˜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)

ÙĕÿÚÈÒ୳̸

ಶȲ’ÕĕöćĞá’ͬ೯ŽͮЏΆ]h:Ńĝ­w’ɰBĝฎBΡS: ǜS:ǥĝ̓˵ΡSŽ:%࿛Ư¦ͼ࿛Ư¦ĀčãŽÛÓĞč‹:oˆ: ̈s’̀o­Ž¯Āčã÷ÅÚåÑÛϧ૏¶È૏Œ{ƒʢ"pΑÒΠ ‹೽¥­°Šn®:̒{hÒ p˨̈s̋­°ˆˆf®¢}; 7ÙĕÿÚÈ˓:w°­’ʢ"ɰญ’Πo­:ìðĝòÆÌΚ—ǥႸ ȏŽ:izΡS¬’āÑďŽ:f¯h“ĀÑďŽϧ૏¶ॾz}¯ɰญ¶È૏Œ {Š:Ąéč̴¨˨ĕওÜýϚ¬’ÙāćĎĞÙĉĕ’çȷ࿥³¯Åᆏˆ hŠ:ƼȎ̅‹1௽{Šh¯êåùÑċےʢ"͵¶ŝΨ{Šਫ਼Ҍóïčখ ਭ¶ࢌh¢};w°¬®:ϣʢ"਒ᆏ̉ ’ਭĝğ࢑Œ:ࣽ˨’ʢ"਒ ᆏȁ೫’¦’p͒­oŽ®:ʢ"਒ᆏ’‡¶୨lƒ¬®̑qŽÒ p̋­ °¯wŒp/˽y°¢};¢ƒ:ͽӑ’̙>¦̈˨xί˕hƒ„q:w’̙ ჳ’ÕĕöćĞáÙāćĎĞÙĉĕʢ"’˲ʵŒÒ ¶ͽӑ̓UŒȁ {ƒh ŒͳlŠh¢};                             

― 3 ―                                                  ùďÒċĂ

  ࿔UƅŬ ÙĕÿÚÈĂએ࿇ƅŬ  ʆǕ Ǟɖ᜖̵7S࢑Uએ   f̑S ˝Dž᜗ ȁŮ͵.ࢢƅŬ ǯΨ ç᜖᜖͂᜗ΡSğ࢑ƊҶɝǻãæʢ"Ǟ೽ൺ ΆȅΪ=ਚň᜗  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 óïčéÅÛÍåÙĉĕ’ʛਫ਼Ň᜖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 óïčéÅÛÍåÙĉĕ’ʛਫ਼Ň᜖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᜗  ]8–8 O‘  –8—–8 óïčéÅÛÍåÙĉĕ ÕĞéÅïĞáᜨʆǕ Ǟɖ  —–8—7 ࿒UƅŬ ؇Ζ ͽ൫  ɢϤϞUᜨΠǕ ႎÏ᜖᜖͂᜗ΡSğ࢑ƊҶɝǻ ᅯɆίϖ᜗

― 5 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ 

ਫ਼ŇȎ”   IùĎìČਫ਼Ňᜟ᜖ìð᜗J

ਫ਼Ňᜟ ɝฐċɰB᜝ฐċ’ìðǛϤᜨ˜ͽΖও܌ቲŒ’ɝžŽǛȬᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ¢ ĀÈď þÊď ƼÛêċÛøčÒ̑SŃ̴̀Sʢ"ô ˝Dž  ਫ਼Ňᜠ ǜɰBďĞáĞ’ÙāćĎĞÙĉĕ ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ8 ÚĉÝ÷ āÑč ůƼÕďċë̑SþĞčâĞ× ˝Dž  ਫ਼Ňᜡ ìðòÆÌDŽ’üáÛÓĞčɰB˿˒SÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ] Πญ 1ͽ൫ ůƼͩÍČ÷ËčíÄ̑S ˝Dž    IùĎìČਫ਼ŇᜠJ

