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arXiv2013

More accurate and efficient bath spectral densities from super-resolution

Quantum transport and other phenomena are typically modeled by coupling the system of interest to an environment, or bath, held at thermal equilibrium. Realistic bath models are at least as challenging to construct as models for the quantum systems themselves, since they must incorporate many degrees of freedom that interact with the system on a wide range of timescales. Owing to computational limitations, the environment is often modeled with simple functional forms, with a few parameters fit to experiment to yield semi-quantitative results. Growing computational resources have enabled the construction of more realistic bath models from molecular dynamics (MD) simulations. In this paper, we develop a numerical technique to construct these atomistic bath models with better accuracy and decreased cost. We apply a novel signal processing technique, known as super-resolution, combined with a dictionary of physically-motivated bath modes to derive spectral densities from MD simulations. Our approach reduces the required simulation time and provides a more accurate spectral density than can be obtained via standard Fourier transform methods. Moreover, the spectral density is provided as a convenient closed-form expression which yields an analytic time-dependent bath kernel. Exciton dynamics of the Fenna-Matthews-Olsen light-harvesting complex are simulated with a second order time-convolutionless master equation, and spectral densities constructed via super-resolution are shown to reproduce the dynamics using only a quarter of the amount of MD data.

quant-ph↗

arXiv2013

Molecular simulation of nano-dispersed fluid phases

Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets, simulation volumes containing a nanoscopic gas bubble surrounded by a subsaturated liquid phase under tension, i.e. at negative pressure, are conducted in the canonical ensemble. The boundary conditions are chosen such that the phase equilibrium at the curved interface is thermodynamically stable. Two distinct size-dependent effects are found: Curvature induces a subsaturation of the system, leading to a smaller liquid density. For the gas in the centre of the bubble, the small diameter has an additional obverse effect, increasing its density. The curvature dependence of the surface tension is discussed by evaluating average radial density profiles to obtain the excess equimolar radius, which is found to be positive, corresponding to a negative Tolman length.

cond-mat.mes-hall↗

arXiv2013

Simultaneous maximum-likelihood reconstruction for x-ray grating based phase-contrast tomography avoiding intermediate phase retrieval

Phase-wrapping artifacts, statistical image noise and the need for a minimum amount of phase steps per projection limit the practicability of x-ray grating based phase-contrast tomography, when using filtered back projection reconstruction. For conventional x-ray computed tomography, the use of statistical iterative reconstruction algorithms has successfully reduced artifacts and statistical issues. In this work, an iterative reconstruction method for grating based phase-contrast tomography is presented. The method avoids the intermediate retrieval of absorption, differential phase and dark field projections. It directly reconstructs tomographic cross sections from phase stepping projections by the use of a forward projecting imaging model and an appropriate likelihood function. The likelihood function is then maximized with an iterative algorithm. The presented method is tested with tomographic data obtained through a wave field simulation of grating based phase-contrast tomography. The reconstruction results are in agreement with the expectations and proof the validity of the concept.

physics.med-ph↗

arXiv2013

New and general framework for adsorption processes on dynamic interfaces

We introduce a new and general continuum thermodynamic framework for the mathematical analysis and computation of adsorption on dynamic interfaces. To the best of our knowledge, there is no formulation available that accounts for the coupled dynamics of interfaces and densities of adsorbants. Our framework leads to analytic adsorption isotherms which also take the interfacial geometry fully into account. We demonstrate the utility and physical consistency of our framework with a new computational multi-level discretization strategy. In the computations, we recover the experimentally observed feature that the adsorption of particles minimizes the interfacial tension.

physics.flu-dyn↗

arXiv2013

GPU peer-to-peer techniques applied to a cluster interconnect

Modern GPUs support special protocols to exchange data directly across the PCI Express bus. While these protocols could be used to reduce GPU data transmission times, basically by avoiding staging to host memory, they require specific hardware features which are not available on current generation network adapters. In this paper we describe the architectural modifications required to implement peer-to-peer access to NVIDIA Fermi- and Kepler-class GPUs on an FPGA-based cluster interconnect. Besides, the current software implementation, which integrates this feature by minimally extending the RDMA programming model, is discussed, as well as some issues raised while employing it in a higher level API like MPI. Finally, the current limits of the technique are studied by analyzing the performance improvements on low-level benchmarks and on two GPU-accelerated applications, showing when and how they seem to benefit from the GPU peer-to-peer method.

physics.comp-ph↗

arXiv2013

Hermitian and non-Hermitian thermal Hamiltonians

Thermal density matrices can be described by a pure quantum state within the thermofield formalism. Here we show how to construct a class of Hamiltonians realizing a thermofield state as their ground state. These Hamiltonians are frustration-free, and can be Hermitian or non-Hermitian, allowing one to use ground-state methods to understand the thermodynamic properties of the system. In particular this approach gives an explicit mapping of thermal phase transitions into quantum phase transitions. In the non-Hermitian case, the quantum phase transition is not accompanied by a change in the spectrum of the Hamiltonian, which remains gapped. We illustrate these ideas for the classical 2D Ising model.

