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Structure Of Biomolecules Through Molecular Dynamics Simulations

Procedia Computer Science 2019年 156卷 69-78页

作者： Maria Arnittali Anastassia N. Rissanou Vagelis Harmandaris Institute of Applied and Computational Mathematics Foundation for Research and Technology Hellas Heraklion Crete GR-70013 Greece Department of Mathematics and Applied Mathematics University of Crete Voutes Campus Heraklion Crete GR-70013 Greece

Proteins are complex biological macromolecules performing a great variety of functions in the living systems. In order to get insight into the atomic structures and the time evolution of proteins, besides experimental techniques, mathematical and computational modeling approaches can be also used. Nowadays, Molecular Dynamics (MD) simulations constitute a powerful technique for understanding the physical basis of the structure of proteins, since via MD simulations someone can obtain information about proteins at the microscopic level and express it in macroscopic properties. In the current work, we present a detailed simulation approach concerning the modeling of two proteins in the native state, through all-atom Molecular Dynamics simulations under specific (physiological) conditions. The homodimeric Rop protein, that is a paradigm of a canonical 4-a-helical bundle, and its loopless mutation (RM6) are studied in aqueous solution. Their structural, conformational properties, as well as their hydrogen bond network, are characterized in atomic detail. Our findings reveal that both Rop and RM6 proteins have stable native states. The stability of the secondary conformation can be attributed to the formation of hydrogen bonds. The calculation of the root mean square deviation (RMSD) verifies that the system is in an equilibrated structure, validating at the same time, our model. Furthermore, the stereochemical quality of our protein models is demonstrated through the calculation of the Ramachandran plot. Finally, the thermal stability of RM6 protein is studied, and the results show that it is a hyperthermostable protein.

关键词： Proteins ROP RM6 Molecular Dynamics Simulations Native State Protein Stability

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A posteriori error estimate for the IPDGFEM of a general problem of the strain gradient elasticity theory in 2D

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AIP Conference Proceedings 2021年第1期2343卷

作者： Konstantinos G. Eptaimeros Institute of Applied and Computational Mathematics Foundation for Research and Technology 100 N. Plastira Str. Vassilika Vouton Heraklion Crete Greece 70013

The strain gradient elasticity theory (SGET) introduces the microstructure to the constitutive equations to explain the material size effects. The constitutive equations of the SGET appear a boundary layer [1, 2]. The interior penalty discontinuous Galerkin finite element method (IPDGFEM) is suitable to handle the boundary layer and the mesh design as well as vary the polynomial degree in the local basis functions. This research objective centers on carrying out an a posteriori error analysis for the (symmetric) IPDGFEM of a general problem of the SGET in 2D.

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The Hydrogen Intensity Real-Time Analysis eXperiment: Overview and Status Update

The Hydrogen Intensity Real-Time Analysis eXperiment: Overvi...

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European Conference on Antennas and Propagation, EuCAP

作者： Anthony Walters Keshav Bechoo Shruti Bhatporia H. Cynthia Chiang Devin Crichton Jacobus Diener Sindhu Gaddam Kit Gerodias Austin Gumba Neeraj Gupta Surajit Kalita Emily Kuhn Martin Kunz Kavilan Moodley Warren Naidoo Viraj Nistane Tasmiya Papiah Aditi Pattabhiraman Aritha Pillay Alice Pisani Isibabale Qhoboshiyane Alexandre Refregier Edwin Retana-Montenegro Benjamin R. B. Saliwanchik Ajith Sampath Tsepo Sekhoasha Mugundhan Vijayaraghavan Amanda Weltman Astrophysics Research Centre University of KwaZulu-Natal Westville Campus Durban South Africa School of Mathematics Statistics & Computer Science University of KwaZulu-Natal Westville Campus Durban South Africa Department of Mathematics and Applied Mathematics High Energy Physics Cosmology & Astrophysics Theory (HEPCAT) Group University of Cape Town Cape Town South Africa Department of Physics McGill University Quebec Canada Institute for Particle Physics and Astrophysics ETH Zürich Zürich Switzerland Department of Physics and Astronomy Botswana International University of Science and Technology Palapye Botswana Inter-University Centre for Astronomy and Astrophysics Pune India NASA Jet Propulsion Laboratory California Institute of Technology Pasadena CA USA Département de Physique Théorique and Centre for Astroparticle Physics Université de Genève Geneva Switzerland Stanford University Stanford CA Center for Computational Astrophysics Flatiron Institute New York NY USA The Cooper Union for the Advancement of Science and Art New York NY USA Department of Electronic and Computer Engineering Durban University of Technology Durban South Africa Department of Astrophysical Sciences Peyton Hall Princeton University Princeton NJ USA Instrumentation Division Brookhaven National Laboratory Upton NY USA Onsala Space Observatory Chalmers University of Technology Gothenburg Sweden

