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Applied Mathematics 2020年第3期11卷 172-183页

作者： Okey Oseloka Onyejekwe Yohannes Demiss Belete Nahom Alemseged Worku Computational Mechanics and Dynamics Systems Group Computational Science Program Addis Ababa University Arat Kilo Campus Addis Ababa Ethiopia

The work presented herein investigates the velocity, heat transfer, Nusselt number and skin friction profiles involved in boundary layer flow past a moving vertical porous plate. Similarity transformations are employed to convert the governing nonlinear unsteady momentum and energy equations from their partial differential equation forms to boundary value ordinary differential equations. The resulting equations are then solved numerically by the Runge-Kutta fourth order method with the help of a shooting technique. Several features of the flow and heat transfer characteristics for different values of problem parameters are analyzed and discussed. These include the effects of the radiation parameter (R), suction and injection parameter (c), Grashof (Gr) and Prandtl (Pr) numbers on the flow and heat profiles. Numerical results show the impact of blowing and sucking as well as radation on boundary layer flows of this type. Both the skin frictions as well as the heat transfer rate are also significantly related to the radiation parameter. For all these cases;the numerical results are found to be in agreement with the physics of the problem.

关键词： Momentum and Energy Grashof Number Prandtl Number Similarity Transformation Radiation Parameter Suction Blowing Radiation Po-rous Plate

Continuity Equation of Left Invariant Gauge Field in Quantum Genotype Of Deltacron

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SSRN

SSRN 2022年

作者： Hannongbua, Supot Kanjamapornkul, Kabin Rungrotmongkol, Thanyada Department of Chemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand Biocatalyst and Environmental Biotechnology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok10330 Thailand

The continuity equation for the invariant gauge field of Deltacron was investigated from the replication and recombination of Delta with Omicron. The new definition of left translation of the invariant gauge field in the quantum genotype of virus and host cell was introduced. The Yang-Mills field in genetic code is an induced curvature in the parallel transport of a unified field between hydrogen bonding between three types of biomolecules. where we defined the invariant gauge field in quantum genotype. This issue allows us to identify the Poincare duality between the nteraction between the behavior field of gene expression in parasitism state and in the curvature of connection in fiber space of Spike protein folding molecule. The Chern Simons current is the anti-self-dual state of mutation between two types of interactive behavior fields in The recombination process of Deltacron was used to plot the Yang-Mills curvature directly from the underlying genetic codes. Further analysis shows that the difference between the tensor correlation with various times of Deltacron the change slope of Omicron BA.1 to the flat curve of the network correlation and closedness centrality of amino acids in receptor binding domain of Spike protein. © 2022, The Authors. All rights reserved.

关键词： Gene expression

Artificial neural network approach for turbulence models: A local framework

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Physical Review Fluids 2021年第8期6卷 084612-084612页

作者： Chenyue Xie Xiangming Xiong Jianchun Wang Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Department of Mechanics and Aerospace Engineering Southern University of Science and Technology Shenzhen 518055 People's Republic of China

A local artificial neural network (LANN) framework is developed for turbulence modeling. The Reynolds-averaged Navier-Stokes (RANS) unclosed terms are reconstructed by the artificial neural network based on the local coordinate system which is orthogonal to the curved walls. We verify the proposed model in the flows over periodic hills. The correlation coefficients of the RANS unclosed terms predicted by the LANN model can be made larger than 0.96 in an a priori analysis, and the relative error of the unclosed terms can be made smaller than 18%. In an a posteriori analysis, detailed comparisons are made on the results of RANS simulations using the LANN, global artificial neural network (GANN), Spalart-Allmaras (SA), and shear stress transport (SST) k−ω models. It is shown that the LANN model performs better than the GANN, SA, and SST k−ω models in the prediction of the average velocity, wall-shear stress, and average pressure, which gives the results that are essentially indistinguishable from the direct numerical simulation data. The LANN model trained at low Reynolds number, Re=2800, can be directly applied to the cases of high Reynolds numbers, Re=5600, 10 595, 19 000, and 37 000, with accurate predictions. Furthermore, the LANN model is verified for flows over periodic hills with varying slopes. These results suggest that the LANN framework has a great potential to be applied to complex turbulent flows with curved walls.

