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A Model of Fluid-Structure and Biochemical Interactions for Applications to Subclinical Leaflet Thrombosis

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arXiv 2022年

作者： Barrett, Aaron Brown, Jordan A. Smith, Margaret Anne Woodward, Andrew Vavalle, John P. Kheradvar, Arash Griffith, Boyce E. Fogelson, Aaron L. Department of Mathematics University of Utah Salt Lake CityUT United States Department of Mathematics University of North Carolina Chapel HillNC United States Advanced Medical Imaging Lab University of North Carolina Medical Center Chapel HillNC United States University of North Carolina School of Medicine Chapel HillNC United States Division of Cardiology Department of Medicine University of North Carolina Chapel HillNC United States Department of Biomedical Engineering University of California Irvine IrvineCA United States Department of Mathematics Applied Physical Sciences and Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina Chapel HillNC United States McAllister Heart Institute University of North Carolina Chapel HillNC United States Department of Mathematics and Biomedical Engineering University of Utah Salt Lake CityUT United States

Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient ischemic attacks and strokes and can progress to clinical leaflet thrombosis. SLT following aortic valve replacement also may be related to subsequent structural valve deterioration, which can impair the durability of the valve replacement. Because of the difficulty in clinical imaging of SLT, models are needed to determine the mechanisms of SLT and could eventually predict which patients will develop SLT. To this end, we develop methods to simulate leaflet thrombosis that combine fluid-structure interaction and a simplified thrombosis model that allows for deposition along the moving leaflets. Additionally, this model can be adapted to model deposition or absorption along other moving boundaries. We present convergence results and quantify the model's ability to realize changes in valve opening and pressures. These new approaches are an important advancement in our tools for modeling thrombosis in which they incorporate both adhesion to the surface of the moving leaflets and feedback to the fluid-structure interaction. © 2022, CC BY-SA.

关键词： Deposition

Potential of fungal thermostable alpha amylase enzyme isolated from Hot springs of Central Anatolia(Turkey)in wheat bread quality

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Food Bioscience 2022年第1期45卷 214-222页

作者： Arzu Unal Asiye Seis Subasi Semra Malkoc Ijlal Ocak SElif Korcan Elif Yetilmezer Seyhun Yurdugül Hülya Yaman Turgay Sanal Alaettin Keceli Igdır University Faculty of AgricultureDepartment of Agricultural BiotechnologyI˘gdırTurkey Ministry of Agriculture and Forestry Field Crops Central Research Institute Department of Quality and TechnologyAnkaraTurkey Eskisehir Technical University Faculty of EngineeringDepartment of Environmental EngineeringEskisehirTurkey Afyon Kocatepe University Faculty of EducationDepartment of Mathematics and Science EducationDivision of Science EducationAfyonTurkey Usak University Vocational School of Health ServicesMedical Laboratory Techniques ProgramUsakTurkey Ministry of Agriculture and Forestry Field Crops Central Research Institute Department of BiotechnologyAnkaraTurkey Bolu Abant Izzet Baysal University Faculty of Arts and ScienceDepartment of BiologyBoluTurkey Bolu Abant Izzet Baysal University Vocational School of the Technical Sciences of BoluFood Technology ProgramBoluTurkey Pamukkale University School of Applied SciencesDepartment of Organic Farming Business ManagementDenizliTurkey

Many industrial processes may quickly proceed with biotechnological and enzymatic *** and production facilitator properties of enzymes have provided variable advantages for ***,enzyme utilization has become inevitable for industry and supplied financial advantages in case of the high energy requirement *** the study,the amylase enzymes were isolated from thermal spring sources,and the effect on bread quality was ***,fungal amylases were isolated from thermal spring sources(29-98◦C)in various places around *** determining the functional properties of amylase enzymes,the most active enzyme was used in bread production to examine their effect on bread *** maximum alpha-amylase activity(38.6 U/mg)has been detected in Aspergillus niger G 2-1 *** compared with the commercially available one,native alpha-amylase increased the bread volume.A significant difference(p<0.01)was found in the color properties and size of the bread between microbial produced in this study and commercially produced *** ppm alpha-amylase addition showed the optimum bread properties for dough processing.

关键词： Alpha-amylase Thermal spring Quality of bread Commercial enzymes

RANDOMLY AGGREGATED LEAST SQUARES FOR SUPPORT RECOVERY

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arXiv 2020年

作者： Steinerberger, Stefan Lindenbaum, Ofir Program in Applied Mathematics Yale University New HavenCT06511 United States Department of Mathematics Yale University New HavenCT06511 United States

We study the problem of exact support recovery: given an (unknown) vector θ ∈ {−1, 0, 1}D, we are given access to the noisy measurement y = Xθ + ω, where X ∈ RN×D is a (known) Gaussian matrix and the noise ω ∈ RN is an (unknown) Gaussian vector. How small we can choose N and still reliably recover the support of θ? We present RAWLS (Randomly Aggregated Unweighted Least Squares Support Recovery): the main idea is to take random subsets of the N equations, perform a least squares recovery over this reduced bit of information and then average over many random subsets. We show that the proposed procedure can provably recover an approximation of θ and demonstrate its use in support recovery through numerical examples. Copyright © 2020, The Authors. All rights reserved.

