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˜ Ü Proceedings ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ The 2nd International Symposium on Large-scale Computational Science and Engineering ਫ਼Ňो̸ႏ Proceedings Ȳ ̵ 4 Nov. 8, 2012, Thursday ̵7S࢑Uએਫ਼ɝ Science Council of Japan, Tokyo, Japan ΪŮ Sponsor Science Council of Japan Japan Science and Technology Agency ȁŮ Co-sponsor ̵7̺µ˨SU (The Japan Society for Industrial and Applied Mathematics) ̵7̴SU᜖The Chemical Society of Japan᜗ ̵7ɝļSU (The Japan Society of Mechanical Engineers) ̵7ওÜǜSU (The Japan Society for Computational Engineering and Science) ̵7ওÜ˨ǜSU (Japan Society for Computational Methods in Engineering) ̵7ওÜ˒SೳϤ JACM (Japan Association for Computational Mechanics) ̵7ÙāćĎĞÙĉĕSU (Japan Society for Simulation Technology) ̵7̀SU (The Physical Society of Japan) ͨଦ Support Ҝ˿తğ࢑U (Society of Automotive Engineers of Japan) ÙĕÿÚÈĂ୳̸ ಶȲÕĕöćĞáͬ೯ͮЏΆ]h:Ńĝ­wɰBĝฎBΡS: ǜS:ǥĝ̓˵ΡS:%࿛Ư¦ͼ࿛Ư¦ĀčãÛÓĞč:o: ̈sï¯̀o­¯Āčã÷ÅÚåÑÛϧ૏¶È૏{ʢ"pΑÒΠ ೽¥­°n®:̒{hÒ p˨̈s̋­°f®¢}; 7ÙĕÿÚÈĂ:w°­ʢ"ɰญΠo­:ìðĝòÆÌΚǥႸ ȏ:izΡS¬āÑď:f¯hĀÑďϧ૏¶ॾz}¯ɰญ¶È૏ {:Ąéč̴¨˨ĕওÜýϚ¬ÙāćĎĞÙĉĕçȷ࿥³¯Åᆏ h:ƼȎ̅1௽{h¯êåùÑċÛʢ"͵¶ŝΨ{ਫ਼Ňóïčখ ਭ¶ࢌh¢};w°¬®:ϣʢ"਒ᆏ̉ਭĝğ࢑:ࣽ˨ʢ"਒ ᆏȁ೫¦p͒­o®:ʢ"਒ᆏ¶୨l¬®̑qÒ p̋­ °¯wp/˽y°¢};¢:ͽӑ̙>¦̈˨xί˕hq:w̙ ჳÕĕöćĞáÙāćĎĞÙĉĕʢ"˲ʵÒ ¶ͽӑ̓Uȁ{h ͳlh¢}; ― 3 ― ùďÒċĂ ࿔UƅŬ ÙĕÿÚÈĂએ࿇ƅŬ ʆǕ Ǟɖ᜖̵7S࢑Uએ f̑S ˝Dž᜗ ȁŮ͵.ࢢƅŬ ǯΨ ç᜖᜖͂᜗ΡSğ࢑ƊҶɝǻãæʢ"Ǟ೽ൺ ΆȅΪ=ਚÅ᜗ 78 ùĎìČਫ਼Ň᜖ìð᜗ ϞUᜨÑŦ Ïͽ᜖̴Sʢ"ôওÜiz̀ʢ" ࿇᜗ ĀÈď þÊď᜖ƼÛêċÛøčÒ̑SŃ̴̀Sʢ"ô ˝Dž᜗ ÚĉÝ÷ āÑč᜖ůƼÕďċë̑SþĞčâĞ× ˝Dž᜗ Πญ 1ͽ൫᜖ůƼͩÍČ÷ËčíÄ̑S ˝Dž᜗ 78]78 ͸O£ ]787] ùĎìČਫ਼Ňᜠ᜖òÆÌ᜗ ϞUᜨİ7 ͐ȶ᜖ϊÿ̑S ˝Dž᜗ ĂĞĕ Ï ÏĂ᜖ᅁƼÒDzᇻ̑S ɀ˝Dž᜗ ÍČĞ× ×ĕþĕĀæ᜖ůƼďÛÄċĄÛƼWʢ"ô ãĞĂČĞâĞ᜗ ÈÉÆáÌ Ćĕ᜖ůƼéćĞÑ̑S ˝Dž᜗ 7]77 O 77878 óïčéÅÛÍåÙĉĕʛਫ਼Ň᜖ᜟ᜗ ϞUᜨ؇Ζ ͽ൫᜖̵7S࢑Uએ ͒φ̑Sǣs˨ΡSÆĕÛèÅèćĞêʲô࿇ĝ˝Dž᜗ » ˯Ï᜖f̑S̑S၄ ˝Dž᜗ ÷˟ çϞ᜖ϊÿǜƿ̑S̑S၄ ˝Dž᜗ Πಧ ͬ᜖ฎB̴Sʢ"ͨU ϖ࿇᜗ ࿇İ ˯ၟ᜖ϊÿ̑S̑S၄ ˝Dž᜗ 878~8 O ~8]8 óïčéÅÛÍåÙĉĕʛਫ਼Ň᜖ᜠ᜗ ϞUᜨ»ದ ૶᜖̴Sʢ"ôওÜΡSʢ"ɝǻ țţ˲᜗ ყ4 ƪϤB᜖ρǖ̑S̑S၄ ˝Dž᜗ ̵÷ ˪)᜖f̑SɰBǭϺ­̀Sʢ"ô ɀ˝Dž᜗ ੆ʃ ̫φ᜖඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞ ÙíÄČ×Ğã÷ÉďĞ᜗ ҫϝ Օε᜖͜î̑S̑S၄ ˝Dž᜗ ϥO ̰᜖f̑S̑S၄ ˝Dž᜗ ]88 O 88 óïčéÅÛÍåÙĉĕ ÕĞéÅïĞáᜨʆǕ Ǟɖ 87 ࿒UƅŬ ؇Ζ ͽ൫ ɢϤϞUᜨΠǕ ႎÏ᜖᜖͂᜗ΡSğ࢑ƊҶɝǻ ᅯɆίϖ᜗ ― 5 ― ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ ਫ਼ŇȎ IùĎìČਫ਼Ňᜟ᜖ìð᜗J ਫ਼Ňᜟ ɝฐċɰB᜝ฐċìðǛϤᜨͽΖওÜቲɝǛȬᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ¢ ĀÈď þÊď ƼÛêċÛøčÒ̑SŃ̴̀Sʢ"ô ˝Dž ਫ਼Ňᜠ ǜɰBďĞáĞÙāćĎĞÙĉĕ ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ8 ÚĉÝ÷ āÑč ůƼÕďċë̑SþĞčâĞ× ˝Dž ਫ਼Ňᜡ ìðòÆÌDŽüáÛÓĞčɰB˿˒SÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ] Πญ 1ͽ൫ ůƼͩÍČ÷ËčíÄ̑S ˝Dž IùĎìČਫ਼ŇᜠJ ਫ਼Ňᜢ ìðòÆÌΡSğ࢑ÙāćĎĞÙĉĕᜨޞƩ଱˿ॾzo­ ìðǻ೰যও¢ᝳᝳᝳ] ĂĞĕ Ï ÏĂ ᅁƼÒDzᇻ̑S ɀ˝Dž ਫ਼Ňᜣ ìðÛÓĞčĀÙĕÙāćĎĞÙĉĕᜨČþßĞĂ̑॔ȵǻ೰˺̴ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ ÍČĞ× ×ĕþĕĀæ ůƼďÛÄċĄÛƼWʢ"ô ãĞĂČĞâĞ ਫ਼Ňᜤ Đn෍Ǣnu¯̴Sη̺ා̴ിǞഓτĀčãÛÓĞčÙāćĎĞÙĉĕᝳᝳᝳ¢ ÈÉÆáÌ Ćĕ ůƼéÅĞÑ̑S ˝Dž ― 6 ― IóïčéÅÛÍåÙĉĕʛਫ਼Ň᜖ᜟ᜗J ਫ਼Ňᜥ ˁǾ࿥ႱB̀଱¥ͽΖϓÄᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ78 » ˯Ï f̑S̑S၄ ˝Dž ਫ਼Ňᜦ ìðÙÛèĂȭÌĞâĞ %࿛ ÃÄ ϊȆɰB˿˒SñÆøČåë̴ᝳᝳᝳᝳ 8 ÷˟ çϞ ϊÿǜƿ̑S̑S၄ ˝Dž ਫ਼Ňᜧ ƝϓÄǟ̑ɰBযওฎB̴S ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 8 Πಧ ͬ ฎB̴Sʢ"ͨU ϖ࿇ ਫ਼Ňᜟ᜞ ɐႏη̺DŽĀčãÛÓĞčÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ ~ ࿇İ ˯ၟ ϊÿ̑S̑S၄ ˝Dž IóïčéÅÛÍåÙĉĕʛਫ਼Ň᜖ᜠ᜗J ਫ਼Ňᜟᜟ ìðĝòÆÌɝЏযও¥୨዇Ɲɐ᜔዇˨ΡฎB̴SŇÜϚᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ~¢ ყ4 ƪϤB ρǖ̑S̑S၄ ˝Dž ਫ਼Ňᜟᜠ ǟ̑òÆÌɰBႏϤwǻ೰âÆìāåÑÛᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ8 ̵÷ ˪) f̑SɰBǭϺ­̀Sʢ"ô ɀ˝Dž ਫ਼Ňᜟᜡ ­wɰBDŽĀčãĎûčÙāćĎ᜛Ùĉĕ ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ ੆ʃ ̫φ ඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞ ÙíÄČ×Ğã÷ÉďĞ ਫ਼Ňᜟᜢ Ϡ͝࿛ӏࢌÙÛèĂ࿔ƦuĀčãÛÓĞčſBÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳ ҫϝ Օε ͜î̑S̑S၄ ˝Dž ਫ਼Ňᜟᜣ ˁhǥႸ¶οu¯ΖB˒ƦႱùċĕêüáÛÓĞčÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳ¢ ϥO ̰ ̵7S࢑Uએ f̑S̑S၄ ˝Dž ― 7 ― ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ The 2nd International Symposium on Large-scale Computational Science and Engineering ɝฐċɰB᜝ฐċìðǛϤᜨ ͽΖওÜቲɝǛȬ Metal-Organic Molecule-Metal Nano-Junctions: A close contact between first-principle simulations and experiments ĀÈď þÊď Mauro BOERO Ƽ ÛêċÛøčÒ̑S Ń̴̀Sʢ"ô ˝Dž Professor, Institut