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Non-orthogonal multi-slater determinant expansions in auxiliary field quantum Monte Carlo

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arXiv 2018年

作者： Borda, Edgar Josué Landinez Gomez, John Morales, Miguel A. Lawrence Livermore National Laboratory LivermoreCA94550 United States Applied Physics Program and Department of Chemistry Rice University HoustonTX77005-1892 United States

The Auxiliary-Field Quantum Monte Carlo (AFQMC) algorithm is a powerful quantum many-body method that can be used successfully as an alternative to standard quantum chemistry approaches to compute the ground state of many body systems, such as molecules and solids, with high accuracy. In this article we use AFQMC with trial wave-functions built from non-orthogonal multi Slater determinant expansions to study the energetics of molecular systems, including the 55 molecules of the G1 test set and the isomerization path of the [Cu2O2]2+molecule. The main goal of this study is to show the ability of non-orthogonal multi Slater determinant expansions to produce high-quality, compact trial wave-functions for quantum Monte Carlo methods. We obtain systematically improvable results as the number of determinants is increased, with high accuracy typically obtained with tens of determinants. Great reduction in the average error and traditional statistical indicators are observed in the total and absorption energies of the molecules in the G1 test set with as few as 10-20 determinants. In the case of the relative energies along the isomerization path of the [Cu2O2]2+, our results compare favorably with other advanced quantum many-body methods, including DMRG and complete-renormalized CCSD(T). Discrepancies in previous studies for this molecular problem are identified and attributed to the differences in the number of electrons and active spaces considered in such calculations. Copyright © 2018, The Authors. All rights reserved.

关键词： Molecules

Probing the Band Structure of Topological Silicon Photonic Lattices in the Visible Spectrum

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Physical Review Letters 2019年第11期122卷 117401-117401页

作者： Siying Peng (彭斯颖) Nick J. Schilder Xiang Ni Jorik van de Groep Mark L. Brongersma Andrea Alù Alexander B. Khanikaev Harry A. Atwater Albert Polman Applied Physics California Institute of Technology Pasadena California 91125 USA Center for Nanophotonics AMOLF Science Park 104 1098 XG Amsterdam Netherlands Department of Electrical Engineering City College of City University of New York New York 10031 USA Physics Program The Graduate Center City University of New York 365 Fifth Avenue New York New York 10016 USA Geballe Laboratory for Advanced Materials Stanford University 476 Lomita Mall Stanford California 94305 USA Photonics Initiative Advanced Science Research Center City University of New York 85 St. Nicholas Terrace New York New York 10031 USA

We study two-dimensional hexagonal photonic lattices of silicon Mie resonators with a topological optical band structure in the visible spectral range. We use 30 keV electrons focused to nanoscale spots to map the local optical density of states in topological photonic lattices with deeply subwavelength resolution. By slightly shrinking or expanding the unit cell, we form hexagonal superstructures and observe the opening of a band gap and a splitting of the double-degenerate Dirac cones, which correspond to topologically trivial and nontrivial phases. Optical transmission spectroscopy shows evidence of topological edge states at the domain walls between topological and trivial lattices.

关键词： Nanophotonics Photonic crystals Topological effects in photonic systems

Phototactic robot tunable by sensorial delays

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arXiv 2018年

作者： Leyman, Maximilian Ogemark, Freddie Wehr, Jan Volpe, Giovanni Department of Physics University of Gothenburg GothenburgSE-41296 Sweden Department of Physics Chalmers University of Technology GothenburgSE-41296 Sweden Department of Mathematics and Program in Applied Mathematics University of Arizona TucsonAZ85721 United States

The presence of a delay between sensing and reacting to a signal can determine the long-term behavior of autonomous agents whose motion is intrinsically noisy. In a previous work [M. Mijalkov, A. McDaniel, J. Wehr, and G. Volpe, Phys. Rev. X 6, 011008 (2016)], we have shown that sensorial delay can alter the drift and the position probability distribution of an autonomous agent whose speed depends on the illumination intensity it measures. Here, using theory, simulations, and experiments with a phototactic robot, we generalize this effect to an agent for which both speed and rotational diffusion depend on the illumination intensity and are subject to two independent sensorial delays. We show that both the drift and the probability distribution are influenced by the presence of these sensorial delays. In particular, the radial drift may have positive as well as negative sign, and the position probability distribution peaks in different regions depending on the delay. Furthermore, the presence of multiple sensorial delays permits us to explore the role of the interaction between them. Copyright © 2018, The Authors. All rights reserved.