cond-mat.stat-mech↗

arXiv2013

Vacancy trapping behaviors of hydrogen atoms in Ti3SiC2: a first-principles study

The behaviors of hydrogen (H) in MAX phase material Ti3SiC2 have been investigated using first-principles method. We show that a single H atom prefers to stay 1.01 Å down of the Si vacancy with solution energy of about -4.07 eV, lowerthan that in bulk Ti3SiC2. Multi H atoms exhibit a repulsive interaction at the Si vacancy. And up to five H atoms can be trapped by a Si vacancy without H2 molecules formation. These results suggest the strong vacancy trapping characteristic of H atoms in Ti3SiC2. Meanwhile, the barrier for H diffusion from an interstitial site to a vacancy is 1.17 eV, which is much larger than that in metals, indicating that to some extent H atoms can not easily migrate or aggregate to form bubble in Ti3SiC.

cond-mat.mtrl-sci↗

arXiv2013

Bateman method for two-body scattering without partial-wave decomposition

The use of Bateman method for solving the two-variable version of the Lippmann-Schwinger equation without recourse to partial-wave decomposition is investigated. Bateman method is based on a special kind of interpolation of the momentum representation of the potential on a multi-variate grid. A suitable scheme for the generation of a multi-variate Cartesian grid is described. The method is tested in the nucleon-nucleon scattering employing a model two-nucleon potential. Our results show that the Bateman method is capable of producing quite accurate solutions with relatively small number of grid points.

physics.comp-ph↗

arXiv2013

Effects of Edge Oxidation on the Structural, Electronic, and Magnetic Properties of Zigzag Boron Nitride Nanoribbons

The effects of edge chemistry on the relative stability and electronic properties of zigzag boron nitride nanoribbons (ZBNNRs) are investigated. Among all functional groups considered, fully hydroxylated ZBNNRs are found to be the most energetically stable. When an in-plane external electric field is applied perpendicular to the axis of both hydrogenated and hydroxylated ZBNNRs, a spin-polarized half-metallic state is induced, whose character is different than that predicted for ZGNRs. The onset field for achieving the half-metallic state is found to mainly depend on the width of the ribbon. Our results indicate that edge functionalization of ZBNNRs may open the way for the design of new nano-electronic and nano-spintronic devices.

cond-mat.mtrl-sci↗

arXiv2013

Geant4 - Current and Future : A Snowmass 2013 White Paper

The US involvement in Geant4 started with its adoption by the BaBar experiment at SLAC in 1997 and the subsequent creation of a group at SLAC supporting BaBar and contributing to Geant4 development. SLAC has provided the leadership of the international Geant4 Collaboration for the recent years and carries major responsibilities for evolutionary development of the existing code with work to implement multithreading and explore new application domains as well as new technologies such as GPUs. This paper presents the current and the future developments being carried by the SLAC Geant4 team.

hep-ex↗

arXiv2013

A multiple-relaxation-time lattice Boltzmann model for convection heat transfer in porous media

In this paper, a two-dimensional (2D) multiple-relaxation-time (MRT) lattice Boltzmann (LB) model is developed for simulating convection heat transfer in porous media at the representative elementary volume scale. In the model, a MRT-LB equation is used to simulate the flow field, while another MRT-LB equation is employed to simulate the temperature field. The effect of the porous media is considered by introducing the porosity into the equilibrium moments, and adding a forcing term to the MRT-LB equation of the flow field in the moment space. The present MRT-LB model is validated by numerical simulations of several 2D convection problems in porous media. The numerical results are in good agreement with the well-documented data reported in the literature.

physics.comp-ph↗

arXiv2013

Open Source Physics

Open Source Physics (Brown, 2012; Christian, 2010; Esquembre, 2012; Hwang, 2010) empowers teachers and students to create and use these free tools with the associated intellectual property rights given to customise (Wee & Mak, 2009) the computer models/tools to suit their teaching and learning needs. Open Source Physics (OSP) focuses on design of computer models, such as Easy Java Simulations (EJS) and the use of video modeling and analysis (Tracker). They allow students to investigate, explore and analyse data which is either real or simulated. The OSP approach helps users overcome barriers in creating, using and scaling up meaningful ICT use in education. In Singapore, teachers and students have created or customised existing computer models to design and re-purpose EJS models to suit their context and learning needs. Tracker tools allow students to analyse different aspects of a physics phenomena to deepen their understanding of abstract physics concepts. Using Tracker, students record the motion of objects and create their own models to test their ideas in the study of kinematics. Essentially, the two main pedagogical approaches (Figure 1) used in OSP are: Guided Inquiry investigating modeled phenomena(EJS) video analysis (Tracker) Constructionism learning by making new models(EJS) video modeling(Tracker)