de Physique et Chimie des Matériaux, University of Strasbourg, France ― 9 ― ਫ਼ Ň ᜟ ùď÷ÅĞč Mauro BOERO᜖ĀÈď þÊď᜗ ÛêċÛøčÒ̀଱̴S̀ʢ"ô᜖IPCMS᜗ʢ "éÅĎÑáĞ:ÛêċÛøčÒ̑S:Strasbourg (France) ̵ၓǣs̑S˝Dž ˊǖΖBɰBওÜÝĕáĞ᜖CECAM᜗˝Dž ওǛ଱ΡSÆíÙÄèÅø᜖f᜗ăĕòĞ 130ý0ΆǾࢢਭ˵᜖100ýΖ؝ਭ˵:5ýॾ ਍ঠϖ:5ý؝:19ýƼၯUએUએ༃᜗;ࣅ ʤµ;˨= 2321:h-index = 28 Ë࿋ᅯɆ ͽΖওÜýϚ:QM/MM᜖ฎB˒S᜝ɰB˒S᜗ñÆøČåëýϚ¬¯̀ ଱ΡSòÆÌ̴S:Đn̴S;1995Ȳ¬®CPMDóåÓĞÚȁò࿔Ʀ͵; þϗɷ 1964Ȳ123̵­ ­ৼǥᜨÆáČĞ:êČð Ҝgsôü æ ̍̃ǣsôü Institute of Physics and Chemistry of Materials (IPCMS), CNRS and University of Strasbourg, 23 Rue du Loess, F-67034 Strasbourg (France) Phone: +33-3-88419931 E-mail: [email protected] S˼ 1988Ȳ87̵ – êČð̑Sͦƿ᜖̀S᜗ 1991Ȳ1᜛1994Ȳ7 – êČð̑Sn¬ ďĞØĕîĝೳൕÊÕĞčĝÿČ èÑíĞÑ᜖EPFL-IRRMA᜗Ph.D. ਒τ᜖ওǛS᜗ 1994Ȳ10 – Ph.D.᜖̀S᜗ ঍ਂ ÆáČÄਂ:÷ċĕÛਂ:Օਂ:ëÆæਂ:̵7ਂ λ˼ 1/1/1995 ~ 31/7/1995 – Post-Doc at EPFL-IRRMA (Switzerland) ― 11 ― 1/8/1995 ~ 31/4/1996 – Post-Doc at IBM Zurich Research Laboratory (Switzerland) 1/5/1995 ~ 7/05/1998 – Post-Doc at Max-Planck-Institut, Stuttgart (Germany) 8/5/1998 ~ 31/3/2001 – Post-Doc. Joint Research Center for Atom Technology, Tsukuba 1/4/2001 ~ 31/8/2002 – NEDO Fellow at Advanced Institute of Science and Technology AIST-RICS, Tsukuba (Japan) 1/9/2002 ~ 30/11/2008 – Associate Professor at University of Tsukuba (Japan) 1/12/2008 ~ to date – Research Director at Institute of Physics and Chemistry of Materials (IPCMS) - Unité Mixte 7504 CNRS / University of Strasbourg, Strasbourg (France) ˝ϡȂቲ - ğ࢑Օਂ I:ğ࢑Օਂ II – ³Ϥ̑S: 2002-2008 - ˨ĕÙāćĎĞÙĉĕ – ³Ϥ̑S̑S၄:2004-2008 - Course "Beyond Xtall: short time dynamics by CPMD. Applications to Biomolecules":ÛêċÛøčÒ̑S:2009 - Course “Introduction to Numerical Simulations: From Materials Science to Biochemistry”.:ÛêċÛøčÒ̑S:2009-2010 - Numerical Modeling:ÛêċÛøčÒ̑S:2010-2011-2012 - CPMD Tutorial – ČĞč̑S᜖÷ċĕÛ᜗:2011Ȳ10 ο଩ - 2001 Ȳ JRCAT Award:“First successful Ziegler-Natta catalysis simulation on a realistic system of industrial relevance” ― 12 ― ɝฐċɰB᜝ฐċìðǛϤᜨ ͽΖওÜቲɝǛȬ Mauro Boero᜖ĀÈď þÊď᜗ Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), CNRS-University