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Coarse molecular-dynamics determination of the onset of structural transitions: Melting of crystalline solids

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Physical Review B 2006年第13期74卷 132201-132201页

作者： Miguel A. Amat Ioannis G. Kevrekidis Dimitrios Maroudas Department of Chemical Engineering University of Massachusetts Amherst Massachusetts 01003 USA Department of Chemical Engineering and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach provides a means for constructing effective free-energy landscapes of structural transitions in condensed matter. The predictions of the approach for the thermodynamic melting point of a model silicon system are in excellent agreement with those of “traditional” techniques for melting-point calculations, as well as with literature values.

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SUBSPACE METHOD OF MOMENTS FOR AB INITIO 3-D SINGLE-PARTICLE CRYO-EM RECONSTRUCTION

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arXiv 2024年

作者： Hoskins, Jeremy Khoo, Yuehaw Mickelin, Oscar Singer, Amit Wang, Yuguan Departments of Statistics and CCAM University of Chicago Chicago IL 60637 USA Departments of Statistics and CCAM University of Chicago Chicago IL 60637 USA Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA Program in Applied and Computational Mathematics and Department of Mathematics Princeton University Princeton NJ 08544 USA Departments of Statistics University of Chicago Chicago IL 60637 USA

Cryo-electron microscopy (Cryo-EM) is a widely-used technique for recovering the 3-D structure of biological molecules from a large number of experimentally generated noisy 2-D tomographic projection images of the 3-D structure, taken from unknown viewing angles. Through computationally intensive algorithms, these observed images are processed to reconstruct the 3-D structures. Many popular computational methods rely on estimating the unknown angles as part of the reconstruction process, which becomes particularly challenging at low signal-to-noise ratio. The method of moments (MoM) offers an alternative approach that circumvents the estimation of viewing angles of individual projection images by instead estimating the underlying distribution of the viewing angles, and is robust to noise given sufficiently many images. However, the method of moments typically entails computing high-order moments of the projection images, incurring significant storage and computational costs. To mitigate this, we propose a new approach called the subspace method of moments (subspace MoM), which compresses the first three moments using data-driven low-rank tensor techniques as well as expansion into a suitable function basis. The compressed moments can be efficiently computed from the set of projection images using numerical quadrature and can be employed to jointly recover the 3-D structure and the distribution of viewing angles. We illustrate the practical applicability of the subspace MoM in numerical experiments using up to the third-order moment, which significantly improves the resolution of MoM reconstructions compared to previous approaches. Copyright © 2024, The Authors. All rights reserved.

关键词： Image reconstruction

Volume growth, curvature, and buser-type inequalities in graphs

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arXiv 2018年

作者： Benson, Brian Ralli, Peter Tetali, Prasad Department of Mathematics University of California RiversideCA United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States School of Mathematics Georgia Institute of Technology AtlantaGA United States

We study the volume growth of metric balls as a function of the radius in discrete spaces, and focus on the relationship between volume growth and discrete curvature. We improve volume growth bounds under a lower bound on the so-called Ollivier curvature, and discuss similar results under other types of discrete Ricci curvature. Following recent work in the continuous setting of Riemannian manifolds (by the first author), we then bound the eigenvalues of the Laplacian of a graph under bounds on the volume growth. In particular, λ2of the graph can be bounded using a weighted discrete Hardy inequality and the higher eigenvalues of the graph can be bounded by the eigenvalues of a tridiagonal matrix times a multiplicative factor, both of which only depend on the volume growth of the graph. As a direct application, we relate the eigenvalues to the Cheeger isoperimetric constant. Using these methods, we describe classes of graphs for which the Cheeger inequality is tight on the second eigenvalue. We also describe a method for proving Buser's Inequality in graphs, particularly under a lower bound assumption on curvature. Copyright © 2018, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

Recursive projection-aggregation decoding of Reed-Muller codes

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arXiv 2019年

作者： Ye, Min Abbe, Emmanuel Mathematics Institute School of Computer and Communication Sciences EPFL Switzerland Program in Applied and Computational Mathematics Department of Electrical Engineering Princeton University Department of Electrical Engineering Princeton University United States

We propose a new class of efficient decoding algorithms for Reed-Muller (RM) codes over binary-input memoryless channels. The algorithms are based on projecting the code on its cosets, recursively decoding the projected codes (which are lower-order RM codes), and aggregating the reconstructions (e.g., using majority votes). We further provide extensions of the algorithms using list-decoding and code concatenation techniques. We run our main algorithm for AWGN channels and Binary Symmetric Channels at the short code length (≤ 1024) and low code rate (≤ 0.5) regime. Simulation results show that the new algorithm not only outperforms the previous decoding algorithms for RM codes, it also outperforms the optimal decoder for polar codes (SCL+CRC) with the same parameters by a wide margin. The performance of the new algorithm for RM codes in those regimes is in fact close to that of the maximal likelihood decoder. Finally, the new decoder naturally allows for parallel implementations. Copyright © 2019, The Authors. All rights reserved.

