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Structure formation and the matter power-spectrum in the Rh = ct universe

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arXiv 2020年

作者： Yennapureddy, Manoj Kumar Melia, Fulvio Department of Physics University of Arizona AZ85721 United States Department of Physics Applied Math Program Department of Astronomy University of Arizona AZ85721 United States

Inflation drives quantum fluctuations beyond the Hubble horizon, freezing them out before the small-scale modes re-enter during the radiation dominated epoch, and subsequently decay, while large-scale modes re-enter later during the matter dominated epoch and grow. This distinction shapes the matter power spectrum and provides observational evidence in support of the standard model. In this paper, we demonstrate that another mechanism, based on the fluctuation growth in the Rh = ct universe, itself an FLRW cosmology with the added constraint of zero active mass (i.e., ρ + 3p = 0), also accounts very well for the observed matter power spectrum, so this feature is not unique to ΛCDM. In Rh = ct, the shape of the matter power spectrum is set by the interplay between the more rapid decay of the gravitational potential for the smaller mode wavelengths and the longer dynamical timescale for the larger wavelengths. This combination produces a characteristic peak that grows in both amplitude and mode number as a function of time. Today, that peak lies at k ≈ 0.02 Mpc−1, in agreement with the Ly-α and Planck data. But there is no need of an inflationary expansion, and a complicated epoch dependence as one finds in ΛCDM. © 2020, CC-BY.

关键词： Gravitation

Relative Alignments Between Magnetic Fields, Velocity Gradients, and Dust Emission Gradients in NGC 1333

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arXiv 2024年

作者： Chen, Michael Chun-Yuan Fissel, Laura M. Sadavoy, Sarah I. Rosolowsky, Erik Doi, Yasuo Arzoumanian, Doris Bastien, Pierre Coudé, Simon Di Francesco, James Friesen, Rachel Furuya, Ray S. Hwang, Jihye Inutsuka, Shu-Ichiro Johnstone, Doug Karoly, Janik Kwon, Jungmi Kwon, Woojin Le Gouellec, Valentin J.M. Liu, Hong-Li Mairs, Steve Onaka, Takashi Pattle, Kate Rawlings, Mark G. Tahani, Mehrnoosh Tamura, Motohide Wang, Jia-Wei Department of Physics Engineering Physics and Astronomy Queen’s University KingstonONK7L 3N6 Canada Department of Physics University of Alberta EdmontonABT6G 2E1 Canada Department of Earth Science and Astronomy The University of Tokyo 3-8-1 Komaba Meguro Tokyo153-8902 Japan National Astronomical Observatory of Japan Osawa 2-21-1 Mitaka Tokyo181-8588 Japan Université de Montréal Département de Physique 1375 Avenue Thérèse-Lavoie-Roux MontréalQCH2V 0B3 Canada Department of Earth Environment and Physics Worcester State University WorcesterMA01602 United States Center for Astrophysics | Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States NRC Herzberg Astronomy and Astrophysics 5071 West Saanich Rd VictoriaBCV9E 2E7 Canada Department of Physics and Astronomy University of Victoria VictoriaBCV8P 5C2 Canada David A. Dunlap Department of Astronomy and Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Institute of Liberal Arts and Sciences Tokushima University Minami Jousanajima-machi 1-1 Tokushima770-8502 Japan Korea Astronomy and Space Science Institute 776 Daedeokdae-ro Yuseong-gu Daejeon34055 Korea Republic of University of Science and Technology Korea 217 Gajeong-ro Yuseong-gu Daejeon34113 Korea Republic of Department of Physics Graduate School of Science Nagoya University Furo-cho Chikusa-ku Nagoya464-8602 Japan Jeremiah Horrocks Institute University of Central Lancashire PrestonPR1 2HE United Kingdom Department of Astronomy Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-0033 Japan Department of Earth Science Education Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of SNU Astronomy Research Center Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of NASA Ames Research Center Space Science and Astrobiology Division M.S. 245-6 Moffett FieldCA94035 United States NASA Postdoc

