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arXiv 2017年

作者： Damasceno, Pablo F. Glotzer, Sharon C. Engel, Michael Applied Physics Program University of Michigan Ann ArborMI48109 United States Department of Cellular and Molecular Pharmacology University of California San Francisco San FranciscoCA94158 United States Department of Materials Science and Engineering University of Michigan Ann ArborMI48109 United States Department of Chemical Engineering University of Michigan Ann ArborMI48109 United States Institute for Multiscale Simulation Friedrich-Alexander-University Erlangen-Nuremberg Erlangen91052 Germany

Quasicrystals are frequently encountered in condensed matter. They are important candidates for equilibrium phases from the atomic scale to the nanoscale. Here, we investigate the computational self-assembly of four quasicrystals in a single model system of identical particles interacting with a tunable isotropic pair potential. We reproduce a known icosahedral quasicrystal and report a decagonal quasicrystal, a dodecagonal quasicrystal, and an octagonal quasicrystal. The quasicrystals have low coordination number or occur in systems with mesoscale density variations. We also report a network gel phase. Copyright © 2017, The Authors. All rights reserved.

关键词： Quasicrystals

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Reply to “Comment on ‘Correlation and relativistic effects in U metal and U-Zr alloy: Validation of ab initio approaches’ ”

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Physical Review B 2016年第15期93卷 157101-157101页

作者： Wei Xie Chris A. Marianetti Dane Morgan Materials Science Program University of Wisconsin-Madison Madison Wisconsin 53706 USA Department of Applied Physics and Applied Mathematics Columbia University New York New York 10027 USA Department of Materials Science and Engineering University of Wisconsin-Madison Madison Wisconsin 53706 USA

In the Comment by Söderlind et al. [Phys. Rev. B 90, 157101 (2014)], the authors argue that (1) density functional theory (DFT), especially with all-electron methods, already models U metal and U-Zr alloy accurately; and (2) DFT+U results calculated at Ueff=1.24 for volume, enthalpy, and magnetic moments that they select from our study [Phys. Rev. B 88, 235128 (2013)] suggest adding the Hubbard U potential in DFT+U reduces accuracy compared to DFT. With respect to argument (1) by Söderlind et al., we argue that previously neglected and very recent experimental data suggest that DFT in Söderlind's full-potential linear muffin-tin orbital calculations [Phys. Rev. B 66, 085113 (2002)] still models the bulk modulus and elastic constants of αU with errors considerably larger than other related elements, e.g., most transition metals. In addition, we demonstrate that the assertion by Söderlind et al. that our DFT results are not satisfactory because deficiency exists in our projector augmented wave calculation is unfounded. With respect to argument (2) by Söderlind et al., we argue that they have inappropriately focused on just one phase [the bcc phase γ(U,Zr)], neglecting the other phases which represent the majority of our evidence; made overgeneralizations based on results at only one Ueff value of 1.24 eV; and supported their argument with inaccurate assertions that DFT+U predicts for γ(U,Zr) an unprecedentedly large positive volume of mixing and an enthalpy of mixing that is inconsistent with the experimental miscibility gap. We therefore hold to our original conclusion that the accuracy of DFT for modeling U and U-Zr has room for improvement and DFT+U is a good candidate.

关键词： physics periodicals URANIUM alloys ZIRCONIUM alloys MAGNETIC moments

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Linear readout of object manifolds

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Physical Review E 2016年第6期93卷 060301(R)-060301(R)页

作者： SueYeon Chung Daniel D. Lee Haim Sompolinsky Program in Applied Physics School of Engineering and Applied Sciences Harvard University Cambridge Massachusetts 02138 USA Center for Brain Science Harvard University Cambridge Massachusetts 02138 USA Department of Electrical and Systems Engineering University of Pennsylvania Philadelphia Pennsylvania 19104 USA Racah Institute of Physics Hebrew University Jerusalem 91904 Israel Edmond and Lily Safra Center for Brain Sciences Hebrew University Jerusalem 91904 Israel

Objects are represented in sensory systems by continuous manifolds due to sensitivity of neuronal responses to changes in physical features such as location, orientation, and intensity. What makes certain sensory representations better suited for invariant decoding of objects by downstream networks? We present a theory that characterizes the ability of a linear readout network, the perceptron, to classify objects from variable neural responses. We show how the readout perceptron capacity depends on the dimensionality, size, and shape of the object manifolds in its input neural representation.

