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Densest local sphere-packing diversity. II. Application to three dimensions

Physical Review E 2011年第1期83卷 011304-011304页

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

The densest local packings of N three-dimensional identical nonoverlapping spheres within a radius Rmin(N) of a fixed central sphere of the same size are obtained for selected values of N up to N=1054. In the predecessor to this paper [A. B. Hopkins, F. H. Stillinger, and S. Torquato, Phys. Rev. E 81, 041305 (2010)], we described our method for finding the putative densest packings of N spheres in d-dimensional Euclidean space Rd and presented those packings in R2 for values of N up to N=348. Here we analyze the properties and characteristics of the densest local packings in R3 and employ knowledge of the Rmin(N), using methods applicable in any d, to construct both a realizability condition for pair correlation functions of sphere packings and an upper bound on the maximal density of infinite sphere packings. In R3, we find wide variability in the densest local packings, including a multitude of packing symmetries such as perfect tetrahedral and imperfect icosahedral symmetry. We compare the densest local packings of N spheres near a central sphere to minimal-energy configurations of N+1 points interacting with short-range repulsive and long-range attractive pair potentials, e.g., 12–6 Lennard-Jones, and find that they are in general completely different, a result that has possible implications for nucleation theory. We also compare the densest local packings to finite subsets of stacking variants of the densest infinite packings in R3 (the Barlow packings) and find that the densest local packings are almost always most similar as measured by a similarity metric, to the subsets of Barlow packings with the smallest number of coordination shells measured about a single central sphere, e.g., a subset of the fcc Barlow packing. Additionally, we observe that the densest local packings are dominated by the dense arrangement of spheres with centers at distance Rmin(N). In particular, we find two “maracas” packings at N=77 and N=93, each consisting of a few unjammed sphere

关键词： DENSITY functionals SPHERES MATHEMATICAL models EUCLIDEAN metric CORRELATION (Statistics) SYMMETRY

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Comprehensive analysis of compositional interface fluctuations in planar lipid bilayer membranes

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Physical Review E 2011年第5期84卷 051903-051903页

作者： Tao Han Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

In this paper we present a comprehensive analysis of line tension-driven compositional interface fluctuations in planar lipid bilayer membranes. Our starting point is the advective Cahn-Hilliard equation for the local lipid composition in symmetric membranes, which explicitly incorporates both advective and diffusive lipid transport processes, and which is coupled to the continuum hydrodynamic equations governing the flow behavior of the membrane and surrounding solvent with finite subphase thickness. In order to extract the interface dynamics from the continuum phase-field formalism, we first derive the appropriate sharp-interface limit equations. We then carry out a linear perturbation analysis for the relaxational dynamics of small-amplitude sinusoidal interface fluctuations to yield the general dispersion relation ωk as a function of perturbation wave number k. The resulting expression incorporates the effects of diffusive and advective lipid transport processes within the membrane, viscous or viscoelastic membrane properties, coupling between membrane and solvent, and inertial effects within the membrane and solvent. It is shown that previously considered scenarios naturally emerge as limiting cases of the general result. Furthermore, we discuss two additional scenarios amenable to analysis, one in which the inertia of the solvent is relevant, and another one in which the membrane displays significant viscoelastic properties. Finally, we numerically evaluate the general dispersion relation for three representative model membrane systems.

关键词： BILAYER lipid membranes FLUCTUATIONS (Physics) PERTURBATION (mathematics) VISCOELASTICITY HYDRODYNAMICS

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Coarse graining the dynamics of heterogeneous oscillators in networks with spectral gaps

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Physical Review E 2011年第3期84卷 036708-036708页

作者： Karthikeyan Rajendran Ioannis G. Kevrekidis Department of Chemical and Biological Engineering Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

We present a computer-assisted approach to coarse graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph Laplacian suggests that the graph dynamics may quickly become low dimensional. Our first choice of coarse variables consists of the components of the oscillator states—their (complex) phase angles—along the leading eigenvectors of this Laplacian. We then use the equation-free framework, circumventing the derivation of explicit coarse-grained equations, to perform computational tasks such as coarse projective integration, coarse fixed-point, and coarse limit-cycle computations. In a second step, we explore an approach to incorporating oscillator heterogeneity in the coarse-graining process. The approach is based on the observation of fast-developing correlations between oscillator state and oscillator intrinsic properties and establishes a connection with tools developed in the context of uncertainty quantification.

