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arXiv 2023年

作者： Xu, Shixin Eisenberg, Robert Song, Zilong Huang, Huaxiong Zu Chongzhi Center for Mathematics and Computational Sciences Duke Kunshan University 8 Duke Ave Jiangsu Kunshan China Department of Applied Mathematics Illinois Institute of Technology ChicagoIL60616 United States Department of Physiology and Biophysics Rush University Chicago IL60612 United States Math and Statistics Department Utah State University Old Main Hill Logan UT84322 United States Research Center for Mathematics Advanced Institute of Natural Sciences Beijing Normal University Guangdong Zhuhai519088 China Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science BNU-HKBU United International College Guangdong Zhuhai519088 China Laboratory of Mathematics and Complex Systems MOE Beijing Normal University Beijing100875 China Department of Mathematics and Statistics York University TorontoONM3J 1P3 Canada

MSC Codes 92E20, 92B05, 35Q92Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical thermodynamics principles. It encompasses both electrostatics and chemical reactions within consistently defined energetic and dissipative functionals. Furthermore, the energy variation method is extended to account for open systems that involve the input and output of charge and mass. Such open systems have the capability to convert one form of input energy into another form of output energy. In particular, a two-domain model is developed to study a reaction system with self-regulation and internal switching, which plays a vital role in the electron transport chain of mitochondria responsible for ATP generation-a crucial process for sustaining life. Simulations are conducted to explore the influence of electric potential on reaction rates and switching dynamics within the two-domain system. It shows that the electric potential inhibits the oxidation reaction while accelerating the reduction reaction. © 2023, CC BY.

关键词： Open systems

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Latent Feature Representations for Human Gene Expression Data Improve Phenotypic Predictions

Latent Feature Representations for Human Gene Expression Dat...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yannis Pantazis Christos Tselas Kleanthi Lakiotaki Vincenzo Lagani Ioannis Tsamardinos Foundation for Research and Technology - Hellas Inst. of Applied and Computational Mathematics Heraklion Greece University of Crete Heraklion Greece Institute of Chemical Biology Ilia State University Tbilisi Georgia

ISBN: (数字)9781728162157

ISBN: (纸本)9781728162164

High-throughput technologies such as microarrays and RNA-sequencing (RNA-seq) allow to precisely quantify transcriptomic profiles, generating datasets that are inevitably high-dimensional. In this work, we investigate whether the whole human transcriptome can be represented in a compressed, low dimensional latent space without loosing relevant information. We thus constructed low-dimensional latent feature spaces of the human genome, by utilizing three dimensionality reduction approaches and a diverse set of curated datasets. We applied standard Principal Component Analysis (PCA), kernel PCA and Autoencoder Neural Networks on 1360 datasets from four different measurement technologies. The latent feature spaces are tested for their ability to (a) reconstruct the original data and (b) improve predictive performance on validation datasets not used during the creation of the feature space. While linear techniques show better reconstruction performance, nonlinear approaches, particularly, neural-based models seem to be able to capture non-additive interaction effects, and thus enjoy stronger predictive capabilities. Despite the limited sample size of each dataset and the biological / technological heterogeneity across studies, our results show that low dimensional representations of the human transcriptome can be achieved by integrating hundreds of datasets. The created space is two to three orders of magnitude smaller compared to the raw data, offering the ability of capturing a large portion of the original data variability and eventually reducing computational time for downstream analyses.