Magnetic fields play an important role in shaping and regulating star formation in molecular clouds. Here, we present one of the first studies examining the relative orientations between magnetic (B) fields and the dust emission, gas column density, and velocity centroid gradients on the 0.02 pc (core) scales, using the BISTRO and VLA+GBT observations of the NGC 1333 star-forming clump. We quantified these relative orientations using the Project Rayleigh Statistic (PRS) and found preferential global parallel alignment between the B field and dust emission gradients, consistent with large-scale studies with Planck. No preferential global alignments, however, are found between the B field and velocity gradients. Local PRS calculated for subregions defined by either dust emission or velocity coherence further revealed that the Bfield does not preferentially align with dust emission gradients in most emission-defined subregions, except in the warmest ones. The velocity-coherent structures, on the other hand, also showed no preferred B field alignments with velocity gradients, except for one potentially bubble-compressed region. Interestingly, the velocity gradient magnitude in NGC 1333 ubiquitously features prominent ripple-like structures that are indicative of magnetohydrodynamic (MHD) waves. Finally, we found B field alignments with the emission gradients to correlate with dust temperature and anticorrelate with column density, velocity dispersion, and velocity gradient magnitude. The latter two anticorrelations suggest that alignments between gas structures and B fields can be perturbed by physical processes that elevate velocity dispersion and velocity gradients, such as infall, accretions, and MHD waves. © 2024, CC BY.

关键词： Plasma magnetohydrodynamic waves

Extrusion of chromatin loops by a composite loop extrusion factor

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Physical Review E 2021年第2期104卷 024414-024414页

作者： Hao Yan Ivan Surovtsev Jessica F. Williams Mary Lou P. Bailey Megan C. King Simon G. J. Mochrie Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06511 USA Department of Physics Yale University New Haven Connecticut 06511 USA Department of Cell Biology Yale School of Medicine New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06511 USA Department of Molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06511 USA

Chromatin loop extrusion by structural maintenance of chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop extrusion by SMCs, such as cohesin and condensin complexes, we introduce and characterize theoretically a composite loop extrusion factor (composite LEF) model. In addition to an SMC complex that creates a chromatin loop by encircling two threads of DNA, this model includes a remodeling complex that relocates or removes nucleosomes as it progresses along the chromatin, and nucleosomes that block SMC translocation along the DNA. Loop extrusion is enabled by SMC motion along nucleosome-free DNA, created in the wake of the remodeling complex, while nucleosome rebinding behind the SMC acts as a ratchet, holding the SMC close to the remodeling complex. We show that, for a wide range of parameter values, this collection of factors constitutes a composite LEF that extrudes loops with a velocity, comparable to the velocity of remodeling complex translocation on chromatin in the absence of SMC, and much faster than loop extrusion by an isolated SMC that is blocked by nucleosomes.

关键词： Biomolecular dynamics Self-organization

First follow-up of transient events with the CTA Large Size Telescope prototype 37

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First follow-up of transient events with the CTA Large Size ...

