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Observation of a single protein by ultrafast X-ray diffraction

Light(Science & Applications) 2024年第1期13卷 80-90页

作者： Tomas Ekeberg Dameli Assalauova Johan Bielecki Rebecca Boll Benedikt J.Daurer Lutz A.Eichacker Linda E.Franken Davide E.Galli Luca Gelisio Lars Gumprecht Laura H.Gunn Janos Hajdu Robert Hartmann Dirk Hasse Alexandr Ignatenko Jayanath Koliyadu Olena Kulyk Ruslan Kurta Markus Kuster Wolfgang Lugmayr Jannik Lübke Adrian P.Mancuso Tommaso Mazza Carl Nettelblad Yevheniy Ovcharenko Daniel E.Rivas Max Rose Amit K.Samanta Philipp Schmidt Egor Sobolev Nicusor Timneanu Sergey Usenko Daniel Westphal Tamme Wollweber Lena Worbs Paul Lourdu Xavier Hazem Yousef Kartik Ayyer Henry N.Chapman Jonas A.Sellberg Carolin Seuring Ivan A.Vartanyants Jochen Küpper Michael Meyer Filipe R.N.C.Maia Laboratory of Molecular Biophysics Department of Cell and Molecular BiologyUppsala UniversityHusargatan 3(Box 596)SE-75124 UppsalaSweden Deutsches Electronen-Synchrotron DESY Notkestrasse 8522607 HamburgGermany European XFEL Holzkoppel 422869 SchenefeldGermany Diamond Light Source Harwell Science&Innovation CampusDidcot OX110DEUK University of Stavanger Centre Organelle ResearchRichard-Johnsensgate 44021 StavangerNorway Leibniz Institute for Experimental Virology(HPI) Centre for Structural Systems BiologyNotkestraße 8522607 HamburgGermany Dipartimento di Fisica“Aldo Pontremoli” Universitàdegli Studi di Milanovia Celoria 1620133 MilanoItaly Center for Free-Electron Laser Science DESY22607 HamburgGermany Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA PNSensor GmbH Otto-Hahn-Ring 6D-81739 MünchenGermany Biomedical and X-Ray Physics Department of Applied PhysicsAlbaNova University CenterKTH Royal Institute of TechnologySE-10691 StockholmSweden ELI Beamlines/IoP Institute of Physics AS CR v.v.i.Na Slovance 218221 Prague 8Czech Republic Multi-User CryoEM Facility Centre for Structural Systems BiologyNotkestr.8522607 HamburgGermany University Medical Center Hamburg-Eppendorf(UKE) Martinistrasse 5220246 HamburgGermany The Hamburg Center for Ultrafast Imaging Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Physics Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Chemistry and Physics La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVIC 3086Australia Division of Scientific Computing Science for Life LaboratoryDepartment of Information TechnologyUppsala UniversityBox 337SE-75105 UppsalaSweden European Molecular Biology Laboratory c/o DESYNotkestrasse 8522607 HamburgGermany Department of Physics and Astronomy Uppsala UniversityBox 516SE-75120 UppsalaSweden Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 14922761 HamburgGe

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired *** was one of the arguments for building X-ray free-electron *** to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably *** was first demonstrated on biological samples a decade ago on the giant *** then,a large collaboration has been pushing the limit of the smallest sample that can be *** ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of *** we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single *** the pattern,it is possible to determine the approximate orientation of the *** experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词： smallest intense ultrafast

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False vacuum decay and nucleation dynamics in neutral atom systems

arXiv

引用

arXiv 2024年

作者： Darbha, Siva Kornjača, Milan Liu, Fangli Balewski, Jan Hirsbrunner, Mark R. Lopes, Pedro L.S. Wang, Sheng-Tao Van Beeumen, Roel Camps, Daan Klymko, Katherine Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory BerkeleyCA94720 United States QuEra Computing Inc. 1284 Soldiers Field Road BostonMA02135 United States Department of Physics Institute for Condensed Matter Theory University of Illinois at Urbana-Champaign UrbanaIL61801 United States

Metastable states of quantum many-body systems with confinement offer a means to simulate false vacuum phenomenology, including non-equilibrium dynamical processes like decay by nucleation, in truncated limits. Recent work has examined the decay process in 1D ferromagnetic Ising spins and superfluids. In this paper, we study nucleation dynamics in 1D antiferromagnetic neutral atom chains with Rydberg interactions, using both numerical simulations and analytic modeling. We apply a staggered local detuning field to generate the metastable and ground states. Our efforts focus on two dynamical regimes: decay and annealing. In the first, we corroborate the phenomenological decay rate scaling and determine the associated parameter range for the decay process;in the second, we uncover and elucidate a procedure to anneal the metastable state from the initial to the final system, with intermediate nucleation events. We further propose experimental protocols to prepare the required states and perform quenches on near-term neutral atom quantum simulators, examining the experimental feasibility of our proposed setup and parameter regime. Copyright © 2024, The Authors. All rights reserved.

