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April 7, 2015 u vol. 112 u no. 14 u 4183–4506 Cover image: Pictured is zebrafish visceral adipose tissue containing lipid droplets (green), plasma membranes (magenta), and collagen (blue). Using genetic analysis and in vivo imag- ing of fluorescently labeled adipocytes, James E. N. Minchin et al. observed lipid deposition patterns in zebrafish. Fish deficient in Plxnd1, a transmembrane receptor that controls the migration of different cell types, displayed altered visceral body fat distribution and were protected from insulin resistance induced by a high-fat diet. The results suggest that Plxnd1 regulates the distribution and morphology of adipose tissue and may have implications in the treatment of metabolic disease. See the article by Minchin et al. on pages 4363–4368. Image courtesy of James E. N. Minchin. From the Cover 4363 Regulation of body fat distribution 4214 Jupiter and evolution of the Solar System 4352 Improving luminescence imaging 4381 Phosphorus sequestration in marine sponges 4459 Evolution of leprosy Contents SCIENCE AND CULTURE—How science intersects with culture 4185 Science and Culture: Using fiction to make the case for basic research Joel Shurkin THIS WEEK IN PNAS 4183 In This Issue COMMENTARIES 4187 Systems approach to metal-based pharmacology LETTERS (ONLINE ONLY) Isolda Romero-Canelón and Peter J. Sadler See companion article on page 3211 in issue 11 of volume 112 E1693 Loss of HtrA1-induced attenuation of TGF-β signaling 4189 Jupiter’s role in sculpting the early Solar System in fibroblasts might not be the main mechanism Smadar Naoz of CARASIL pathogenesis See companion article on page 4214 Ju Liu, Fengyun Dong, and Josephine Hoh 4191 Sponge symbionts and the marine P cycle E1694 Reply to Liu et al.: Loss of TGF-β signaling in Albert S. Colman CARASIL pathogenesis See companion article on page 4381 Nathalie Beaufort, Eva Scharrer, Vanda Lux, Michael Ehrmann, Christof Haffner, and Martin Dichgans PNAS PLUS E1695 Highly productive sown biodiverse pastures with low invasion risk Vânia Proença, Carlos Aguiar, and Tiago Domingos 4193 Significance Statements Brief statements written by the authors about the significance of E1696 Reply to Proença et al.: Sown biodiverse pastures their papers. are not a universal solution to invasion risk Don A. Driscoll, Jane A. Catford, Jacob N. Barney, Philip E. Hulme, Inderjit, Tara G. Martin, Aníbal INAUGURAL ARTICLE Pauchard, Petr Pysek, David M. Richardson, Sophie Riley, and Vernon Visser 4195 Candidate ionotropic taste receptors in the Drosophila larva Shannon Stewart, Tong-Wey Koh, Arpan C. Ghosh, Free online through the PNAS open access option. and John R. Carlson PNAS u April 7, 2015 u vol. 112 u no. 14 u iii–vii Downloaded by guest on September 30, 2021 ENVIRONMENTAL SCIENCES PHYSICAL SCIENCES 4251 Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite APPLIED MATHEMATICS oligotrophic lifestyle 4202 Using wavelength and slope to infer the historical Nathan Walworth, Ulrike Pfreundt, William C. Nelson, origin of semiarid vegetation bands Tracy Mincer, John F. Heidelberg, Feixue Fu, John B. Jonathan A. Sherratt Waterbury, Tijana Glavina del Rio, Lynne Goodwin, Nikos C. Kyrpides, Miriam L. Land, Tanja Woyke, 4208 Route to thermalization in the α-Fermi–Pasta– David A. Hutchins, Wolfgang R. Hess, and Eric A. Webb Ulam system Miguel Onorato, Lara Vozella, Davide Proment, SUSTAINABILITY SCIENCE and Yuri V. Lvov 4257 Criticality of metals and metalloids T. E. Graedel, E. M. Harper, N. T. Nassar, Philip Nuss, and Barbara K. Reck ASTRONOMY 4214 Jupiter’s decisive role in the inner Solar System’s early evolution Konstantin Batygin and Greg Laughlin SOCIAL SCIENCES See Commentary on page 4189 ANTHROPOLOGY 4263 Late Pleistocene horse and camel hunting at the CHEMISTRY southern margin of the ice-free corridor: Reassessing 4218 Evidence for tunneling