关键词： Recovery

Biwhitening reveals the rank of a count matrix

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arXiv 2021年

作者： Landa, Boris Zhang, Thomas T.C.K. Kluger, Yuval Program in Applied Mathematics Yale University United States Department of Electrical and Systems Engineering University of Pennsylvania United States Interdepartmental Program in Computational Biology and Bioinformatics Yale University United States Department of Pathology Yale University School of Medicine United States

Estimating the rank of a corrupted data matrix is an important task in data analysis, most notably for choosing the number of components in PCA. Significant progress on this task was achieved using random matrix theory by characterizing the spectral properties of large noise matrices. However, utilizing such tools is not straightforward when the data matrix consists of count random variables, e.g., Poisson, in which case the noise can be heteroskedastic with an unknown variance in each entry. In this work, we consider a Poisson random matrix with independent entries, and propose a simple procedure termed biwhitening for estimating the rank of the underlying signal matrix (i.e., the Poisson parameter matrix) without any prior knowledge. Our approach is based on the key observation that one can scale the rows and columns of the data matrix simultaneously so that the spectrum of the corresponding noise agrees with the standard Marchenko-Pastur (MP) law, justifying the use of the MP upper edge as a threshold for rank selection. Importantly, the required scaling factors can be estimated directly from the observations by solving a matrix scaling problem via the Sinkhorn-Knopp algorithm. Aside from the Poisson, our approach is extended to families of distributions that satisfy a quadratic relation between the mean and the variance, such as the generalized Poisson, binomial, negative binomial, gamma, and many others. This quadratic relation can also account for missing entries in the data. We conduct numerical experiments that corroborate our theoretical findings, and showcase the advantage of our approach for rank estimation in challenging regimes. Furthermore, we demonstrate the favorable performance of our approach on several real datasets of single-cell RNA sequencing (scRNA-seq), High-Throughput Chromosome Conformation Capture (Hi-C), and document topic *** Codes 62H12, 62H25. Copyright © 2021, The Authors. All rights reserved.

关键词： Random variables

A SEMICIRCLE LAW FOR DERIVATIVES OF RANDOM POLYNOMIALS

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arXiv 2020年

作者： Hoskins, Jeremy G. Steinerberger, Stefan Program in Applied Mathematics Yale University New HavenCT06511 United States Department of Mathematics Yale University New HavenCT06511 United States

Let x1, . . ., xn be n independent and identically distributed random variables with mean zero, unit variance, and finite moments of all remaining orders. We study the random polynomial pn having roots at x1, . . ., xn. We prove that for ` ∈ N fixed as n → ∞, the (n − `)−th derivative of pn behaves like a Hermite polynomial: for x in a compact interval, n`/2n`!! · p(nn−`) ( √xn ) → He`(x + γn), where He` is the `−th probabilists’ Hermite polynomial and γn is a random variable converging to the standard N(0, 1) Gaussian as n → ∞. Thus, there is a universality phenomenon when differentiating a random polynomial many times: the remaining roots follow a Wigner semicircle distribution. Copyright © 2020, The Authors. All rights reserved.

关键词： Polynomials

Hyperuniformity classes of quasiperiodic tilings via diffusion spreadability

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Physical Review E 2024年第6期109卷 064108-064108页

作者： Adam Hitin-Bialus Charles Emmett Maher Paul J. Steinhardt Salvatore Torquato Department of Physics <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA. Department of Chemistry <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA. Jefferson Physical Laboratory <a href="https://***/03vek6s52">Harvard University</a> Cambridge Massachusetts 02138 USA and Department of Physics <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA. Department of Chemistry <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA Department of Physics <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA Princeton Institute of Materials <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA and Program in Applied and Computational Mathematics <a href="https://***/00hx57361">Princeton University</a> Princeton New Jersey 08544 USA.

Hyperuniform point patterns can be classified by the hyperuniformity scaling exponent α>0, that characterizes the power-law scaling behavior of the structure factor S(k) as a function of wave number k≡|k| in the vicinity of the origin, e.g., S(k)∼|k|α in cases where S(k) varies continuously with k as k→0. In this paper, we show that the spreadability is an effective method for determining α for quasiperiodic systems where S(k) is discontinuous and consists of a dense set of Bragg peaks. It has been shown in [Phys. Rev. E 104, 054102 (2021)] that, for media with finite α, the long-time behavior of the excess spreadability S(∞)−S(t) can be fit to a power law of the form t−(d−α)/2, where d is the space dimension, to accurately extract α for the continuous case. We first transform quasiperiodic and limit-periodic point patterns into two-phase media by mapping them onto packings of identical nonoverlapping disks, where space interior to the disks represents one phase and the space in exterior to them represents the second phase. We then compute the spectral density χ̃V(k) of the packings, and finally compute and fit the long-time behavior of their excess spreadabilities. Specifically, we show that the excess spreadability can be used to accurately extract α for the one-dimensional (1D) limit-periodic period-doubling chain (α=1) and the 1D quasicrystalline Fibonacci chain (α=3) to within 0.02% of the analytically known exact results. Moreover, we obtain a value of α=5.97±0.06 for the two-dimensional Penrose tiling and present plausible theoretical arguments strongly suggesting that α is exactly equal to six. We also show that, due to the self-similarity of the structures examined here, one can truncate the small-k region of the scattering information used to compute the spreadability and obtain an accurate value of α, with a small deviation from the untruncated case that decreases as the system size increases. This strongly suggests that one can obtain a good estimate of

