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arXiv 2025年

作者： Logan, Jack A. Sumner, Jacob Grigas, Alex T. Shattuck, Mark D. O'Hern, Corey S. Department of Mechanical Engineering Yale University New HavenCT06520 United States Graduate Program in Computational Biology & Biomedical Informatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department The City College of New York New YorkNY10031 United States Department of Applied Physics Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States

Proteins are composed of linear chains of amino acids that fold into complex three-dimensional structures. A general feature of folded proteins is that they are compact with a radius of gyration Rg(N) ∼ Nν that obeys power-law scaling with the number of amino acids N in each protein and ν ∼ 1/3. In this study, we investigate the internal scaling of the radius of gyration Rg(n) versus the chemical separation n between amino acids for all subchains of length n. We show that for globular proteins Rg(n) ∼ nν1,2 with a larger exponent ν1 > 1/3 for small n and a smaller exponent ν2 g(N) ∝ Nν. To describe this scaling behavior for Rg(n), we carry out folding simulations for a series of coarse-grained models for proteins beginning with the freely-jointed and freely-rotating chain models composed of spherical monomers and varying degrees of stereochemical constraints. We show that a minimal model, which coarse-grains amino acids into a single spherical backbone atom and one variable-sized spherical side-chain atom, and enforces bend- and dihedral-angle constraints, can recapitulate Rg(n) for x-ray crystal structures of globular proteins. In addition, this model predicts the correct average packing fraction and size of the hydrophobic core, which are two key physical features that can be used to distinguish between computational 'decoys' and correctly folded proteins in protein design applications. © 2025, CC BY.

关键词： Spheres

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Analytical approach to the mean-return-time phase of isotropic stochastic oscillators

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Physical Review E 2022年第2期105卷 024202-024202页

作者： Konstantin Holzhausen Peter J. Thomas Benjamin Lindner Bernstein Center for Computational Neuroscience Berlin Philippstr. 13 Haus 2 10115 Berlin Germany Physics Department of Humboldt University Berlin Newtonstr. 15 12489 Berlin Germany Department of Mathematics Applied Mathematics and Statistics 212 Yost Hall Case Western Reserve University 10900 Euclid Avenue Cleveland Ohio USA

One notion of phase for stochastic oscillators is based on the mean return-time (MRT): a set of points represents a certain phase if the mean time to return from any point in this set to this set after one rotation is equal to the mean rotation period of the oscillator (irrespective of the starting point). For this so far only algorithmically defined phase, we derive here analytical expressions for the important class of isotropic stochastic oscillators. This allows us to evaluate cases from the literature explicitly and to study the behavior of the MRT phase in the limits of strong noise. We also use the same formalism to show that lines of constant return time variance (instead of constant mean return time) can be defined, and that they in general differ from the MRT isochrons.

关键词： Stochastic processes Stochastic analysis Stochastic processes & statistics

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Coarse-graining conformational dynamics with multi-dimensional generalized Langevin equation: how, when, and why

arXiv

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arXiv 2024年

作者： Xie, Pinchen Qiu, Yunrui Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Chemistry University of Wisconsin-Madison MadisonWI53706 United States AI for Science Institute Beijing100080 China Center for Machine Learning Research School of Mathematical Sciences Peking University Beijing100084 China

A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained conformational dynamics. Constrained by the fluctuation-dissipation theorem, the approach can build coarse-grained models in dynamical consistency with all-atom molecular dynamics. We also propose practical criteria for AIGLE to enforce long-term dynamical consistency. Case studies of a toy polymer, with 20 coarse-grained sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling coarse-grained conformational dynamics in practice. © 2024, CC BY.

关键词： Coarse-grained modeling

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Thermodynamics and a Definite Large Half-Metallic Spin Gap Along with a Sizeable Magnetic Anisotropy in La-Doped Ba2niiro6

SSRN

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SSRN 2022年

作者： Naseem, Shahnila Alay-E-Abbas, Syed Muhammad Alay-e-Abbas Nazir, Safdar Department of Physics University of Sargodha Sargodha40100 Pakistan Applied Physics Division of Materials Science Department of Engineering Sciences and Mathematics Lulea University of Technology Lulea97187 Sweden Computational Materials Modeling Laboratory Department of Physics Government College University Faisalabad Faisalabad38040 Pakistan