关键词： Dimensionality reduction Gene expression Principal component analysis Biology Training Neural networks Bioinformatics

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Multidomain Model for Optic Nerve Potassium Clearance: Roles of Glial Cells and Perivascular Spaces

arXiv

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arXiv 2024年

作者： Xiao, Shanfeng Huang, Huaxiong Eisenberg, Robert Song, Zilong Xu, Shixin School of Mathematical Sciences Soochow University 1 Shi-Zi Street Jiangsu Province Suzhou215006 China Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science BNU-HKBU United International College Zhuhai519088 China Laboratory of Mathematics and Complex Systems MOE Beijing China Normal University Beijing100875 China Department of Mathematics and Statistics York University TorontoONM3J 1P3 Canada Department of Applied Mathematics Illinois Institute of Technology ChicagoIL60616 United States Math and Statistics Department Utah State University Old Main Hill LoganUT84322 United States Zu Chongzhi Center for Mathematics and Computational Sciences Duke Kunshan University 8 Duke Ave Kunshan China

The accumulation of potassium in the extracellular space surrounding nerve cells is a fundamental aspect of biophysics that has garnered significant attention in recent research. This phenomenon holds implications for various neurological conditions, including spreading depression, migraine, certain types of epilepsy, and potentially, learning processes. A quantitative analysis is essential for understanding the dynamics of potassium clearance following a series of action potentials. This clearance process involves multiple structures along the nerve, including glia, the extracellular space, axons, and the perivascular space, necessitating a spatially distributed systems approach akin to the cable equations of nerve physiology. In this study, we propose a multi-domain model for the optic nerve to investigate potassium accumulation and clearance dynamics. The model accounts for the convection, diffusion, and electrical migration of fluid and ions, revealing the significant roles of glia and the perivascular space in potassium buffering. Specifically, our findings suggest that potassium clearance primarily occurs through convective flow within the syncytia of glia, driven by osmotic pressure differences. Additionally, the perivascular space serves as a crucial pathway for potassium buffering and fluid circulation, further contributing to the overall clearance process. Importantly, our model’s adaptability allows for its application to diverse structures with distinct channel and transporter distributions across the six compartments, extending its utility beyond the optic nerve. © 2024, CC BY-SA.

关键词： Neurons

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First-principles study of the role of surface in the heavy-fermion compound CeRh2Si2

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Physical Review B 2021年第16期103卷 165140-165140页

作者： Yue-Chao Wang Yuan-Ji Xu Yu Liu Xing-Jie Han Xie-Gang Zhu Yi-feng Yang Yan Bi Hai-Feng Liu Hai-Feng Song Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing 100088 China Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing 100190 China Science and Technology on Surface Physics and Chemistry Laboratory Jiangyou Sichuan 621908 China School of Physical Sciences University of Chinese Academy of Sciences Beijing 100190 China Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China Center for High Pressure Science and Technology Advanced Research Beijing 100094 China

In the heavy-fermion materials, the characteristic energy scales of many exotic strongly correlated phenomena (Kondo effect, magnetic order, superconductivity, etc.) are at millielectron-volt order, implying that the heavy-fermion materials are surface sensitive. Here, we investigate the electronic structures for Si- and Ce-terminated surfaces of CeRh2Si2 by first-principles methods. Our research reveals three notable impacts of surface effects on electronic structures, which are consistent with recent angle-resolved photoemission spectroscopy experiments. First, the relaxation of surface crystal structures changes the relative position of Fermi level, adjusts the dispersion of bands, and enhances the Kondo resonance. Second, the decrease of the hybridization between the Ce−4f and conduction electrons in the surface layer leads to a weaker Kondo resonance peak and the shift of spin-orbit bands. Third, the variation of crystal electric field around surface Ce atoms affects the splitting of Kondo resonance peaks, and also pushes down the lower Hubbard bands of surface 4f electrons. Moreover, we find the characteristic of bulk's lower Hubbard bands, which was overlooked in previous works. Our investigation suggests that these surface effects are potentially important and highlighted in the future researches on properties of strongly correlated materials.