The Hydrogen Intensity Real-time Analysis eXperiment (HIRAX) will be a large interferometric array of drift-scan radio telescopes designed to map the large-scale spatial fluctuations of neutral hydrogen in the Universe, in order to better understand the nature of dark energy. It will operate between 400–800 MHz, and is currently under construction in the Karoo desert of South Africa. It will also be a powerful tool for studying astronomical transients and the evolution of galaxies. Here we present an overview of the project, its anticipated deployment timelines, and highlight some of the characterisation and calibration efforts that are currently underway, or planned for the future.

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(f, Γ)-divergences: Interpolating between f-divergences and integral probability metrics

arXiv

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arXiv 2020年

作者： Birrell, Jeremiah Dupuis, Paul Katsoulakis, Markos A. Pantazis, Yannis Rey-Bellet, Luc TRIPODS Institute for Theoretical Foundations of Data Science University of Massachusetts Amherst AmherstMA01003 United States Division of Applied Mathematics Brown University ProvidenceRI02912 United States Department of Mathematics and Statistics University of Massachusetts Amherst AmherstMA01003 United States Institute of Applied and Computational Mathematics Foundation for Research and Technology - Hellas HeraklionGR-70013 Greece

We develop a rigorous and general framework for constructing information-theoretic divergences that subsume both f-divergences and integral probability metrics (IPMs), such as the 1-Wasserstein distance. We prove under which assumptions these divergences, hereafter referred to as (f, Γ)- divergences, provide a notion of 'distance' between probability measures and show that they can be expressed as a two-stage mass-redistribution/mass-transport process. The (f, Γ)-divergences inherit features from IPMs, such as the ability to compare distributions which are not absolutely continuous, as well as from f-divergences, namely the strict concavity of their variational representations and the ability to control heavy-tailed distributions for particular choices of f. When combined, these features establish a divergence with improved properties for estimation, statistical learning, and uncertainty quantification applications. Using statistical learning as an example, we demonstrate their advantage in training generative adversarial networks (GANs) for heavy-tailed, not-absolutely continuous sample distributions. We also show improved performance and stability over gradientpenalizedWasserstein GAN in image generation. Copyright © 2020, The Authors. All rights reserved.

关键词： Generative adversarial networks

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Evolutionary convergence of sensory circuits in the pallium of amniotes

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Science (New York, N.Y.) 2025年第6735期387卷 eadp3411页

作者： Rueda-Alaña, Eneritz Senovilla-Ganzo, Rodrigo Grillo, Marco Vázquez, Enrique Marco-Salas, Sergio Gallego-Flores, Tatiana Ordeñana-Manso, Aitor Ftara, Artemis Escobar, Laura Benguría, Alberto Quintas, Ana Dopazo, Ana Rábano, Miriam Vivanco, María dM Aransay, Ana María Garrigos, Daniel Toval, Ángel Ferrán, José Luis Nilsson, Mats Encinas-Pérez, Juan Manuel De Pittà, Maurizio García-Moreno, Fernando Achucarro Basque Center for Neuroscience Scientific Park of the University of the Basque Country (UPV/EHU) Leioa Spain Department of Neuroscience Faculty of Medicine and Odontology UPV/EHU Barrio Sarriena s/n Leioa Bizkaia Spain Science for Life Laboratory Department of Biophysics and Biochemistry Stockholm University Solna Sweden Genomics Unit Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) Madrid Spain Center for Cooperative Research in Biosciences (CIC bioGUNE) Basque Research and Technology Alliance (BRTA) Bizkaia Technology Park Derio Spain Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) Madrid Spain Department of Human Anatomy Medical School University of Murcia and Murcia Arrixaca Institute for Biomedical Research Murcia Spain IKERBASQUE Foundation Bilbao Spain Basque Center for Applied Mathematics Bilbao Spain Computational Neuroscience Hub Krembil Research Institute University Health Network Toronto ON Canada Department of Physiology Temerty Faculty of Medicine University of Toronto Toronto ON Canada

The amniote pallium contains sensory circuits that are structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. We used birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko), and mammals (mouse). We reveal that neurons within these circuits' stations are generated at varying developmental times and brain regions across species and found an early developmental divergence in the transcriptomic progression of glutamatergic neurons. Our research highlights developmental distinctions and functional similarities in the sensory circuit between birds and mammals, suggesting the convergence of high-order sensory processing across amniote lineages.