physics.ed-ph↗

arXiv2013

Gradient type optimization methods for electronic structure calculations

The density functional theory (DFT) in electronic structure calculations can be formulated as either a nonlinear eigenvalue or direct minimization problem. The most widely used approach for solving the former is the so-called self-consistent field (SCF) iteration. A common observation is that the convergence of SCF is not clear theoretically while approaches with convergence guarantee for solving the latter are often not competitive to SCF numerically. In this paper, we study gradient type methods for solving the direct minimization problem by constructing new iterations along the gradient on the Stiefel manifold. Global convergence (i.e., convergence to a stationary point from any initial solution) as well as local convergence rate follows from the standard theory for optimization on manifold directly. A major computational advantage is that the computation of linear eigenvalue problems is no longer needed. The main costs of our approaches arise from the assembling of the total energy functional and its gradient and the projection onto the manifold. These tasks are cheaper than eigenvalue computation and they are often more suitable for parallelization as long as the evaluation of the total energy functional and its gradient is efficient. Numerical results show that they can outperform SCF consistently on many practically large systems.

physics.comp-ph↗

arXiv2014

Real time quantum dynamics preaveraged over imaginary time path integral: A formal basis for both Centroid Molecular Dynamics and Ring Polymer Molecular Dynamics

An exact real time quantum dynamics preaveraged over imaginary time path integral is formulated for general condensed phase equilibrium ensemble. This formulation results in the well-known centroid dynamics approach upon filtering of centroid constraint, and provides a rigorous framework to understand and analyze a related quantum dynamics approximation method called ring polymer molecular dynamics. The formulation also serves as the basis for developing new kinds of quantum dynamics that utilize the cyclic nature of the imaginary time path integral.

quant-ph↗

arXiv2013

Molecular dynamics (MD) calculation of the zeta potential of neutral surfaces

Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions 'apparent'. Here we demonstrate how zeta potentials that agree with measured values can be calculated by: (1) integrating the net average charge in surface-parallel layers from the midpoint of the fluid layer (where the electrostatic potential is zero) to and then into two solid caps, (2) determining the position of slipping plane with separate Couette flow models, and (3) calculating the charge distribution and electrostatic potential under static conditions. The solids we model are charge neutral surfaces composed of atoms with zero charge or charge balanced monovalent or divalent ions. The zeta potentials calculated are within a few millivolts of measured values, and the measured values fall within the simulation error bars. Insights provided by the improved MD simulations into the complex phenomena that affect surface charge and zeta potential are discussed.

physics.comp-ph↗

arXiv2013

Onsager reciprocity principle for kinetic models and kinetic schemes

Boltzmann equation requires some alternative simpler kinetic model like BGK to replace the collision term. Such a kinetic model which replaces the Boltzmann collision integral should preserve the basic properties and characteristics of the Boltzmann equation and comply with the requirements of non equilibrium thermodynamics. Most of the research in development of kinetic theory based methods have focused more on entropy conditions, stability and ignored the crucial aspect of non equilibrium thermodynamics. The paper presents a new kinetic model formulated based on the principles of non equilibrium thermodynamics. The new kinetic model yields correct transport coefficients and satisfies Onsager's reciprocity relationship. The present work also describes a novel kinetic particle method and gas kinetic scheme based on this linkage of non-equilibrium thermodynamics and kinetic theory. The work also presents derivation of kinetic theory based wall boundary condition which complies with the principles of non-equilibrium thermodynamics, and can simulate both continuum and rarefied slip flow in order to avoid extremely costly multi-scale simulation.

physics.flu-dyn↗

arXiv2013

Intrinsic Magnetism of Grain Boundaries in Two-dimensional Metal Dichalcogenides

Grain boundaries (GBs) are structural imperfections that typically degrade the performance of materials. Here we show that dislocations and GBs in two-dimensional (2D) metal dichalcogenides MX2 (M = Mo, W; X = S, Se) can actually improve the material by giving it a qualitatively new physical property: magnetism. The dislocations studied all have a substantial magnetic moment of ~1 Bohr magneton. In contrast, dislocations in other well-studied 2D materials are typically non-magnetic. GBs composed of pentagon-heptagon pairs interact ferromagnetically and transition from semiconductor to half-metal or metal as a function of tilt angle and/or doping level. When the tilt angle exceeds 47° the structural energetics favor square-octagon pairs and the GB becomes an antiferromagnetic semiconductor. These exceptional magnetic properties arise from an interplay of dislocation-induced localized states, doping, and locally unbalanced stoichiometry. Purposeful engineering of topological GBs may be able to convert MX2 into a promising 2D magnetic semiconductor.

cond-mat.mtrl-sci↗

arXiv2013

Upper Bound for Critical Probability of Site Percolation on Triangular Lattice

In site percolation, vertices (sites) of a graph are open with probability p, and there is critical p, for which open vertices form an open path the long way across a graph, so a vertex at the origin is a part of an infinite connected open vertex set. Smirnov found that for triangular lattice critical p is 0.5, but there is the traversal, from the origin upwards, so that an infinite connected open vertex set exists for critical p=0.3535.

math-ph↗