37th International Cosmic Ray Conference, ICRC 2021

作者： Kobayshi, Yukiho Sanchez, David Abe, H. Aguasca, A. Agudo, I. Antonelli, L.A. Aramo, C. Armstrong, T. Artero, M. Asano, K. Ashkar, H. Aubert, P. Baktash, A. Bamba, A. Baquero Larriva, A. Baroncelli, L. Barres de Almeida, U. Barrio, J.A. Batkovic, I. Becerra González, J. Bernardos, M.I. Berti, A. Biederbeck, N. Bigongiari, C. Blanch, O. Bonnoli, G. Bordas, P. Bose, D. Bulgarelli, A. Burelli, I. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Cassol, F. Cerruti, M. Chai, Y. Cheng, K. Chikawa, M. Chytka, L. Contreras, J.L. Cortina, J. Costantini, H. Dalchenko, M. De Angelis, A. de Bony de Lavergne, M. Deleglise, G. Delgado, C. Delgado Mengual, J. della Volpe, D. Depaoli, D. Di Pierro, F. Di Venere, L. Díaz, C. Dominik, R.M. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Elsässer, D. Emery, G. Escudero, J. Fiasson, A. Foffano, L. Fonseca, M.V. Freixas Coromina, L. Fukami, S. Fukazawa, Y. Garcia, E. Garcia López, R. Giglietto, N. Giordano, F. Gliwny, P. Godinovic, N. Green, D. Grespan, P. Gunji, S. Hackfeld, J. Hadasch, D. Hahn, A. 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. Inada, T. Inome, Y. Iori, M. Ishio, K. Iwamura, Y. Jacquemont, M. Jimenez Martinez, I. Jouvin, L. Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kerszberg, D. Kobayashi, Y. Kong, A. Kubo, H. Kushida, J. Lamanna, G. Lamastra, A. Le Flour, T. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Luque-Escamilla, P.L. Majumdar, P. Makariev, M. Mandat, D. Manganaro, M. Mannheim, K. Mariotti, M. Marquez, P. Marsella, G. Martí, J. Martinez, O. Martínez, G. Martínez, M. Marusevec, P. Mas, A. Maurin, G. Mazin, D. Mestre Guillen, E. Micanovic, S. Miceli, D. Miener, T. Miranda, J.M. Miranda, L.D.M. Mirzoyan, R. Mizuno, T. Molina, E. Montaruli, T. Monteiro, I. Moralejo, A. Morcuende, D. Moretti, E. Morselli, A. Mrakovcic, K. Murase, K. Nagai, A. LAPP Université de Savoie Mont-Blanc CNRS/IN2P3 Annecy74941 France Institute for Cosmic Ray Research The University of Tokyo Kashiwa Japan Institute for Cosmic Ray Research University of Tokyo Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Spain Instituto de Astrofísica de Andalucía CSIC INAF - Osservatorio Astronomico di Roma Italy INFN Sezione di Napoli Italy Aix Marseille Univ CNRS/IN2P3 CPPM France The Barcelona Institute of Science and Technology Spain IRFU CEA Université Paris-Saclay France LAPP Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS/IN2P3 Annecy France Universität Hamburg Institut für Experimentalphysik Germany Graduate School of Science University of Tokyo Japan EMFTEL department IPARCOS Universidad Complutense de Madrid Spain INAF - Osservatorio di Astrofisica Scienza dello Spazio di Bologna Italy Centro Brasileiro de Pesquisas Físicas Brazil INFN Sezione di Padova Università degli Studi di Padova Italy Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Spain Max-Planck-Institut für Physik Germany Department of Physics TU Dortmund University Germany Saha Institute of Nuclear Physics INFN Sezione di Trieste Università degli Studi di Udine Italy INFN Sezione di Catania Italy Italy University of Geneva Département de Physique Nucléaire et Corpusculaire Switzerland Palacky University Olomouc Faculty of Science Czech Republic CIEMAT Port d'Informació Científica INFN Sezione di Torino Italy Dipartimento di Fisica Universitá degli Studi di Torino Italy INFN Sezione di Bari Università di Bari Italy University of Rijeka Department of Physics Croatia Institute for Theoretical Physics and Astrophysics Universität Würzburg Germany Physics Program Graduate School of Advanced Science and Engineering Hiroshima University Japan INFN Sezione di Bari Politecnico di Bari Italy Faculty of Physics and Applied Informatics University of L