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Studies of laser-plasma interaction physics with low-density targets for direct-drive inertial confinement fusion on the Shenguang III prototype

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Matter and Radiation at Extremes 2021年第2期6卷 54-66页

作者： V.T.Tikhonchuk T.Gong N.Jourdain O.Renner F.P.Condamine K.Q.Pan W.Nazarov L.Hudec J.Limpouch R.Liska M.Krus F.Wang D.Yang S.W.Li Z.C.Li Z.Y.Guan Y.G.Liu T.Xu X.S.Peng X.M.Liu Y.L.Li J.Li T.M.Song J.M.Yang S.E.Jiang B.H.Zhang W.Y.Huo G.Ren Y.H.Chen W.Zheng Y.K.Ding K.Lan S.Weber ELI-Beamlines Institute of PhysicsCzech Academy of Sciences25241 Dolni BrezanyCzech Republic Centre Lasers Intenses et Applications University of Bordeaux-CNRS-CEA33405 TalenceFrance Laser Fusion Research Center China Academy of Engineering PhysicsMianyang 621900China Institute of Plasma Physics Czech Academy of Sciences18200 PragueCzech Republic Independent Foam Target Supplier CarnoustieDD76DPUnited Kingdom Faculty of Nuclear Sciences and Physical Engineering Czech Technical University in Prague11519 PragueCzech Republic Institute of Applied Physics and Computational Mathematics Beijing 100088China Center for Applied Physics and Technology Peking UniversityBeijing 100871China School of Science Xi’an Jiaotong UniversityXi’an 710049China

The physics of laser-plasma interaction is studied on the Shenguang III prototype laser facility under conditions relevant to inertial confinement fusion designs.A sub-millimeter-size underdense hot plasma is created by ionization of a low-density plastic foam by four high-energy(3.2 kJ)laser *** interaction beam is fired with a delay permitting evaluation of the excitation of parametric instabilities at different stages of plasma *** diagnostics are used for plasma characterization,scattered radiation,and accelerated *** experimental results are analyzed with radiation hydrodynamic simulations that take account of foam ionization and *** measured level of stimulated Raman scattering is almost one order of magnitude larger than that measured in experiments with gasbags and hohlraums on the same installation,possibly because of a greater plasma *** amplification is achieved in high-intensity speckles,indicating the importance of implementing laser temporal smoothing techniques with a large bandwidth for controlling laser propagation and absorption.

关键词： density. interaction scattered

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The Deterministic and Stochastic Shallow Lake Problem 1

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Conference in Honor of the 75th Birthday of S.R.S. Varadhan, 2016

作者： Kossioris, G.T. Loulakis, M. Souganidis, P.E. Department of Mathematics and Applied Mathematics Voutes Campus University of Crete Heraklion700 13 Greece School of Applied Mathematical and Physical Sciences National Technical University of Athens Athens157 80 Greece Institute of Applied and Computational Mathematics-Foundation of Research and Technology Hellas Heraklion700 13 Greece Department of Mathematics University of Chicago 5734 S. University Avenue ChicagoIL60637 United States

ISBN: (数字)9783030153380

ISBN: (纸本)9783030153373

We study the welfare function of the deterministic and stochastic shallow lake problem. We show that the welfare function is the viscosity solution of the associated Bellman equation, we establish several properties including its asymptotic behaviour at infinity and we present a convergent monotone numerical scheme. © Springer Nature Switzerland AG 2019.

关键词： Stochastic systems

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First polar direct-drive exploding-pusher target experiments on the ShenGuang laser facility

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Chinese Physics B 2019年第9期28卷 288-294页

作者： Bo Yu Jiamin Yang Tianxuan Huang Peng Wang Wanli Shang Xiumei Qiao Xuewei Deng Zhanwen Zhang Zifeng Song Qi Tang Xiaoshi Peng Jiabin Chen Yulong Li Wei Jiang Yudong Pu Ji Yan Zhongjing Chen Yunsong Dong Wudi Zheng Feng Wang Shaoen Jiang Yongkun Ding Jian Zheng Laser Fusion Research Center China Academy of Engineering PhysicsMianyang 621900China Department of Modern Physics University of Science and Technology of ChinaHefei 230026China Institute of Applied Physics and Computational Mathematics Beijing 100088China IFSA Collaborative Innovation Center Shanghai Jiao Tong UniversityShanghai 200240China