of Strasbourg, ÛêċÛøčÒ̀଱̴̀Sʢ"ô:CNRS-ÛêċÛøčÒ̑S 23 rue du Loess, F- 67034 Strasbourg (France) 5^ႱBéòÆÛ{:ɝЏͮ¶}¯ฐċɰBǛϤ¶ϧ}¯¥ :w°­ïϘ̀଱¶ɰBĎûčȆϤy:ÒჳႱB̧Rͮ଱ ƊӉh¶ॾ}¯wpϒोf¯#$%;®³u:ฐċ÷ÉčāýqಶŘ ÊïčÐж¦:ùǞ{hhÒჳႱB̧R:ǛϤႱ֤/Ǹ7 ଱Ư˲ʵ¶}¯#1%;wÒჳჰùǞ̴:ȅ>̴SƯ:ǻ೰Ư:˟RƯोƩ Μ{y°:°­pȑ£ϤϤ˿࿥˨ჰùǞ̴˫ᅚ{h¯;7ਫ਼Ň :ᜠၥʋòÛ˟̧ɝฐċɰBf¯÷ÉďÝĕ[Fe(C5H5)2] λႣ}¯ ɝฐċɰ: wsCu(111)ࢢჳΆ٘Ȭy¯wpq¯w:Ȇ B᜝ฐċÒჳ:Ȭ:Òჳ̧R:ჰùǞͮ¶ਚ¯͒þӉϖf¯ w¶̿}#N%;ȅwƯ:Ȭ{÷ÉďÝĕ:ÙĉåêÏĞࢢჳ̧R ෎e{1ˇǞÒჳ̧R¶˟Ò}¯wp͒­o®:wɰBđΆ:y ˺ฐċΖB¶٘Ȭ}¯w¬®:ÒჳႱB̧RpÒჳÿèĕÙąč­ ਚτɐ˔4f¯o¶ॾz}¯wpq¯;˯˴ȏ॔ȵ˿ƯÙ ȬႱ֤Ȕɰǰ࿥āćĎĞÙĉĕቲ¶Ǽ£Ϥ³¯w¬®#a%: Èp͒­o;Ƨ̋­°ʉ॒:̴Sη̺¶1µ}¯w¬®: ɰB᜝ฐċÒჳႱBƊӉh¶˺ਚ}¯wpϕЏf¯w¶̿{h ¯; [1] See e.g. Introducing Molecular Electronics, by G. Cuniberti, G. Fagas, and K. Richter, Springer, Berlin, (2005). [2] X.-Y. Zhu, Surf. Sci. Rep., 56, 1 (2004). [3] T. Komeda, H. Isshiki, J. Liu, Y.-F.Zahng, N. Lorente, K. Katoh, B. K. Breedlove, M. Yamashita, Nature Comm. 2, 217 (2011). [4] B.W. Heinrich, L. Limot, M.V. Rastei, C. Iacovita, J. P. Bucher, D. Mbongo Djimbi, C. Massobrio, M. Boero, Phys. Rev. Lett. 107, 216801 (2011). ― 13 ― (Note) ― 14 ― ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ The 2nd International Symposium on Large-scale Computational Science and Engineering ǜɰBďĞáĞÙāćĎĞÙĉĕ Simulations of Artificial Molecular Rotors ÚĉÝ÷ āÑč Josef MICHL ůƼ Õďċë̑SþĞčâĞ×˝Dž Professor, University of Colorado at Boulder, USA ― 15 ― ਫ਼ Ň ᜠ ùď÷ÅĞč Josef Michl᜖ÚĉÝ÷ āÑč᜗ ɧ­: 1939 Ȳ 3 12 ̵, ùċñ᜖ãÉÕĝÛďòÏÄ᜗ Õďċë̑S ̴Sĝ­̴SSൺ˝Dž ᜖ÄăČÍϤࢇƼÕďċëǖþĞčâĞ᜗ ãÉÕȁTƼΡSÄÍéāĞ ɝĝ­̴Sʢ"ô ÒčĞùČĞâĞ S˼ 1961 Ȳ Sç˨ᜨãÉÕĝÛďòÏÄ ãąĞčÜ̑S᜖ùċñ᜗᜚ Václav Horák ˝Džδ Petr Zuman ͬ˨ 1965 Ȳ Ph.D.ᜨãÉÕĝÛďòÏÄ ãÉÕĝÛďòÏÄΡSÄÍéāĞ ᜖ùċñ᜗᜚Rudolf Zahradník ͬ˨ Ȃ˼ 1965-66 ͬ˨ʢ"᜖ôćĞÛêĕ̑S᜖èÏ×ÛǖôćĞÛêĕ᜗᜗ 1966-67 ͬ˨ʢ"᜖èÏ×Û̑S᜖èÏ×ÛǖÌĞÛèÅĕ᜗᜗ 1967-8/68 ʢ"᜖ãÉÕĝÛďòÏÄΡSÄÍéāĞ᜗ 9/68-7/69 ˛ý᜖ÌĞ÷Û̑S᜗ 9/69-6/70 ͬ˨ʢ"᜖Ĉá̑S᜖ĈáǖßčêĎĞÑǯ᜗᜗ 7/70-7/71 ɀʢ"˝Dž᜖Ĉá̑S᜖ĈáǖßčêĎĞÑǯ᜗᜗ 7/71-6/75 ɀ˝Dž᜖Ĉá̑S᜖ĈáǖßčêĎĞÑǯ᜗᜗ 7/75-8/86 ˝Dž᜖Ĉá̑S᜖ĈáǖßčêĎĞÑǯ᜗᜗ 10/79-6/84 Sൺ࿇᜖Ĉá̑S᜖ĈáǖßčêĎĞÑǯ᜗᜗ 8/86-ϧǞ ჰȎ̍˝Dž᜖Ĉá̑S᜖ĈáǖßčêĎĞÑǯ᜗᜗ 9/86-5/91 M. K. Collie-Welch ϖ࿇᜖èÏ×Û̑SÌĞÛèÅĕ× ᜖èÏ×ÛǖÌĞÛèÅĕ᜗᜗ 