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arXiv 2024年

作者： Barton, Brandon Sagal, Jacob Feeney, Sean Grattan, George Patnaik, Pratik Oganesyan, Vadim Carr, Lincoln D. Kapit, Eliot Quantum Engineering Program Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Colorado School of Mines 1523 Illinois St GoldenCO80401 United States Department of Computer Science Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Physics and Astronomy College of Staten Island City University of New York Staten IslandNY10314 United States Physics program and Initiative for the Theoretical Sciences The Graduate Center City University of New York New YorkNY10016 United States

In this work, we introduce a new iterative quantum algorithm, called Iterative Symphonic Tunneling for Satisfiability problems (IST-SAT), which solves quantum spin glass optimization problems using high-frequency oscillating transverse fields. IST-SAT operates as a sequence of iterations, in which bitstrings returned from one iteration are used to set spin-dependent phases in oscillating transverse fields in the next iteration. Over several iterations, the novel mechanism of the algorithm steers the system toward the problem ground state. We benchmark IST-SAT on sets of hard MAX-3-XORSAT problem instances with exact state vector simulation, and report polynomial speedups over trotterized adiabatic quantum computation (TAQC) and the best known semi-greedy classical algorithm. When IST-SAT is seeded with a sufficiently good initial approximation, the algorithm converges to exact solution(s) in a polynomial number of iterations. Our numerical results identify a critial Hamming radius(CHR), or quality of initial approximation, where the time-to-solution crosses from exponential to polynomial scaling in problem size. By combining IST-SAT with future classical or quantum approximation algorithms, larger gains may be achieved. The mechanism we present in this work thus presents a new path toward achieving quantum advantage in optimization. © 2024, CC BY.

关键词： Combinatorial optimization

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On the importance of assessing topological convergence in Bayesian phylogenetic inference

arXiv

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arXiv 2024年

作者： Brusselmans, Marius Carvalho, Luiz Max Hong, Samuel L. Gao, Jiansi Matsen, Frederick A. Rambaut, Andrew Lemey, Philippe Suchard, Marc A. Dudas, Gytis Baele, Guy Department of Microbiology Immunology and Transplantation Rega Institute KU Leuven Leuven Belgium School of Applied Mathematics Getulio Vargas Foundation Praia de Botafogo 190 Rio de Janeiro22250-900 Brazil Computational Biology Program Fred Hutchinson Cancer Center SeattleWA98109 United States Howard Hughes Medical Institute Computational Biology Program Fred Hutchinson Cancer Research Center SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Department of Statistics University of Washington SeattleWA United States Institute of Ecology and Evolution University of Edinburgh EdinburghEH9 3FL United Kingdom Department of Biostatistics Fielding School of Public Health University of California Los AngelesCA90095 United States Institute of Biotechnology Life Sciences Center Vilnius University Vilnius Lithuania

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the effective sample size (ESS) and to investigate trace graphs of the sampled parameters. A major limitation of these approaches is that they are developed for continuous parameters and therefore incompatible with a crucial parameter in these inferences: the tree topology. Several recent advancements have aimed at extending these diagnostics to topological space. In this reflection paper, we present two case studies – one on Ebola virus and one on HIV – illustrating how these topological diagnostics can contain information not found in standard diagnostics, and how decisions regarding which of these diagnostics to compute can impact inferences regarding MCMC convergence and mixing. Our results show the importance of running multiple replicate analyses and of carefully assessing topological convergence using the output of these replicate analyses. To this end, we illustrate different ways of assessing and visualizing the topological convergence of these replicates. Given the major importance of detecting convergence and mixing issues in Bayesian phylogenetic analyses, the lack of a unified approach to this problem warrants further action, especially now that additional tools are becoming available to researchers. © 2024, CC BY-SA.

关键词： Phylogenetic

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Local two-sample testing over graphs and point-clouds by random-walk distributions

arXiv

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arXiv 2020年

作者： Landa, Boris Qu, Rihao Chang, Joseph Kluger, Yuval Program in Applied Mathematics Yale University Department of Pathology Yale University School of Medicine Department of Statistics and Data Science Yale University Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Immunology Yale School of Medicine

Rejecting the null hypothesis in two-sample testing is a fundamental tool for scientific discovery. Yet, aside from concluding that two samples do not come from the same probability distribution, it is often of interest to characterize how the two distributions differ. Given samples from two densities f1and f0, we consider the task of localizing occurrences of the inequality f1> f0. To avoid the challenges associated with high-dimensional space, we propose a general hypothesis testing framework where hypotheses are formulated adaptively to the data by conditioning on the combined sample from the two densities. We then investigate a special case of this framework where the notion of locality is captured by a random walk on a weighted graph constructed over this combined sample. We derive a tractable testing procedure for this case employing a type of scan statistic, and provide non-asymptotic lower bounds on the power and accuracy of our test to detect whether f1> f0in a local sense. Furthermore, we characterize the test's consistency according to a certain problem-hardness parameter, and show that our test achieves the minimax detection rate for this parameter. We conduct numerical experiments to validate our method, and demonstrate our approach on two real-world applications: detecting and localizing arsenic well contamination across the United States, and analyzing two-sample single-cell RNA sequencing data from melanoma *** Codes 62G10 Copyright © 2020, The Authors. All rights reserved.