关键词： GRAINING COMPUTER-aided design LAPLACIAN operator EIGENVECTORS HARMONIC oscillators

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Direct minimization of the optimized effective problem based on efficient finite differences

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Physical Review B 2011年第16期84卷 165122-165122页

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

To avoid the difficult-to-solve optimized effective potential (OEP) integral equation, we introduce an efficient direct minimization scheme for performing OEP calculations within Kohn–Sham density functional theory (KS-DFT). We reformulated the functional derivative of the total energy with respect to the KS effective potential in terms of efficient finite differences. Our method only uses the orbitals involved in the construction of the KS exchange-correlation functionals. We demonstrate our scheme by performing exact-exchange OEP for sodium clusters, in which only occupied KS orbitals are needed to obtain the OEP. Our efficient direct minimization scheme should aid future development of orbital-dependent density functionals and render OEP to be a practical choice for various applications.

关键词： INTEGRAL equations DENSITY functionals TOTAL energy systems (On-site electric power production) FINITE differences PHYSICS

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Frame coherence and sparse signal processing

Frame coherence and sparse signal processing

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IEEE International Symposium on Information Theory

作者： Dustin G. Mixon Waheed U. Bajwa Robert Calderbank Program in Applied and Computational Mathematics Princeton University Princeton NJ USA Department of Electrical and Computer Engineering Duke University Durham NC USA

The sparse signal processing literature often uses random sensing matrices to obtain performance guarantees. Unfortunately, in the real world, sensing matrices do not always come from random processes. It is therefore desirable to evaluate whether an arbitrary matrix, or frame, is suitable for sensing sparse signals. To this end, the present paper investigates two parameters that measure the coherence of a frame: worst-case and average coherence. We first provide several examples of frames that have small spectral norm, worst-case coherence, and average coherence. Next, we present a new lower bound on worst-case coherence and compare it to the Welch bound. Later, we propose an algorithm that decreases the average coherence of a frame without changing its spectral norm or worst-case coherence. Finally, we use worst-case and average coherence, as opposed to the Restricted Isometry Property, to garner near-optimal probabilistic guarantees on both sparse signal detection and reconstruction in the presence of noise. This contrasts with recent results that only guarantee noiseless signal recovery from arbitrary frames, and which further assume independence across the nonzero entries of the signal-in a sense, requiring small average coherence replaces the need for such an assumption.

关键词： Coherence Signal processing algorithms Noise Harmonic analysis Noise measurement Geometry

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Parsimonious reconstruction of network evolution

Parsimonious reconstruction of network evolution

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Lecture Notes in Computer Science

作者： Patro, Rob Sefer, Emre Malin, Justin Marçais, Guillaume Navlakha, Saket Kingsford, Carl Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 United States Department of Computer Science University of Maryland College Park MD 20742 United States Computational Biology Bioinformatics and Genomics Concentration Biological Sciences Graduate Program University of Maryland College Park MD 20742 United States Program in Applied Mathematics Statistics and Scientific Computation University of Maryland College Park MD 20742 United States School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 United States

ISBN: (纸本)9783642230370

We consider the problem of reconstructing a maximally parsimonious history of network evolution under models that support gene duplication and loss and independent interaction gain and loss. We introduce a combinatorial framework for encoding network histories, and we give a fast procedure that, given a set of duplication histories, in practice finds network histories with close to the minimum number of interaction gain or loss events. In contrast to previous studies, our method does not require knowing the relative ordering of unrelated duplication events. Results on simulated histories suggest that common ancestral networks can be accurately reconstructed using this parsimony approach. © 2011 Springer-Verlag.

关键词： Genes

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4D seismic monitoring of CO2 sequestration based upon spectral-element and adjoint methods: Comparison of acoustic, elastic and poroelastic theories 80

4D seismic monitoring of CO2 sequestration based upon spectr...

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Society of Exploration Geophysicists International Exposition and 80th Annual Meeting 2010, SEG 2010

作者： Morency, Christina Luo, Yang Tromp, Jeroen Department of Geosciences Princeton University United States Department of Geosciences and Program in Applied and Computational Mathematics Princeton University United States

ISBN: (纸本)9781617389801

The key issues in CO2 sequestration monitoring involve accurate monitoring, from the injection stage to prediction & verification, of CO2 movement over time for environmental considerations. A natural non-intrusive monitoring technique is referred to as "4D seismics", which involves 3D time-lapse seismic surveys. The success of monitoring the CO2 movement is subject to a proper description of the physical properties of the structure. We realize time-lapse migrations comparing acoustic, elastic, and poroelastic simulations of 4D seismic imaging to characterize the storage zone, based solely upon the first arrival traveltime anomaly arising from the injection of CO2. This approach highlights the influence of using different physical theories on interpreting seismic data, and, more importantly, on extracting the CO2 signature from the seismic wave field. Simulations are performed using a spectral-element method, which allows for highly accurate results. Biot? Equations are implemented to account for poroelastic effects. The sensitivity of observables to the model parameters is quantified based upon finite-frequency sensitivity kernels calculated using an adjoint method. © 2010 SEG.

