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作者： Nadler, Boaz Lafon, Stephane Coifman, Ronald Kevrekidis, Ioannis G. Department of Computer Science and Applied Mathematics Weizmann Institute of Science Rehovot 76100 Israel Google Inc. United States Department of Mathematics Yale University New Haven CT 06520-8283 United States Department of Chemical Engineering Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 United States

ISBN: (纸本)9783540737490

Spectral embedding and spectral clustering are common methods for non-linear dimensionality reduction and clustering of complex high dimensional datasets. In this paper we provide a diffusion based probabilistic analysis of algorithms that use the normalized graph Laplacian. Given the pairwise adjacency matrix of all points in a dataset, we define a random walk on the graph of points and a diffusion distance between any two points. We show that the diffusion distance is equal to the Euclidean distance in the embedded space with all eigenvectors of the normalized graph Laplacian. This identity shows that characteristic relaxation times and processes of the random walk on the graph are the key concept that governs the properties of these spectral clustering and spectral embedding algorithms. Specifically, for spectral clustering to succeed, a necessary condition is that the mean exit times from each cluster need to be significantly larger than the largest (slowest) of all relaxation times inside all of the individual clusters. For complex, multiscale data, this condition may not hold and multiscale methods need to be developed to handle such situations.

关键词： Relaxation time

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Locality and low-dimensions in the prediction of natural experience from fMRI

Locality and low-dimensions in the prediction of natural exp...

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21st Annual Conference on Neural Information Processing Systems, NIPS 2007

作者： Meyer, François G. Stephens, Greg J. Center for the Study of Brain Mind and Behavior Program in Applied and Computational Mathematics Princeton University United States Center for the Study of Brain Mind and Behavior Department of Physics Princeton University United States

ISBN: (纸本)160560352X

Functional Magnetic Resonance Imaging (fMRI) provides dynamical access into the complex functioning of the human brain, detailing the hemodynamic activity of thousands of voxels during hundreds of sequential time points. One approach towards illuminating the connection between fMRI and cognitive function is through decoding;how do the time series of voxel activities combine to provide information about internal and external experience? Here we seek models of fMRI decoding which are balanced between the simplicity of their interpretation and the effectiveness of their prediction. We use signals from a subject immersed in virtual reality to compare global and local methods of prediction applying both linear and nonlinear techniques of dimensionality reduction. We find that the prediction of complex stimuli is remarkably low-dimensional, saturating with less than 100 features. In particular, we build effective models based on the decorrelated components of cognitive activity in the classically-defined Brodmann areas. For some of the stimuli, the top predictive areas were surprisingly transparent, including Wernicke's area for verbal instructions, visual cortex for facial and body features, and visual-temporal regions for velocity. Direct sensory experience resulted in the most robust predictions, with the highest correlation (c ∼ 0:8) between the predicted and experienced time series of verbal instructions. Techniques based on non-linear dimensionality reduction (Laplacian eigenmaps) performed similarly. The interpretability and relative simplicity of our approach provides a conceptual basis upon which to build more sophisticated techniques for fMRI decoding and offers a window into cognitive function during dynamic, natural experience.

关键词： Forecasting

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Domain Formation in the Plasma Membrane: Roles of Nonequilibrium Lipid Transport and Membrane Proteins

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Physical Review Letters 2008年第17期100卷 178102-178102页

作者： Jun Fan Maria Sammalkorpi 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

Compositional lipid domains (“lipid rafts”) in plasma membranes are believed to be important components of many cellular processes. The mechanisms by which cells regulate the sizes and lifetimes of these spatially extended domains are poorly understood at the moment. Here we show that the competition between phase separation in an immiscible lipid system and active cellular lipid transport processes naturally leads to the formation of such domains. Furthermore, we demonstrate that local interactions with immobile membrane proteins can spatially localize the rafts and lead to further clustering.

关键词： Lipids

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Analytic form for a nonlocal kinetic energy functional with a density-dependent kernel for orbital-free density functional theory under periodic and Dirichlet boundary conditions

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Physical Review B 2008年第4期78卷 045105-045105页

作者： Gregory S. Ho Vincent L. Lignères Emily A. Carter Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544-5263 USA

We derive an analytic form of the Wang-Govind-Carter (WGC) [Wang et al., Phys. Rev. B 60, 16350 (1999)] kinetic energy density functional (KEDF) with the density-dependent response kernel. A real-space aperiodic implementation of the WGC KEDF is then described and used in linear scaling orbital-free density functional theory (OF-DFT) calculations.

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First-principles characterization of Ni diffusion kinetics in β-NiAl

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Physical Review B 2008年第18期78卷 184105-184105页

作者： Kristen A. Marino Emily A. Carter Department of Chemical Engineering Princeton University Princeton New Jersey 08544-5263 USA Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544-5263 USA

First-principles density functional theory calculations are performed to examine five postulated diffusion mechanisms for Ni in NiAl: next-nearest-neighbor (NNN) jumps, the triple defect mechanism, and three variants of the six-jump cycle. In contrast to most previous theoretical work, which employed empirical interatomic potentials, we provide a more accurate nonempirical description of the mechanisms. For each pathway, we calculate the activation energy and the pre-exponential factor for the diffusion constant. Although our quantum mechanics calculations are performed at 0 K, we show that it is critical to include the effect of temperature on the pre-exponential factor. We predict that the triple defect mechanism and [110] six-jump cycle both are likely contributors to Ni diffusion in NiAl since their activation energies and pre-exponential factors are in very good agreement with experimental data. Although the activation energy and pre-exponential factor of NNN jumps agree well with experiment, experimental evidence suggests that this is not a dominant contributor to Ni diffusion. Lastly, the activation energies of the [100] bent and straight six-jump cycles are 1 eV higher than the experimental value, allowing us to exclude both [100] cycle mechanisms.