关键词： Random processes

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Towards Autonomous Synchrotron Fourier Transform Infrared Microscopy

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Zwart, Petrus Tas, Neslihan Noack, Marcus Holman, HoiYing Berkeley Synchrotron Infrared Structural Biology Program Lawrence Berkeley National Laboratory Berkeley California USA Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory Berkeley California USA Center for Advanced Mathematics in Energy Research Applications Lawrence Berkeley National Laboratory Berkeley California USA Climate and Ecosystem Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA Applied Mathematics & Computational Research Lawrence Berkeley National Laboratory Berkeley California USA

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Active learning of uniformly accurate interatomic potentials for materials simulation

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Physical Review Materials 2019年第2期3卷 023804-023804页

作者： Linfeng Zhang De-Ye Lin Han Wang Roberto Car Weinan E Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA and Beijing Institute of Big Data Research Beijing 100871 People's Republic of China

An active learning procedure called deep potential generator (DP-GEN) is proposed for the construction of accurate and transferable machine learning-based models of the potential energy surface (PES) for the molecular modeling of materials. This procedure consists of three main components: exploration, generation of accurate reference data, and training. Application to the sample systems of Al, Mg, and Al-Mg alloys demonstrates that DP-GEN can produce uniformly accurate PES models with a minimal number of reference data.

关键词： Atomic & molecular structure Potential energy surfaces Alloys Amorphous materials Liquids Density functional theory First-principles calculations Molecular dynamics

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Reducing bias and variance for CTF estimation in single particle cryo-EM

arXiv

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arXiv 2019年

作者： Heimowitz, Ayelet Andén, Joakim Singer, Amit Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Center for Computational Mathematics Flatiron Institute New YorkNY10010 United States Program in Applied and Computational Mathematics Department of Mathematics Princeton University PrincetonNJ08544 United States

When using an electron microscope for imaging of particles embedded in vitreous ice, the recorded image, or micrograph, is a significantly degraded version of the tomographic projection of the sample. Apart from noise, the image is affected by the optical configuration of the microscope. This transformation is typically modeled as a convolution with a point spread function. The Fourier transform of this function, known as the contrast transfer function (CTF), is oscillatory, attenuating and amplifying different frequency bands, and sometimes flipping their signs. High-resolution reconstruction requires this CTF to be accounted for, but as its form depends on experimental parameters, it must first be estimated from the micrograph. We present a new method for CTF estimation based on multitaper methods, which reduces bias and variance in the estimate. We also use known properties of the CTF and the background noise power spectrum to further reduce the variance through background subtraction and steerable basis projection. We show that the resulting power spectrum estimates better capture the zero-crossings of the CTF and yield accurate CTF estimates on several experimental micrographs. Copyright © 2019, The Authors. All rights reserved.

关键词： Linear programming

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A comparative analysis of lead (Pb) and cadmium heavy metals contents in bottled and refilled drinking water in Sukarame District, Bandar Lampung

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AIP Conference Proceedings 2024年第1期3058卷

作者： Welly Anggraini Iqlima Amelia Anisa Oktina Sari Pratama Mala Pratama Devi Cendekia Rizkia Dita Farenda Biology Education Department Tarbiyah and Teacher Training Faculty Raden Intan State Islamic University of Lampung Lampung Indonesia Mathematics and Natural Science Education Faculty Universitas Pendidikan Indonesia Bandung Indonesia Department of Agricultural Technology Applied Chemistry Study Program D4 Politeknik Negeri Lampung Lampung Indonesia

The primary need of humans is access to safe drinking water. These requirements expand the availability of water supply facilities, refilled drinking water, and bottled drinking water. Heavy metals are transition elements with large atomic masses. This study aims to assess the heavy metals lead (Pb) and cadmium (Cd) in bottled and refilled drinking water using Ministry of Health Regulation No. 492/Menkes/Per/IV/2010. An atomic absorption spectrophotometer was used to test samples of five local bottled drinking water brands and twelve refilled drinking water Sukarame sub-district. The tests found that certain heavy metals exceeded the government’s maximum level. The AMDK5, with a Pb content of-0.007 mg/L and a Cd concentration of 0.001 mg/L, was one of five bottled water samples with acceptable quality. The Pb and Cd content in the other four samples, on the other hand, surpassed the maximum standard. Pb and Cd levels in refilled drinking water were measured, and the results were mixed. Pb values in five of the twelve refilled drinking water samples exceeded the maximum standard of 0.01 mg/L. Furthermore, the Cd content in twelve samples of refilled drinking water exceeded 0.003 mg/L, which violated the requirement.