关键词： Electronic structure First-principles calculations Strongly correlated systems DFT+DMFT DFT+U Density functional theory

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An adaptive response surface methodology based on active subspaces for mixed random and interval uncertainties

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Journal of Verification, Validation and Uncertainty Quantification 2019年第2期4卷 021006页

作者： Hu, Xingzhi Duan, Yanhui Wang, Ruili Liang, Xiao Chen, Jiangtao China Aerodynamics Research and Development Center Mianyang621000 China Institute of Applied Physics and Computational Mathematics Beijing100094 China School of Math Shandong University of Science and Technology Qingdao266590 China

The popular use of response surface methodology (RSM) accelerates the solutions of parameter identification and response analysis issues. However, accurate RSM models subject to aleatory and epistemic uncertainties are still challenging to construct, especially for multidimensional inputs, which is widely existed in real-world problems. In this study, an adaptive interval response surface methodology (AIRSM) based on extended active subspaces is proposed for mixed random and interval uncertainties. Based on the idea of subspace dimension reduction, extended active subspaces are given for mixed uncertainties, and interval active variable representation is derived for the construction of AIRSM. A weighted response surface strategy is introduced and tested for predicting the accurate boundary. Moreover, an interval dynamic correlation index is defined, and significance check and cross validation are reformulated in active subspaces to evaluate the AIRSM. The effectiveness of AIRSM is demonstrated on two test examples: three-dimensional nonlinear function and speed reducer design. They both possess a dominant one-dimensional active subspace with small estimation error, and the accuracy of AIRSM is verified by comparing with full-dimensional Monte Carlo simulates, thus providing a potential template for tackling high-dimensional problems involving mixed aleatory and interval uncertainties. Copyright © 2019 by ASME

关键词： Uncertainty analysis

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Pattern change of precipitation extremes in Bear Island

arXiv

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arXiv 2023年

作者： Ray, Arnob Chakraborty, Tanujit Radhakrishnan, Athulya Hens, Chittaranjan Dana, Syamal K. Ghosh, Dibakar Murukesh, Nuncio Physics and Applied Mathematics Unit Indian Statistical Institute Kolkata700108 India Roux Institute Northeastern University Portland04101 United States Institute for Experiential AI Northeastern University Boston02115 United States Department of Science and Engineering Sorbonne University Abu Dhabi United Arab Emirates Sorbonne Center for Artificial Intelligence Sorbonne University Paris75005 France Ocean Atmospheric Studies National Centre for Antarctic and Ocean Research Vasco Da Gama403804 India Center for Computational Natural Science and Bioinformatics International Institute of Informational Technology Hyderabad500032 India Division of Dynamics Lodz University of Technology postcode Lodz90-924 Poland

Extreme precipitation in the Arctic region plays a crucial role in global weather and climate patterns. Bear Island (Bjørnøya) is located in the Norwegian Svalbard archipelago, which is, therefore, selected for our study on extreme precipitation. The island occupies a unique geographic position at the intersection of the high and low Arctic, characterized by a flat and lake-filled northern region contrasting with mountainous terrain along its southern shores. Its maritime-polar climate is influenced by North Atlantic currents, resulting in relatively mild winter temperatures. An increase in precipitation level in Bear Island is a significant concern linked to climate change and has global implications. We have collected the amount of daily precipitation as well as daily maximum temperatures from the meteorological station of Bjørnøya located on the island, operated by the Norwegian Centre for Climate Services in Svalbard for a period spanning from January 1, 1960 to December 31, 2021. We observe that the trend of yearly mean precipitation during this period linearly increases. Also, the number of extreme precipitation events is also increasing. Motivating from this observation, we analyze the recorded data to investigate the changing pattern of precipitation extremes over the climate scales. We employ the generalized extreme value distribution to model yearly and seasonal maxima of daily precipitation amount and determine the return levels and return period of precipitation extremes. We compare the variability of precipitation extremes between the two time periods: (i) 1960-1990 and (ii) 1991-2021. Our analysis reveals an increase in the frequency of precipitation extremes occurrences between 1991 and 2021. A relationship between temperature and precipitation in the area is discerned using wavelet transform coherence. Our findings establish a better understanding of precipitation extremes in Bear Island from a statistical viewpoint, with an observation of seasonal a

关键词： Wavelet transforms

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Momentum Spectroscopy for Multiple Ionization of Cold Rubidium in the Elliptically Polarized Laser Field

