 eV.

For decades following its introduction in 1968, the resistively and capacitively shunted junction (RCSJ) model, sometimes referred to as the Stewart-McCumber model, was successfully applied to study the dynamics of Josephson junctions embedded in a variety of superconducting circuits. In 1980 a theoretical conjecture by A.J. Leggett suggested a possible new and quite different behavior for Josephson junctions at very low temperatures. A number of experiments seemed to confirm this prediction and soon it was taken as a given that junctions at tens of millikelvins should be regarded as macroscopic quantum entities. As such, they would possess discrete levels in their effective potential wells, and would escape from those wells (with the appearance of a finite junction voltage) via a macroscopic quantum tunneling process. A zeal to pursue this new physics led to a virtual abandonment of the RCSJ model in this low temperature regime. In this paper we consider a selection of essentially prototypical experiments that were carried out with the intention of confirming aspects of anticipated macroscopic quantum behavior in Josephson junctions. We address two questions: (1) How successful is the non-quantum theory (RCSJ model) in replicating those experiments? (2) How strong is the evidence that data from these same experiments does indeed reflect macroscopic quantum behavior?, Comment: 40 pages, 51 figures

We present experimental evidence for the existence of a unique molecular-level order in the vicinity of the bilayer's edge. Discrete patches of substrate-supported lipid bilayers exhibiting stable edge defects are prepared by confining vesicle fusion to hydrophilic patches of a chemically patterned substrate exhibiting hydrophilic patches in hydrophobic surrounding, and edge properties are characterized by fluorescence and vibrational spectroscopy based measurements. Specifically, wide-field fluorescence microscopy using phase-sensitive dyes, temperature-programmed fluorescence recovery measurements, and temperature-dependent attenuated total reflection Fourier transform infrared spectroscopy measurements are performed to characterize the local chain conformational properties, local diffusional characteristics, and phase discrimination afforded by phase-sensitive DiI fluorescent probes. We find that the bilayer structure near the edge is characterized by (1) an increase in intramolecular conformational order; (2) reduced effective lateral mobility; and (3) a distinctly higher local, effective gel-fluid transition temperature in comparison to their bulk counterpart. Together, these features signal the emergence of unique ordering presumably triggered by the hemimicellar configuration of the edge. These results are consistent with simulations of lyso-lipid micelles predicting the presence of dynamic clusters of ordered lipids in comparable micellar topology and disagrees with some recent interpretations of mobility near the edges of supported bilayers. Our results also offer the structural basis for the stability of defects and edges in fluid supported bilayers, and may be relevant in understanding the ordering and stabilization of pores, edges, and defects generated in membrane bilayers by proteins, curvature-sensitive lipids, antimicrobial peptides, and detergents.

This work presents the results of first principles electronic structure calculations for Cerium (Ce) doped Yttrium (Y) and Lanthanum (La) oxyhalides performed using the pseudopotential method based on the local density approximation in the density functional theory. The relative position of the Ce 4f and 5d levels in the energy gap of the host are determined from the ground-state density of states for the Ce-doped material. Localization of the excited electron is determined from the calculations of the (Ce3+)* excited state. A qualitative prediction of Ce-activated scintillation is made based on these theoretical calculations. Our approach indicates that Ce-doped Y and La oxyhalides show progressively better luminescence as we move down the periodic table from oxyfluorides to oxyiodides. These families of materials have been synthesized and the experimental results agree qualitatively with our calculations.

We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show dramatic DNA compaction down to essentially close packed DNA arrays with a DNA interaxial spacing $d_{\rm DNA}=25\AA$. A gradual increase in $\Phi_{\rm NL}$ does not lead to a continuous increase in $d_{\rm DNA}$ as observed for DNA complexes of monovalent cationic lipids (CLs). Instead, distinct spacing regimes exist, with sharp transitions between them. Three packing states have been identified: (i) close packed, (ii) condensed, but not close packed, with $d_{\rm DNA}=27-28\AA$, and (iii) an expanded state, where $d_{\rm DNA}$ increases gradually with $\Phi_{\rm NL}$. Based on our experimental and computational results, we conclude that the DNA condensation is mediated by the multivalent cationic lipids, which assemble between the negatively charged DNA rods. Quite remarkably, the computational results show that the less tightly packed structure in regime (ii) is thermodynamically more stable than the close packed structure in regime (i). Accordingly, the constant DNA spacing observed in regime (ii) is attributed to lateral phase coexistence between this stable CL-DNA complex and neutral membranes. This finding may explain the reduced transfection efficiency measured for such complexes: Transfection involves endosomal escape and disassembly of the complex, and these processes are inhibited by the high thermodynamic stability. Our results, which demonstrate the existence of an inverse correlation between the stability and transfection activity of lamellar CL-DNA complexes are, therefore, consistent with a recently proposed model of cellular entry., Comment: Accepted for publication in Biophys. J