关键词： Compressible boundary layers Turbulence Artificial neural networks

The phase diagram of a deep potential water model

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arXiv 2021年

作者： Zhang, Linfeng Wang, Han Car, Roberto Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China Department of Chemistry Department of Physics Program in Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50 GPa, excluding the vapor stability region. The computational efficiency of the model makes it possible to predict its phase diagram using molecular dynamics. Satisfactory overall agreement with experimental results is obtained. The fluid phases, molecular and ionic, and all the stable ice polymorphs, ordered and disordered, are predicted correctly, with the exception of ice III and XV that are stable in experiments, but metastable in the model. The evolution of the atomic dynamics upon heating, as ice VII transforms first into ice VII′′ and then into an ionic fluid, reveals that molecular dissociation and breaking of the ice rules coexist with strong covalent fluctuations, explaining why only partial ionization was inferred in experiments. © 2021, CC BY-NC-ND.

关键词： Phase diagrams

Minuscule corrections to near-surface solar internal rotation using mode-coupling

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arXiv 2023年

作者： Das, Srijan Bharati Kashyap, Samarth G. Oktay, Deniz Hanasoge, Shravan M. Tromp, Jeroen Department of Geosciences Princeton University PrincetonNJ United States Department of Astronomy and Astrophysics Tata Institute of Fundamental Research Mumbai India Department of Computer Science Princeton University PrincetonNJ United States Department of Geosciences and Program in Applied & Computational Mathematics Princeton University PrincetonNJ United States

The observed solar oscillation spectrum is influenced by internal perturbations such as flows and structural asphericities. These features induce splitting of characteristic frequencies and distort the resonant-mode eigenfunctions. Global axisymmertric flow — differential rotation — is a very prominent perturbation. Tightly constrained rotation profiles as a function of latitude and radius are products of established helioseismic pipelines that use observed Dopplergrams to generate frequency-splitting measurements at high precision. However, the inference of rotation using frequency-splittings do not consider the effect of mode-coupling. This approximation worsens for high-angular-degree modes, as they become increasingly proximal in frequency. Since modes with high angular degrees probe the near-surface layers of the Sun, inversions considering coupled modes could potentially lead to more accurate estimates of rotation very close to the surface. In order to investigate if this is indeed the case, we perform inversions for solar differential rotation, considering coupling of modes for angular degrees 160 ≤ ` ≤ 300 in the surface gravity f-branch and first-overtone p modes. In keeping with the character of mode coupling, we carry out a non-linear inversion using an eigenvalue solver. Differences in inverted profiles for frequency splitting measurements from MDI and HMI are compared and discussed. We find that corrections to the near-surface differential rotation profile, when accounting for mode-coupling effects, are smaller than 0.003 nHz and hence are insignificant. These minuscule corrections are found to be correlated with the solar cycle. We also present corrections to even-order splitting coefficients, which could consequently impact inversions for structure and magnetic fields. © 2023, CC BY.

关键词： Rotation

Global dispersal and adaptive evolution of domestic cattle:a genomic perspective

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Stress Biology 2023年第1期3卷 98-110页

作者： Xiaoting Xia Kaixing Qu Yan Wang Mikkel-Holger SSinding Fuwen Wang Quratulain Hanif Zulfiqar Ahmed Johannes A.Lenstra Jianlin Han Chuzhao Lei Ningbo Chen Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Academy of Science and Technology Chuxiong Normal UniversityChuxiong 675000China Qingdao Municipal Bureau of Agriculture and Rural Affairs Qingdao 266000China Section for Computational and RNA Biology Department of BiologyUniversity of CopenhagenCopenhagen 1350Denmark National Institute for Biotechnology and Genetic Engineering FaisalabadPakistan Faculty of Veterinary and Animal Sciences University of Poonch RawalakotAzad Jammu and Kashmir 12350Pakistan Faculty of Veterinary Medicine Utrecht UniversityUtrechtThe Netherlands Livestock Genetic Program International Livestock Research Institute(ILRI)Nairobi 00100Kenya CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources Institute of Animal ScienceChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China