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Chinese Physics Letters 2020年第5期37卷 33-37页

作者： Junyang Yuan Yixuan Ma Renyuan Li Huanyu Ma Yizhu Zhang Difa Ye Zhenjie Shen Tianmin Yan Xincheng Wang Matthias Weidemüller Yuhai Jiang Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210 University of Chinese Academy of Sciences Beijing 100049 School of Physical Science and Technology ShanghaiTech UniversityShanghai 201210 Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering Key Laboratory of the Ministry of EducationTianjin UniversityTianjin 300072 Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing 100088 Hefei National Laboratory for Physical Sciences at the Microscale and Shanghai Branch University of Science and Technology of ChinaShanghai 201315 CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics University of Science and Technology of ChinaShanghai 201315 Physikalisches Institut Universitat HeidelbergIm Neuenheimer Feld 22669120 HeidelbergGermany

Employing recently developed magneto-optical trap recoil ion momentum spectroscopy(MOTRIMS)combined with cold atoms,strong laser pulse,and ultrafast technologies,we study momentum distributions of the multiply ionized cold rubidium(Rb)induced by the elliptically polarized laser pulses(35 fs,1.3×10^15 W/cm^2).The complete vector momenta of Rb^n+ions up to charge state n=4 are recorded with extremely high resolution(0.12 *** Rb^+).Variations of characteristic multi-bands are displayed in momentum distributions because the ellipticity varies from the linear to circular polarization,are interpreted qualitatively with the classical overbarrier ionization *** momentum spectroscopy of cold heavy alkali atoms presents novel strong-field phenomena beyond the noble gases.

关键词： polarization momentum alkali

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Dynamics and rheology of polymer melts via hierarchical atomistic, coarse-grained, and slip-spring simulations

arXiv

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arXiv 2021年

作者： Behbahani, Alireza Foroozani Schneider, Ludwig Rissanou, Anastassia Chazirakis, Anthony Bačová, Petra Jana, Pritam Kumar Li, Wei Doxastakis, Manolis Polińska, Patrycja Burkhart, Craig Müller, Marcus Harmandaris, Vagelis A. Institute of Applied and Computational Mathematics Foundation for Research and Technology - Hellas HeraklionGR-71110 Greece Institute for Theoretical Physics Georg-August University Göttingen Germany Department of Chemical and Biomolecular Engineering University of Tennessee KnoxvilleTN37996 United States Goodyear S.A. Avenue Gordon Smith Colmar-BergL-7750 Luxembourg The Goodyear Tire and Rubber Company 142 Goodyear Blvd. AkronOH44305 United States Department of Mathematics and Applied Mathematics University of Crete HeraklionGR-71110 Greece Computation-based Science and Technology Research Center The Cyprus Institute Nicosia2121 Cyprus

A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular weight entangled polymer melts. The methodology consists of atomistic, moderately coarse-grained (mCG), and highly coarse-grained slip-spring (SLSP) simulations. At the mCG level, a few chemically bonded atoms are lumped into one coarse-grained bead. At this level, the chemical identity of the underlying atomistic system, and the interchain topological constraints (entanglements) are preserved. The mCG interaction potentials are derived by matching local structural distributions of the mCG model to those of the atomistic model through iterative Boltzmann inversion. For matching mCG and atomistic dynamics, the mCG time is scaled by a time scaling factor, which compensates for the lower monomeric friction coefficient of the mCG model than that of the atomistic one. At the SLSP level, multiple Kuhn segments of a polymer chain are represented by one coarse-grained bead. The very soft nonbonded interactions between beads do not prevent chain crossing and, hence, can not capture entanglements. The topological constraints are represented by slip-springs, restricting the lateral motion of polymer chains. A compensating pair potential is used in the SLSP model, to keep the static macromolecular properties unaltered upon the introduction of slip-springs. The static and kinetic parameters of the SLSP model are determined based on the lower level simulation models. Particularly, matching the orientational autocorrelation of the end-to-end vector, we determine the number of slip-springs and calibrate the timescale of the SLSP model. As the test case, the hierarchical methodology is applied to cis-1,4-polybutadiene (cPB) at 413 K. Dynamical single-chain and linear viscoelastic properties of cPB melts are calculated for a broad range of molecular weights, ranging from unentangled to well-entangled chains. The calculations are compared,