The recent detection of a very high energy (VHE) emission from Gamma-Ray Bursts (GRBs) above 100 GeV performed by the MAGIC and H.E.S.S. collaborations, has represented a significant, long-awaited result for the VHE astrophysics community. Although these results' scientific impact has not yet been fully exploited, the possibility to detect VHE gamma-ray signals from GRBs has always been considered crucial for clarifying the poorly known physics of these objects. Furthermore, the discovery of high-energy neutrinos and gravitational waves associated with astrophysical sources have definitively opened the era of multi-messenger astrophysics, providing unique insights into the physics of extreme cosmic accelerators. In the near future, the Cherenkov Telescope Array (CTA) will play a major role in these observations. Within this framework, the Large Size Telescopes (LSTs) will be the instruments best suited to significantly impact on short time-scale transients follow-up thanks to their fast slewing and large effective area. The observations of the early emission phase of a wide range of transient events with good sensitivity below 100 GeV will allow us to open new opportunities for time-domain astrophysics in an energy range not affected by selective absorption processes typical of other wavelengths. In this contribution, we will report about the observational program and first transients follow-up observations performed by the LST-1 telescope currently in its commissioning phase on La Palma, Canary Islands, the CTA northern hemisphere site. © Copyright owned by the author(s) under the terms of the Creative Commons.

关键词： Telescopes

Superdiffusion from Emergent Classical Solitons in Quantum Spin Chains

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Physical Review Letters 2020年第7期125卷 070601-070601页

作者： Jacopo De Nardis Sarang Gopalakrishnan Enej Ilievski Romain Vasseur Department of Physics and Astronomy University of Ghent Krijgslaan 281 9000 Gent Belgium Department of Physics and Astronomy CUNY College of Staten Island Staten Island New York 10314 Physics Program and Initiative for the Theoretical Sciences The Graduate Center CUNY New York New York 10016 USA Faculty for Mathematics and Physics University of Ljubljana Jadranska ulica 19 1000 Ljubljana Slovenia Department of Physics University of Massachusetts Amherst Massachusetts 01003 USA

Finite-temperature spin transport in the quantum Heisenberg spin chain is known to be superdiffusive, and has been conjectured to lie in the Kardar-Parisi-Zhang (KPZ) universality class. Using a kinetic theory of transport, we compute the KPZ coupling strength for the Heisenberg chain as a function of temperature, directly from microscopics; the results agree well with density-matrix renormalization group simulations. We establish a rigorous quantum-classical correspondence between the “giant quasiparticles” that govern superdiffusion and solitons in the classical continuous Landau-Lifshitz ferromagnet. We conclude that KPZ universality has the same origin in classical and quantum integrable isotropic magnets: a finite-temperature gas of low-energy classical solitons.

关键词： Transport phenomena 1-dimensional spin chains Kardar–Parisi–Zhang equation Solitons

New Approach to Designing Functional Materials for Stealth Technology: Radar Experiment with Bilayer Absorbers and Optimization of the Reflection Loss

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arXiv 2023年

作者： Calvo-De la Rosa, Jaume Bou-Comas, Aleix Hernàndez, Joan Manel Marín, Pilar Lopez-Villegas, Jose Maria Tejada, Javier Chudnovsky, Eugene M. Departament de Física de la Matèria Condensada Universitat de Barcelona Martí i Franquès 1 Barcelona08028 Spain Universitat de Barcelona Barcelona08028 Spain Graduate Program in Physics and Initiative for the Theoretical Sciences Graduate Center The City University of New York New YorkNY10016 United States Madrid28230 Spain Madrid28040 Spain Departament d’Enginyeria Electrònica i Biomèdica Universitat de Barcelona Barcelona08028 Spain Department of Physics and Astronomy Herbert H. Lehman College The City University of New York BronxNY10468-1589 United States

Microwave power absorption by a two-layer system deposited on a metallic surface is studied in the experimental setup emulating the response to a radar signal. Layers containing hexaferrite and iron powder in a dried paint of thickness under 1mm are used. The data is analyzed within a theoretical model derived for a bilayer system from the transmission line theory. Good agreement between experimental and theoretical results is found. The advantage of using a bilayer system over a single-layer system is demonstrated. We show how the maximum microwave absorption (minimum reflection) can be achieved through the optimization of the filling factors and thicknesses of the two layers. © 2023, CC BY-NC-SA.

