arXiv subjects

Niels Grønbech-Jensen

Publications and source records attributed to Niels Grønbech-Jensen.

At least 55 records · Page 3Linked to original sources

arXiv2008

Efficient Parallel Algorithm for Statistical Ion Track Simulations in Crystalline Materials

We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been successfully applied to studies of, e.g., ion implantation into crystalline semiconductor wafers. We discuss the strategies for parallelizing the method, and we settle on a host-client type polling scheme in which a multiple of asynchronous processors are continuously fed to the host, which, in turn, distributes the resulting feed-back information to the clients. This real-time feed-back consists of, e.g., cumulative damage information or statistics updates necessary for the cloning in the rare event algorithm. We finally demonstrate the algorithm for radiation effects in a nuclear oxide fuel, and we show the balanced parallel approach with high parallel efficiency in multiple processor configurations.

physics.comp-ph↗

arXiv2008

Transitions between distinct compaction regimes in complexes of multivalent cationic lipids and DNA

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), $Φ_{\rm NL}$, the complexes show dramatic DNA compaction down to essentially close packed DNA arrays with a DNA interaxial spacing $d_{\rm DNA}=25Å$. A gradual increase in $Φ_{\rm NL}$ 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 $d_{\rm DNA}=27-28Å$, and (iii) an expanded state, where $d_{\rm DNA}$ increases gradually with $Φ_{\rm NL}$. 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.

cond-mat.soft↗

arXiv2007

Thiol density dependent classical potential for methyl-thiol on a Au(111) surface

A new classical potential for methyl-thiol on a Au(111) surface has been developed using density functional theory electronic structure calculations. Energy surfaces between methyl-thiol and a gold surface were investigated in terms of symmetry sites and thiol density. Geometrical optimization was employed over all the configurations while minimum energy and thiol height were determined. Finally, a new interatomic potential has been generated as a function of thiol density, and applications to coarse-grained simulations are presented.

cond-mat.mtrl-sci↗

arXiv2007

Parallel TREE code for two-component ultracold plasma analysis

The TREE method has been widely used for long-range interaction {\it N}-body problems. We have developed a parallel TREE code for two-component classical plasmas with open boundary conditions and highly non-uniform charge distributions. The program efficiently handles millions of particles evolved over long relaxation times requiring millions of time steps. Appropriate domain decomposition and dynamic data management were employed, and large-scale parallel processing was achieved using an intermediate level of granularity of domain decomposition and ghost TREE communication. Even though the computational load is not fully distributed in fine grains, high parallel efficiency was achieved for ultracold plasma systems of charged particles. As an application, we performed simulations of an ultracold neutral plasma with a half million particles and a half million time steps. For the long temporal trajectories of relaxation between heavy ions and light electrons, large configurations of ultracold plasmas can now be investigated, which was not possible in past studies.

physics.comp-ph↗

arXiv2006

Computational and Analytical Modeling of Cationic Lipid-DNA Complexes

We present a theoretical study of the physical properties of cationic lipid-DNA (CL-DNA) complexes - a promising synthetically based nonviral carrier of DNA for gene therapy. The study is based on a coarse-grained molecular model, which is used in Monte Carlo (MC) simulations of mesoscopically large systems over time scales long enough to address experimental reality. In the present work we focus on the statistical-mechanical behavior of lamellar complexes, which in MC simulations self-assemble spontaneously from a disordered random initial state.

cond-mat.soft↗

arXiv2006

Vacancy clustering and diffusion in silicon: Kinetic lattice Monte Carlo simulations

Diffusion and clustering of lattice vacancies in silicon as a function of temperature, concentration, and interaction range are investigated by Kinetic Lattice Monte Carlo simulations. It is found that higher temperatures lead to larger clusters with shorter lifetimes on average, which grow by attracting free vacancies, while clusters at lower temperatures grow by aggregation of smaller clusters. Long interaction ranges produce enhanced diffusivity and fewer clusters. Greater vacancy concentrations lead to more clusters, with fewer free vacancies, but the size of the clusters is largely independent of concentration. Vacancy diffusivity is shown to obey power law behavior over time, and the exponent of this law is shown to increase with concentration, at fixed temperature, and decrease with temperature, at fixed concentration.

cond-mat.mtrl-sci↗

arXiv2006

Simulating Ramsey-Type Fringes in a Pulsed Microwave-Driven Classical Josephson Junction

We present evidence for a close analogy between the nonlinear behavior of a pulsed microwave-driven Josephson junction at low temperature and the experimentally observed behavior of Josephson systems operated below the quantum transition temperature under similar conditions. We specifically address observations of Ramsey-type fringe oscillations, which can be understood in classical nonlinear dynamics as results of slow transient oscillations in a pulsed microwave environment. Simulations are conducted to mimic experimental measurements by recording the statistics of microwave-induced escape events from the anharmonic potential well of a zero-voltage state. Observations consistent with experimentally found Ramsey-type oscillations are found in the classical model.