关键词： Neuronal networks Machine learning

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Tomographic reconstruction of time-bin-entangled qudits

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Physical Review A 2016年第4期94卷 042328-042328页

作者： Samantha J. Nowierski Neal N. Oza Prem Kumar Gregory S. Kanter Center for Photonic Communication and Computing EECS Department Northwestern University 2145 Sheridan Road Evanston Illinois 60208-3118 USA Graduate Program in Applied Physics Northwestern University Evanston Illinois 60208 USA Department of Physics and Astronomy Northwestern University 2145 Sheridan Road Evanston Illinois 60208-3112 USA

We describe an experimental implementation to generate and measure high-dimensional time-bin-entangled qudits. Two-photon time-bin entanglement is generated via spontaneous four-wave mixing in single-mode fiber. Unbalanced Mach-Zehnder interferometers transform selected time bins to polarization entanglement, allowing standard polarization-projective measurements to be used for complete quantum state tomographic reconstruction. Here we generate maximally entangled qubits (d=2), qutrits (d=3), and ququarts (d=4), as well as other phase-modulated nonmaximally entangled qubits and qutrits. We reconstruct and verify all generated states using maximum-likelihood estimation tomography.

关键词： Entanglement detection Entanglement manipulation Quantum entanglement Quantum tomography

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NWChem: Past, present, and future

arXiv

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arXiv 2020年

作者： Aprà, E. Bylaska, E.J. de Jong, W.A. Govind, N. Kowalski, K. Straatsma, T.P. Valiev, M. van Dam, H.J.J. Alexeev, Y. Anchell, J. Anisimov, V. Aquino, F.W. Atta-Fynn, R. Autschbach, J. Bauman, N.P. Becca, J.C. Bernholdt, D.E. Bhaskaran-Nair, K. Bogatko, S. Borowski, P. Boschen, J. Brabec, J. Bruner, A. Cauët, E. Chen, Y. Chuev, G.N. Cramer, C.J. Daily, J. Deegan, M.J.O. Dunning, T.H. Dupuis, M. Dyall, K.G. Fann, G.I. Fischer, S.A. Fonari, A. Früchtl, H. Gagliardi, L. Garza, J. Gawande, N. Ghosh, S. Glaesemann, K. Götz, A.W. Hammond, J. Helms, V. Hermes, E.D. Hirao, K. Hirata, S. Jacquelin, M. Jensen, L. Johnson, B.G. Jónsson, H. Kendall, R.A. Klemm, M. Kobayashi, R. Konkov, V. Krishnamoorthy, S. Krishnan, M. Lin, Z. Lins, R.D. Littlefield, R.J. Logsdail, A.J. Lopata, K. Ma, W. Marenich, A.V. Martin del Campo, J. Mejia-Rodriguez, D. Moore, J.E. Mullin, J.M. Nakajima, T. Nascimento, D.R. Nichols, J.A. Nichols, P.J. Nieplocha, J. Otero-de-la-Roza, A. Palmer, B. Panyala, A. Pirojsirikul, T. Peng, B. Peverati, R. Pittner, J. Pollack, L. Richard, R.M. Sadayappan, P. Schatz, G.C. Shelton, W.A. Silverstein, D.W. Smith, D.M.A. Soares, T.A. Song, D. Swart, M. Taylor, H.L. Thomas, G.S. Tipparaju, V. Truhlar, D.G. Tsemekhman, K. van Voorhis, T. Vázquez-Mayagoitia, Á. Verma, P. Villa, O. Vishnu, A. Vogiatzis, K.D. Wang, D. Weare, J.H. Williamson, M.J. Windus, T.L. Woliński, K. Wong, A.T. Wu, Q. Yang, C. Yu, Q. Zacharias, M. Zhang, Z. Zhao, Y. Harrison, R.J. Pacific Northwest National Laboratory RichlandWA99352 United States Lawrence Berkeley National Laboratory BerkeleyCA94720 United States National Center for Computational Sciences Oak Ridge National Laboratory Oak RidgeTN37831 United States Brookhaven National Laboratory UptonNY11973 United States Argonne Leadership Computing Facility Argonne National Laboratory ArgonneIL60439 United States Intel Corporation Santa ClaraCA95054 United States QSimulate CambridgeMA02139 United States Department of Physics University of Texas at Arlington ArlingtonTX76019 United States Department of Chemistry University at Buffalo State University of New York BuffaloNY14260 United States Department of Chemistry Pennsylvania State University University ParkPA16802 United States Oak Ridge National Laboratory Oak RidgeTN37831 United States Washington University St. LouisMO63130 United States 4G Clinical WellesleyMA02481 United States Faculty of Chemistry Maria Curie-Sklodowska University in Lublin Lublin20-031 Poland Department of Chemistry Iowa State University AmesIA50011 United States J. Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic Prague 818223 Czech Republic Department of Chemistry and Physics University of Tennessee at Martin MartinTN38238 United States Université libre de Bruxelles BrusselsB-1050 Belgium Facebook Menlo ParkCA94025 United States Institute of Theoretical and Experimental Biophysics Russian Academy of Science Pushchino Moscow142290 Russia Department of Chemistry Chemical Theory Center Supercomputing Institute University of Minnesota MinneapolisMN55455 United States SKAO Jodrell Bank Observatory MacclesfieldSK11 9DL United Kingdom Department of Chemistry University of Washington SeattleWA98195 United States Dirac Solutions PortlandOR97229 United States Chemistry Division U. S. Naval Research Laboratory WashingtonDC20375 United States School of Chemistry and Biochemis

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the last few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach and outlook. Copyright © 2020, The Authors. All rights reserved.

