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Static structural signatures of nearly jammed disordered and ordered hard-sphere packings: Direct correlation function

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Physical Review E 2016年第3期94卷 032902-032902页

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

The nonequilibrium process by which hard-particle systems may be compressed into disordered, jammed states has received much attention because of its wide utility in describing a broad class of amorphous materials. While dynamical signatures are known to precede jamming, the task of identifying static structural signatures indicating the onset of jamming have proven more elusive. The observation that compressing hard-particle packings towards jamming is accompanied by an anomalous suppression of density fluctuations (termed “hyperuniformity”) has paved the way for the analysis of jamming as an “inverted critical point” in which the direct correlation function c(r), rather than the total correlation function h(r), diverges. We expand on the notion that c(r) provides both universal and protocol-specific information as packings approach jamming. By considering the degree and position of singularities (discontinuities in the nth derivative) as well as how they are changed by the convolutions found in the Ornstein-Zernike equation, we establish quantitative statements about the structure of c(r) with regards to singularities it inherits from h(r). These relations provide a concrete means of identifying features that must be expressed in c(r) if one hopes to reproduce various details in the pair correlation function accurately and provide stringent tests on the associated numerics. We also analyze the evolution of systems of three-dimensional monodisperse hard spheres of diameter D as they approach ordered and disordered jammed configurations. For the latter, we use the Lubachevsky-Stillinger (LS) molecular dynamics and Torquato-Jiao (TJ) sequential linear programming algorithms, which both generate disordered packings, but can show perceptible structural differences. We identify a short-ranged scaling c(r)∝−1/r as r→0 that accompanies the formation of the delta function at c(D) that indicates the formation of contacts in all cases, and show that this scaling behavior is,

关键词： Jamming

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Critical slowing down and hyperuniformity on approach to jamming

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Physical Review E 2016年第1期94卷 012902-012902页

作者： Steven Atkinson Ge Zhang Adam B. Hopkins Salvatore Torquato Department of Chemistry Department of Physics Princeton Center for Theoretical Science Program of Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

Hyperuniformity characterizes a state of matter that is poised at a critical point at which density or volume-fraction fluctuations are anomalously suppressed at infinite wavelengths. Recently, much attention has been given to the link between strict jamming (mechanical rigidity) and (effective or exact) hyperuniformity in frictionless hard-particle packings. However, in doing so, one must necessarily study very large packings in order to access the long-ranged behavior and to ensure that the packings are truly jammed. We modify the rigorous linear programming method of Donev et al. [J. Comput. Phys. 197, 139 (2004)] in order to test for jamming in putatively collectively and strictly jammed packings of hard disks in two dimensions. We show that this rigorous jamming test is superior to standard ways to ascertain jamming, including the so-called “pressure-leak” test. We find that various standard packing protocols struggle to reliably create packings that are jammed for even modest system sizes of N≈103 bidisperse disks in two dimensions; importantly, these packings have a high reduced pressure that persists over extended amounts of time, meaning that they appear to be jammed by conventional tests, though rigorous jamming tests reveal that they are not. We present evidence that suggests that deviations from hyperuniformity in putative maximally random jammed (MRJ) packings can in part be explained by a shortcoming of the numerical protocols to generate exactly jammed configurations as a result of a type of “critical slowing down” as the packing's collective rearrangements in configuration space become locally confined by high-dimensional “bottlenecks” from which escape is a rare event. Additionally, various protocols are able to produce packings exhibiting hyperuniformity to different extents, but this is because certain protocols are better able to approach exactly jammed configurations. Nonetheless, while one should not generally expect exact hyperuniformity for d

关键词： Granular materials Packing & jamming problems

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Systems-level approach to uncovering diffusive states and their transitions from single-particle trajectories

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Physical Review E 2016年第5期94卷 052412-052412页

作者： Peter K. Koo Simon G. J. Mochrie Department of Physics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

The stochastic motions of a diffusing particle contain information concerning the particle's interactions with binding partners and with its local environment. However, an accurate determination of the underlying diffusive properties, beyond normal diffusion, has remained challenging when analyzing particle trajectories on an individual basis. Here, we introduce the maximum-likelihood estimator (MLE) for confined diffusion and fractional Brownian motion. We demonstrate that this MLE yields improved estimation over traditional mean-square displacement analyses. We also introduce a model selection scheme (that we call mleBIC) that classifies individual trajectories to a given diffusion mode. We demonstrate the statistical limitations of classification via mleBIC using simulated data. To overcome these limitations, we introduce a version of perturbation expectation-maximization (pEMv2), which simultaneously analyzes a collection of particle trajectories to uncover the system of interactions that give rise to unique normal and/or non-normal diffusive states within the population. We test and evaluate the performance of pEMv2 on various sets of simulated particle trajectories, which transition among several modes of normal and non-normal diffusion, highlighting the key considerations for employing this analysis methodology.