6/91-ϧǞ ˝Dž᜖Õďċë̑S᜖ÕďċëǖþĞčâĞ᜗᜗ 1/06-ϧǞ ÒčĞùČĞâĞ᜖ãÉÕȁTƼΡSÄÍéāĞ᜗ ʢ"È૏ ϧǞ/˒{h¯ɰญ:(i) ዇˨ῬၗႱ΍¶ǸŶ{ͽฌᅟˢୣBɰ࣓ (singlet fission)Ǥ̴SδǤ̀:(ii) ̒{háÆùႱBĝÆÌĕW×̴ͮ Ϥ̀዇ɰB:(iii) ɝ̴SƯβҜǣǼʺ̴ƯϤÒy°:ɝ̴S: ɝฐċ̴Sδɓɝ̴Sɖs:ࢢჳࣖɰBďĞáĞɰBƧ஠᜖w°­ ìðႱBǜS:ìð6wǜSδǤăáĀèČÄčɰญnhµ̴ ― 17 ― ¶¥z{h¯᜗:(iv) “ࣴ”ČãÈĂÍãÌĕঀϙη̺:̉ÄčÓĕ:Ä čÏĕδÄčÍÚÊĕċÚÍčฌϤ:(v) Άঠ (i)ᝬ(iv) ʢ"࿥ೳ{: ýÈǢ:ÓÆǢ:÷åǢδČãÈĂ̴Sçz{̒॔̀଱ǻ೰:(vi) Άঠ (i) ᝬ(iv) ʢ"࿥ೳ{ਭ̴S̺µ:Π¦ɰBǻ೰ਭδɰBâÆì āÑÛ; w°¢hɰBႱBǜS{:ƧయႱɹ¨6w6˿¬ቁ˿{ࢢჳ Ά̘o°ζLJͮɰBďĞáĞǓ͍¶Ó>࿔ŕ{¬j{h¯;w° ­ďĞáж 2 ˇǞóáĞĕΠප̘y¯৘£{:èíÛïåê¨ ฐɉȅ˟¶{ɰBϤÒýϚ¶࿔ŕ{h¯; ̒॔Íčþċĕ°࿥ೳ{ǻ೰¶ŲɰB{୨ˁා୨ˁ˒ා̴ ʫpʉ­°h¯;w°­ÎÛΠ{ő­°hhp:Ó>òčÑ {̋¯৘£¶ࢌh¯;w°ჰȎɖ̧ƯΡSf¯p:ఏಶ̺ µ{:ČãÈĂÿČĀĞႱ΍Ⴑॾ଱¨ʞ́Ⴑ΍ѧpƂv­°¯; ― 18 ― ǜɰBďĞáĞÙāćĎĞÙĉĕ Jin Wen, AlexandrProkop, JaroslavVacek, Josef Michl Õďċë̑S̴Sĝ­̴SSൺ(ÄăČÍϤࢇƼÕďċëǖþĞčâĞ CO 80309) δ ãÉÕȁTƼΡSÄÍéāĞɝĝ­̴Sʢ"ô (ãÉÕȁTƼ 16610 ùċñ 6) ǜζLJͮɰBďĞáĞ॔ʖƯපɼǻ೰:ìð6wǜS¨ɰBႱBǜS ɰญҶApŲ°h¯;Π¦ɰBႱBǜSɰญnh:ˁ৿Ⴑͮ ɖɇ̧Rපɼp̉n¦{±h¦¯f±jp:5ϤÒy°h h;Ó>ɰBâÆìāÑÛওܶࢌhቲ¶ࢌn®:Ƨయቁ˿˒ È}¯þ>ďĞáĞ̺µ¶˴o¥¬j{h¯;¦ҶAhቁ˿˒ {:ƧయႱɹ6w6˿ϗpƂv­°¯;wϗɹϤÈ}¯: UFF(Universal Force Field)ÿèĕÙąč¶µhͼওÜȆ :δҜʛɰB âÆìāÑÛùďÒċöµhͼওÜȆ ¶Ʀࢢ}¯;¢Ó>:ɰ BĎûčɆʏÈ}¯५͍µͮh¦Ɛখ¶ࢌq;Ȇ :ɰBĎûčɆʏ:ĀÑďÛÓĞčɆʏhsoȬnh ჰȎen®:wǓ͍h&A¶Ųwp͒­o;þ>ď ĞáĞâÆìāÑÛʢ"˕l:Ó>ʢ"ϤÒ{ϗˇǞ΅ॵ˟ පɼ¶¦ζLJͮďĞáĞഐ˿h¦ʢ"{n®:̉ďĞáĞ࿛ Ǿ࿥ฌȬ¶nhh¯; ੠಑ 7ʢ" European Research Council (FP7/2007-2013/ERC 227756) δ U.S. National Science Foundation (CHE-0848663)¬ʽȌy°h¢}; ― 19 ― (Note) ― 20 ― ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ The 2nd International Symposium on Large-scale Computational Science and Engineering ìðòÆÌDŽüáÛÓĞčɰB˿˒SÙāćĎĞÙĉĕ Petascale Molecular Dynamics Simulations of Nano-bio-systems Πญ 1ͽ൫ Aiichiro NAKANO ůƼ ͩÍČ÷ËčíÄ̑S ˝Dž Professor, University of Southern California, USA ― 21 ― ਫ਼ Ň ᜡ ùď÷ÅĞč Πญ1ͽ൫ ͩÍČ÷ËčíÄ̑SÚÄăČÍϤࢇƼÛ ÕĕöćĞáĞΡSΡÜ ̀̓˵SΡÜ
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  • Challenges Across Large-Scale Biomolecular and Polymer Simulations