关键词： Computational chemistry

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Epitaxial growth following crystal nucleation in laser-quenched Si filins on SiO2

Epitaxial growth following crystal nucleation in laser-quenc...

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2015 MRS Spring Meeting

作者： Wong, Vemon K. Chitu, A.M. Limanov, A.B. Im, James S. Program in Materials Science and Engineering Department of Applied Physics and Applied Mathematics Columbia University New YorkNY United States

ISBN: (纸本)9781510826267

We have investigated the solidified microstructure of nucleation-generated grains obtained via complete melting of Si films on SiO2 at high nucleation temperatures. This was achieved using a high-temperature-capable hot stage in conjunction with excimer laser irradiation. As predicted by the direct-growth model that considers (1) the evolution in the temperature of the solidifying interface and (2) the subsequent modes of growth (consisting of amorphous, defective, and epitaxial) as key factors, we were able to observe the appearance of "normal" grains that possess a single-crystal core area. These grains, which are in contrast to previously reported flower-shaped grains that fully make up the microstructure of the solidified films obtained via irradiation at lower preheating temperatures (and amongst which these "normal" grains emerge), indicate that epitaxial growth of nucleated crystals must have taken place within the grains. We discuss the implications of our findings regarding (1) the validity of the direct-growth model, (2) the nature of the heterogeneous nucleation mechanism, and (3) the alternative explanations and assumptions that have been previously employed in order to explain the microstructure of Si films obtained via nucleation and growth within the complete melting regime. © 2015 Materials Research Society.

关键词： Silica

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Packing in protein cores

arXiv

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arXiv 2017年

作者： Gaines, J.C. Clark, A.H. Regan, L. O'Hern, C.S. Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Yale University New HavenCT06520 United States Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Department of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Department of Chemistry 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

Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and predicting protein structure and stability. It is well-established that a large contribution to protein stability originates from the sequestration from solvent of hydrophobic residues in the protein core. How are such hydrophobic residues arranged in the core? And how can one best model the packing of these residues? Here we show that to properly model the packing of residues in protein cores it is essential that amino acids are represented by appropriately calibrated atom sizes, and that hydrogen atoms are explicitly included. We show that protein cores possess a packing fraction of φ ≈ 0.56, which is significantly less than the typically quoted value of 0.74 obtained using the extended atom representation. We also compare the results for the packing of amino acids in protein cores to results obtained for jammed packings from disrete element simulations composed of spheres, elongated particles, and particles with bumpy surfaces. We show that amino acids in protein cores pack as densely as disordered jammed packings of particles with similar values for the aspect ratio and bumpiness as found for amino acids. Knowing the structural properties of protein cores is of both fundamental and practical importance. Practically, it enables the assessment of changes in the structure and stability of proteins arising from amino acid mutations (such as those identified as a result of the massive human genome sequencing efforts) and the design of new folded, stable proteins and protein-protein interactions with tunable specificity and affinity. Copyright © 2017, The Authors. All rights reserved.

关键词： Proteins

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A new phase-field approach to variational implicit solvation of charged molecules with the coulomb-field approximation

arXiv

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arXiv 2017年

作者： Zhao, Yanxiang Ma, Yanping Sun, Hui Li, Bo Du, Qiang Department of Mathematics George Washington University 801 22nd St. NW Phillips 739 WashingtonDC20052 United States Department of Mathematics Loyola Marymount University 1 LMU drive Los AngelesCA90045 United States Department of Mathematics and Statistics California State University Long BeachCA90840-1001 United States Department of Mathematics and Quantitative Biology Graduate Program University of California San Diego 9500 Gilman Drive Mail code: 0112 La JollaCA92093-0112 United States Department of Applied Physics and Applied Mathematics Columbia University NY10027 United States