关键词： Atoms

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Long-lived oscillations of metastable states in neutral atom systems

arXiv

引用

arXiv 2024年

作者： Darbha, Siva Kornjača, Milan Liu, Fangli Balewski, Jan Hirsbrunner, Mark R. Lopes, Pedro L.S. Wang, Sheng-Tao Van Beeumen, Roel Klymko, Katherine Camps, Daan Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory BerkeleyCA94720 United States QuEra Computing Inc. 1284 Soldiers Field Road BostonMA02135 United States Department of Physics Institute for Condensed Matter Theory University of Illinois at Urbana-Champaign UrbanaIL61801 United States

Metastable states arise in a range of quantum systems and can be observed in various dynamical scenarios, including decay, bubble nucleation, and long-lived oscillations. The phenomenology of metastable states has been examined in quantum many-body systems, notably in 1D ferromagnetic Ising spin systems and superfluids. In this paper, we study long-lived oscillations of metastable and ground states in 1D antiferromagnetic neutral atom chains with long-range Rydberg interactions. We use a staggered local detuning field to achieve confinement. Using theoretical and numerical models, we identify novel spectral signatures of quasiparticle oscillations distinct to antiferromagnetic neutral atom systems and interpret them using a classical energy model of short-range meson repulsion. Finally, we evaluate the experimental accessibility of our proposed setup on current neutral-atom platforms and discuss experimental feasibility and constraints. Copyright © 2024, The Authors. All rights reserved.

关键词： Atoms

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Vaccine efficacy and SARS-CoV-2 control in California and *** the session 2020e2026:A modeling study

引用

Infectious Disease Modelling 2022年第1期7卷 62-81页

作者： Md Shahriar Mahmud Md Kamrujjaman Md Mashih Ibn Yasin Adan Md Alamgir Hossain Md Mizanur Rahman Md Shahidul Islam Muhammad Mohebujjaman Md Mamun Molla Department of Computer Science and Engineering State University of BangladeshDhaka1205Bangladesh Department of Mathematics University of DhakaDhaka1000Bangladesh Department of Mathematics and Statistics University of CalgaryCalgaryABCanada Computational Biology Research Lab(CBRL) Department of PharmacyJagannath UniversityDhaka1100Bangladesh Hitotsubashi Institute for Advanced Study Hitotsubashi UniversityNaka KunitachiTokyo186-8601Japan Department of Mathematics and Physics Texas A&M International UniversityLaredoTX78041USA Department of Mathematics&Physics North South UniversityDhaka1229Bangladesh Center for Applied Scientific Computing(CASC) North South UniversityDhaka1229Bangladesh

Background:Besides maintaining health precautions,vaccination has been the only prevention from SARS-CoV-2,though no clinically proved 100%effective vaccine has been developed till *** this stage,to withhold the debris of this pandemic-experts need to know the impact of the vaccine efficacy rates,the threshold level of vaccine effectiveness and how long this pandemic may extent with vaccines that have different efficacy *** this article,a mathematical model study has been done on the importance of vaccination and vaccine efficiency rate during an ongoing ***:We simulated a five compartment mathematical model to analyze the pandemic scenario in both California,and whole *** considered four vaccines,Pfizer(95%),Moderna(94%),AstraZeneca(79%),and Johnson&Johnson(72%),which are being used rigorously to control the SARS-CoV-2 pandemic,in addition with two special cases:a vaccine with 100%efficacy rate and no vaccine under ***-CoV-2 related data of California,and *** used in this ***:Both the infection and death rates are very high in *** model suggests that the pandemic situation in California will be under control in the last quartile of the year 2023 if vaccination program is continued with the Pfizer *** this time,six waves may happen from the beginning of the immunization where the case fatality and recovery rates will be 1.697%and 98.30%,***,according to the considered model,this period might be extended to the mid of 2024 when vaccines with lower efficacy rates are *** the other hand,the daily cases and deaths in the *** be under control at the end of 2026 with multiple *** the number of susceptible people will fall down to none in the beginning of 2027,there is less chance to stop the vaccination program if vaccinated with a vaccine other than a 100%effective vaccine or Pfizer,and at that case vaccination program must run till the mid of *** to this s