关键词： Fractional Brownian motion Imaging & optical processing

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Signatures of quantum spin liquid in kitaev-like frustrated magnets

arXiv

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arXiv 2017年

作者： Gohlke, Matthias Wachtel, Gideon Yamaji, Youhei Pollmann, Frank Kim, Yong Baek Max-Planck-Institut für Physik Komplexer Systeme Dresden01187 Germany Department of Physics University of Toronto TorontoONM5S 1A7 Canada Department of Applied Physics University of Tokyo Hongo Bunkyo-ku Tokyo113-8656 Japan JST PRESTO Hongo Bunkyo-ku Tokyo113-8656 Japan Technische Universität München Garching85747 Germany Canadian Institute for Advanced Research/Quantum Materials Program TorontoONMSG 1Z8 Canada School of Physics Korea Institute for Advanced Study Seoul130-722 Korea Republic of

Motivated by recent experiments on α-RuCl3, we investigate a possible quantum spin liquid ground state of the honeycomb-lattice spin model with bond-dependent interactions. We consider the K - Γ model, where K and Γ represent the Kitaev and symmetric-anisotropic interactions between spin-1/2 moments on the honeycomb lattice. Using the infinite density matrix renormalization group (iDMRG), we provide compelling evidence for the existence of quantum spin liquid phases in an extended region of the phase diagram. In particular, we use transfer matrix spectra to show the evolution of two-particle excitations with well-defined two-dimensional dispersion, which is a strong signature of quantum spin liquid. These results are compared with predictions from Majorana mean-field theory and used to infer the quasiparticle excitation spectra. Further, we compute the dynamical structure factor using finite size cluster computations and show that the results resemble the scattering continuum seen in neutron scattering experiments on α-RuCl3. We discuss these results in light of recent and future experiments. Copyright © 2017, The Authors. All rights reserved.

关键词： Honeycomb structures

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Edge states in dynamical superlattices

arXiv

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arXiv 2017年

作者： Zhang, Yiqi Kartashov, Yaroslav V. Li, Feng Zhang, Zhaoyang Zhang, Yanpeng Belić, Milivoj R. Xiao, Min Key Laboratory for Physical Electronics and Devices of the Ministry of Education & Shaanxi Key Lab of Information Photonic Technique Xi’an Jiaotong University Xi’an710049 China Department of Applied Physics School of Science Xi’an Jiaotong University Xi’an710049 China 08860 Spain Institute of Spectroscopy Russian Academy of Sciences Troitsk Moscow Region142190 Russia Department of Physics University of Bath BathBA2 7AY United Kingdom Science Program Texas A&M University at Qatar P.O. Box 23874 Doha Qatar Department of Physics University of Arkansas FayettevilleAR72701 United States National Laboratory of Solid State Microstructures and School of Physics Nanjing University Nanjing210093 China

We address edge states and rich localization regimes available in the one-dimensional (1D) dynamically modulated superlattices, both theoretically and numerically. In contrast to conventional lattices with straight waveguides, the quasi-energy band of infinite modulated superlattice is periodic not only in the transverse Bloch momentum, but it also changes periodically with increase of the coupling strength between waveguides. Due to collapse of quasi-energy bands dynamical superlattices admit known dynamical localization effect. If, however, such a lattice is truncated, periodic longitudinal modulation leads to appearance of specific edge states that exist within certain periodically spaced intervals of coupling constants. We discuss unusual transport properties of such truncated superlattices and illustrate different excitation regimes and enhanced robustness of edge states in them, that is associated with topology of the quasi-energy band. Copyright © 2017, The Authors. All rights reserved.