Domestic cattle have spread across the globe and inhabit variable and unpredictable *** have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions,including UV exposure,diseases,and stall-feeding *** selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/*** efforts to sequence the genomes of local and commercial cattle breeds/populations,along with the growing availability of ancient bovid DNA data,have significantly advanced our understanding of the genomic architecture,recent evolution of complex traits,common diseases,and local adaptation in ***,we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.

关键词： Cattle Origin Domestication Migration route Environmental adaptation Selective pressure

Cyclic ferroelectric switching and quantized charge transport in CuInP2S6

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Physical Review B 2023年第18期108卷 L180101-L180101页

作者： Daniel Seleznev Sobhit Singh John Bonini Karin M. Rabe David Vanderbilt Department of Physics and Astronomy Center for Materials Theory Rutgers University Piscataway New Jersey 08854 USA Department of Mechanical Engineering University of Rochester Rochester New York 14627 USA Materials Science Program University of Rochester Rochester New York 14627 USA Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New York New York 10010 USA

The van der Waals layered ferroelectric CuInP2S6 has been found to exhibit a variety of intriguing properties arising from the fact that the Cu ions are unusually mobile in this system. While the polarization switching mechanism is usually understood to arise from Cu ion motion within the monolayers, a second switching path involving Cu motion across the van der Waals gaps has been suggested. In this work, we perform zero-temperature first-principles calculations on such switching paths, focusing on two types that preserve the periodicity of the primitive unit cell: “cooperative” paths preserving the system's glide mirror symmetry, and “sequential” paths in which the two Cu ions in the unit cell move independently of each other. We find that CuInP2S6 features a rich and varied energy landscape, and that sequential paths are clearly favored energetically both for cross-gap and through-layer paths. Importantly, these segments can be assembled to comprise a globally insulating cycle with the out-of-plane polarization evolving by a quantum as the Cu ions shift to neighboring layers. In this sense, we argue that CuInP2S6 embodies the physics of a quantized adiabatic charge pump.

关键词： Electric polarization Electronic structure Ferroelectricity Phonons Structural phase transition

Development, Biological Evaluation, and Molecular Modelling of Novel Isocytosine and Guanidine Derivatives as Bace1 Inhibitors Using a Fragment Growing Strategy

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SSRN

SSRN 2024年

作者： Atta, Asmaa M. Rihan, Nouran Abdelwaly, Ahmad M. Nafie, Mohamed S. Elgawish, Mohamed S. Moustafa, Samia M. Helal, Mohamed A. Darwish, Khaled M. Badr City Cairo11829 Egypt Biomedical Sciences Program University of Science and Technology Zewail City of Science and Technology Giza12587 Egypt Institute for Computational Molecular Science Department of Chemistry Temple University PhiladelphiaPA19122 United States Department of Chemistry College of Sciences University of Sharjah Sharjah27272 United Arab Emirates Chemistry Department Faculty of Science Suez Canal University Ismailia41522 Egypt Medicinal Chemistry Department Faculty of Pharmacy Suez Canal University Ismailia41522 Egypt Center for Molecular Spectroscopy and Dynamic Institute of Basic Science Korea University Seoul02841 Korea Republic of

