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Importance of reference Hamiltonians containing exact exchange for accurate one-shot GW calculations of Cu2O

Physical Review B 2012年第23期85卷 235142-235142页

作者： Leah Y. Isseroff Emily A. Carter Department of Chemical and Biological Engineering Princeton University Princeton New Jersey 08544-5263 USA Department of Mechanical and Aerospace Engineering Program in Applied and Computational Mathematics and Andlinger Center for Energy and the Environment Princeton University Princeton New Jersey 08544-5263 USA

We show that a “one-shot” GW approach (denoted G0W0) can accurately calculate the photoemission/inverse-photoemission properties of Cu2O. As the results of any perturbative method are heavily dependent on the reference state, the appropriate reference Hamiltonian for G0W0 is identified by evaluating the performance of density-functional-theory-based input wave functions and eigenvalues generated with selected exchange-correlation functionals. It is shown that a reference Hamiltonian employing the hybrid Heyd-Scuseria-Ernzerhof functional used in conjunction with G0W0 produces an accurate photoemission/inverse-photoemission band gap and photoemission spectrum whose character is then further analyzed. The physical origin of why a hybrid functional is required for the zeroth-order wave function is discussed, giving insight into the unique electronic structure of Cu2O in comparison to other transition-metal oxides.

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Efficient coarse simulation of a growing avascular tumor

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Physical Review E 2012年第3期85卷 031912-031912页

作者： Michail E. Kavousanakis Ping Liu Andreas G. Boudouvis John Lowengrub Ioannis G. Kevrekidis School of Chemical Engineering National Technical University of Athens 9 Heroon Polytechniou St. Zographos Athens GR-15780 Greece Department of Chemical and Biological Engineering Princeton University Princeton New Jersey 08544 USA Department of Mathematics University of California 103 MSTB Irvine California 92697 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

The subject of this work is the development and implementation of algorithms which accelerate the simulation of early stage tumor growth models. Among the different computational approaches used for the simulation of tumor progression, discrete stochastic models (e.g., cellular automata) have been widely used to describe processes occurring at the cell and subcell scales (e.g., cell-cell interactions and signaling processes). To describe macroscopic characteristics (e.g., morphology) of growing tumors, large numbers of interacting cells must be simulated. However, the high computational demands of stochastic models make the simulation of large-scale systems impractical. Alternatively, continuum models, which can describe behavior at the tumor scale, often rely on phenomenological assumptions in place of rigorous upscaling of microscopic models. This limits their predictive power. In this work, we circumvent the derivation of closed macroscopic equations for the growing cancer cell populations; instead, we construct, based on the so-called “equation-free” framework, a computational superstructure, which wraps around the individual-based cell-level simulator and accelerates the computations required for the study of the long-time behavior of systems involving many interacting cells. The microscopic model, e.g., a cellular automaton, which simulates the evolution of cancer cell populations, is executed for relatively short time intervals, at the end of which coarse-scale information is obtained. These coarse variables evolve on slower time scales than each individual cell in the population, enabling the application of forward projection schemes, which extrapolate their values at later times. This technique is referred to as coarse projective integration. Increasing the ratio of projection times to microscopic simulator execution times enhances the computational savings. Crucial accuracy issues arising for growing tumors with radial symmetry are addressed by applying th

关键词： SIMULATION methods & models TUMORS -- Growth MATHEMATICAL models CANCER invasiveness STOCHASTIC models computational biology BIONICS PHENOMENOLOGY

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Model reduction for agent-based social simulation: Coarse-graining a civil violence model

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Physical Review E 2012年第6期85卷 066106-066106页

作者： Yu Zou Vladimir A. Fonoberov Maria Fonoberova Igor Mezic Ioannis G. Kevrekidis Department of Chemical and Biological Engineering and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Aimdyn Inc. 1919 State Street Suite 207 Santa Barbara California 93101 USA Department of Mechanical Engineering University of California Santa Barbara Santa Barbara California 93106 USA

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

关键词： VIOLENCE SOCIAL dynamics STOCHASTIC models CITIZENS SOCIAL interaction DEGREES of freedom

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Seismic Probes of Solar Interior Magnetic Structure