关键词： Polymer melts

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Formulation of the Electric Vehicle Charging and Routing Problem for a Hybrid Quantum-Classical Search Space Reduction Heuristic

Formulation of the Electric Vehicle Charging and Routing Pro...

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International Conference on Intelligent Transportation

作者： Mikel Garcia De Andoin Alberto Bottarelli Sebastian Schmitt Izaskun Oregi Philipp Hauke Mikel Sanz Department of Physical Chemistry University of the Basque Country UPV/EHU Leioa Spain TECNALIA Basque Research and Technology Alliance (BRTA) Derio Spain EHU Quantum Center University of the Basque Country UPV/EHU Leioa Spain Dipartimento di Fisica Pitaevskii BEC Center CNR-INO Università di Trento Trento Italy INFN-TIFPA Trento Institute for Fundamental Physics and Applications Trento Italy Honda Research Institute Europe GmbH Offenbach Germany IKERBASQUE Basque Foundation for Science Bilbao Spain Basque Center for Applied Mathematics BCAM Bilbao Spain

Combinatorial optimization problems have attracted much interest in the quantum computing community in the recent years as a potential testbed to showcase quantum advantage. In this paper, we show how to exploit multilevel carriers of quantum information—qudits—for the construction of algorithms for constrained quantum optimization. These systems have been recently introduced in the context of quantum optimization and they allow us to treat more general problems than the ones usually mapped into qubit systems. In particular, we propose a hybrid classical quantum heuristic strategy that allows us to sample constrained solutions while greatly reducing the search space of the problem, thus optimizing the use of fewer quantum resources. As an example, we focus on the Electric Vehicle Charging and Routing Problem (EVCRP). We translate the classical problem and map it into a quantum system, obtaining promising results on a toy example which shows the validity of our technique.

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Spatiotemporal Switches in Progenitor Cell Fate Govern Upper Hair Follicle Growth and Maintenance

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Journal of Investigative Dermatology 2025年

作者： Andersen, Marianne S. Ulyanchenko, Svetlana Schweiger, Pawel J. Hannezo, Edouard Simons, Benjamin D. Jensen, Kim B. Biotech Research and Innovation Centre (BRIC) Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Novo Nordisk Foundation Center for Stem Cell Medicine ReNEW Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Institute of Science and Technology Austria Klosterneuburg Austria Centre for Mathematical Science Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom The Wellcome Trust/Cancer Research UK Gurdon Institute University of Cambridge Cambridge United Kingdom The Wellcome Trust/Medical Research Council Stem Cell Institute University of Cambridge Cambridge United Kingdom Department of Biomedical Sciences Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark

The epidermis provides a protective barrier against hostile environments. However, our knowledge of how this barrier forms during development and is subsequently maintained remains incomplete. The infundibulum is a cylindrical epidermal tissue compartment that serves as an outlet for hair follicles protruding from the skin and the excretion of the sebaceous glands that are essential for proper skin function. In this study, we applied quantitative fate mapping to address how infundibulum are maintained during adulthood. We demonstrate that progenitors build and maintain tissues through stochastic cell fate choices. Long-term analysis identified a preferential transient contribution from cells initially located at the bottom of the structure to the maintenance of the tissue, with bursts of local progenitor expansion associated with the phases of hair growth. Beyond providing compartment-wide insights into progenitor cell dynamics in infundibulum, these findings demonstrate how spatiotemporal regulation controls transient progenitor dominance. © 2025 The Authors

关键词： Epidermis Infundibulum Quantitative fate mapping Skin Stem cells

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