    Challenges across Large-Scale Biomolecular and Polymer Simulations February 21, 2017 - February 24, 2017 CECAM-AT Ivan Coluzza University of Vienna, Austria Samuela Pasquali Paris Descartes University, France Barbara Capone University of Vienna, Austria Christoph Dellago University of Vienna, Austria Tamar Schlick New York University, USA 1 Description The goal of this workshop is to bring together scientists who study large scale molecular systems both in the biological world and those from the polymer science community. This workshop aims to bring broad-minded scientists interested in these challenges to discuss state-of-the-art approaches and issues with the goal of advancing structural biophysics and applied fields. By discussing various approaches and ways to integrate knowledge on multiple scales, we hope to build a community to advance this important field. The increase in computer power in tandem with algorithmic and force-field improvements are opening opportunities for modeling large biomolecular systems as never before. Yet, many challenges in modeling and simulations of such complex systems, in realistic environments, require innovations to make the necessary experimental connections and develop new theories and mechanistic details of the associated processes. The workshop that we propose will follow and build upon the first workshop organized in Telluride (June 14-18, 2015) by Tamar Schlick and Klaus Schulten entitled "Challenges in Simulating Large-Scale Biomolecular Complexes", by focusing on the following subjects: - Large scale simulations with respect to time and system size. We will include recent advances in atomistic force-fields and technological advances in algorithms and hardware that make possible simulations on the millisecond time scales for systems composed of millions of atoms, such as large solvated biomolecules.
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  • Poster Session 10: Translation 21:00 - 22:00 Friday, 29Th May, 2020 Poster
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  • ABSTRACT Title of Document: BUILDING a MAP of the DYNAMIC RIBOSOME. Suna Pelin Gulay, Doctor of Philosophy, 2015 Directed By