ਫ਼Ňᜢ ìðòÆÌΡSğ࢑ÙāćĎĞÙĉĕᜨޞƩ଱˿ॾzo­ ˜™š ìðǻ೰যও¢‹ᝳᝳᝳ] ĂĞĕ Ï ÏĂ ᅁƼÒDzᇻ̑S ɀ˝Dž  ਫ਼Ňᜣ ìðÛÓĞčĀÙĕ’ÙāćĎĞÙĉĕᜨČþßĞÒ̑॔ȵǻ೰˺̴ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ–– ÍČĞ× ×ĕþĕĀæ ůƼďÛÄċĄÛƼWʢ"ô ãĞĂČĞâĞ  ਫ਼Ňᜤ ĐnŒ෍Ǣnu¯̴Sη̺Œා̴ിǞഓτ’ĀčãÛÓĞčÙāćĎĞÙĉĕᝳᝳᝳ–¢ ÈÉÆáÌ Ćĕ ůƼéÅĞÑ̑S ˝Dž         

― 6 ―  IóïčéÅÛÍåÙĉĕ’ʛਫ਼Ň᜖ᜟ᜗J

ਫ਼Ňᜥ ˁǾ࿥ႱB̀଱’ƒ¥’˜ͽΖϓÄᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ78 » ˯Ï f̑S̑S၄ ˝Dž  ਫ਼Ňᜦ ìðÙÛèÒȭ’ÌĞâĞ™ %࿛ ˜ÃÄ ŒϊȆɰB˿˒SŒ’ñÆøČåë̴ᝳᝳᝳᝳ 8 ÷˟ çϞ 
ϊÿǜƿ̑S̑S၄ ˝Dž

ਫ਼Ňᜧ ƝžϓČǟ̑ɰBযও’ฎB̴S ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 8 Πಧ ͬ ฎB̴Sʢ"ͨU ϖ࿇  ਫ਼Ňᜟ᜞ ɐႏη̺DŽ’ĀčãÛÓĞčÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ ~– ࿇İ ˯ၟ
ϊÿ̑S̑S၄ ˝Dž    IóïčéÅÛÍåÙĉĕ’ʛਫ਼Ň᜖ᜠ᜗J

ਫ਼Ňᜟᜟ ìðĝòÆÌɝЏযও’ƒ¥’୨዇Ɲɐ᜔዇˨ΡฎB̴SŇÜϚᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ~¢ ყ4 ƪϤB ρǖ̑S̑S၄ ˝Dž  ਫ਼Ňᜟᜠ ǟ̑òÆÌɰBႏϤw’ǻ೰âÆìāåÑÛᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ8 ̵÷ ˪)  f̑SɰBǭϺ­̀Sʢ"ô ɀ˝Dž  ਫ਼Ňᜟᜡ ­wɰBDŽ’ĀčãĎûčÙāćĎ᜛Ùĉĕ ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ— ੆ʃ ̫φ ඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞ ÙíÄČ×Ğã÷ÉďĞ  ਫ਼Ňᜟᜢ Ϡ͝࿛ӏࢌÙÛèĂ࿔ƦuƒĀčãÛÓĞčſBÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳ— ҫϝ Օε ͜î̑S̑S၄ ˝Dž  ਫ਼Ňᜟᜣ ˁhǥႸ¶οu¯ΖB˒ƦႱùċĕê’üáÛÓĞčÙāćĎĞÙĉĕᝳᝳᝳᝳᝳᝳᝳᝳᝳ¢– ϥO ̰ ̵7S࢑Uએ   f̑S̑S၄ ˝Dž   

― 7 ―                                          ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ɝฐċɰB᜝ฐċ’ìðǛϤᜨ ˜ͽΖও܌ቲŒ’ɝžŽǛȬ   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€ˆ˝Dž  ˊǖΖBɰBওÜÝĕáĞ᜖CECAM᜗€ˆ˝Dž  ওǛ଱ΡSÆíÙÄèÅø᜖f᜗ăĕòĞ 130ý0Ά’Ǿࢢਭ˵᜖100ý’Ζ؝ਭ˵:5ý’ॾ  ਍ঠϖ:5ý’؝:19ý’ƼၯUએUએ༃᜗;ࣅ ʤµ;˨= 2321:h-index = 28

Ë࿋ᅯɆ ˜ͽΖওÜýϚ:QM/MM᜖ฎB˒S᜝ɰB˒S᜗ñÆøČåëýϚ¬¯̀ ଱ΡSŒòÆÌ̴S:Đn̴S;1995Ȳ¬®CPMDóåÓĞڒȁò࿔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᜝ฐċ’ìðǛϤᜨ ˜ͽΖও܌ቲŒ’ɝžŽǛȬ

