519 research outputs found
Preface: Special Topic on Enhanced Sampling for Molecular Systems
No full textThis special topic highlights recent developments in enhanced sampling methods for molecular-level simulations of chemical and biological systems. These methods are designed to enable more efficient exploration of phase space and extend the time scales that can be explored by simulations
Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations
No full textABSTRACT: Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (Lettieri, S.; Zuckerman, D. M. J. Comput. Chem. 2012, 33, 268−275) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent inter-actions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70−90 % of the α-helical structure while providing a factor of 3−10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding− unfolding transitions of the peptide were observed, along with a factor of 10−100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a “resolution exchange ” setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (Lyman, E.; Zuckerman, D. M. J. Chem. Theory Comput. 2006, 2, 656−666). 1
The Book of Daniel and manticism: a critical assessment of the view that the Book of Daniel derives from a mantic tradition
No full textThis dissertation examines the consensus view that is based on Hans-Peter
Müller's 1969 and 1972 articles: Daniel was a mantic wise man in the Mesopotamian
ASA
court, and this was the self-understanding or aspiration of the maskilim of Dan 11:33, 35,
12:3, 10, who wrote the book. Chapter 1 reviews the arguments that make the mantic connection and Chapter 2 concludes that a direct connection with the Danes of Aqht, Ezek, and Jub, and with the angel in 1 Enoch should be rejected. There is evidence that the
tradition of a priest in Ezra 8: 2 and Neh 10: 7, and found also in the superscription to
the Old Greek of Bel, and 4 Ezra 12:10-11, and suggested the name.
Chapter 3 concludes that the portrayal of the court diviners in Dan 1-6 is wholly
negative and includes both the diviners, and the essence of the professions, i. e., the
ability to interpret a divine revelation. The critique is conveyed through the story line,
explicit criticisms, irony, and humour. Chapter 4 concludes that Daniel, the interpreter
of dreams and the writing on the wall, is distinguished from every other character and role. In the final form of Dan, Daniel as the divinely assisted each time he interprets, just as when he receives help from an interpreting angel in Dan 7-12.
Chapter 5 demonstrates that the portrayal of Daniel as the divinely assisted
interpreter makes sense of the reinterpretation of old prophecies against the Assyrians
as prophecies against Antiochus IV Epiphanes. Hab 2:2-4 and Isa 52-53 were also
understood as predictions about the maskilim themselves. Comparisons are then made
with the Teacher of Righteousness, the writers of the Hodayot, and with three Essenes
portrayed by Josephus. These too were portrayed as divinely assisted interpreters
Heraclius in 625
No full textREB 60 2002 France p. 189-197
Constantin Zuckerman, He radius in 625. — Comparing the evidence of the Ps. -Sebeos with that of Theophanes, the author revises the itinerary of Heraclius and the chronology of his battles during the key years of the Persian campaign (625-626). One year's campaign in Theophanes, A. M. 61 15, is reduced to two months of hostilities during the winter of 625, and the events described in A. M. 61 16 to the following two months. This analysis eliminates certain contradictions in Theophanes's account which have hitherto puzzled commentators.L'itinéraire d'Héraclius et la chronologie de ses batailles durant deux années clef de la campagne perse, 625-626, subissent ici une révision, le témoignage de Théophane étant revu à la lumière de celui de Pseudo-Sébéos. Une année de campagne, placée par Théophane sub a.m. 61 15, se réduit désormais à deux mois d'hostilités durant l'hiver 625, et les événements décrits sub a.m. 6116 se placent dans les mois qui suivent. Cette analyse tenant compte tant des réalités du terrain que des données des sources élimine les contradictions du récit de Théophane qui ont jusqu'ici défié les commentateurs.Zuckerman Constantin. Heraclius in 625. In: Revue des études byzantines, tome 60, 2002. pp. 189-197
The long-wavelength view of GG Tau A: rocks in the ring world
No full textWe present the first detection of GG Tau A at centimetre wavelengths, made with the Arcminute Microkelvin Imager Large Array at a frequency of 16 GHz (λ = 1.8 cm). The source is detected at >6 σrms with an integrated flux density of S16GHz = 249 ± 45 µJy. We use these new centimetre-wave data, in conjunction with additional measurements compiled from the literature, to investigate the long-wavelength tail of the dust emission from this unusual protoplanetary system. We use an MCMC-based method to determine maximum likelihood parameters for a simple parametric spectral model and consider the opacity and mass of the dust contributing to the microwave emission. We derive a dust mass of Md ~ 0.1 Msun, constrain the dimensions of the emitting region and find that the opacity index at λ > 7 mm is less than unity, implying a contribution to the dust population from grains exceeding ~4 cm in size. We suggest that this indicates coagulation within the GG Tau A system has proceeded to the point where dust grains have grown to the size of small rocks with dimensions of a few centimetres. Considering the relatively young age of the GG Tau association in combination with the low derived disc mass, we suggest that this system may provide a useful test case for rapid core accretion planet formation models
