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Comprehensive analysis of compositional interface fluctuations in planar lipid bilayer membranes

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： Dispersions

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Towards a mathematical understanding of neural network-based machine learning: What we know and what we don't

arXiv

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arXiv 2020年

作者： Weinan, E. Ma, Chao Wojtowytsch, Stephan Wu, Lei Department of Mathematics Princeton University United States Program in Applied and Computational Mathematics Princeton University United States Department of Mathematics Stanford University United States Beijing Institute of Big Data Research China

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Landscape of unitary transformations in controlled quantum dynamics

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Physical Review A 2009年第1期79卷 013422-013422页

作者： Tak-San Ho Jason Dominy Herschel Rabitz Department of Chemistry Princeton University Princeton NJ 08544-1009 United States Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544-1000 United States

We consider the control problem of generating unitary transformations, which is especially relevant to current research in quantum information processing and computing, in contrast to the usual state-to-state or the more general observable expectation value control problems. A previous analysis of optimal control landscapes for unitary transformations from a kinematic perspective in the finite-dimensional unitary matrices is extended to a dynamical one in the infinite-dimensional function space of the time-dependent external field. The underlying dynamical landscape is defined as the Frobenius square norm of the difference between the control unitary matrix and the target matrix. A nonsingular adaptation matrix is introduced to provide additional freedom for exploring and manipulating key features, specifically the slope and curvature, of the control landscapes. The dynamical analysis reveals many essential geometric features of optimal control landscapes for unitary transformations, including bounds on the local landscape slope and curvature. Close examination of the curvatures at the critical points shows that the unitary transformation control landscapes are free of local traps and proper choices of the adaptation matrix may facilitate the search for optimal control fields producing desired unitary transformations, in particular, in the neighborhood of the global extrema.

关键词： Linear transformations

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Lipid Microdomains: Structural Correlations, Fluctuations, and Formation Mechanisms

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Physical Review Letters 2010年第11期104卷 118101-118101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) Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Compositional lipid microdomains (“lipid rafts”) in mammalian plasma membranes are believed to facilitate many important cellular processes. While several physically distinct scenarios predicting the presence of finite-sized microdomains in vivo have been proposed in the past, direct experimental verification or falsification of model predictions has remained elusive. Herein, we demonstrate that the combination of the spatial correlation and temporal fluctuation spectra of the lipid domains can be employed to unambiguously differentiate between the existing theoretical scenarios. Furthermore, the differentiation of the raft formation mechanisms using this methodology can be achieved by collecting data at physiologically relevant conditions without the need to tune control parameters.

关键词： Cell membranes

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Critical dynamics in multicomponent lipid membranes

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Physical Review E 2009年第2期80卷 020902(R)-020902(R)页

作者： 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

The formation and dynamics of spatially extended compositional domains in multicomponent lipid membranes both in vivo and in vitro lie at the heart of many important biological and biophysical phenomena. While the thermodynamic basis for domain formation has been explored extensively in the past, the roles of membrane and exterior fluid hydrodynamics on domain formation kinetics have received less attention. A case in point is the impact of hydrodynamics on the dynamics of compositional heterogeneities in lipid membranes in the vicinity of a critical point. In this Rapid Communication it is argued that the asymptotic dynamic behavior of a lipid membrane system in the vicinity of a critical point is strongly influenced by hydrodynamic interactions. More specifically, a mode-coupling argument is developed which predicts a scaling behavior of lipid transport coefficients near the critical point for both symmetric and asymmetric bilayers immersed in a bulk fluid.

关键词： Hydrodynamics

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The Nystrom Extension for Signals Defined on a Graph

The Nystrom Extension for Signals Defined on a Graph

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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Ayelet Heimowitz Yonina C. Eldar The Program in Applied and Computational Mathematics Princeton University Princeton NJ USA Department of Electrical Engineering Technion Haifa Israel

ISBN: (纸本)9781538646595

In this paper we introduce a computationally efficient solution to the problem of graph signal interpolation. Our solution is derived using the Nyström extension and is due to the properties of the Markov matrix which we use as our graph shift operator, inspired by diffusion maps. We focus on graph signals that are smooth over the graph. This assumption cements the relationship between the graph and the graph signal. We experimentally verify our suggested framework on the MNIST data set of handwritten digits.