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^’ႱBéòÆی{Š:ɝЏͮ¶ }¯ฐċŒɰB’ǛϤ¶ϧ}¯ƒ¥ “:w°­’ïϘ̀଱¶ɰBĎûč‹ȆϤy:Òჳ‹’ႱB̧R’ͮ଱Œ ƊӉh¶ॾ}¯wŒpϒो‹f¯#$%;Œ®³u:ฐċ’÷Éčāýqಶؒ ÊïčÐж¦ˆ:ùǞ{ŠhŽhÒჳႱB̧R“:ǛϤ‹’Ⴑ֤’/Ǹ7 ଱Ư˲ʵ¶}¯#1%;w’ÒჳჰùǞ̴“:ȅ>Ž̴SƯ:ǻ೰Ư:˟RƯोƩ ‹Μ{y°:°­pȑ£Ϥ‡ŠϤ˿࿥˨’ჰùǞ̴˫ᅚ{Šh¯;7ਫ਼Ň

‹“:ᜠၥʋòÛ˟̧’ ɝฐċɰB‹f¯÷ÉďÝĕ[Fe(C5H5)2] “λႣ}¯ ɝฐċɰ : wŒŽsCu(111)ࢢჳΆ٘Ȭy¯wŒp‹q¯wŒ:’Ȇ B᜝ฐċÒჳ‹’:Ȭ:Òჳ̧R:’ჰùǞͮ¶ਚ¯͒þ’Ӊϖ‹f¯ wŒ¶̿}#N%;ȅwƯ“:Ȭ{ƒ÷ÉďÝĕ“:ÙĉåêÏĞࢢჳ̧R ෎e{ƒ1ˇǞÒჳ̧R¶˟Ò}¯wŒp͒­oŒŽ®:w’ɰBđ’Ά:y ˺ฐċΖB¶٘Ȭ}¯wŒ¬®:ÒჳႱB̧RpÒჳ‹’ÿèĕÙąč­ ਚ’τɐ˔4‹f¯o¶ॾz}¯wŒp‹q¯;˯˴oˆ̑॔ȵŽ˿ƯÙ ȬŒႱ֤Ȕɰǰ’࿥āćĎĞÙĉĕŒቲŒ¶Ǽ£Ϥ³¯wŒ¬®#a%: Èp͒­oŽ‡ƒ;Ƨ̋­°ƒʉ॒“:̴Sη̺¶1µ}¯wŒ¬®: ɰB᜝ฐċÒჳ‹’ႱB’ƊӉh¶˺ਚ}¯wŒpϕЏ‹f¯wŒ¶̿{Šh ¯;

[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).

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                                               (Note)

― 14 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ǜɰBďĞáĞ’ÙāćĎĞÙĉĕ 

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"ˆ᜖ôćĞÛêĕ̑S᜖èÏ×ÛǖôćĞÛêĕ᜗᜗  1966-67   ͬ˨ʢ"ˆ᜖èÏ×Û̑S᜖èÏ×ÛǖÌĞÛèÅĕ᜗᜗  1967-8/68 ʢ"ˆ᜖ãÉÕĝÛďòÏÄΡSÄÍéāĞ᜗  9/68-7/69  ˛ý᜖ÌĞ÷Û̑S᜗  9/69-6/70  ͬ˨ʢ"ˆ᜖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/˒{Šh¯ɰญ“:(i) ዇˨ῬၗႱ΍¶ǸŶ{ƒͽฌᅟˢୣBɰ࣓ (singlet fission)’Ǥ̴Sδ—Ǥ̀:(ii) ̒{háÆù’ႱBĝÆÌĕW×̴ͮ Ϥ̀Œ዇ɰB:(iii) ɝ̴SƯβ“ҜǣǼʺ̴ƯϤÒy°ƒ: ɝ̴S: ɝฐċ̴Sδ—ɓɝ̴Sɖ‰s:ࢢჳࣖɰBďĞáĞŒɰBƧ஠᜖w°­ “ìðႱBǜS:ìð6wǜSδ—ǤăáĀèČÄč’ɰญnhŠ’µ̴