    ABSTRACT Title of Document: BUILDING A MAP OF THE DYNAMIC RIBOSOME. Suna Pelin Gulay, Doctor of Philosophy, 2015 Directed By: Professor Jonathan D. Dinman Cell Biology and Molecular Genetics Our understanding of the static structure of the 80S eukaryotic ribosome has been enhanced by the emergence of high resolution cryo-electron microscopy and crystallography data over the past 15 years. However our understanding of the dynamic nature of the ribosome has lagged. High-throughput Selective 2’-Hydroxyl Acylation analyzed by Primer Extension (hSHAPE) is easily amenable for interrogation of rRNA dynamics. Here we report an improved method of hSHAPE data analysis and apply it to translation initiation and elongation complexes of the yeast ribosome to identify the changes in rRNA flexibility that occur during these processes. Most importantly, we have obtained complete analyses of tRNA binding and intersubunit bridge dynamics, as well as overall expansion segment dynamics, as the ribosome progresses through the translation elongation cycle. The results from these analyses suggest that (1) the yeast P site tRNA binding site is a “hybrid” between the prokaryotic and mammalian P sites, (2) there may be substates of intersubunit rotation, (3) expansion segments may have roles in accommodation. We are also able to identify a network of information pathways that connect elongation factor binding sites to all tRNA binding sites, five intersubunit bridges and two expansion segments. Future directions of this project will focus on improving the visualization of our data to better reflect the highly dynamic nature of the yeast ribosome and to reveal the underlying causes of the observed rRNA flexibility changes.
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  • Current Challenges of Computational Intelligent Techniques for Functional Annotation of Ncrna Genes
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  • ESI Annual Report 2017
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