in base-catalyzed isomerization the age of Wally’s Beach, Canada of glyceraldehyde to dihydroxyacetone by hydride Michael R. Waters, Thomas W. Stafford Jr., Brian Kooyman, shift under formose conditions and L. V. Hills Liang Cheng, Charles Doubleday, and Ronald Breslow 4268 Development of sedentary communities in the Maya 4221 Multiplexed metagenome mining using short DNA lowlands: Coexisting mobile groups and public sequence tags facilitates targeted discovery of ceremonies at Ceibal, Guatemala epoxyketone proteasome inhibitors Takeshi Inomata (猪俣 健), Jessica MacLellan, Daniela Jeremy G. Owen, Zachary Charlop-Powers, Triadan, Jessica Munson, Melissa Burham, Kazuo Alexandra G. Smith, Melinda A. Ternei, Paula Y. Aoyama (青山 和夫), Hiroo Nasu (那須 浩郎), Calle, Boojala Vijay B. Reddy, Daniel Montiel, Flory Pinzón, and Hitoshi Yonenobu (米延 仁志) and Sean F. Brady PSYCHOLOGICAL AND COGNITIVE SCIENCES 4227 Tunable molecular orientation and elevated 4274 Leader emergence through interpersonal thermal stability of vapor-deposited neural synchronization organic semiconductors Jing Jiang (蒋静), Chuansheng Chen (陈传升), Bohan Shakeel S. Dalal, Diane M. Walters, Ivan Lyubimov, Dai (代博涵), Guang Shi (时光), Guosheng Ding (丁国盛), Juan J. de Pablo, and M. D. Ediger Li Liu (刘丽), and Chunming Lu (卢春明) 4233 Engineering three-dimensional hybrid supercapacitors and microsupercapacitors for high-performance SUSTAINABILITY SCIENCE integrated energy storage 4375 Area burned in the western United States is unaffected Maher F. El-Kady, Melanie Ihns, Mengping Li, Jee Youn by recent mountain pine beetle outbreaks Hwang, Mir F. Mousavi, Lindsay Chaney, Andrew T. Lech, Sarah J. Hart, Tania Schoennagel, Thomas T. Veblen, and Richard B. Kaner and Teresa B. Chapman EARTH, ATMOSPHERIC, AND PLANETARY SCIENCES BIOLOGICAL SCIENCES 4239 Continental erosion and the Cenozoic rise of marine diatoms Pedro Cermeño, Paul G. Falkowski, Oscar E. Romero, APPLIED BIOLOGICAL SCIENCES Morgan F. Schaller, and Sergio M. Vallina 4280 Sparse feature selection methods identify unexpected global cellular response to 4245 Evidence for indigenous nitrogen in sedimentary and strontium-containing materials aeolian deposits from the Curiosity rover investigations Hélène Autefage, Eileen Gentleman, Elena Littmann, at Gale crater, Mars Martin A. B. Hedegaard, Thomas Von Erlach, Matthew Jennifer C. Stern, Brad Sutter, Caroline Freissinet, O’Donnell, Frank R. Burden, David A. Winkler, Rafael Navarro-González, Christopher P. McKay, and Molly M. Stevens P. Douglas Archer Jr., Arnaud Buch, Anna E. Brunner, Patrice Coll, Jennifer L. Eigenbrode, Alberto G. Fairen, Heather B. Franz, Daniel P. Glavin, Srishti Kashyap, BIOCHEMISTRY Amy C. McAdam, Douglas W. Ming, Andrew Steele, E1697 Motion of proximal histidine and structural allosteric Cyril Szopa, James J. Wray, F. Javier Martín-Torres, transition in soluble guanylate cyclase Maria-Paz Zorzano, Pamela G. Conrad, Paul R. Byung-Kuk Yoo, Isabelle Lamarre, Jean-Louis Martin, Mahaffy, and the MSL Science Team Fabrice Rappaport, and Michel Negrerie iv u www.pnas.org Downloaded by guest on September 30, 2021 E1705 Altered cofactor regulation with disease-associated 4334 N-Glycosylation as determinant of epidermal growth p97/VCP mutations factor receptor conformation in membranes Xiaoyi Zhang, Lin Gui, Xiaoyan Zhang, Stacie L. Bulfer, Karol Kaszuba, Michał Grzybek, Adam Orłowski, Reinis Valentina Sanghez, Daniel E. Wong, YouJin Lee, Lynn Danne, Tomasz Róg, Kai Simons, Ünal Coskun, Lehmann, James Siho Lee, Pei-Yin Shih, Henry J. Lin, and Ilpo Vattulainen Michelina Iacovino, Conrad C. Weihl, Michelle R. Arkin, Yanzhuang Wang, and Tsui-Fen Chou CELL BIOLOGY 4218 Evidence for tunneling in base-catalyzed isomerization E1724 Oncogenesis driven by the Ras/Raf pathway requires of glyceraldehyde to dihydroxyacetone by hydride the SUMO E2 ligase Ubc9 shift under formose conditions Bing Yu, Stephen