cond-mat.supr-con↗

arXiv2006

Classical analysis of phase-locking transients and Rabi-type oscillations in microwave-driven Josephson junctions

We present a classical analysis of the transient response of Josephson junctions perturbed by microwaves and thermal fluctuations. The results include a specific low frequency modulation in phase and amplitude behavior of a junction in its zero-voltage state. This transient modulation frequency is linked directly to an observed variation in the probability for the system to switch to its non-zero voltage state. Complementing previous work on linking classical analysis to the experimental observations of Rabi-oscillations, this expanded perturbation method also provides closed form analytical results for attenuation of the modulations and the Rabi-type oscillation frequency. Results of perturbation analysis are compared directly (and quantitatively) to numerical simulations of the classical model as well as published experimental data, suggesting that transients to phase-locking are closely related to the observed oscillations.

cond-mat.supr-con↗

arXiv2006

The Influence of Interatomic Bonding Potentials on Detonation Properties

The dependence of macroscopic detonation properties of a two-dimensional diatomic (AB) molecular system on the fundamental properties of the molecule were investigated. This includes examining the detonation velocity, reaction zone thickness, and critical width as a function of the exothermicity of the gas-phase reaction and the gas-phase dissociation energy for. Following previous work, molecular dynamics (MD) simulations with a reactive empirical bond-order potential were used to characterize the shock-induced response of a diatomic AB molecular solid, which exothermically reacts to produce gaseous products. MD simulations reveal that there is a linear dependence between the square of the detonation velocity and each of these molecular parameters. The detonation velocities were shown to be consistent with the Chapman-Jouguet model, demonstrating that these dependencies arise from how the Equation of State of the products and reactants are affected.

cond-mat.mtrl-sci↗

arXiv2005

Meso-scale computer modeling of lipid-DNA complexes for gene therapy

We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a coarse-grained representation of the intra-molecular details, and via inter-molecular potentials, which effectively mimic the hydrophobic effect {\em without} explicit solvent. In addition to showing spontaneous self-assembly of complexes, the broad utility of the model is illustrated by demonstrating excellent agreement with X-ray diffraction experimental data for the dependence of the spacing between DNA chains on the concentration of CLs. At high concentrations, the large electrostatic pressure induce the formation of pores in the membranes through which the DNA molecules may escape the complex. We relate this observation to the origin of recently observed enhanced transfection efficiency of lamellar CL-DNA complexes at high charge densities.

cond-mat.soft↗

arXiv2004

Non-iterative and exact method for constraining particles in a linear geometry

We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations, and is limited in accuracy only by the numerical methods for solving small systems of linear equations. As a result of the non-iterative and exact (within numerical accuracy) nature of the procedure there is no drift in the constrained geometry, and the method is therefore readily applied to molecular dynamics simulations of, e.g., rigid linear molecules or materials of non-spherical grains. We illustrate the approach through implementation in the commonly used second-order velocity explicit Verlet method.

cond-mat.mtrl-sci↗

arXiv2004

Vacancy assisted arsenic diffusion and time dependent clustering effects in silicon

We present results of kinetic lattice Monte Carlo (KLMC) simulations of substitutional arsenic diffusion in silicon mediated by lattice vacancies. Large systems are considered, with 1000 dopant atoms and long range \textit{ab initio} interactions, to the 18th nearest lattice neighbor, and the diffusivity of each defect species over time is calculated. The concentration of vacancies is greater than equilibrium concentrations in order to simulate conditions shortly after ion implantation. A previously unreported time dependence in the applicability of the pair diffusion model, even at low temperatures, is demonstrated. Additionally, long range interactions are shown to be of critical importance in KLMC simulations; when shorter interaction ranges are considered only clusters composed entirely of vacancies form. An increase in arsenic diffusivity for arsenic concentrations up to $10^{19} \text{cm}^{-3}$ is observed, along with a decrease in arsenic diffusivity for higher arsenic concentrations, due to the formation of arsenic dominated clusters. Finally, the effect of vacancy concentration on diffusivity and clustering is studied, and increasing vacancy concentration is found to lead to a greater number of clusters, more defects per cluster, and a greater vacancy fraction within the clusters.

cond-mat.mtrl-sci↗

arXiv1999

Effective Interactions Between Rigid Polyelectrolytes and Like-charged Planar Surfaces

We study the effective interaction between a planar array of uniformly negatively charged, stiff rods parallel to a negatively charged planar substrate in the absence of salt in a continuous, isotropic dielectric medium. Using Brownian dynamics simulations, we examine the general effects of counterion valence, rod spacing, macroion charge densities, and the rod size on the attractive rod-surface interaction force. At room temperature divalent as well as monovalent counterions mediate an interaction that can be repulsive or attractive upon adjusting either the macroion charge densities or the rod radius. Finally, we examine the effects of discretizing the surface charge as laterally mobile monovalent anions and of electrostatic images in the substrate.