关键词： Lattice constants

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Low field nuclear polarization using nitrogen vacancy centers in diamonds

arXiv

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arXiv 2017年

作者： Hovav, Y. Naydenov, B. Jelezko, F. Bar-Gill, N. Dept. of Applied Physics Rachel and Selim School of Engineering Hebrew University Jerusalem9190401 Israel Institute of Quantum Optics Ulm University Albert Einstein Allee 11 UlmD-89081 Germany Albert Einstein Allee 11 UlmD-89081 Germany Racah Institute of Physics Hebrew University of Jerusalem Jerusalem9190401 Israel Quantum Information Science Program Canadian Institute for Advanced Research 661 University Ave. TorontoONM5G 1M1 Canada

It was recently demonstrated that bulk nuclear polarization can be obtained using Nitrogen Vacancy (NV) color centers in diamonds, even at ambient conditions. This is based on the optical polarization of the NV electron spin, and using several polarization transfer methods. One such method is the NOVEL sequence, where a spin-locked sequence is applied on the NV spin, with a microwave power equal to the nuclear precession frequency. This was performed at relatively high fields, to allow for both polarization transfer and noise decoupling. As a result, this scheme requires accurate magnetic field alignment in order preserve the NV properties. Such a requirement may be undesired or impractical in many practical scenareios. Here we present a new sequence, termed the refocused NOVEL, which can be used for polarization transfer (and detection) even at low fields. Numerical simulations are performed, taking into account both the spin Hamiltonian and spin-decoherence, and we show that, under realistic parameters, it can outperform the NOVEL sequence. Copyright © 2017, The Authors. All rights reserved.

关键词： Color centers

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The Effects of Chemical Fixation on the Cellular Nanostructure: A Correlative Study of Back-Scattered Interference Spectrometry Microscopy and TEM

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Microscopy and Microanalysis 2016年第S3期22卷 234-235页

作者： Yue Li Luay Almassalha John Chandler Yolanda Cyrus Reiner Bleher Hariharan Subramanian Igal Szleifer Vadim Backman Vinayak Dravid Applied Physics Program Northwestern University Interdisciplinary Biological Sciences Graduate Program Northwestern University Biomedical Engineering Department Northwestern University Materials Sciences and Engineering Department Northwestern University Chemistry of Life Processes Institute Northwestern University

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Deep Learning Models of the Retinal Response to Natural Scenes 16

Deep Learning Models of the Retinal Response to Natural Scen...

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Annual Conference on Neural Information Processing Systems

作者： Lane T. McIntosh Niru Maheswaranathan Aran Nayebi Surya Ganguli Stephen A. Baccus Neurosciences PhD Program Stanford University Department of Applied Physics Stanford UniversityNeurobiology Department Stanford University Neurobiology Department Stanford University

ISBN: (纸本)9781510838819

A central challenge in sensory neuroscience is to understand neural computations and circuit mechanisms that underlie the encoding of ethologically relevant, natural stimuli. In multilayered neural circuits, nonlinear processes such as synaptic transmission and spiking dynamics present a significant obstacle to the creation of accurate computational models of responses to natural stimuli. Here we demonstrate that deep convolutional neural networks (CNNs) capture retinal responses to natural scenes nearly to within the variability of a cell's response, and are markedly more accurate than linear-nonlinear (LN) models and Generalized Linear Models (GLMs). Moreover, we find two additional surprising properties of CNNs: they are less susceptible to overfitting than their LN counterparts when trained on small amounts of data, and generalize better when tested on stimuli drawn from a different distribution (e.g. between natural scenes and white noise). An examination of the learned CNNs reveals several properties. First, a richer set of feature maps is necessary for predicting the responses to natural scenes compared to white noise. Second, temporally precise responses to slowly varying inputs originate from feedforward inhibition, similar to known retinal mechanisms. Third, the injection of latent noise sources in intermediate layers enables our model to capture the sub-Poisson spiking variability observed in retinal ganglion cells. Fourth, augmenting our CNNs with recurrent lateral connections enables them to capture contrast adaptation as an emergent property of accurately describing retinal responses to natural scenes. These methods can be readily generalized to other sensory modalities and stimulus ensembles. Overall, this work demonstrates that CNNs not only accurately capture sensory circuit responses to natural scenes, but also can yield information about the circuit's internal structure and function.

关键词： natural scenes Stimuli circuit response Retinaldehyde feature map Computational modeling Noise sources

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In-situThermal Testing on Nanostructures in TEM

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Microscopy and Microanalysis 2016年第S3期22卷 770-771页

作者： Hua Guo Will J. Hardy Panpan Zhou Douglas Natelson Jun Lou Department of Materials Science and NanoEngineering Rice University Houston Texas USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas USA Department of Physics and Astronomy Rice University Houston Texas USA

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