Alzheimer’s disease (AD) is a neurodegenerative condition characterized by significant synaptic loss and neuronal death in brain regions critical for cognitive functions. The disease is characterized by the formation of amyloid plaques, which are extracellular constructs consisting mainly of aggregated Aβ42. The latter is a peptide formed by the proteolytic cleavage of β-amyloid precursor protein (APP) by two enzymes, β- and ɣ-secretase. Therefore, inhibition of the aspartic protease β-secretase (BAXE1) is considered a promising therapeutic approach for the treatment and prevention of Alzheimer’s disease. Unfortunately, a limited number of β-secretase inhibitors have reached human trials and eventually failed due to inconclusive therapeutic and/or safety profiles. In this study, we developed drug-like molecules with a β-secretase inhibitory activity using a fragment growing strategy on isocytosine and acyl guanidine warheads. Our approach is based on optimizing the hydrophobic part of the molecules to obtain a conformationally restrained scaffold complementary to the hydrophobic pockets within the enzyme active site. We developed 32 compounds with promising in vitro inhibitory activity against BACE1 down to sub-micromolar IC50. Docking simulation studies were performed to understand the mode of binding of the prepared compounds. We demonstrated that the possible justification for the superior activity of compound which provides the best balance between size and position of the polar substituent for achieving preferential anchoring at S1’/S3 across S1/S2 sub-pockets. Further, in vivo, characterization of the most active benzimidazole series AMK-IV demonstrated its ability to reduce oxidation stress and its safety in brain and liver tissues. © 2024, The Authors. All rights reserved.

关键词： Molecular modeling

Efficient First-Principles Framework for Overdamped Phonon Dynamics and Anharmonic Electron-Phonon Coupling in Superionic Materials

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arXiv 2025年

作者： Wang, Yuxuan Zacharias, Marios Zhang, Xiao Pant, Nick Even, Jacky Poudeu, Pierre F.P. Kioupakis, Emmanouil Department of Materials Science and Engineering University of Michigan Ann ArborMI48109 United States Univ Rennes INSA Rennes CNRS Institut FOTON - UMR 6082 RennesF-35000 France Applied Physics Program University of Michigan Ann ArborMI48109 United States Oden Institute for Computational Engineering and Sciences The University of Texas at Austin AustinTX78712 United States

Relying on the anharmonic special displacement method, we introduce an ab initio quasistatic polymorphous framework to describe local disorder, anharmonicity, and electron-phonon coupling in superionic conductors. Using the example of cubic Cu2Se, we show that positional polymorphism yields extremely overdamped anharmonic vibrations while preserving transverse acoustic phonons, consistent with experiments. We also demonstrate well-defined electronic band structures with large band gap openings due to polymorphism of 1.0 eV and calculate anharmonic electron-phonon renormalization, yielding band gap narrowing with increasing temperature in agreement with previous measurements. Our approach opens the way for efficient ab initio electronic structure calculations in superionic crystals to elucidate their compelling high figure-of-merit. © 2025, CC BY-NC-ND.

关键词： Energy gap

Dimension reduction of dynamical systems on networks with leading and non-leading eigenvectors of adjacency matrices

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arXiv 2022年

作者： Masuda, Naoki Kundu, Prosenjit Department of Mathematics State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Dimension reduction techniques for dynamical systems on networks are considered to promote our understanding of the original high-dimensional dynamics. One strategy of dimension reduction is to derive a low-dimensional dynamical system whose behavior approximates the observables of the original dynamical system that are weighted linear summations of the state variables at the different nodes. Recently proposed methods use the leading eigenvector of the adjacency matrix of the network as the mixture weights to obtain such observables. In the present study, we explore performances of this type of one-dimensional reductions of dynamical systems on networks when we use non-leading eigenvectors of the adjacency matrix as the mixture weights. Our theory predicts that non-leading eigenvectors can be more efficient than the leading eigenvector and enables us to select the eigenvector minimizing the error. We numerically verify that the optimal non-leading eigenvector outperforms the leading eigenvector for some dynamical systems and networks. We also argue that, despite our theory, it is practically better to use the leading eigenvector as the mixture weights to avoid misplacing the bifurcation point too distantly and to be resistant against dynamical noise. © 2022, CC BY.

关键词： Eigenvalues and eigenfunctions