We investigate the results of recently published experiments on the quantum behavior of Josephson circuits in terms of the classical modelling based on the resistively and capacitively-shunted (RCSJ) junction model. Our analysis shows evidence for a close analogy between the nonlinear behavior of a pulsed microwave-driven Josephson junction at low temperature and low dissipation and the experimental observations reported for the Josephson circuits. Specifically, we demonstrate that Rabi-oscillations, Ramsey-fringes, and spin-echo observations are not phenomena with a unique quantum interpretation. In fact, they are natural consequences of transients to phase-locking in classical nonlinear dynamics and can be observed in a purely classical model of a Josephson junction when the experimental recipe for the application of microwaves is followed and the experimental detection scheme followed. We therefore conclude that classical nonlinear dynamics can contribute to the understanding of relevant experimental observations of Josephson response to various microwave perturbations at very low temperature and low dissipation., Comment: 16 pages, 7 figures

A stack of inductively coupled long Josephson junctions are modeled as a system of coupled sine-Gordon equations. One boundary of the stack is coupled electrically to a resonant cavity. With one fluxon in each Josephson junction, the inter-junction fluxon forces are repulsive. We look at a possible transition, induced by the cavity, to a bunched state.

Complexes of cationic and neutral lipids and DNA (lipoplexes) are emerging as promising vectors for gene therapy applications. Their appeal stems from their non pathogenic nature and the fact that they self-assemble under conditions of thermal equilibrium. Lipoplex adhesion to the cell plasma membrane initiates a three-stage process termed transfection, consisting of (i) endocytosis, (ii) lipoplex breakdown, and (iii) DNA release followed by gene expression. As successful transfection requires lipoplex degradation, it tends to be hindered by the lipoplex thermodynamic stability; nevertheless, it is known that the transfection process may proceed spontaneously. Here, we use a simple model to study the thermodynamic driving forces governing transfection. We demonstrate that after endocytosis [stage (i)], the lipoplex becomes inherently unstable. This instability, which is triggered by interactions between the cationic lipids of the lipoplex and the anionic lipids of the enveloping plasma membrane, is entropically controlled involving both remixing of the lipids and counterions release. Our detailed calculation shows that the free energy gain during stage (ii) is approximately linear in $\Phi_+$, the mole fraction of cationic lipids in the lipoplex. This free energy gain, $\Delta F$, reduces the barrier for fusion between the enveloping and the lipoplex bilayers, which produces a hole allowing for DNA release [stage (iii)]. The linear relationship between $\Delta F$ and the fraction of cationic lipids explains the experimentally observed exponential increase of transfection efficiency with $\Phi_+$ in lamellar lipoplexes., Comment: 7 pages, 3 figures, to appear in Phys. Chem. Chem. Phys. New version similar to older, but with corrected fig.2

We present a simple molecular model for the self-assembly of alkanethiols on gold. The model, a rigid rod representation of a molecule which is constrained to a given distance from the gold surface, allows direct long-time simulations of large-scale molecular ensembles (104−105 molecules) on desktop workstations. As a result, the model allows for efficient studies of evolution and ordering of, for example, orientational order and domain patterns in a full range of monolayer coverages. The model is parametrized entirely by existing literature on atomic and molecular scale interactions. Extensive simulations of molecular self-assembled monolayer domain formation at optimal (packing commensurate with a gold surface (111) structure) and suboptimal packing are conducted and presented. The results show close correspondence between the model features and the existing, and emerging, picture observed through experimental characterization of self-assembled monolayers on Au(111). This strong experimental validation ...

We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems - a one dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb & Dunweg, show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation., 14 pages, 12 figures

We use coarse-grained Monte Carlo simulations to study the elastic properties of charged membranes in solutions of monovalent and pentavalent counterions. The simulation results of the two cases reveal trends opposite to each other. The bending rigidity and projected area increase with the membrane charge density for monovalent counterions, while they decrease for the pentavalent ions. These observations can be related to the counterion screening of the lipid charges. While the monovalent counterions only weakly screen the Coulomb interactions, which implies a repulsive Coulomb system, the multivalent counterions condense on the membrane and, through spatial charge correlations, make the effective interactions due the charged lipids attractive. The differences in the elastic properties of the charged membranes in monovalent and multivalent counterion solutions are reflected in the mechanisms leading to their mechanical instability at high charge densities. In the former case, the membranes develop pores to relieve the electrostatic tensile stresses, while in the latter case, the membrane exhibit large wavelength bending instability., 10 pages, 6 figures, to appear in Eur. Phys. J. E

The reaction of UO2Cl2·3THF with the tridentate nitrogen donor ligand 2,6-bis(2-benzimidazolyl)pyridine (H2BBP) in pyridine leads to the formation of three different complexes: [(UO2)(H2BBP)Cl2] (1), [(UO)2(HBBP)(Py)Cl] (2), and [(UO2)(BBP)(Py)2] (3) after successive deprotonation of H2BBP with a strong base. Crystallographic determination of 1-3 reveals that increased charge through ligand deprotonation and displacement of chloride leads to equatorial planarity about uranyl as well as a more compact overall coordination geometry. Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectra of 1-3 at the U-4d edges have been recorded using a soft X-ray Scanning Transmission X-ray Microscope (STXM) and reveal the uranium 4d5/2 and 4d3/2 transitions at energies associated with uranium in the hexavalent oxidation state. First-principles Density Functional Theory (DFT) electronic structure calculations for the complexes have been performed to determine and validate the coordination characteristics, which correspond well to the experimental results.