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Physical Review Letters 2012年第10期109卷 101101-101101页

作者： Shravan Hanasoge Aaron Birch Laurent Gizon Jeroen Tromp Department of Geosciences Princeton University New Jersey 08544 USA Max-Planck Institut für Sonnensystemforschung 37191 Kalenburg-Lindau Germany Georg-August-Universität Institut für Astrophysik D-37077 Göttingen Germany Program for Applied and Computational Mathematics Princeton University New Jersey 08544 USA

Sun spots are prominent manifestations of solar magnetoconvection, and imaging their subsurface structure is an outstanding problem of wide physical importance. Travel times of seismic waves that propagate through these structures are typically used as inputs to inversions. Despite the presence of strongly anisotropic magnetic waveguides, these measurements have always been interpreted in terms of changes to isotropic wave speeds and flow-advection-related Doppler shifts. Here, we employ partial-differential-equation-constrained optimization to determine the appropriate parametrization of the structural properties of the magnetic interior. Seven different wave speeds fully characterize helioseismic wave propagation: the isotropic sound speed, a Doppler-shifting flow-advection velocity, and an anisotropic magnetic velocity. The structure of magnetic media is sensed by magnetoacoustic slow and fast modes and Alfvén waves, each of which propagates at a different wave speed. We show that even in the case of weak magnetic fields, significant errors may be incurred if these anisotropies are not accounted for in inversions. Translation invariance is demonstrably lost. These developments render plausible the accurate seismic imaging of magnetoconvection in the Sun.

关键词： SEISMIC waves -- Speed MAGNETIC structure PARTIAL differential equations DOPPLER effect THEORY of wave motion SUN INTERNAL structure

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Semi-Eulerian and High Order Gaussian Beam Methods for the Schrödinger Equation in the Semiclassical Regime

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Communications in computational Physics 2011年第3期9卷 668-687页

作者： Shi Jin Hao Wu Xu Yang Department of Mathematics University of WisconsinMadisonWI 53706USA Department of Mathematical Sciences Tsinghua UniversityBeijing 10084China Program in Applied and Computational Mathematics Princeton UniversityNJ 08544USA

A novel Eulerian Gaussian beam method was developed in[8]to compute the Schrödinger equation efficiently in the semiclassical *** this paper,we introduce an efficient semi-Eulerian implementation of this *** new algorithm inherits the essence of the Eulerian Gaussian beam method where the Hessian is computed through the derivatives of the complexified level set functions instead of solving the dynamic ray tracing *** difference lies in that,we solve the ray tracing equations to determine the centers of the beams and then compute quantities of interests only around these *** yields effectively a local level set implementation,and the beam summation can be carried out on the initial physical space instead of the phase *** a consequence,it reduces the computational cost and also avoids the delicate issue of beam summation around the caustics in the Eulerian Gaussian beam ***,the semi-Eulerian Gaussian beam method can be easily generalized to higher order Gaussian beam methods,which is the topic of the second part of this *** numerical examples are provided to verify the accuracy and efficiency of both the first order and higher order semi-Eulerian methods.

关键词： Schrödinger equation semi-Eulerian Gaussian beam method high order methods

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Nonequilibrium static diverging length scales on approaching a prototypical model glassy state

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Physical Review E 2012年第2期86卷 021505-021505页

作者： Adam B. Hopkins Frank H. Stillinger Salvatore Torquato Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Maximally random jammed states of hard spheres are prototypical glasses. We study the small wavenumber k behavior of the structure factor S(k) of overcompressed million-sphere packings as a function of density up to the jammed state. We find both a precursor to the glassy jammed state evident long before the jamming density is reached and two associated growing length scales, one extracted from the volume integral of the direct correlation function c(r) and the other from the small-k behavior of the structure factor S(k), that can diverge at the “critical” jammed state. We also define a nonequilibrium index X and use it to demonstrate that the packings studied are intrinsically nonequilibrium in nature well before the critical state is reached. The extension of the results reported in the present work to supercooled atomic-liquid models in which the atoms interact with both repulsive and attractive forces is also discussed.