Factors Influencing Physical Risk Taking in Rock Climbing
No full textThis study was designed to investigate factors influencing physical risk taking in the sport of rock climbing. Specifically, the relationships between physical risk taking, sensation seeking, spheres of control, and desirability of control were examined. One hundred five rock climbers from the United States completed a series of surveys measuring each of the above-mentioned psychological variables. As predicted, physical risk taking demonstrated significant positive relationships to both total sensation seeking and thrill/adventure seeking (TAS). The expected relationships between physical risk taking, personal control and desirability of control were not supported. As hypothesized, no substantive patterns were revealed between physical risk taking and interpersonal control or sociopolitical control. Finally, comparisons between high and low physical risk taking rock climbers revealed significant group differences for total sensation seeking, TAS, and disinhibition. The identification of predictors of physical risk taking is a key step toward identifying individuals likely to engage in high physical risk behavior, and under what circumstances they are likely to do so
Scientometric portrait of Nobel laureate Leland H. Hartwell
No full textLeland H. Hartwell was honoured with the Nobel Prize in Physiology or Medicine (2001) at his 62 years age and at 41 years of research publishing career. The first contribution of the author was in 1961 at the age of 22. The number of his contributions in a year peaked in 1997 when it touched 8. He had 108 publications during 1961 – 2001 in domains: Molecular Biology of Cell Cycle Regulation (43), Genetics of Cell Division (48), Genomic Re-arrangement and DNA Repair (9), Molecular Genetics of Yeast Cell Fission (5), and Drug Target Interaction (3) which were analysed for authorship pattern with his 101 collaborators. Most active researchers having number of publications with Leland H. Hartwell were : Weinert, T. A. (10), Garvik, B. M. (8), McLaughlin, C. S. (8), Jenness, D. D. (5). His productivity coefficient was 0.76 which clearly indicates that his productivity increased after 50 percentile age. Highest collaboration coefficient (1) for Leland H. Hartwell was found during 1963-1965, 1968-1969, 1977, 1981-1983, 1985-1990, 1996 and 1998-2001. Journals have been the most preferred channel of communication where, as many as 96 papers out of 108 have been published. The core journals publishing his papers were: Cell (14), Genetics (12), Mol. Cell Biol. (8), J. Bactariol. (7), J. Cell Biol. ( 7), Science (7) J. Mol. Biol.(6), Exp. Cell Res. (5), and Proc. Nat. Acad. Sci.(5). Publication density is 2.63 and Publication concentration is 14.63. Most prolific keywords in titles of publications were: Saccharomyces cerevisiae , Yeast , Cell division cycle , RAD9, DNA Damage , Genes , Cell cycle, Genetic control , Check point (s) , Cell division , Mutant of Yeast
ALMA and Herschel observations of the prototype dusty and polluted white dwarf G29-38
No full textJF gratefully acknowledges the support of the STFC via an Ernest Rutherford Fellowship. AB acknowledges the support of the ANR-2010 BLAN-0505-01 (EXOZODI). MCW and OP are grateful for the support of the European Union through ERC grant number 279973.ALMA Cycle 0 and Herschel PACS observations are reported for the prototype, nearest, and brightest example of a dusty and polluted white dwarf, G29-38. These long-wavelength programmes attempted to detect an outlying, parent population of bodies at 1–100 au, from which originates the disrupted planetesimal debris that is observed within 0.01 au and which exhibits LIR/L* = 0.039. No associated emission sources were detected in any of the data down to LIR/L* ∼ 10−4, generally ruling out cold dust masses greater than 1024–1025 g for reasonable grain sizes and properties in orbital regions corresponding to evolved versions of both asteroid and Kuiper belt analogues. Overall, these null detections are consistent with models of long-term collisional evolution in planetesimal discs, and the source regions for the disrupted parent bodies at stars like G29-38 may only be salient in exceptional circumstances, such as a recent instability. A larger sample of polluted white dwarfs, targeted with the full ALMA array, has the potential to unambiguously identify the parent source(s) of their planetary debris.Peer reviewe
Moving Through Diasporic Dancescapes in the 21st Century
No full textLa thèse explore les interrelations et interactions entre mémoire, mouvement, diaspora et espace-temps dans la danse au XXIème siècle. Dans une approche transculturelle, transdisciplinaire et transtemporelle, la publication se concentre sur des pièces solo chorégraphiées et interprétées par sept chorégraphes contemporain.e.s basé.e.s en Allemagne, France, Martinique, Palestine, à Taiwan et aux Etats-Unis. Estimant que les corps humains sont objets et sujets de relations de pouvoir, la thèse étudie ce qui se passe lorsque les corps dansent le passé au temps présent, au sens propre et au sens figuré. L'auteure introduit un nouveau concept: (to) perforMemory, à la fois un substantif et un verbe en anglais. Elle met en relief la spécificité de la danse comme forme de production et transmission de la mémoire culturelle, en relation avec des traumas historiques tels que l'Holocauste, la Traite triangulaire ou Maafa, la Nakba ainsi que des défis sociopolitiques contemporains.