Low density and low convergence implosion occurs in the exploding-pusher target experiment, and generates neutrons isotropically to develop a high yield *** order to validate the performance of ShenGuang(SG) laser facility and test nuclear diagnostics, all 48-beam lasers with an on-target energy of 48 kJ were firstly used to drive room-temperature, DT gas-filled glass *** optimization has been carried out and optimal drive uniformity was obtained by the combination of beam repointing and *** final irradiation uniformity of less than 5% on polar direct-drive capsules of 540 μm in diameter was achieved, and the highest thermonuclear yield of the polar direct-drive DT fuel implosion at the SG was 1.04 × 10^(13).The experiment results show neutron yields severely depend on the irradiation uniformity and laser timing,and decrease with the increase of the diameter and fuel pressure of the *** thin CH ablator does not impact the implosion performance, but the laser drive uniformity is *** simulated results validate that the cos γ distribution laser design is reasonable and can achieve a symmetric pressure *** optimization will focus on measuring the symmetry of the hot spot by self-emission imaging, increasing the diameter, and decreasing the fuel pressure.

关键词： polar direct-drive exploding-pusher target neutron yield irradiation uniformity

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A machine learning-based high-precision density functional method for drug-like molecules

Artificial Intelligence Chemistry

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Artificial Intelligence Chemistry 2024年第1期2卷

作者： Jin Xiao YiXiao Chen LinFeng Zhang Han Wang Tong Zhu Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development Shanghai Frontiers Science Center of Molecule Intelligent Syntheses School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 P.R. China Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 USA AI for Science Institute Beijing 100080 P.R. China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing 100088 P.R. China NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 P.R. China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518005 P.R. China

In computer-aided drug discovery, accurately determining the structure and properties of drug-like molecules is of utmost importance. This necessitates the use of precise and efficient electronic structure methods. Here, we developed two deep learning-based density functional methods, namely DeePHF and DeePKS, specifically tailored for drug-like molecules. Notably, DeePKS incorporates self-consistency into its framework. With a limited dataset labelled at the CCSD(T)/def2-TZVP level, both models have been able to achieve chemical accuracy in calculating molecular energies and have demonstrated excellent transferability. We anticipate that further advancements in this field will lead to the development of high-quality density functional methods designed specifically for drug discovery purposes. This research showcases the capabilities of deep learning approaches in simplifying the construction complexity associated with traditional DFT methods.

关键词： Machine Learning Density Functional Theory DeePHF DeePKS

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The underestimation of high pressure in DFT+U simulation for the wide range cold-pressure of lanthanide metals

arXiv

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arXiv 2021年

作者： Wang, Yue-Chao Liu, Bei-Lei Liu, Yu Liu, Hai-Feng Bi, Yan Gao, Xing-Yu Sheng, Jie Song, Hong-Zhou Tian, Ming-Feng Song, Hai-Feng Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China School of Mathematical Sciences Beijing Normal University Beijing100875 China Center for High Pressure Science and Technology Advanced Research Beijing100094 China National Key Laboratory for Shock Wave and Detonation Physics Institute of Fluid Physics CAEP Mianyang621900 China Graduate School of China Academy of Engineering Physics Beijing100088 China

Density functional theory plus U (DFT+U) is one of the most efficient first-principles methods to simulate the cold pressure properties of strongly-correlated materials. However, the applicability of DFT+U at ultra-high pressure is not sufficiently studied, especially in the widely-used augmented schemes [such as projector augmented wave (PAW) and linearized augmented plane wave (LAPW)]. This work has systematically investigated the performance of DFT+U in PAW and LAPW at the pressure up to several hundred GPa for the lanthanide metals, which is a typical strongly-correlated series. We found DFT+U simulation in PAW exhibits an unphysical underestimation of pressure in high-pressure region, which was not observed in conventional DFT simulation. By delicate analysis and comparison with local-orbital-independent hybrid functional results, we have demonstrated that this unphysical behavior is related to a normalization problem on the local density matrix caused by the overlap of local orbitals in PAW under high pressure. Additionally, we observed a slight underestimating of pressure in correlation correction methods in heavy lanthanides (Tm, Yb and Lu) in high-pressure region comparing with the DFT results without the influence of local orbital overlap, and it might be related to the enhancement of binding between atoms in correlation correction methods at high pressure. Our work reveals the underestimation of high pressure in DFT+U simulation, analyses two sources of this unusual behavior and proposes their mechanism. Most importantly, our investigation highlights the breakdown of DFT+U for high pressure simulation in VASP package based on PAW framework. Copyright © 2021, The Authors. All rights reserved.

关键词： Density functional theory

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