关键词： Decoding

Random conical tilt reconstruction without particle picking in cryo-electron microscopy

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arXiv 2021年

作者： Lan, Ti-Yen Boumal, Nicolas Singer, Amit Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Institute of Mathematics EPFL LausanneCH-1015 Switzerland Department of Mathematics Princeton University PrincetonNJ08544 United States

We propose a method to reconstruct the 3-D molecular structure from micrographs collected at just one sample tilt angle in the random conical tilt scheme in cryo-electron microscopy. Our method uses autocorrelation analysis on the micrographs to estimate features of the molecule which are invariant under certain nuisance parameters such as the positions of molecular projections in the micrographs. This enables us to reconstruct the molecular structure directly from micrographs, completely circumventing the need for particle picking. We demonstrate reconstructions with simulated data and investigate the effect of the missing-cone region. These results show promise to reduce the size limit for single particle reconstruction in cryo-electron microscopy. © 2021, CC BY.

关键词： Electron microscopes

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

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Physical Review Letters 2018年第14期120卷 143001-143001页

作者： Linfeng Zhang Jiequn Han Han Wang Roberto Car Weinan E Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA and Center for Data Science Beijing International Center for Mathematical Research Peking University Beijing Institute of Big Data Research Beijing 100871 People’s Republic of China

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

关键词： Classical statistical mechanics Density functional theory First-principles calculations Interatomic & molecular potentials Learning Neuronal networks Potential energy surfaces Solid-state chemistry Thermal properties Van der Waals interaction Molecular dynamics

Structural Effects and Aggregation in a Social-Network Model of Natural Resource Consumption

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IFAC-PapersOnLine 2017年第1期50卷 7675-7680页

作者： Manzoor T. Rovenskaya E. Muhammad A. Department of Electrical Engineering Lahore University of Management Sciences (LUMS) Lahore Pakistan Center for Water Informatics & Technology (WIT) Lahore University of Management Sciences (LUMS) Pakistan Advanced Systems Analysis Program International Institute for Applied Systems Analysis (IIASA) Laxenburg Austria Faculty of Computational Mathematics and Cybernetics Lomonosov Moscow State University Moscow Russian Federation

In this paper we consider a networked system of natural-resource consumption, where the agents are governed by a recently reported model of consumer psychology Dynamics of the consumption for each agent are influenced by the state of the resource and consumption of her neighbors. The process is parameterized by the psychological characteristics of each agent. This study extends the original model to incorporate the underlying network topology and explores the effects of aggregation via densely-connected communities present in the network. The exercise yields new interpretations of the predictions made by the original model in context of the influence network. We present aggregation mechanisms first for certain canonical structures of the consuming population and later on for a class of non-canonically structured populations. In the end we present an approximate aggregation scheme for populations where only some inaccurate information of the consumer characteristics is available. © 2017

关键词： Control in economics identification of environmental systems Modeling Multi-agent systems Natural resources management Social Networks

Pair correlation function characteristics of nearly jammed disordered and ordered hard-sphere packings

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Physical Review E 2005年第1期71卷 011105-011105页

作者： Aleksandar Donev Salvatore Torquato Frank H. Stillinger Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA PRISM Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA

We study the approach to jamming in hard-sphere packings and, in particular, the pair correlation function g2(r) around contact, both theoretically and computationally. Our computational data unambiguously separate the narrowing δ-function contribution to g2 due to emerging interparticle contacts from the background contribution due to near contacts. The data also show with unprecedented accuracy that disordered hard-sphere packings are strictly isostatic: i.e., the number of exact contacts in the jamming limit is exactly equal to the number of degrees of freedom, once rattlers are removed. For such isostatic packings, we derive a theoretical connection between the probability distribution of interparticle forces Pf(f), which we measure computationally, and the contact contribution to g2. We verify this relation for computationally generated isostatic packings that are representative of the maximally random jammed state. We clearly observe a maximum in Pf and a nonzero probability of zero force, shedding light on long-standing questions in the granular-media literature. We computationally observe an unusual power-law divergence in the near-contact contribution to g2, persistent even in the jamming limit, with exponent −0.4 clearly distinguishable from previously proposed inverse-square-root divergence. Additionally, we present high-quality numerical data on the two discontinuities in the split-second peak of g2 and use a shared-neighbor analysis of the graph representing the contact network to study the local particle clusters responsible for the peculiar features. Finally, we present the computational data on the contact contribution to g2 for vacancy-diluted fcc crystal packings and also investigate partially crystallized packings along the transition from maximally disordered to fully ordered packings. We find that the contact network remains isostatic even when ordering is present. Unlike previous studies, we find that ordering has a significant impact on the sh

关键词： MOLECULAR-DYNAMICS SIMULATION DISK PACKINGS CRYSTALLIZATION DISTRIBUTIONS GENERATION PARTICLES PRESSURE

Designed interaction potentials via inverse methods for self-assembly

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Physical Review E 2006年第1期73卷 011406-011406页

作者： Mikael Rechtsman Frank 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

We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and greater control over colloidal interaction potentials, we propose and discuss two computational algorithms that search for optimal potentials for self-assembly of a given target configuration. The first optimizes the potential near the ground state and the second near the melting point. We begin by applying these techniques to assembling open structures in two dimensions (square and honeycomb lattices) using only circularly symmetric pair interaction potentials; we demonstrate that the algorithms do indeed cause self-assembly of the target lattice. Our approach is distinguished from previous work in that we consider (i) lattice sums, (ii) mechanical stability (phonon spectra), and (iii) annealed Monte Carlo simulations. We also devise circularly symmetric potentials that yield chainlike structures as well as systems of clusters.

关键词： THERMAL-EXPANSION MICROSTRUCTURES SYSTEM PORES MODEL