Conçu comme une spirale, le livre est une invitation au voyage à travers des paysages diasporiques dansés, dans lequel les notions d'identité, d'appartenance, de spatialité, de temporalité et de représentation émergent tour à tour, et s'illuminent mutuellement dans l'analyse de séquences de danse concrètes. Le corpus théorique puise dans des domaines aussi variés que les études de genre, la danse, les études postcoloniales, la litérature, les Cultural Studies, la physique quantique, les études queer et la poésie. Basée sur des recherches doctorales conduites de 2013 à 2017 à travers le monde, cette publication électronique comprend également les transcriptions intégrales des entretiens personnels menés avec les artistes Oxana Chi, Zufit Simon, Chantal Loïal, Christiane Emmanuel, Farah Saleh, Wan-Chao Chang, et André M. Zachery, ainsi que des liens vers des extraits audiovisuels de spectacles.Die Dissertation von L. Zuckerman (auch bekannt als Layla Zami)
erforscht die Wechselbeziehungen zwischen Erinnerung, Bewegung, Diaspora und Zeit/Raum in Tanzproduktionen des 21. Jahrhunderts. In einer innovativen transkulturellen, transdisziplinären und transtemporalen Perspektive setzt die Publikation den Akzent auf die Solo-Arbeiten von sieben zeitgenössischen Choreograph_innen, die in Deutschland, Frankreich, Taiwan, Martinique, Palästina und den USA leben, und Interpret_innen ihrer eigenen Stücke sind. Ausgehend von der Hypothese, dass Körper eine zentrale Rolle in der Aushandlung und Überwindung von Machtverhältnissen spielen, fragt die Forschung was geschehen kann, wenn tanzende Körper die Vergangenheit in die Gegenwart transportieren, im materiellen und im metaphorischen Sinne. Die Autorin leitet ein neues Konzept ein, das im Englischen sowohl Substantiv als auch Verb ist: (to) perforMemory. Sie reflektiert die Besonderheiten der Ausdruckform Tanz in der Darstellung, Herstellung, und Tradierung von kultureller Erinnerung im Bezug auf historische Traumata wie der Holocaust, der Transatlantische Sklavenhandel, die Maafa, die Nakba und zeitgenössische gesellschaftspolitische Herausforderungen.
Das als Spirale konzipierte Buch lädt zu einer Wanderung durch diasporische Tanz_schaften, in denen sich Fragestellungen zu Identität, Körperlichkeit, Zugehörigkeit, Räumlichkeit und Zeitlichkeit entfalten, und sich in der Diskussion von bestimmten Tanzsequenzen wechselseitig beleuchten. Die Doktorarbeit basiert auf den Ergebnissen einer vierjährigen internationalen Forschung. Die Quellen schöpfen aus unterschiedlichen Fachrichtungen, u.a. Gender und Queer Studies, Tanz/Performance, Kulturwissenschaften, Erinnerung, Postkoloniale Studien, Literatur, Quantenphysik, und Lyrik. Die Veröffentlichung beinhaltet ebenfalls die vollständigen Transkripte von persönlichen Gesprächen, die die Autorin mit den Künstler_innen Oxana Chi, Zufit Simon, Wan-Chao Chang, André M. Zachery, Farah Saleh, Christiane Emmanuel und Chantal Loïal aufgenommen hat, sowie Links zu Performance-Ausschnitten.The dissertation by L. Zuckerman (aka Layla Zami) explores the
interrelations and interactions between memory, movement, diaspora, and spacetime in 21st century dance productions. In an innovative transcultural, transdisciplinary and transtemporal approach, the publication focuses on solo works by seven contemporary dancers-choreographers based in Germany, France, Taiwan, Martinique, Palestine and the USA. Contending that corporeality is a site and a source of power, the research asks what happens when moving bodies propel the past into the present, metaphorically and materially. The author introduces a new concept: (to) perforMemory, which is both a noun and a verb, and discusses the specificity of dance in the production and transmission of cultural memory in relation to historical trauma such as the Holocaust, the Transatlantic Slave Trade, Maafa, the Nakba and contemporary sociopolitical challenges.
Conceived in a spiral-like fashion, the book takes the reader through diasporic dancescapes in which notions of identity, home, embodiment, spatiality and temporality unfold and are brought into resonance with each other in the discussion of specific dance examples. The theoretical references connect such various fields as gender studies, dance and performance studies, cultural memory studies, postcolonial studies, literature, quantum physics, queer studies and poetry. Based on doctoral research conducted across the globe from 2013 to 2017, the electronic publication also features the full interview transcripts of personal conversations recorded by the author with the artists Oxana Chi, Zufit Simon, Wan-Chao Chang, André M. Zachery, Farah Saleh, Christiane Emmanuel and Chantal Loïal, as well as links to audiovisual performance excerpts
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