关键词： Autonomous agents

Controlled Continuous Evolution of Enzymatic Activity Screened at Ultrahigh Throughput Using Drop-Based Microfluidics

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Angewandte Chemie 2023年第24期135卷

作者： R. G. Rosenthal X. Diana Zhang K. Ilić Đurđić J. J. Collins D. A. Weitz School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA Institute for Medical Engineering and Science Massachusetts Institute of Technology 77 Massachusetts Ave Cambridge MA 02139 USA Wyss Institute for Biologically Inspired Engineering Harvard University 3 Blackfan Circle Boston MA 02115 USA University of Belgrade-Faculty of Chemistry Studentski trg 12–16 11000 Belgrade Serbia Department of Biological Engineering Massachusetts Institute of Technology 77 Massachusetts Ave Cambridge MA 02139 USA Synthetic Biology Center Massachusetts Institute of Technology 77 Massachusetts Ave Cambridge MA 02139 USA Harvard-MIT Program in Health Sciences and Technology Massachusetts Institute of Technology 77 Massachusetts Ave Cambridge MA 02139 USA Broad Institute of MIT and Harvard 415 Main St Cambridge MA 02142 USA Department of Physics Harvard University Cambridge MA 02138 USA

Enzymes are highly specific catalysts delivering improved drugs and greener industrial processes. Naturally occurring enzymes must typically be optimized which is often accomplished through directed evolution; however, this is still a labor- and capital-intensive process, due in part to multiple molecular biology steps including DNA extraction, in vitro library generation, transformation, and limited screening throughput. We present an effective and broadly applicable continuous evolution platform that enables controlled exploration of fitness landscape to evolve enzymes at ultrahigh throughput based on direct measurement of enzymatic activity. This drop-based microfluidics platform cycles cells between growth and mutagenesis followed by screening with minimal human intervention, relying on the nCas9 chimera with mutagenesis polymerase to produce in vivo gene diversification using sgRNAs tiled along the gene. We evolve alditol oxidase to change its substrate specificity towards glycerol, turning a waste product into a valuable feedstock. We identify a variant with a 10.5-fold catalytic efficiency.

关键词： CRISPR-Directed Evolution Continuous Evolution Droplet Microfluidics Protein Engineering Sustainable Chemistry

Early Detection of Preeclampsia using a Rule-Based System Information System

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Journal of physics: Conference Series 2019年第1期1179卷

作者： F N Aini M N Widyawati S Suryono Purwokerto Midwifery Program Poltekkes Kemenkes Semarang Indonesia Postgraduate Applied Science Midwifery Program Poltekkes Kemenkes Semarang Indonesia Department of Physics Faculty of Science and Mathematics University Diponegoro Semarang Indonesia

Preeclampsia is the highest cause of maternal death. One program to reduce Maternal Mortality Rate (MMR) is by early detection. The incomplete history of maternal history that has occurred has led to the determination of an incorrect diagnosis and has resulted in errors in decision making. The results of the survey in the detection of preeclampsia include midwives not conducting a history of past medical history, physical examination during the first antenatal care visit is incomplete. During this time the detection and diagnosis model is still done manually, so it was not effective and efficient. The inspection data obtained using the information system becomes more complete and faster. Data obtained with information systems can be seen anywhere and anytime. This study produced innovations for the detection of preeclampsia in pregnant women using a rule-based system information system. This study uses the Quasy experimental posttest-only design. The subjects of this study were 66 pregnant women. Data collection was carried out using questionnaires and checklists. The results showed that early detection of preeclampsia using a rule-based system information system could improve the completeness of data on pregnant women up to 35.66%, and speed up the detection time of preeclampsia up to 35.60%. This system also has an effectivenessvalue 84.8%.