关键词： Vaccine Model California Control measurement SARS-CoV-2

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Issues in the comparison of particle perturbations and numerical relativity for binary black hole mergers

arXiv

引用

arXiv 2022年

作者： Price, Richard H. Khanna, Gaurav Department of Physics MIT 77 Massachusetts Ave. CambridgeMA02139 United States Department of Physics East Hall University of Rhode Island KingstonRI02881 United States Department of Physics Center for Scientific Computing & Data Research University of Massachusetts DartmouthMA02747 United States

Recent work on improved efficiency of calculations for extreme mass ratio inspirals has produced the useful byproduct of comparisons of inspirals of comparable mass by particle perturbation (PP) methods and by numerical relativty (NR). Here we point out: (1) In choosing the rescaling of the masses, consideration must be given to the differences in the PP and NR methods even in the earliest, least nonlinear regime;in particular barycenter effects must be addressed. (2) Care must be given to the comparison of the nonspinning remnant in PP and the rapidly spinning remnant in NR. Copyright © 2022, The Authors. All rights reserved.

关键词： Black holes

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Testing eccentric corrections to the radiation-reaction force in the test-mass limit of effective-one-body models

arXiv

引用

arXiv 2024年

作者： Faggioli, Guglielmo van de Meent, Maarten Buonanno, Alessandra Gamboa, Aldo Khalil, Mohammed Khanna, Gaurav Am Mühlenberg 1 Potsdam14476 Germany Niels Bohr International Academy Niels Bohr Institute Blegdamsvej 17 Copenhagen2100 Denmark Department of Physics University of Maryland College ParkMD20742 United States Perimeter Institute for Theoretical Physics 31 Caroline Street North WaterlooONN2L 2Y5 Canada Department of Physics Center for Computational Research University of Rhode Island KingstonRI02881 United States Department of Physics University of Massachusetts DartmouthMA02747 United States Center for Scientific Computing and Data Science Research University of Massachusetts DartmouthMA02747 United States

In this work, we test an effective-one-body radiation-reaction force for eccentric planar orbits of a test mass in a Kerr background, which contains third-order post-Newtonian (PN) non-spinning and second-order PN spin contributions. We compare the analytical fluxes connected to two different resummations of this force, truncated at different PN orders in the eccentric sector, with the numerical fluxes computed through the use of frequency- and time-domain Teukolsky-equation codes. We find that the different PN truncations of the radiation-reaction force show the expected scaling in the weak gravitational-field regime, and we observe a fractional difference with the numerical fluxes that is 2/3 = 0.06, corresponding to the mildly strong-field regime with semilatera recta 9M Copyright © 2024, The Authors. All rights reserved.

关键词： Black holes

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Gravitational waves from black hole emission

arXiv

引用

arXiv 2024年

作者： Islam, Tousif Khanna, Gaurav Liebling, Steven L. Kavli Institute of Theoretical Physics University of California Santa Barbara Santa BarbaraCA93106 United States Theoretical Astrophysics Walter Burke Institute for Theoretical Physics California Institute of Technology PasadenaCA91125 United States Department of Physics University of Massachusetts DartmouthMA02747 United States Department of Mathematics University of Massachusetts DartmouthMA02747 United States Center for Scientific Computing and Data Science Research University of Massachusetts DartmouthMA02747 United States Department of Physics Center for Computational Research University of Rhode Island KingstonRI02881 United States Long Island University BrookvilleNY11548 United States

Using adiabatic point-particle black hole perturbation theory, we simulate plausible gravitational wave (GW) signatures in two exotic scenarios (i) where a small black hole is emitted by a larger one (‘black hole emission’) and (ii) where a small black hole is emitted by a larger one and subsequently absorbed back (‘black hole absorption’). While such scenarios are forbidden in general relativity!(GR), alternative theories (such as certain quantum gravity scenarios obeying the weak gravity conjecture, white holes, and Hawking radiation) may allow them. By leveraging the phenomenology of black hole emission and absorption signals, we introduce straightforward modifications to existing gravitational waveform models to mimic gravitational radiation associated with these exotic events. We anticipate that these (incomplete but) initial simulations, coupled with the adjusted waveform models, will aid in the development of null tests for GR using GWs. Copyright © 2024, The Authors. All rights reserved.