We construct a new phase-field model for the solvation of charged molecules with a variational implicit solvent. Our phase-field free-energy functional includes the surface energy, solute-solvent van der Waals dispersion energy, and electrostatic interaction energy that is described by the Coulomb-field approximation, all coupled together self-consistently through a phase field. By introducing a new phase-field term in the description of the solute-solvent van der Waals and electrostatic interactions, we can keep the phase-field values closer to those describing the solute and solvent regions, respectively, making it more accurate in the free-energy estimate. We first prove that our phase-field functionals Γ-converge to the corresponding sharp-interface limit. We then develop and implement an efficient and stable numerical method to solve the resulting gradient-flow equation to obtain equilibrium conformations and their associated free energies of the underlying charged molecular system. Our numerical method combines a linear splitting scheme, spectral discretization, and exponential time differencing Runge-Kutta approximations. Applications to the solvation of single ions and a two-plate system demonstrate that our new phase-field implementation improves the previous ones by achieving the localization of the system forces near the solute-solvent interface and maintaining more robustly the desirable hyperbolic tangent profile for even larger interfacial width. This work provides a scheme to resolve the possible unphysical feature of negative values in the phase-field function found in the previous phase-field modeling (cf. H. Sun, et al. J. Chem. Phys., 2015) of charged molecules with the Poisson-Boltzmann equation for the electrostatic interaction. Copyright © 2017, The Authors. All rights reserved.

关键词： Free energy

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Comparative studies of commercial window with standard shielding concretes on the basis of photon interaction parameters 2nd

Comparative studies of commercial window with standard shiel...

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2nd International Conference on applied physics and Material Applications, ICAPMA 2015

作者： Sangwaranatee, N.W. Sangwaranatee, N. Kaewkhao, J. Chanthima, N. Informatics Mathematics Faculty of Science and Technology Suan Sunandha Rajabhat University Bangkok10300 Thailand Applied Physics Faculty of Science and Technology Suan Sunandha Rajabhat University Bangkok10300 Thailand Science Program Faculty of Science and Technology Nakhon Pathom Rajabhat University Nakhon Pathom73000 Thailand Nakhon Pathom Rajabhat University Nakhon Pathom73000 Thailand

ISBN: (纸本)9783038356837

Commercial window added with BaSO4 have been studies on the mass attenuation coefficient and compared it with some standard shielding concretes. This parameter has been investigated at photon energy from 1 keV to 100 GeV on the basis of calculation. The theoretical values of photon interaction were obtained by the WinXCom program. The variations of mass attenuation coefficient of commercial window and standard shielding concretes are shown graphically with photon energy. It has been observed that the commercial window added with 30% BaSO4 has higher value of mass attenuation coefficient than all of standard shielding concretes at the photon energy range above 40-400 keV. Also, discontinuous jump of mass attenuation coefficient at the lower energy has been discusses. © 2016 Trans Tech Publications, Switzerland.

关键词： Radiation shielding

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Engineering Sensorial Delay to Control Phototaxis and Emergent Collective Behaviors

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Physical Review X 2016年第1期6卷 011008-011008页

作者： Mite Mijalkov Austin McDaniel Jan Wehr Giovanni Volpe Soft Matter Lab Department of Physics Bilkent University Cankaya 06800 Ankara Turkey UNAM-National Nanotechnology Research Center Bilkent University Ankara 06800 Turkey Department of Mathematics and Program in Applied Mathematics University of Arizona Tucson Arizona 85721 USA

Collective motions emerging from the interaction of autonomous mobile individuals play a key role in many phenomena, from the growth of bacterial colonies to the coordination of robotic swarms. For these collective behaviors to take hold, the individuals must be able to emit, sense, and react to signals. When dealing with simple organisms and robots, these signals are necessarily very elementary; e.g., a cell might signal its presence by releasing chemicals and a robot by shining light. An additional challenge arises because the motion of the individuals is often noisy; e.g., the orientation of cells can be altered by Brownian motion and that of robots by an uneven terrain. Therefore, the emphasis is on achieving complex and tunable behaviors from simple autonomous agents communicating with each other in robust ways. Here, we show that the delay between sensing and reacting to a signal can determine the individual and collective long-term behavior of autonomous agents whose motion is intrinsically noisy. We experimentally demonstrate that the collective behavior of a group of phototactic robots capable of emitting a radially decaying light field can be tuned from segregation to aggregation and clustering by controlling the delay with which they change their propulsion speed in response to the light intensity they measure. We track this transition to the underlying dynamics of this system, in particular, to the ratio between the robots’ sensorial delay time and the characteristic time of the robots’ random reorientation. Supported by numerics, we discuss how the same mechanism can be applied to control active agents, e.g., airborne drones, moving in a three-dimensional space. Given the simplicity of this mechanism, the engineering of sensorial delay provides a potentially powerful tool to engineer and dynamically tune the behavior of large ensembles of autonomous mobile agents; furthermore, this mechanism might already be at work within living organisms such as chemo

关键词： Pattern formation Active matter Coarse graining Exact solutions for many-body systems Imaging & optical processing Molecular dynamics

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