Electron doping (i. e., by replacing Ba+2 with La+3) impact on the electronic and magnetic properties of Ba2NiIrO6 system is investigated using ab-initio calculations with the inclusion of Hubbard parameter U along with spin-orbit coupling effects. The calculated formation energies affirm the experimental realization of all motifs at ambient conditions. Whereas, the elastic properties confirm the mechanical stability, ductility, and thermal conductivity of all the structures. It is revealed that anti-ferromagnetic/ferromagnetic (FM) interaction between Ni and Ir ions are energetically stable in pristine motif having an energy band gap (Eg) of 0.70/0.35 eV using the GGA+U method without/with the inclusion of SOC effects, which is in good agreement with the recent experimental results [Inorg. Chem. 60, 1241 (2021)]. Interestingly, La-doped structures depict the half-metallic FM behavior except for 50% concentration, which results in conductivity of the spin-minority channel owing to the admixture of Ir 5d states. On the other hand, the spin-majority channels exhibit an insulating nature having a large E g of 2.53/2.63/2.49 eV for 12.5%/25%/37.5%, which looks sufficient to restrict the spin reversal and assure high spin filtering efficiency. Moreover, a substantial reduction in the moment of Ir ion for 37.5% and 50% La concentrations lead to the existence of the mixed-valence state of +6/+7 having a configuration of 5d3 (t32g↑t02g↓e0g↑e0g↓)/5d2(t22g↑t02g↓e0g↑e0g↓). Finally, a reasonable magneto-crystalline anisotropic constant of ∼×106 erg/cm3 in all La-doped Ba2NiIrO6 systems is predicted, which is a good signal for their potential utilization in data storage devices. © 2022, The Authors. All rights reserved.

关键词： Calculations

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Thermodynamics and a Definite Large Half-Metallic Spin Gap Along with a Sizeable Magnetic Anisotropy in La-Doped Ba2niiro6

SSRN

引用

SSRN 2022年

作者： Naseem, Shahnila Alay-E-Abbas, Syed Muhammad Nazir, Safdar Department of Physics University of Sargodha Sargodha40100 Pakistan Applied Physics Division of Materials Science Department of Engineering Sciences and Mathematics Lulea University of Technology Lulea97187 Sweden Computational Materials Modeling Laboratory Department of Physics Government College University Faisalabad Faisalabad38040 Pakistan

Electron doping (i. e., by replacing Ba+2 with La+3 ) impact on the electronic and magnetic properties of Ba2NiIrO6 system is investigated using ab-initio calculations with the inclusion of Hubbard parameter U along with spin-orbit coupling effects. The calculated formation energies affirm the experimental realization of all motifs at ambient conditions. Whereas, the elastic properties confirm the mechanical stability, ductility, and thermal conductivity of all the structures. It is revealed that anti-ferromagnetic/ferromagnetic (FM) interaction between Ni and Ir ions are energetically stable in pristine motif having an energy band gap (E g ) of 0.70/0.35 eV using the GGA+U method without/with the inclusion of SOC effects, which is in good agreement with the recent experimental results [Inorg. Chem. 60, 1241 (2021)]. Interestingly, La-doped structures depict the half-metallic FM behavior except for 50% concentration, which results in conductivity of the spin-minority channel owing to the admixture of Ir 5d states. On the other hand, the spin-majoritychannels exhibit an insulating nature having a large E g of 2.53/2.63/2.49 eV for 12.5%/25%/37.5%, which looks sufficient to restrict the spin reversal and assure high spin filtering efficiency. Moreover, La-doping leads to the existence of mixed-valence state of +6/+5 having a configuration 5d3 (t 32g ↑ t 02g ↓ e 0 g ↑ e 0 g ↓)/5d4 (t 32g ↑ t 12g ↓ e 0 g ↑ e 0 g ↓) for Ir ion. Finally, a reasonable magneto-crystallineanisotropic constant of ∼ ×10 6 erg/cm 3 in all La-doped Ba2NiIrO6 systems is predicted, which is agood signal for their potential utilization in data storage devices. © 2022, The Authors. All rights reserved.