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The Athena++ Adaptive Mesh Refinement Framework: Design and Magnetohydrodynamic Solvers

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Astrophysical Journal, Supplement Series 2020年第1期249卷

作者： Stone, James M. Tomida, Kengo White, Christopher J. Felker, Kyle G. Department of Astrophysical Sciences Princeton University Princeton 08544 NJ United States Program in Applied and Computational Mathematics Princeton University Princeton 08544 NJ United States Department of Earth and Space Science Osaka University Toyonaka Osaka 560-0043 Japan Kavli Institute for Theoretical Physics University of California Santa Barbara Santa Barbara 93107 CA United States School of Natural Sciences Institute for Advanced Study Princeton 08544 NJ United States Astronomical Institute Tohoku University Sendai Miyagi 980-8578 Japan Argonne National Laboratory Lemont 60439 IL United States

The design and implementation of a new framework for adaptive mesh refinement calculations are described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use for a wide variety of physics. The framework works with both uniform and nonuniform grids in Cartesian and curvilinear coordinate systems. It adopts a dynamic execution model based on a simple design called a "task list"that improves parallel performance by overlapping communication and computation, simplifies the inclusion of a diverse range of physics, and even enables multiphysics models involving different physics in different regions of the calculation. We describe physics modules implemented in this framework for both nonrelativistic and relativistic magnetohydrodynamics (MHD). These modules adopt mature and robust algorithms originally developed for the Athena MHD code and incorporate new extensions: support for curvilinear coordinates, higher-order time integrators, more realistic physics such as a general equation of state, and diffusion terms that can be integrated with super-time-stepping algorithms. The modules show excellent performance and scaling, with well over 80% parallel efficiency on over half a million threads. The source code has been made publicly available. © 2020. The American Astronomical Society. All rights reserved..