关键词： PROTOTYPES GLASS FACTOR structure DENSITY functionals NONEQUILIBRIUM thermodynamics MATHEMATICAL models CORRELATION (Statistics) CRITICAL point

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Microstructural degeneracy associated with a two-point correlation function and its information content

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Physical Review E 2012年第5期85卷 051140-051140页

作者： C. J. Gommes Y. Jiao S. Torquato Department of Chemical Engineering University of Liège Liège 4000 Belgium Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

A two-point correlation function provides a crucial yet an incomplete characterization of a microstructure because distinctly different microstructures may have the same correlation function. In an earlier Letter [Gommes, Jiao, and Torquato, Phys. Rev. Lett. 108, 080601 (2012)], we addressed the microstructural degeneracy question: What is the number of microstructures compatible with a specified correlation function? We computed this degeneracy, i.e., configurational entropy, in the framework of reconstruction methods, which enabled us to map the problem to the determination of ground-state degeneracies. Here, we provide a more comprehensive presentation of the methodology and analyses, as well as additional results. Since the configuration space of a reconstruction problem is a hypercube on which a Hamming distance is defined, we can calculate analytically the energy profile of any reconstruction problem, corresponding to the average energy of all microstructures at a given Hamming distance from a ground state. The steepness of the energy profile is a measure of the roughness of the energy landscape associated with the reconstruction problem, which can be used as a proxy for the ground-state degeneracy. The relationship between this roughness metric and the ground-state degeneracy is calibrated using a Monte Carlo algorithm for determining the ground-state degeneracy of a variety of microstructures, including realizations of hard disks and Poisson point processes at various densities as well as those with known degeneracies (e.g., single disks of various sizes and a particular crystalline microstructure). We show that our results can be expressed in terms of the information content of the two-point correlation functions. From this perspective, the a priori condition for a reconstruction to be accurate is that the information content, expressed in bits, should be comparable to the number of pixels in the unknown microstructure. We provide a formula to calculate the

关键词： MICROSTRUCTURE CORRELATION (Statistics) INFORMATION theory ENTROPY (Information theory) GROUND state (Quantum mechanics) MONTE Carlo method POISSON processes

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Effective Maxwell Equations from Time-dependent Density Functional Theory

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Acta Mathematica Sinica,English Series 2011年第2期27卷 339-368页

作者： Weinan E Jianfeng LU Xu YANG Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA Beijing International Center for Mathematical Research and School of Mathematical Sciences Peking University Beijing 100871 P. R. China Department of Mathematics Courant Institute of Mathematical Sciences New York University New York NY 10012 USA

The behavior of interacting electrons in a perfect crystal under macroscopic external electric and magnetic fields is studied. Effective Maxwell equations for the macroscopic electric and magnetic fields are derived starting from time-dependent density functional theory. Effective permittivity and permeability coefficients are obtained.

关键词： Time-dependent density functional theory Maxwell equations effective permittivity electromagnetic fields

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Momentum distribution, vibrational dynamics, and the potential of mean force in ice

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Physical Review B 2011年第22期83卷 220302(R)-220302(R)页

作者： Lin Lin Joseph A. Morrone Roberto Car Michele Parrinello Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA Department of Chemistry Princeton University Princeton NJ 08544 USA Department of Physics Princeton University Princeton NJ 08544 USA Computational Science Department of Chemistry and Applied Biosciences Eidgenössische Technische Hochschule Zürich USI Campus Via Giuseppe Buffi 12 CH-6900 Lugano Switzerland

By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasiharmonic context, anharmonicity in the ground-state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.

关键词： PHYSICS research PHONONS ICE ANISOTROPY PROTON beams SPECTROSCOPIC imaging

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Manifold learning techniques and model reduction for dissipative dynamics

Manifold learning techniques and model reduction for dissipa...

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Computing and Systems Technology Division - Core programming Topic at the 2011 AIChE Annual Meeting

作者： Sonday, Benjamin Rajendran, Karthikeyan Gear, William Singer, Amit Kevrekidis, Ioannis G. Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Chemical and Biological Engineering Princeton University PrincetonNJ United States Mathematics and PACM Princeton University PrincetonNJ United States

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