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Quantum simulation of materials at micron scales and beyond

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Physical Review B 2008年第5期78卷 054118-054118页

作者： Qing Peng Xu Zhang Linda Hung Emily A. Carter Gang Lu Department of Physics and Astronomy California State University Northridge Northridge California USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey USA Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey USA

We present a multiscale modeling approach that can simulate multimillion atoms effectively via density-functional theory. The method is based on the framework of the quasicontinuum (QC) approach with orbital-free density-functional theory (OFDFT) as its sole energetics formulation. The local QC part is formulated by the Cauchy-Born hypothesis with OFDFT calculations for strain energy and stress. The nonlocal QC part is treated by an OFDFT-based embedding approach, which couples OFDFT nonlocal atoms to local region atoms. The method—QCDFT—is applied to a nanoindentation study of an Al thin film, and the results are compared to a conventional QC approach. The results suggest that QCDFT represents a new direction for the quantum simulation of materials at length scales that are relevant to experiments.

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Edge-Stress-Induced Warping of Graphene Sheets and Nanoribbons

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Physical Review Letters 2008年第24期101卷 245501-245501页

作者： V. B. Shenoy C. D. Reddy A. Ramasubramaniam Y. W. Zhang Division of Engineering Brown University Providence Rhode Island 02912 USA Institute of High Performance Computing Singapore 138632 Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Department of Materials Science and Engineering National University of Singapore Singapore 119260

We show that edge stresses introduce intrinsic ripples in freestanding graphene sheets even in the absence of any thermal effects. Compressive edge stresses along zigzag and armchair edges of the sheet cause out-of-plane warping to attain several degenerate mode shapes. Based on elastic plate theory, we identify scaling laws for the amplitude and penetration depth of edge ripples as a function of wavelength. We also demonstrate that edge stresses can lead to twisting and scrolling of nanoribbons as seen in experiments. Our results underscore the importance of accounting for edge stresses in thermal theories and electronic structure calculations for freestanding graphene sheets.

关键词： Nanoribbons

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The Elastic Continuum Limit of the Tight Binding Model

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Chinese Annals of mathematics,Series B 2007年第6期28卷 665-676页

作者： Weinan E Jianfeng LU Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA

The authors consider the simplest quantum mechanics model of solids, the tight binding model, and prove that in the continuum limit, the energy of tight binding model converges to that of the continuum elasticity model obtained using Cauchy-Born rule. The technique in this paper is based mainly on spectral perturbation theory for large matrices.

关键词： Continuum limit Elasticity theory Cauchy-Born rule Tight binding model

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Rate-achievability strategies for two-hop interference flows

Rate-achievability strategies for two-hop interference flows

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Annual Allerton Conference on Communication, Control, and Computing

作者： P.S. Chandrashekhar Thejaswi Amir Bennatan Junshan Zhang Robert Calderbank Douglas Cochran Department of Electrical Engineering Arizona Stare University Tempe 85287 USA Program in Applied and Computational Mathematics (PACM) at Princeton University Princeton NJ USA Department of Electrical Engineering Arizona State University Tempe AZ USA Department of Electrical Engineering Arizona Stare University Tempe AZ USA

We consider a basic model for two-hop transmissions of two information flows which interfere with each other. In this model, two sources simultaneously transmit to two relays (in the first hop), which then simultaneously transmit to two destinations (in the second hop). While the transmission during the first hop is essentially the transmission over a classical interference channel, the transmission in the second hop enjoys an interesting advantage. Specifically, as a byproduct of the Han-Kobayashi transmission scheme applied to the first hop, each of the relays (in the second hop) has access to some of the data that is intended to the other destination, in addition to its own data. As recently observed by Simeone et al., this opens the door to cooperation between the relays. In this paper, we observe that the cooperation can take the form of distributed MIMO broadcast, thus greatly enhancing its effectiveness at high SNR. However, since each relay is only aware of part of the data beyond its own, full cooperation is not possible. We propose several approaches that combine MIMO broadcast strategies (including ldquodirty paperrdquo) with standard non-cooperative strategies for the interference channel. Numerical results are provided, which indicate that our approaches provide substantial benefits at high SNR.

关键词： Relays Interference channels Decoding MIMO Broadcasting Context Wireless networks mathematics Electronic mail

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Negative Poisson’s Ratio Materials via Isotropic Interactions

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Physical Review Letters 2008年第8期101卷 085501-085501页

作者： Mikael C. Rechtsman Frank H. Stillinger Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics and PRISM Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08544 USA

We show that under tension a classical many-body system with only isotropic pair interactions in a crystalline state can, counterintuitively, have a negative Poisson’s ratio, or auxetic behavior. We derive the conditions under which the triangular lattice in two dimensions and lattices with cubic symmetry in three dimensions exhibit a negative Poisson’s ratio. In the former case, the simple Lennard-Jones potential can give rise to auxetic behavior. In the latter case, a negative Poisson’s ratio can be exhibited even when the material is constrained to be elastically isotropic.

关键词： Lennard-Jones potential

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