关键词： Astronomy software Magnetohydrodynamics

Multi-wavelength study of the galactic PeVatron candidate LHAASO J2108+5157

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arXiv 2022年

作者： Abe, S. Aguasca-Cabot, A. Agudo, I. Alvarez Crespo, N. Antonelli, L.A. Aramo, C. Arbet-Engels, A. Artero, M. Asano, K. Aubert, P. Baktash, A. Bamba, A. Baquero Larriva, A. Baroncelli, L. Barres de Almeida, U. Barrio, J.A. Batkovic, I. Baxter, J. Becerra González, J. Bernardini, E. Bernardos, M.I. Bernete Medrano, J. Berti, A. Bhattacharjee, P. Biederbeck, N. Bigongiari, C. Bissaldi, E. Blanch, O. Bordas, P. Buisson, C. Bulgarelli, A. Burelli, I. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Cassol, F. Cauz, D. Ceribella, G. Chai, Y. Cheng, K. Chiavassa, A. Chikawa, M. Chytka, L. Cifuentes, A. Contreras, J.L. Cortina, J. Costantini, H. D'Amico, G. Dalchenko, M. De Angelis, A. de Bony de Lavergne, M. De Lotto, B. de Menezes, R. Deleglise, G. Delgado, C. Delgado Mengual, J. della Volpe, D. Dellaiera, M. Di Piano, A. Di Pierro, F. Di Tria, R. Di Venere, L. Díaz, C. Dominik, R.M. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Elsässer, D. Emery, G. Escudero, J. Fallah Ramazani, V. Ferrara, G. Fiasson, A. Freixas Coromina, L. Fröse, S. Fukami, S. Fukazawa, Y. Garcia, E. Garcia López, R. Gasparrini, D. Geyer, D. Giesbrecht Paiva, J. Giglietto, N. Giordano, F. Giro, E. Gliwny, P. Godinovic, N. Grau, R. Green, D. Green, J. Gunji, S. Hackfeld, J. Hadasch, D. Hahn, A. Hashiyama, K. Hassan, T. Hayashi, K. Heckmann, L. Heller, M. Herrera Llorente, J. Hirotani, K. Hoffmann, D. Horns, D. Houles, J. Hrabovsky, M. Hrupec, D. Hui, D. Hütten, M. Imazawa, R. Inada, T. Inome, Y. Ioka, K. Iori, M. Ishio, K. Iwamura, Y. Jacquemont, M. Jimenez Martinez, I. Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kerszberg, D. Kobayashi, Y. Kong, A. Kubo, H. Kushida, J. Lainez, M. Lamanna, G. Lamastra, A. Le Flour, T. Linhoff, M. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Loporchio, S. Lorini, A. Luque-Escamilla, P.L. Majumdar, P. Makariev, M. Mandat, D. Manganaro, M. Manicò, G. Mannheim, K. Mariotti, M. Marquez, P. Marsella, G. Martí, J. Martinez, O. Institute for Cosmic Ray Research University of Tokyo 5-1-5 Kashiwa-no-ha Kashiwa Chiba277-8582 Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Martí i Franquès 1 Barcelona08028 Spain Instituto de Astrofísica de Andalucía CSIC Glorieta de la Astronomía s/n Granada18008 Spain Grupo de Electronica Universidad Complutense de Madrid Av. Complutense s/n Madrid28040 Spain INAF - Osservatorio Astronomico di Roma Via di Frascati 33 Monteporzio Catone00040 Italy INFN Sezione di Napoli Via Cintia ed. G Napoli80126 Italy Max-Planck-Institut für Physik Föhringer Ring 6 München80805 Germany The Barcelona Institute of Science and Technology Campus UAB Bellaterra Barcelona08193 Spain Univ. Savoie Mont Blanc CNRS Laboratoire d'Annecy de Physique des Particules - IN2P3 Annecy74000 France Universität Hamburg Institut für Experimentalphysik Luruper Chaussee 149 Hamburg22761 Germany Graduate School of Science University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-0033 Japan EMFTEL department IPARCOS Universidad Complutense de Madrid Madrid28040 Spain INAF - Osservatorio di Astrofisica e Scienza dello spazio di Bologna Via Piero Gobetti 93/3 Bologna40129 Italy Centro Brasileiro de Pesquisas Físicas Rua Xavier Sigaud 150 RJ Rio de Janeiro22290-180 Brazil INFN Sezione di Padova Università degli Studi di Padova Via Marzolo 8 Padova35131 Italy Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Tenerife La Laguna Spain CIEMAT Avda. Complutense 40 Madrid28040 Spain Department of Physics TU Dortmund University Otto-Hahn-Str. 4 Dortmund44227 Germany INFN Sezione di Bari Politecnico di Bari via Orabona 4 Bari70124 Italy INFN Sezione di Trieste Università degli studi di Udine via delle scienze 206 Udine33100 Italy INFN Sezione di Catania Via S. Sofia 64 Catania95123 Italy Via del Fosso del Cavaliere 100 Roma00133 Italy Aix Marseill

Context: Several new ultrahigh-energy (UHE) gamma-ray sources have recently been discovered by the Large High Altitude Air Shower Observatory (LHAASO) collaboration. These represent a step forward in the search for the so-called Galactic PeVatrons, the enigmatic sources of the Galactic cosmic rays up to PeV energies. However, it has been shown that multi-TeV gamma-ray emission does not necessarily prove the existence of a hadronic accelerator in the source;indeed this emission could also be explained as inverse Compton scattering from electrons in a radiation-dominated environment. A clear distinction between the two major emission mechanisms would only be made possible by taking into account multi-wavelength data and detailed morphology of the source. Aims: We aim to understand the nature of the unidentified source LHAASO J2108+5157, which is one of the few known UHE sources with no very high-energy (VHE) counterpart. Methods: We observed LHAASO J2108+5157 in the X-ray band with XMM-Newton in 2021 for a total of 3.8 hours and at TeV energies with the Large-Sized Telescope prototype (LST-1), yielding 49 hours of good-quality data. In addition, we analyzed 12 years of Fermi-LAT data, to better constrain emission of its high-energy (HE) counterpart 4FGL J2108.0+5155. We used naima and jetset software packages to examine the leptonic and hadronic scenario of the multi-wavelength emission of the source. Results: We found an excess (3.7σ) in the LST-1 data at energies E > 3 TeV. Further analysis of the whole LST-1 energy range, assuming a point-like source, resulted in a hint (2.2σ) of hard emission, which can be described with a single power law with a photon index of Γ = 1.6 ± 0.2 the range of 0.3 − 100 TeV. We did not find any significant extended emission that could be related to a supernova remnant (SNR) or pulsar wind nebula (PWN) in the XMM-Newton data, which puts strong constraints on possible synchrotron emission of relativistic electrons. We revealed a new pote