关键词： Black holes

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Gaussian Process Emulators for Few-Shot Segmentation in Cardiac MRI

arXiv

引用

arXiv 2024年

作者： Viti, Bruno Thaler, Franz Kapper, Kathrin Lisa Urschler, Martin Holler, Martin Karabelas, Elias Department of Mathematics and Scientific Computing University of Graz Graz Austria Institute for Medical Informatics Statistics and Documentation Medical University of Graz Graz Austria Institute of Computer Graphics and Vision Graz University of Technology Graz Austria Gottfried Schatz Research Center: Medical Physics and Biophysics Medical University of Graz Graz Austria BioTechMed-Graz Graz Austria

Segmentation of cardiac magnetic resonance images (MRI) is crucial for the analysis and assessment of cardiac function, helping to diagnose and treat various cardiovascular diseases. Most recent techniques rely on deep learning and usually require an extensive amount of labeled data. To overcome this problem, few-shot learning has the capability of reducing data dependency on labeled data. In this work, we introduce a new method that merges few-shot learning with a U-Net architecture and Gaussian Process Emulators (GPEs), enhancing data integration from a support set for improved performance. GPEs are trained to learn the relation between the support images and the corresponding masks in latent space, facilitating the segmentation of unseen query images given only a small labeled support set at inference. We test our model with the M&Ms-2 public dataset to assess its ability to segment the heart in cardiac magnetic resonance imaging from different orientations, and compare it with state-of-the-art unsupervised and few-shot methods. Our architecture shows higher DICE coefficients compared to these methods, especially in the more challenging setups where the size of the support set is considerably small. The code is available on GitLab 6 © 2024, CC BY-NC-ND.

关键词： Gaussian distribution

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Evaluating the Potential of Disaggregated Memory Systems for HPC applications

arXiv

引用

arXiv 2023年

作者： Ding, Nan Maris, Pieter Nam, Hai Ah Groves, Taylor Awan, Muaaz Gul Lindsey, LeAnn Daley, Christopher Selvitopi, Oguz Oliker, Leonid Wright, Nicholas Williams, Samuel Computational Research Division Lawrence Berkeley National Laboratory CA United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory CA United States Department Of Physics and Astronomy Iowa State University IA United States 1 Cyclotron Road BerkeleyCA94720 United States

Disaggregated memory is a promising approach that addresses the limitations of traditional memory architectures by enabling memory to be decoupled from compute nodes and shared across a data center. Cloud platforms have deployed such systems to improve overall system memory utilization, but performance can vary across workloads. High-performance computing (HPC) is crucial in scientific and engineering applications, where HPC machines also face the issue of underutilized memory. As a result, improving system memory utilization while understanding workload performance is essential for HPC operators. Therefore, learning the potential of a disaggregated memory system before deployment is a critical step. This paper proposes a methodology for exploring the design space of a disaggregated memory system. It incorporates key metrics that affect performance on disaggregated memory systems: memory capacity, local and remote memory access ratio, injection bandwidth, and bisection bandwidth, providing an intuitive approach to guide machine configurations based on technology trends and workload characteristics. We apply our methodology to analyze thirteen diverse workloads, including AI training, data analysis, genomics, protein, fusion, atomic nuclei, and traditional HPC bookends. Our methodology demonstrates the ability to comprehend the potential and pitfalls of a disaggregated memory system and provides motivation for machine configurations. Our results show that eleven of our thirteen applications can leverage injection bandwidth disaggregated memory without affecting performance, while one pays a rack bisection bandwidth penalty and two pay the system-wide bisection bandwidth penalty. In addition, we also show that intra-rack memory disaggregation would meet the application’s memory requirement and provide enough remote memory bandwidth. © 2023, CC BY-NC-SA.

关键词： Bandwidth

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Algebraic Compression of Free Fermionic Quantum Circuits: Particle Creation, Arbitrary Lattices and Controlled Evolution

arXiv

引用

arXiv 2023年

作者： Kökcü, Efekan Camps, Daan Oftelie, Lindsay Bassman de Jong, Wibe A. Van Beeumen, Roel Kemper, A.F. Department of Physics North Carolina State University RaleighNC27695 United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

Recently we developed a local and constructive algorithm based on Lie algebraic methods for compressing Trotterized evolution under Hamiltonians that can be mapped to free fermions [1, 2]. The compression algorithm yields a circuit which scales linearly in the number of qubits, is fixed depth for for arbitrarily long evolution times and is applicable to time dependent Hamiltonians, although is limited to simple nearest-neighbor spin interactions and fermionic hopping. In this work, we extend the algorithm to compress circuits simulating evolution with long-range spin interactions and fermionic hopping, thereby enabling embedding of arbitrary lattices onto a chain of qubits. Moreover, we show that controlled time evolution, as well as fermion creation and annihilation operators can also be compressed. We demonstrate our results by adiabatically preparing the ground state for a half-filled fermionic chain, and simulating a 4×4 tight binding model on ibmq washington. With these new developments, our results enable the simulation of a wider range of models of interest and the efficient compression of subcircuits. Copyright © 2023, The Authors. All rights reserved.

关键词： Ground state

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