关键词： Iron powder

Status and results of the prototype LST of CTA 37

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Status and results of the prototype LST of CTA

37th International Cosmic Ray Conference, ICRC 2021

作者： Mazin, D. Abe, H. Aguasca, A. Agudo, I. Antonelli, L.A. Aramo, C. Armstrong, T. Artero, M. Asano, K. Ashkar, H. Aubert, P. Baktash, A. Bamba, A. Baquero Larriva, A. Baroncelli, L. Barres de Almeida, U. Barrio, J.A. Batkovic, I. Becerra González, J. Bernardos, M.I. Berti, A. Biederbeck, N. Bigongiari, C. Blanch, O. Bonnoli, G. Bordas, P. Bose, D. Bulgarelli, A. Burelli, I. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Cassol, F. Cerruti, M. Chai, Y. Cheng, K. Chikawa, M. Chytka, L. Contreras, J.L. Cortina, J. Costantini, H. Dalchenko, M. De Angelis, A. de Bony de Lavergne, M. Deleglise, G. Delgado, C. Delgado Mengual, J. della Volpe, D. Depaoli, D. Di Pierro, F. Di Venere, L. Díaz, C. Dominik, R.M. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Elsässer, D. Emery, G. Escudero, J. Fiasson, A. Foffano, L. Fonseca, M.V. Freixas Coromina, L. Fukami, S. Fukazawa, Y. Garcia, E. Garcia López, R. Giglietto, N. Giordano, F. Gliwny, P. Godinovic, N. Green, D. Grespan, P. Gunji, S. Hackfeld, J. Hadasch, D. Hahn, A. 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. Inada, T. Inome, Y. Iori, M. Ishio, K. Iwamura, Y. Jacquemont, M. Jimenez Martinez, I. Jouvin, L. Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kerszberg, D. Kobayashi, Y. Kong, A. Kubo, H. Kushida, J. Lamanna, G. Lamastra, A. Le Flour, T. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Luque-Escamilla, P.L. Majumdar, P. Makariev, M. Mandat, D. Manganaro, M. Mannheim, K. Mariotti, M. Marquez, P. Marsella, G. Martí, J. Martinez, O. Martínez, G. Martínez, M. Marusevec, P. Mas, A. Maurin, G. Mestre Guillen, E. Micanovic, S. Miceli, D. Miener, T. Miranda, J.M. Miranda, L.D.M. Mirzoyan, R. Mizuno, T. Molina, E. Montaruli, T. Monteiro, I. Moralejo, A. Morcuende, D. Moretti, E. Morselli, A. Mrakovcic, K. Murase, K. Nagai, A. Nakamori, T. Nickel, L. Nieto, D. Institute for Cosmic Ray Research University of Tokyo 5-1-5 Kashiwa-no-ha Chiba Kashiwa277-8582 Japan Max-Planck-Institut für Physik München80805 Germany Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Spain Instituto de Astrofísica de Andalucía-CSIC Spain INAF - Osservatorio Astronomico di Roma Italy INFN Sezione di Napoli Italy Aix Marseille Univ CNRS IN2P3 CPPM France The Barcelona Institute of Science and Technology Spain IRFU CEA Université Paris-Saclay France LAPP Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS-IN2P3 Annecy France Universität Hamburg Institut für Experimentalphysik Germany Graduate School of Science University of Tokyo Japan EMFTEL department IPARCOS Universidad Complutense de Madrid Spain INAF - Osservatorio di Astrofisica e Scienza dello spazio di Bologna Italy Centro Brasileiro de Pesquisas Físicas Brazil INFN Sezione di Padova Università degli Studi di Padova Italy Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Spain Department of Physics TU Dortmund University Germany Saha Institute of Nuclear Physics India INFN Sezione di Trieste Università degli Studi di Udine Italy INFN Sezione di Catania Italy Italy University of Geneva Département de Physique Nucléaire et Corpusculaire Switzerland Palacky University Olomouc Faculty of Science Czech Republic CIEMAT Port d'Informació Científica INFN Sezione di Torino Italy Dipartimento di Fisica Universitá degli Studi di Torino Italy INFN Sezione di Bari Università di Bari Italy University of Rijeka Department of Physics Croatia Institute for Theoretical Physics and Astrophysics Universität Würzburg Germany Physics Program Graduate School of Advanced Science and Engineering Hiroshima University Japan INFN Sezione di Bari Politecnico di Bari Italy Faculty of Physics and Applied Informatics University of Lodz Poland University of Split FESB Croatia Department of Physics