cond-mat.soft↗

arXiv1999

Theoretical and Experimental Adsorption Studies of Polyelectrolytes on an Oppositely Charged Surface

Using self-assembly techniques, x-ray reflectivity measurements, and computer simulations, we study the effective interaction between charged polymer rods and surfaces. Long-time Brownian dynamics simulations are used to measure the effective adhesion force acting on the rods in a model consisting of a planar array of uniformly positively charged, stiff rods and a negatively charged planar substrate in the presence of explicit monovalent counterions and added monovalent salt ions in a continuous, isotropic dielectric medium. This electrostatic model predicts an attractive polymer-surface adhesion force that is weakly dependent on the bulk salt concentration and that shows fair agreement with a Debye-Huckel approximation for the macroion interaction at salt concentrations near 0.1 M. Complementary x-ray reflectivity experiments on poly(diallyldimethyl ammonium) chloride (PDDA) monolayer films on the native oxide of silicon show that monolayer structure, electron density, and surface roughness are likewise independent of the bulk ionic strength of the solution.

cond-mat.soft↗

arXiv1998

$π$-kinks in strongly ac driven sine-Gordon systems

We demonstrate that $π$-kinks exist in non-parametrically ac driven sine-Gordon systems if the ac drive is sufficiently fast. It is found that, at a critical value of the drive amplitude, there are two stable and two unstable equilibria in the sine-Gordon phase. The pairwise symmetry of these equilibria implies the existence of a one-parameter family of $π$-kink solutions in the reduced system. In the dissipative case of the ac driven sine-Gordon systems, corresponding to Josephson junctions, the velocity is selected by the balance between the perturbations. The results are derived from a perturbation analysis and verified by direct numerical simulations.

patt-sol↗

arXiv1998

Higher order Shapiro steps in ac-driven Josephson junctions

We demonstrate that the well known phase-locking mechanism leading to Shapiro steps in ac-driven Josephson junctions is always accompanied by a higher order phase-locking mechanism similar to that of the parametrically driven pendulum. This effect, resulting in a $π$-periodic effective potential for the phase, manifests itself clearly in the parameter regions where the usual Shapiro steps are expected to vanish.

patt-sol↗

arXiv1998

Pressure Calculation in Polar and Charged Systems using Ewald Summation: Results for the Extended Simple Point Charge Model of Water

Ewald summation and physically equivalent methods such as particle-mesh Ewald, kubic-harmonic expansions, or Lekner sums are commonly used to calculate long-range electrostatic interactions in computer simulations of polar and charged substances. The calculation of pressures in such systems is investigated. We find that the virial and thermodynamic pressures differ because of the explicit volume dependence of the effective, resummed Ewald potential. The thermodynamic pressure, obtained from the volume derivative of the Helmholtz free energy, can be expressed easily for both ionic and rigid molecular systems. For a system of rigid molecules, the electrostatic energy and the forces at the atom positions are required, both of which are readily available in molecular dynamics codes. We then calculate the virial and thermodynamic pressures for the extended simple point charge (SPC/E) water model at standard conditions. We find that the thermodynamic pressure exhibits considerably less system size dependence than the virial pressure. From an analysis of the cross correlation between the virial and thermodynamic pressure, we conclude that the thermodynamic pressure should be used to drive volume fluctuations in constant-pressure simulations.

physics.chem-ph↗

arXiv1994

Kinks in the Presence of Rapidly Varying Perturbations

Dynamics of sine-Gordon kinks in the presence of rapidly varying periodic perturbations of different physical origins is described analytically and numerically. The analytical approach is based on asymptotic expansions, and it allows to derive, in a rigorous way, an effective nonlinear equation for the slowly varying field component in any order of the asymptotic procedure as expansions in the small parameter $ω^{-1}$, $ω$ being the frequency of the rapidly varying ac driving force. Three physically important examples of such a dynamics, {\em i.e.}, kinks driven by a direct or parametric ac force, and kinks on rotating and oscillating background, are analysed in detail. It is shown that in the main order of the asymptotic procedure the effective equation for the slowly varying field component is {\em a renormalized sine-Gordon equation} in the case of the direct driving force or rotating (but phase-locked to an external ac force) background, and it is {\em the double sine-Gordon equation} for the parametric driving force. The properties of the kinks described by the renormalized nonlinear equations are analysed, and it is demonstrated analytically and numerically which kinds of physical phenomena may be expected in dealing with the renormalized, rather than the unrenormalized, nonlinear dynamics. In particular, we predict several qualitatively new effects which include, {\em e.g.}, the perturbation-induced

cond-mat↗