― 17 ― ¶¥z{Šh¯᜗:(iv) “ࣴ’”ČãÈĂÍãÌĕ’ঀϙη̺:̉ÄčÓĕ:Ä čÏĕδ—ÄčÍÚÊĕ’ċÚÍčฌϤ:(v) Άঠ (i)ᝬ(iv) ’ʢ"࿥ೳ{ƒ: ýÈǢ:ÓÆǢ:÷åǢδ—ČãÈĂ̴Sçz{ƒ̒॔̀଱ǻ೰:(vi) Άঠ (i) ᝬ(iv) ’ʢ"࿥ೳ{ƒਭ̴S’̺µ:Π‹¦ɰBǻ೰ਭδ—ɰBâÆì āÑÛ;

 w°¢‹ŽhɰBႱBǜSŒ{Š:ƧయႱɹ¨6w6˿¬‡Šቁ˿{ࢢჳ Ά̘o°ƒζLJͮɰBďĞáĞ’Ǔ͍¶Ó>“࿔ŕ{¬jŒ{Šh¯;w° ­’ďĞáж 2 ˇǞóáĞĕ’Џප̘y¯৘£Œ{Š:èíÛïåê¨ ฐɉ’ȅŽ˟¶{ƒɰB’ϤÒýϚ¶࿔ŕ{Šh¯;

̒॔ÍčþċĕŒ°࿥ೳ{ƒǻ೰¶ŲˆɰBŒ{Š୨ˁාŒ୨ˁ˒ා̴ ʫpʉ­°Šh¯;w°­“ÎÛΠ‹{ő­°ŠhŽhp:Ó>“òčь {Š̋¯৘£¶ࢌ‡Šh¯;w°“ჰȎɖ̧ƯŽΡS‹“f¯p:ఏಶŽ̺ µŒ{Š:ČãÈĂÿČĀĞႱ΍’Ⴑॾ଱¨ʞ́Ⴑ΍ѧpƂv­°¯;

                      

― 18 ― ǜɰBďĞáĞ’ÙāćĎĞÙĉĕ

Jin Wen, AlexandrProkop, JaroslavVacek, Josef Michl

Õďċë̑S̴Sĝ­̴SSൺ(ÄăČÍϤࢇƼÕďċëǖþĞčâĞ CO 80309) δ— ãÉÕȁTƼΡSÄÍéāĞ ɝĝ­̴Sʢ"ô (ãÉÕȁTƼ 16610 ùċñ 6)

ǜζLJͮɰBďĞáĞ’॔ʖƯපɼǻ೰“:ìð6wǜS¨ɰBႱBǜS’ ɰญ‹ҶApŲƒ°Šh¯;Π‹¦ɰBႱBǜS’ɰญnhŠ“:ˁ৿Ⴑͮ ɖɇ̧R’පɼp̉n¦{±h¦’Ž¯‹f±jp:5„ϤÒy°ŠhŽ h;Ó>“ɰBâÆìāÑÛওܶࢌhˆˆቲ¶ࢌ‡Šn®:Ƨయ’ቁ˿˒ È}¯þ>’ďĞáĞ’̺µ¶˴o¥¬jŒ{Šh¯;¦ҶAhቁ˿˒ Œ{Š:ƧయႱɹŒ6w6˿’ϗˆpƂv­°¯;w’ϗˆ’ɹϤÈ}¯: UFF(Universal Force Field)ÿèĕÙąč¶µhƒͼ’ওÜȆ :δ—Ҝʛ’ɰB âÆìāÑےùďÒċöµhƒͼ’ওÜȆ ¶Ʀࢢ}¯;¢ƒÓ>“:ɰ BĎû苒ɆʏÈ}¯५͍’ µͮˆhŠ¦Ɛখ¶ࢌ‡Šqƒ;’Ȇ :ɰBĎû苒Ɇʏ“:ĀÑďÛÓĞ苒ɆʏŒhsˆo’ȬnhŠ ჰȎeŠn®:w’Ǔ͍“h&A¶ŲˆwŒp͒­oŒŽ‡ƒ;þ>’ď ĞáĞ’âÆìāÑےʢ"˕lŠ:Ó>’ʢ"‚‹ϤÒ{ƒϗˇǞ΅ॵ˟ පɼ¶¦ˆζLJͮďĞáĞ’ഐ˿ˆhŠ¦ʢ"{Šn®:̉ďĞáĞ࿛’ Ǿ࿥ฌȬ¶nhŠh¯;

੠಑ 7ʢ"“ European Research Council (FP7/2007-2013/ERC 227756) δ— U.S. National Science Foundation (CHE-0848663)¬‡ŠʽȌy°Šh¢};                 

― 19 ―                                                 (Note)