Swatkoski, Alesia Holly, Liam C. Lee, Liang Cheng, Charles Doubleday, and Ronald Breslow Valentin Giroux, Chih-Shia Lee, Dennis Hsu, Jordan L. 4286 Human RECQ1 helicase-driven DNA unwinding, Smith, Garmen Yuen, Junqiu Yue, David K. Ann, R. Mark annealing, and branch migration: Insights Simpson, Chad J. Creighton, William D. Figg, Marjan Gucek, from DNA complex structures and Ji Luo Ashley C. W. Pike, Shivasankari Gomathinayagam, 4340 KLHL3 regulates paracellular chloride transport in the Paolo Swuec, Matteo Berti, Ying Zhang, Christina kidney by ubiquitination of claudin-8 Schnecke, Francesca Marino, Frank von Delft, Yongfeng Gong, Jinzhi Wang, Jing Yang, Ernie Gonzales, Ludovic Renault, Alessandro Costa, Opher Gileadi, Ronaldo Perez, and Jianghui Hou and Alessandro Vindigni 4346 TRAPPII regulates exocytic Golgi exit by mediating 4292 Structural mechanisms of DNA binding and unwinding nucleotide exchange on the Ypt31 in bacterial RecQ helicases ortholog RabERAB11 Kelly A. Manthei, Morgan C. Hill, Jordan E. Burke, Mario Pinar, Herbert N. Arst Jr., Areti Pantazopoulou, Samuel E. Butcher, and James L. Keck Víctor G. Tagua, Vivian de los Ríos, Javier Rodríguez-Salarichs, J. Fernando Díaz, 4298 Phosphorylation of ORF1p is required for and Miguel A. Peñalva L1 retrotransposition Pamela R. Cook, Charles E. Jones, and Anthony V. Furano 4352 Expanded palette of Nano-lanterns for real-time multicolor luminescence imaging 4304 SWI/SNF chromatin-remodeling complexes function in Akira Takai, Masahiro Nakano, Kenta Saito, Remi Haruno, noncoding RNA-dependent assembly of nuclear bodies Tomonobu M. Watanabe, Tatsuya Ohyanagi, Takashi Jin, Tetsuya Kawaguchi, Akie Tanigawa, Takao Naganuma, Yasushi Okada, and Takeharu Nagai Yasuyuki Ohkawa, Sylvie Souquere, Gerard Pierron,
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  • Viscosity from Newton to Modern Non-Equilibrium Statistical Mechanics

    Viscosity from Newton to Modern Non-Equilibrium Statistical Mechanics

    Viscosity from Newton to Modern Non-equilibrium Statistical Mechanics S´ebastien Viscardy Belgian Institute for Space Aeronomy, 3, Avenue Circulaire, B-1180 Brussels, Belgium Abstract In the second half of the 19th century, the kinetic theory of gases has probably raised one of the most impassioned de- bates in the history of science. The so-called reversibility paradox around which intense polemics occurred reveals the apparent incompatibility between the microscopic and macroscopic levels. While classical mechanics describes the motionof bodies such as atoms and moleculesby means of time reversible equations, thermodynamics emphasizes the irreversible character of macroscopic phenomena such as viscosity. Aiming at reconciling both levels of description, Boltzmann proposed a probabilistic explanation. Nevertheless, such an interpretation has not totally convinced gen- erations of physicists, so that this question has constantly animated the scientific community since his seminal work. In this context, an important breakthrough in dynamical systems theory has shown that the hypothesis of microscopic chaos played a key role and provided a dynamical interpretation of the emergence of irreversibility. Using viscosity as a leading concept, we sketch the historical development of the concepts related to this fundamental issue up to recent advances. Following the analysis of the Liouville equation introducing the concept of Pollicott-Ruelle resonances, two successful approaches — the escape-rate formalism and the hydrodynamic-mode method — establish remarkable relationships between transport processes and chaotic properties of the underlying Hamiltonian dynamics. Keywords: statistical mechanics, viscosity, reversibility paradox, chaos, dynamical systems theory Contents 1 Introduction 2 2 Irreversibility 3 2.1 Mechanics. Energyconservationand reversibility . ........................ 3 2.2 Thermodynamics.