关键词： Carbon dioxide

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Continuum model of irradiation-induced spinodal decomposition in the presence of dislocations

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Physical Review B 2011年第17期83卷 174106-174106页

作者： J. J. Hoyt M. Haataja Department of Materials Science and Engineering McMaster University Hamilton Ontario Canada L8S4L7 Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544

A model of phase-separation kinetics in systems exposed to energetic particle irradiation has been extended to include the effects of mobile dislocations. It is shown that when dislocations are allowed to participate in the decomposition reaction, phase separation can occur at temperatures above the coherent spinodal, which is in agreement with several experiments on irradiated alloys. A linear stability analysis of the governing kinetic equations is performed and three regimes of microstructural evolution are identified within the parameter space of damage cascade size vs incident flux: complete phase separation, solid-solution behavior, and compositional patterning. In addition, numerical simulations of the evolving dislocation density and composition fields are performed. The numerical results provide the amplitude and wavelength of the stable patterns that can form under irradiation and elucidate the role of misfit dislocations in reducing the coherency strain due to atomic size mismatch.

关键词： PHASE transformations (Physics) THERMODYNAMICS PARTICLES (Nuclear physics) ALLOYS IRRADIATION STRAINS & stresses (Mechanics)

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Reducing time delays on congested road networks using social navigation

Reducing time delays on congested road networks using social...

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IEEE Forum on Integrated and Sustainable Transportation System (FISTS)

作者： Alje van den Bosch Bart van Arem Mohamed Mahmod James Misener Department of Applied Mathematics Faculty of Electrical Engineering Mathematics and Computer Science University of Twente Netherlands Partners for Advanced Transit and Highways (PATH) program University of California Berkeley USA Department of Transport and Planning at the Faculty of Civil Engineering and Geosciences Delft University of Technnology Netherlands Centre of Transport Studies Faculty of Engineering University of Twente Enschede Netherlands

Social navigation provides drivers with an advice that aims to shift traffic flows in a network from a user equilibrium to a system optimum. The advice is based on minimizing a combination of the individual travel time and the marginal total travel time in the network. The level of altruism defines the extent to which a driver is willing to sacrifice his own travel time in favor of other drivers. Fuel consumption and CO2 emission are taking into account by converting them into time equivalent. Experimental results for a small network loosely representing the Bay area show that social navigation can reduce time delays by 10%. The reduction is positively correlated with network load, market penetration and level of altruism.

关键词： Navigation Driver circuits Vehicles Fuels Vehicle dynamics Roads Approximation methods

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Improved reconstructions of random media using dilation and erosion processes

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Physical Review E 2011年第5期84卷 056102-056102页

作者： Chase E. Zachary Salvatore Torquato Department of Chemistry 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 Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

By using the most sensitive two-point correlation functions introduced to date, we reconstruct the microstructures of two-phase random media with heretofore unattained accuracy. Such media arise in a host of contexts, including porous and composite media, ecological structures, biological media, and astrophysical structures. The aforementioned correlation functions are special cases of the so-called canonical n-point correlation function Hn and generalize the ones that have been recently employed to advance our ability to reconstruct complex microstructures [Y. Jiao, F. H. Stillinger, and S. Torquato, Proc. Natl. Acad. Sci. 106, 17634 (2009)]. The use of these generalized correlation functions is tantamount to dilating or eroding a reference phase of the target medium and incorporating the additional topological information of the modified media, thereby providing more accurate reconstructions of percolating, filamentary, and other topologically complex microstructures. We apply our methods to a multiply connected “donut” medium and a dilute distribution of “cracks” (a set of essentially zero measure), demonstrating improved accuracy in both cases with implications for higher-dimensional and biconnected two-phase systems. The high information content of the generalized two-point correlation functions suggests that it would be profitable to explore their use to characterize the structural and physical properties of not only random media, but also molecular systems, including structural glasses.

关键词： FUNCTIONS (mathematics) MICROSTRUCTURE TOPOLOGY COMPOSITE materials PROBABILITY theory STATISTICS

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