― 20 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ìðòÆÌDŽ’üáÛÓĞčɰB˿˒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 ̴SǜSŃΡSΡ᜚ ǣ೽ওÜÙāćĎĞÙĉĕʢ"ô ˝Dž  $ÝÞ$ Ȳ a  Þ ̵­  Sͬ˨᜖f̑S᜗$ÝßÝ Ȳ

λ˼   $ÝßÝ Ȳ  ÄčÖĕîƼWʢ"ô᜚âã ʢ"ˆ  $ÝÝä Ȳ čÆÚÄìǖW̑S᜚âã ʢ"ˆ  $ÝÝå Ȳ  čÆÚÄìǖW̑S᜚˛˝  $ÝÝÝ Ȳ čÆÚÄìǖW̑S᜚ɀ˝Dž  1ää1 ȲͩÍČ÷ËčíÄ̑S᜚ɀ˝Dž  1ääÞ ȲͩÍČ÷ËčíÄ̑S᜚˝Dž

 €؝  ɧ˧̀ɢও˨: 296; Å਎$qÚąĞìčਭ˵˨: 183

ʢ"ɰญ   ýÛÓĞċøčŽΡSওÜÄčÖČÜĂ᜚዇ ɐ ΚɼওÜ᜚ΡSƯŽõåÒé Ğá’ϕख̴़Œॾz᜚ওÜŃΡS᜜ 

       

― 23 ―                                                 ANote)

― 24 ― ìðòÆÌDŽ’üáÛÓĞčɰB˿˒SÙāćĎĞÙĉĕ

Πญ 1ͽ൫

ǣ೽ওÜÙāćĎĞÙĉĕʢ"ô᜚ ÕĕöćĞáĞΡSΡ᜝̀̓˵SΡ᜝̴SǜSŃΡSΡ᜚ ͩÍČ÷ËčíÄ̑S ďÛÄĕÚÉčǯ᜚CA 90089-0242, ÄăČÍϤࢇƼ Email: [email protected]

Ó>“᜚ýÛÓĞċøč᜖ˆ¢®᜚ÕĞë¶ͽɐযও}¯Œ᜚ওÜɝϤ³ ŠওÜ॔ȵpÛÓĞčϕЏ᜗ŽΚɼওÜϚ¶᜚ȹ¥ನ£ɰʵțφ’ÄčÖČÜ Ă¶ɖ̧Œ{Š᜚̑qŽͼ%࿛ÛÓĞč’ɰB˿˒S᜖MD᜗ÙāćĎĞÙĉĕ ¶ŇÜЏ˒p˨ PFLOPS ’ÛóÕĕ‹ࢌjƒ¥࿔Ʀ{Šqƒ᜜w’ΚɼওÜ Ϛ¬®᜚163,840 þ’ùďÝå×o­Ž¯ IBM BlueGene ¶µhŠ᜚95ᜓ0Ά ’Κɼ̴˨Ρ¶᜚1.0 ǡΖBDŽ’ϊȆ MD᜚y­žɐͿ࿥˨Ϛ’‡Ǽ£‹ 2.58 ǡþ’ႱBƯŽҜ¼ɐ’ฎB MD ‹ϧ{Šh¯᜜Ó>’ÙāćĎĞÙĉĕ ¬®᜚ìðÛÓĞ苒Ǥˢୣ᜚˒S᜚6°᜚̴Sη̺’࿛’7଱ƯŽǾϛ࿥ Èp͒­oŒŽ‡ƒ᜜ਫ਼ҋ“̉᜚0·ˆhŠ’ΖBਭƯŽăÍíÜÏ ˆhŠએਭ}¯ϓ{‹f¯ᜨ(1) ฐċìðÑċÛáжµhƒͰo­’ͰǢ’዇ ೯­Ò᜚(2) ̔ၗႱ΍Ýč࿥ೳ{ƒ᜚Ⴑ֤λ˿᜚Ⴑ֤ȔȆϤ᜚ÙĕÒĎåȩ̂ Rźˏ’ɰBĎû苒ʌ̒᜚(3) ìðòøč¨ìðÚÉåêΠ‹ୣw¯̴Sη ̺’˒SƯŽÉ೽᜚(4) Ǿϛ€µ{ƒ RNA ’Čĕා଱ѧ¶೫|ƒλǸ᜜

― 25 ―                                                 (Note)