关键词： Cosmology

Current md forcefields fail to capture key features of protein structure and fluctuations: a case study of cyclophilin a and t4 lysozyme

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arXiv 2020年

作者： Mei, Zhe Grigas, Alex T. Treado, John D. Corres, Gabriel Melendez Vuorte, Maisa Sammalkorpi, Maria Regan, Lynne Levine, Zachary A. O’Hern, Corey S. Department of Chemistry Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Biology UPR Humacao Puerto RicoHumacao00792 Puerto Rico Department of Chemistry and Materials Science School of Chemical Engineering Aalto University Aalto Finland Department of Bioproducts and Biosystems School of Chemical Engineering Aalto University Aalto Finland Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Edinburgh United Kingdom Department of Pathology Yale School of Medicine New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectroscopy. Given these discrepancies, it is unclear whether molecular dynamics (MD) simulations can accurately recapitulate protein conformations. We therefore perform extensive MD simulations across multiple force fields and sampling techniques to investigate the degree to which computer simulations can capture the ensemble of conformations observed in experiments. By analyzing fluctuations in the atomic coordinates and core packing, we show that conformations sampled in MD simulations both move away from and sample a larger conformational space than the ensemble of structures observed in NMR experiments. However, we find that adding inter-residue distance restraints that match those obtained via Nuclear Overhauser Effect measurements enables the MD simulations to sample more NMR-like conformations, though significant differences between the core packing features in restrained MD and the NMR ensemble remain. Given that the protein structures obtained from the MD simulations possess smaller and less dense protein cores compared to those solved by NMR, we suggest that future improvements to MD forcefields should aim to increase the packing of hydrophobic residues in protein cores. © 2020, CC BY.

关键词： Molecular dynamics

Estimation of Shear Wave Velocity of Darul Imarah District, Aceh Besar, Indonesia by Using 1D HVSR Inversion

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IOP Conference Series: Materials Science and Engineering 2020年第1期846卷

作者： Y Yusran Aulia Khalqillah Umar Muksin Muhammad Syukri Syamsul Rizal Nazli Ismail Doctoral Program of Mathematics and Applied Sciences Universitas Syiah Kuala Banda Aceh Indonesia Education of Physics Universitas Islam Negeri Ar-Raniry Banda Aceh Indonesia Department of Physics Universitas Syiah Kuala Banda Aceh Indonesia Tsunami and Disaster Mitigation Research Center (TDMRC) Universitas Syiah Kuala Banda Aceh Indonesia Department of Marine Sciences Universitas Syiah Kuala Banda Aceh Indonesia

A total of 19 locations of Horizontal to Vertical Spectral Ratio (HVSR) measurements was conducted in Darul Imarah District, Aceh Besar, Indonesia. The objective of the research is to investigate the shear wave velocity (Vs) structure. This survey is important to analyze a structural characteristic through a Vs, considering the measurement points intersect to Aceh Segment Fault. One of the methods to obtain Vs is 1D HVSR inversion. In this paper, we analyzed only four of 19 measurement points of HVSR data to estimate Vs, they are AB03, AB08, AB09 and AB19 points. The inversion results show that the four points have four layers with different Vs. The average of Vs30 of AB03, AB08, AB09 and AB19 were calculated, they are 150.90 m/s, 197.16 m/s, 150.45 m/s and 316.80 m/s, respectively. The AB09 has the lowest average of Vs30 (highest amplification) than the other points and has soft soil composition. Furthermore, based on the average of Vs30 and amplification, the subsurface of AB03, AB08 and AB19 may have combination soft soil and stiff soil in 30 m depth. The complete analysis of average of Vs30 structure will be conducted at all sites including a 3D velocity structure will be derived from the interpolation of 1D velocity.

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