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Development of a biodegradable smart packaging film with ZnO nanoparticles and anthocyanins for real-time freshness monitoring of shrimps

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Food Bioscience 2025年 69卷

作者： Heryanto Heryanto Muh Ade Artasasta Dahlang Tahir Ali Alomari Juliasih Partini Abdelillah Akouibaa Department of Physics Faculty of Mathematics and Natural Science Hasanuddin University Makassar 90425 Indonesia Biotechnology Program Study Department of Applied Science Faculty of Mathematics and Natural Science Universitas Negeri Malang Malang 65145 Indonesia Physics Department Al-Qunfudah University College Umm Al-Qura University Makkah Saudi Arabia Department of Physics Universitas Gadjah Mada Yogyakarta 55281 Indonesia Rue Tarik Bnou Ziad Casablanca 20100 Casablanca-Settat LPPSMM Physics Department Hassan II University Casablanca 7955 Morocco

This research introduces a biodegradable smart packaging film designed for real-time freshness monitoring of shrimp, incorporating zinc oxide nanoparticles (ZnO NPs) and anthocyanin extracted from Hibiscus rosa-sinensis L. as a pH-responsive indicator. The film matrix, composed of cassava starch, chitosan, and glycerin, was reinforced with varying concentrations of ZnO (0 %, 6 %, and 10 %). Structural characterization via X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR) confirmed the successful incorporation of ZnO into the biopolymer matrix. Notably, the film containing 6 % ZnO exhibited the highest crystallinity index (12.23 %) compared to the control (10.29 %) and the 10 % ZnO variant (10.81 %). Mechanical property assessments indicated that the 6 % ZnO film demonstrated superior tensile strength (0.78 MPa) and Young's modulus (2.84 MPa). However, increasing the ZnO content resulted in a decrease in elongation at break, from 41.52 % in the control to 27.65 % in the 10 % ZnO film. Water interaction analyses revealed improved water resistance with ZnO incorporation, as evidenced by a reduction in water solubility from 38.12 % (control) to 28.45 % (10 % ZnO). Biodegradation assays showed a slower degradation rate in ZnO-reinforced films (56.42 % for 6 % ZnO and 49.87 % for 10 % ZnO) compared to the control (68.15 %) over 15 days, likely attributable to the hydrophobic nature of ZnO nanoparticles. Functionally, the film demonstrated effective spoilage detection through visible colorimetric transitions, shifting from reddish-purple to bluish-green within 24 h of shrimp storage, corresponding to pH changes associated with degradation. Overall, the findings underscore the potential of ZnO-reinforced, starch-based films as eco-friendly and smart packaging materials for enhancing food safety and quality monitoring.

关键词： Biodegradable film pH indicator Shrimp Smart packaging ZnO NPs

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Gap sensitivity reveals universal behaviors in optimized photonic crystal and disordered networks

arXiv

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arXiv 2021年

作者： Klatt, Michael Andreas Steinhardt, Paul J. Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Institut für Theoretische Physik University of Erlangen-Nürnberg Staudtstr. 7 Erlangen91058 Germany Department of Chemistry Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Through an extensive series of high-precision numerical computations of the optimal complete photonic band gap (PBG) as a function of dielectric contrast α for a variety of crystal and disordered heterostructures, we reveal striking universal behaviors of the gap sensitivity S(α) ≡ d∆(α)/dα, the first derivative of the optimal gap-to-midgap ratio ∆(α). In particular, for all our crystal networks, S(α) takes a universal form that is well approximated by the analytic formula for a one-dimensional quarter-wave stack, SQWS(α). Even more surprisingly, the values of S(α) for our disordered networks converge to SQWS(α) for sufficiently large α. A deeper understanding of the simplicity of this universal behavior may provide fundamental insights about PBG formation and guidance in the design of novel photonic *** Codes 78A48, 78M50 (Primary) 82D25, 82D30, 52C99 (Secondary) © 2021, CC BY-SA.

关键词： Photonic band gap

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Bayesian quantum phase estimation with fixed photon states

arXiv

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arXiv 2023年

作者： Zhou, Boyu Guha, Saikat Gagatsos, Christos N. Department of Physics The University of Arizona 1118 E 4th St TucsonAZ85721 United States Department of Electrical and Computer Engineering University of Maryland 2410 A.V. Williams Building College ParkMD20742 United States Wyant College of Optical Sciences The University of Arizona 1630 E University Blvd TucsonAZ85721 United States Department of Electrical and Computer Engineering The University of Arizona 1230 E Speedway Blvd TucsonAZ85721 United States Program in Applied Mathematics The University of Arizona 617 N. Santa Rita TucsonAZ85721 United States

We consider a two-mode bosonic state with fixed photon number n ∈ N, whose upper and lower modes pick up a phase and − respectively. We compute the optimal Fock coefficients of the input state, such that the mean square error (MSE) for estimating is minimized while the minimum MSE is always attainable by a measurement. Our setting is Bayesian, i.e., we consider to be a random variable that follows a prior probability distribution function (PDF). Initially, we consider the flat prior PDF and we discuss the well-known fact that the MSE is not an informative tool for estimating a phase when the variance of the prior PDF is large. Therefore, we move on to study truncated versions of the flat prior in both single-shot and adaptive approaches. For our adaptive technique we consider n = 1 and truncated prior PDFs. Each subsequent step utilizes as prior PDF the posterior probability of the previous step and at the same time we update the optimal state and optimal measurement. Copyright © 2023, The Authors. All rights reserved.

关键词： Distribution functions

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