关键词： Lanthanum compounds

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Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics

arXiv

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arXiv 2021年

作者： Wang, Dongdong Zhang, Linfeng Wang, Yanze Chang, Junhan Wang, Han Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States DP Technology Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China School of Mathematical Sciences Peking University Beijing China Department of Mathematics Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

Enhanced sampling methods such as metadynamics and umbrella sampling have become essential tools for exploring the configuration space of molecules and materials. At the same time, they have long faced a number of issues such as the inefficiency when dealing with a large number of collective variables (CVs) or systems with high free energy barriers. In this work, we show that with the clustering and adaptive tuning techniques, the reinforced dynamics (RiD) scheme can be used to efficiently explore the configuration space and free energy landscapes with a large number of CVs or systems with high free energy barriers. We illustrate this by studying various representative and challenging examples. Firstly we demonstrate the efficiency of adaptive RiD compared with other methods, and construct the 9-dimensional free energy landscape of peptoid trimer which has energy barriers of more than 8 kcal/mol. We then study the folding of the protein chignolin using 18 CVs. In this case, both the folding and unfolding rates are observed to be equal to 4.30 µs−1. Finally, we propose a protein structure refinement protocol based on RiD. This protocol allows us to efficiently employ more than 100 CVs for exploring the landscape of protein structures and it gives rise to an overall improvement of 14.6 units over the initial Global Distance Test-High Accuracy (GDT-HA) score. © 2021, CC BY.

关键词： Wave functions

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Doping-Induced Charge Density Wave and Ferromagnetism in the Van der Waals Semiconductor CrSBr

arXiv

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arXiv 2024年

作者： Feuer, Margalit L. Thinel, Morgan Huang, Xiong Cui, Zhi-Hao Shao, Yinming Kundu, Asish K. Chica, Daniel G. Han, Myung-Geun Pokratath, Rohan Telford, Evan J. Cox, Jordan York, Emma Okuno, Saya Huang, Chun-Ying Bukula, Owethu Nashabeh, Luca M. Qiu, Siyuan Nuckolls, Colin P. Dean, Cory R. Billinge, Simon J.L. Zhu, Xiaoyang Zhu, Yimei Basov, Dmitri N. Millis, Andrew J. Reichman, David R. Pasupathy, Abhay N. Roy, Xavier Ziebel, Michael E. Columbia University Department of Chemistry New YorkNY United States Columbia University Department of Physics New YorkNY United States Pennsylvania State University Department of Physics University ParkPA United States Brookhaven National Laboratory Condensed Matter Physics and Materials Science Department UptonNY United States Brookhaven National Laboratory National Synchrotron Light Source II UptonNY United States University of Basel Department of Chemistry Basel Switzerland Columbia University Department of Mechanical Engineering New YorkNY United States Columbia University Department of Applied Physics and Applied Mathematics New YorkNY United States Flatiron Institute Center for Computational Quantum Physics New YorkNY United States

In materials with one-dimensional electronic bands, electron-electron interactions can produce intriguing quantum phenomena, including spin-charge separation and charge density waves (CDW). Most of these systems, however, are non-magnetic, motivating a search for anisotropic materials where the coupling of charge and spin may affect emergent quantum states. Here, electron doping the van der Waals magnetic semiconductor CrSBr induces an electronically driven quasi-1D CDW, which survives above room temperature. Lithium intercalation also increases the magnetic ordering temperature to 200 K and changes its interlayer magnetic coupling from antiferromagnetic to ferromagnetic. The spin-polarized nature of the anisotropic bands that give rise to this CDW enforces an intrinsic coupling of charge and spin. The coexistence and interplay of ferromagnetism and charge modulation in this exfoliatable material provides a promising platform for studying tunable quantum phenomena across a range of temperatures and thicknesses. Copyright © 2024, The Authors. All rights reserved.

关键词： Van der Waals forces

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High-order accurate structure-preserving finite volume schemes on adaptive moving meshes for shallow water equations: well-balancedness and positivity

arXiv

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arXiv 2024年

作者： Zhang, Zhihao Tang, Huazhong Wu, Kailiang Center for Applied Physics and Technology HEDPS and LMAM School of Mathematical Sciences Peking University Beijing100871 China Nanchang Hangkong University Jiangxi Province Nanchang330000 China Department of Mathematics Shenzhen International Center for Mathematics Southern University of Science and Technology Guangdong Shenzhen518055 China Guangdong Provincial Key Laboratory of Computational Science and Material Design Shenzhen518055 China