关键词： Quasicrystals

Machine learning based non-Newtonian fluid model with molecular fidelity

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arXiv 2020年

作者： Lei, Huan Wu, Lei Weinan, E. Department of Computational Mathematics Science & Engineering Department of Statistics & Probability Michigan State University MI48824 United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University NJ08544 United States

We introduce a machine-learning-based framework for constructing continuum non-Newtonian fluid dynamics model directly from a micro-scale description. Polymer solution is used as an example to demonstrate the essential ideas. To faithfully retain molecular fidelity, we establish a micro-macro correspondence via a set of encoders for the micro-scale polymer configurations and their macro-scale counterparts, a set of nonlinear conformation tensors. The dynamics of these conformation tensors can be derived from the micro-scale model and the relevant terms can be parametrized using machine learning. The final model, named the deep non-Newtonian model (DeePN2), takes the form of conventional non-Newtonian fluid dynamics models, with a new form of the objective tensor derivative. Numerical results demonstrate the accuracy of DeePN2. Copyright © 2020, The Authors. All rights reserved.

关键词： Viscous flow

Liquid-Liquid Transition in Water from First Principles

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Physical Review Letters 2022年第25期129卷 255702-255702页

作者： Thomas E. Gartner, III Pablo M. Piaggi Roberto Car Athanassios Z. Panagiotopoulos Pablo G. Debenedetti Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics 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 Department of Chemical and Biological Engineering Princeton University Princeton New Jersey 08544 USA

A long-standing question in water research is the possibility that supercooled liquid water can undergo a liquid-liquid phase transition (LLT) into high- and low-density liquids. We used several complementary molecular simulation techniques to evaluate the possibility of an LLT in an ab initio neural network model of water trained on density functional theory calculations with the SCAN exchange correlation functional. We conclusively show the existence of a first-order LLT and an associated critical point in the SCAN description of water, representing the first definitive computational evidence for an LLT in water from first principles.

关键词： Classical statistical mechanics First order phase transitions First-principles calculations Liquid-liquid phase transition Phase transitions Thermodynamics Deep learning Density functional theory Molecular dynamics

Realizability of Iso-g2 Processes via Effective Pair Interactions

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arXiv 2022年

作者： Wang, Haina Stillinger, Frank H. Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Princeton Institute of Materials and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States School of Natural Sciences Institute for Advanced Study 1 Einstein Drive PrincetonNJ08540 United States

An outstanding problem in statistical mechanics is the determination of whether prescribed functional forms of the pair correlation function g2(r) [or equivalently, structure factor S(k)] at some number density ρ can be achieved by d-dimensional many-body systems. The Zhang-Torquato conjecture states that any realizable set of pair statistics, whether from a nonequilibrium or equilibrium system, can be achieved by equilibrium systems involving up to two-body interactions. In light of this conjecture, we study the realizability problem of the nonequilibrium iso-g2 process, i.e., the determination of density-dependent effective potentials that yield equilibrium states in which g2 remains invariant for a positive range of densities. Using a precise inverse methodology that determines effective potentials that match hypothesized functional forms of g2(r) for all r and S(k) for all k, we show that the unit-step function g2, which is the zero-density limit of the hard-sphere potential, is remarkably numerically realizable up to the packing fraction = 0.49 for d = 1. For d = 2 and 3, it is realizable up to the maximum "terminal" packing fraction c = 1/2d, at which the systems are hyperuniform, implying that the explicitly known necessary conditions for realizability are sufficient up through c. For near but below c, the large-r behaviors of the effective potentials are given exactly by the functional forms exp[−κ()r] for d = 1, r−1/2 exp[−κ()r] for d = 2, and r−1 exp[−κ()r] (Yukawa form) for d = 3, where κ−1() is a screening length, and for = c, the potentials at large r are given by the pure Coulomb forms in the respective dimensions, as predicted by Torquato and Stillinger [Phys. Rev. E, 68, 041113 1-25 (2003)]. We also find that the effective potential for the pair statistics of the 3D "ghost" random sequential addition at the saturation density c = 1/8 is much shorter-ranged than that for the 3D unit-step-function g2 at c, and thus does not constrain the realizability

关键词： Inverse problems