The Large-Sized Telescopes (LSTs) of Cherenkov Telescope Array (CTA) are designed for gamma-ray studies focusing on low energy threshold, high flux sensitivity, rapid telescope repositioning speed and a large field of view. Once the CTA array is complete, the LSTs will be dominating the CTA performance between 20 GeV and 150 GeV. During most of the CTA Observatory construction phase, however, the LSTs will be dominating the array performance until several TeVs. In this presentation we will report on the status of the LST-1 telescope inaugurated in La Palma, Canary islands, Spain in 2018. We will show the progress of the telescope commissioning, compare the expectations with the achieved performance, and give a glance of the first physics results. © Copyright owned by the author(s) under the terms of the Creative Commons.

关键词： Telescopes

Light-induced topological superconductivity via Floquet interaction engineering

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Physical Review Research 2021年第2期3卷 023039-023039页

作者： Hossein Dehghani Mohammad Hafezi Pouyan Ghaemi Joint Quantum Institute College Park Maryland 20742 USA The Institute for Research in Electronics and Applied Physics University of Maryland College Park Maryland 20742 USA Physics Department City College of the City University of New York New York New York 10031 USA Physics Program Graduate Center of the City University of New York New York New York 10031 USA

We propose a mechanism for light-induced unconventional superconductivity in a two-valley semiconductor with a massive Dirac-type band structure. The superconducting phase results from the out-of-equilibrium excitation of carriers in the presence of Coulomb repulsion and is stabilized by coupling the driven semiconductor to a bosonic or fermionic thermal bath. We consider a circularly polarized light pump and show that by controlling the detuning of the pump frequency relative to the band gap, different types of chiral superconductivity would be induced. The emergence of novel superconducting states, such as the chiral p-wave pairing, results from the Floquet engineering of the interaction. This is realized by modifying the form of the Coulomb interaction by projecting it into the states that are resonant with the pump frequency. We show that the resulting unconventional pairing in our system can host topologically protected chiral bound states. We discuss a promising experimental platform to realize our proposal and detect the signatures of the emergent superconducting state.

关键词： Band gap Superconducting fluctuations Superconducting order parameter Superconducting phase transition Floquet systems Honeycomb lattice Low-temperature superconductors Quantum wells Semiconductors Two-dimensional electron system Methods in superconductivity Optical absorption spectroscopy

Core packing of well-defined x-ray and NMR structures is the same

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arXiv 2022年

作者： Grigas, Alex T. Liu, Zhuoyi Regan, Lynne O’Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh United Kingdom Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies, or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared to those of high-resolution x-ray crystal structures. Our current work investigates this result in more detail, and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and side chain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by x-ray crystallography at high-resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and x-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments. Significance: Dense packing of hydrophobic residues is key to protein structure and stability. Previously, it has been noted that structures solved by NMR spectroscopy have denser cores than x-ray crystal structures. Here, we calculate the core size and packing fraction of NMR structures with experimental restraints in the PDB. Their cores are typically smaller, but denser. However, NMR structures with accurate stereochemistry possess core pa

关键词： X ray crystallography