This paper develops high-order accurate, well-balanced (WB), and positivity-preserving (PP) finite volume schemes for shallow water equations on adaptive moving structured meshes. The mesh movement poses new challenges in maintaining the WB property, which not only depends on the balance between flux gradients and source terms but is also affected by the mesh movement. To address these complexities, the WB property in curvilinear coordinates is decomposed into flux source balance and mesh movement balance. The flux source balance is achieved by suitable decomposition of the source terms, the numerical fluxes based on hydrostatic reconstruction, and appropriate discretization of the geometric conservation laws (GCLs). Concurrently, the mesh movement balance is maintained by integrating additional schemes to update the bottom topography during mesh adjustments. The proposed schemes are rigorously proven to maintain the WB property by using the discrete GCLs and these two balances. We provide rigorous analyses of the PP property under a sufficient condition enforced by a PP limiter. Due to the involvement of mesh metrics and movement, the analyses are nontrivial, while some standard techniques, such as splitting high-order schemes into convex combinations of formally first-order PP schemes, are not directly applicable. Various numerical examples validate the high-order accuracy, high efficiency, WB, and PP properties of the proposed schemes. Copyright © 2024, The Authors. All rights reserved.

关键词： Mesh generation

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Intelligent Attractors for Singularly Perturbed Dynamical Systems

arXiv

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arXiv 2024年

作者： Serino, Daniel A. Loya, Allen Alvarez Burby, Joshua W. Kevrekidis, Ioannis G. Tang, Qi Los Alamos National Laboratory Los Alamos NM United States Department of Physics University of Texas at Austin AustinTX United States Department of Chemical and Biomolecular Engineering Department of Applied Mathematics and Statistics Johns Hopkins University BaltimoreMD United States School of Computational Science and Engineering Georgia Institute of Technology AtlantaGA United States

Singularly perturbed dynamical systems play a crucial role in climate dynamics and plasma physics. A powerful and well-known tool to address these systems is the Fenichel normal form, which significantly simplifies fast dynamics near slow manifolds through a transformation. However, this normal form is difficult to realize in conventional numerical algorithms. In this work, we explore an alternative way of realizing it through structure-preserving machine learning. Specifically, a fast-slow neural network (FSNN) is proposed for learning data-driven models of singularly perturbed dynamical systems with dissipative fast timescale dynamics. Our method enforces the existence of a trainable, attracting invariant slow manifold as a hard constraint. Closed-form representation of the slow manifold enables efficient integration on the slow time scale and significantly improves prediction accuracy beyond the training data. We demonstrate the FSNN on examples including the Grad moment system, two-scale Lorenz96 equations, and Abraham-Lorentz dynamics modeling radiation reaction of electrons. © 2024, CC BY.

关键词： Neural networks

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Explicitly correlated configuration interaction investigation on low-lying states of SiO^+ and SiO

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Chinese physics B 2019年第4期28卷 157-164页

作者： Rui Li Gui-Ying Liang Xiao-He Lin Yu-Hao Zhu Shu-Tao Zhao Yong Wu Department of Physics College of Science Qiqihar University Institute of Applied Physics and Computational Mathematics School of Physics and Electronic Science Fuyang Normal University HEDPS Center for Applied Physics and Technology Peking University

SiO^+ and SiO, which play vital roles in astrophysics and astrochemistry, have long attracted considerable ***, accurate information about excited states of SiO^+ is still limited. In this work, the structures of 14 Λ–S states and 30? states of SiO^+ are computed with explicitly correlated configuration interaction method. On the basis of the calculated potential energy curves of those Λ–S states and ? states, the spectroscopic constants of bound states are evaluated, which are in good agreement with the latest experimental results. The predissociation mechanism of B^2Σ^+ state is illuminated with the aid of spin–orbit coupling matrix elements. On the basis of the calculated potential energy curves and transition dipole moments, the radiative lifetime for each of low-lying vibrational states B^2Σ^+and A^2Π is estimated. The laser cooling scheme of SiO^+ is proposed by employing B^2Σ^+–X^2Σ^+ transition. Finally, the vertical ionization energy values from SiO(X^1Σ^+) to ionic states: SiO^+ , X^2Σ^+, B^2Σ^+, and A^2Π are calculated, which agree well with experimental measurements.

关键词： SiO+ explicitly correlated configuration interaction transition dipole moment ionization energy

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