We describe a simple and fast rate-equation model for surface growth during ion beam assisted metal-on-metal deposition. In terms of the rate coefficients the model describes how island detachment and breakup, adatom diffusion and interlayer transitions of adatoms affect the growth. Results from our model can be directly compared to experimental data, also for coverages of several layers. We identify parameter values corresponding to different modes of growth and locate the phase boundary between them as a function of temperature. We also show that in ideal layer-by-layer growth island size distributions retain the regular scaling form. Our model shows that in order to obtain thin films of good quality, both efficient detachment of adatoms and sufficiently fast interlayer transitions are needed. The results validate the approximations made in an earlier, more coarse-grained model.

We present a systematic application of reaction path sampling to computer simulations of the folding of peptides and small proteins at atomic resolution in the presence of solvent. We use a simulated annealing protocol to generate an ensemble of room temperature folding trajectories of fixed length, which connect predetermined initial and final states. The trajectories are distributed according to a discretized version of the Onsager–Machlup action functional. We show that, despite the enormous practical restrictions placed on the number of time slices which can be explored, some of the basic kinetic features found experimentally for the folding of peptides and small proteins are exhibited in the nature of the reaction paths sampled. We test the method on three systems: A 12 residue α-helical peptide, a 16 residue β-hairpin peptide, and the 36 residue avian Pancreatic Polypeptide (aPP). All systems are represented at atomic resolution, and include explicit water molecules. For the 12 residue α-helix, we find that (i,i+3) hydrogen bonds can play a significant role in the folding pathway, with specific (i,i+3) bonds appearing, then transforming to the corresponding (i,i+4) hydrogen bond for some, but not all of the native hydrogen bonds. For the β-hairpin and aPP, hydrophobic interactions play a dominant role, with nonbonded interactions consistently appearing before hydrogen bonds. This is true both at the level of tertiary structure, and at the level of individual hydrogen bonds which tend to form only after stabilizing nonbonded interactions have already formed between the residues involved.

Advanced nuclear fuel concepts sometimes involve metal oxide interfaces between fissile and nonfissile phases. During operation, cascade damage as secondary events from a fission track will occur throughout the material. Some of that damage will take place at the interface between phases. Here we simulate representative secondary events of this nature. As a model system, ongoing experiments consider a composite in which the nonfissile material is magnesia and the fissile phase is modeled via hafnia as a surrogate. In correspondence the experiments, the atomistic simulation cells are composed of hafnia in the fluorite structure and magnesia in the rocksalt structure. Molecular dynamics simulations of cascade damage across interfaces of these materials shows Hf cations becoming kinetically trapped in the magnesia phase. The Hf cations remained trapped for the duration of the 20-ps simulations. When the primary-knock-on atom energy is above a few hundred eV in the direction of the interface and is within five lattice spacings, the propensity for trapping is very high. Under these same conditions, an Mg cation will occasionally become trapped in the hafnia. Complementary electronic structure calculations indicate that Hf cations are thermodynamically unstable in magnesia. Furthermore, these calculations indicate that the charge on the Hf ions reduces by one electron if no compensating defect is present, but reverts to the charge in HfO2 bulk in the presence of a defect such as an oxygen interstitial. Extensions of these observations to the behavior of urania and ceria are mentioned.

We study a three-dimensional model of driven vortices in weakly coupled layered superconductors with strong pinning. Above the critical force F{sub c}, we find a plastic flow regime in which pancakes in different layers are uncoupled, corresponding to a pancake gas. At a higher F, there is a ''smectic flow'' regime with short-range interlayer order, corresponding to an entangled line liquid. Later, the transverse displacements freeze and vortices become correlated along the c axis, resulting in a transverse solid. Finally, at a force F{sub s} the longitudinal displacements freeze and we find a coherent solid of rigid lines.

We present molecular dynamics simulations of driven vortices in layered superconductors in the presence of an external homogeneous force and point disorder. We use a model introduced by J.R.Clem for describing 3D vortex lines as stacks of 2D pancake vortices where only magnetic interactions are considered and the Josephson interlayer coupling is neglected. We numerically evaluate the long-range magnetic interaction between pancake vortices exactly. We analyze the vortex correlation along the field direction on (c-axis). We find that above the critical current, in the ``plastic flow'' regime, pancakes are completely uncorrelated in the c-direction. When increasing the current, there is an onset of correlation along the c-axis at the transition from plastic flow to a moving smectic phase. This transition coincides with the peak in the differential resistance., 4 pages, 3 figures, needs espcrc2.sty. Submitted to the proceedings of the M2S-HTSC-IV Conference