关键词： Markov processes Signal processing Interpolation Laplace equations Symmetric matrices Image edge detection Eigenvalues and eigenfunctions

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Geometrical ambiguity of pair statistics. II. Heterogeneous media

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Physical Review E 2010年第1期82卷 011106-011106页

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

In the first part of this series of two papers [Y. Jiao, F. H. Stillinger, and S. Torquato, Phys. Rev. E 81, 011105 (2010)], we considered the geometrical ambiguity of pair statistics associated with point configurations. Here we focus on the analogous problem for heterogeneous media (materials). Heterogeneous media are ubiquitous in a host of contexts, including composites and granular media, biological tissues, ecological patterns, and astrophysical structures. The complex structures of heterogeneous media are usually characterized via statistical descriptors, such as the n-point correlation function Sn. An intricate inverse problem of practical importance is to what extent a medium can be reconstructed from the two-point correlation function S2 of a target medium. Recently, general claims of the uniqueness of reconstructions using S2 have been made based on numerical studies, which implies that S2 suffices to uniquely determine the structure of a medium within certain numerical accuracy. In this paper, we provide a systematic approach to characterize the geometrical ambiguity of S2 for both continuous two-phase heterogeneous media and their digitized representations in a mathematically precise way. In particular, we derive the exact conditions for the case where two distinct media possess identical S2, i.e., they form a degenerate pair. The degeneracy conditions are given in terms of integral and algebraic equations for continuous media and their digitized representations, respectively. By examining these equations and constructing their rigorous solutions for specific examples, we conclusively show that in general S2 is indeed not sufficient information to uniquely determine the structure of the medium, which is consistent with the results of our recent study on heterogeneous-media reconstruction [Y. Jiao, F. H. Stillinger, and S. Torquato, Proc. Natl. Acad. Sci. U.S.A. 106, 17634 (2009)]. The analytical examples include complex patterns composed of building blo

关键词： Inverse problems

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

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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： Packing

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Densest binary sphere packings

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Physical Review E 2012年第2期85卷 021130-021130页

作者： Adam B. Hopkins Frank H. Stillinger Salvatore Torquato Department of Chemistry 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 binary sphere packings in the α-x plane of small to large sphere radius ratio α and small sphere relative concentration x have historically been very difficult to determine. Previous research had led to the prediction that these packings were composed of a few known “alloy” phases including, for example, the AlB2 (hexagonal ω), HgBr2, and AuTe2 structures, and to XYn structures composed of close-packed large spheres with small spheres (in a number ratio of n to 1) in the interstices, e.g., the NaCl packing for n=1. However, utilizing an implementation of the Torquato-Jiao sphere-packing algorithm [Torquato and Jiao, Phys. Rev. E 82, 061302 (2010)], we have discovered that many more structures appear in the densest packings. For example, while all previously known densest structures were composed of spheres in small to large number ratios of one to one, two to one, and very recently three to one, we have identified densest structures with number ratios of seven to three and five to two. In a recent work [Hopkins et al., Phys. Rev. Lett. 107, 125501 (2011)], we summarized these findings. In this work, we present the structures of the densest-known packings and provide details about their characteristics. Our findings demonstrate that a broad array of different densest mechanically stable structures consisting of only two types of components can form without any consideration of attractive or anisotropic interactions. In addition, the structures that we have identified may correspond to currently unidentified stable phases of certain binary atomic and molecular systems, particularly at high temperatures and pressures.

关键词： Spheres

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Hyperuniformity and its generalizations

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Physical Review E 2016年第2期94卷 022122-022122页

作者： 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

Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystal and liquid: They are like perfect crystals in the way they suppress large-scale density fluctuations and yet are like liquids or glasses in that they are statistically isotropic with no Bragg peaks. These exotic states of matter play a vital role in a number of problems across the physical, mathematical as well as biological sciences and, because they are endowed with novel physical properties, have technological importance. Given the fundamental as well as practical importance of disordered hyperuniform systems elucidated thus far, it is natural to explore the generalizations of the hyperuniformity notion and its consequences. In this paper, we substantially broaden the hyperuniformity concept along four different directions. This includes generalizations to treat fluctuations in the interfacial area (one of the Minkowski functionals) in heterogeneous media and surface-area driven evolving microstructures, random scalar fields, divergence-free random vector fields, and statistically anisotropic many-particle systems and two-phase media. In all cases, the relevant mathematical underpinnings are formulated and illustrative calculations are provided. Interfacial-area fluctuations play a major role in characterizing the microstructure of two-phase systems (e.g., fluid-saturated porous media), physical properties that intimately depend on the geometry of the interface, and evolving two-phase microstructures that depend on interfacial energies (e.g., spinodal decomposition). In the instances of random vector fields and statistically anisotropic structures, we show that the standard definition of hyperuniformity must be generalized such that it accounts for the dependence of the relevant spectral functions on the direction in which the origin in Fourier space is approached (nonanalyticities at the origin). Using this analysis, we place some well-known energy spectr

关键词： Amorphous materials Glasses

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