― 26 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ìðòÆÌΡSğ࢑ÙāćĎĞÙĉĕᜨ ޞƩ଱˿ॾzo­ DNA ìðǻ೰যও¢‹   Simulation Based Nano-Bio Science & Engineering: From Protein Dynamics to DNA Nanostructure Design                     ⁞⁺ⁱូ ‫ូ ‫⁞ូ Moon Ki KIM

ᅁƼូ ÒDzᇻ̑Sូ ɀ˝Džូ Associate Professor, Sungkyunkwan University, Korea

― 27 ―

ਫ਼ Ň ᜢ

ùď÷ÅĞč  Moon Ki Kim᜖ĂĞĕ Ï ÏĂ᜗

ᅁƼ ÒDzᇻ̑SɝļǜSΡ ɀ˝Dž 1974 Ȳ 2  16 ̵­¢°

S˼   PhD, 2004, The Johns Hopkins University  MS, 1999, ßÈčƼW̑S  BS, 1997, ßÈčƼW̑S   λ˼   2004, University of Massachusetts-Amherst, Assistant Professor  2008, ÒDzᇻ̑S Assistant Professor  2009, ÒDzᇻ̑S Associate Professor

Ϊोਭ˵   "Efficient transfer of large-area graphene films onto rigid substrates by hot pressing", ACS Nano, Vol. 6, pp. 5360-5365, 2012  "KOSMOS: A universal morph server for nucleic acids, proteins and their complexes", Nucleic Acids Research, Vol. 40, pp. W531-W536, 2012  "DNA nanotube formation based on normal mode analysis", Nanotechnology, Vol. 23, Article No. 105704, 2012  "Rigid Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies", Biophysical Journal, Vol. 89, pp. 43-55, 2005.  "Efficient Generation of Feasible Pathways for Protein Conformational Transitions", Biophysical Journal, Vol. 83, pp. 1620-1630, 2002.

ʢ"È૏   ޞƩ଱’˿˒S  DNA ìðǜS  ĀčãÛÓĞčॾz  6wǻ೰ೳÒÙāćĎĞÙĉĕ

― 29 ―                                                 (Note)

― 30 ― ìðòÆÌΡSğ࢑’ÙāćĎĞÙĉĕᜨ ޞƩ଱˿˒So­ DNA ìðǻ೰যও¢‹   Moon Ki Kim᜖ĂĞĕ Ï ÏĂ᜗   ìðòÆÌΡSğ࢑’ÙāćĎĞÙĉĕ’ +ŽýϚŒ{Š:ಶ:ÙāćĎ ĞÙĉĕğ࢑p/Ǹy°Šh¯;7ਫ਼ҋ“:CNT ¨ DNA Ž’ìðòÆÌǻ ೰’ĄéČĕÒ¨যও࿥}¯ýϚ‹f¯ˆͮïåêđĞÑĄéč᜖ENM᜗’ ĀčãÛÓĞčýϚˆhŠએਭ}¯; ENM “:ìðòÆÌÙÛèĂp”‘଱ฎDŽ‹ࢢϧy°:ΖB࿛’Ǿϛ€µ“: ”‘È˨¬‡ŠĶͪÕĕêďĞč‹q¯;ENM ĄĞëॾz¬‡Š:ìð òÆÌǻ೰’ɖ7ƯŽƊ˿Ƃ˿¶ਚ¯wŒp‹q¯;¢ƒ:NMA ’£¶Ϙ> ˺l¯wŒ¬®:ǻ೰ŒɝЏ’࿥ȶਚ¯wŒpϕЏŒŽ¯;y­:w ’̙Ϛ“:­w’ঠ˜̘ࣖ¶¤ 2 ˇǞ:3 ˇǞìðǻ೰ÙÛèܒϕЏͮ¶ Φ¥¯ DNA áÆč’˨ΡƯযওĆ࿔y°¬j; }Ž³ :w’˒SûĞےÙāćĎĞÙĉĕýϚ“ϧ’ìðòÆÌDŽ’ǻ ೰¶ਚ¯wŒp‹q¯”o®‹Žs:ቲ¶ࢌjʛ’ÕĕöćĞáÙāćĎ ĞÙĉĕnhŠċࣥযও’èÛꒃ¥ ˨‹f¯; ូ ូ ូ 

― 31 ―                                          

   

(Note)

― 32 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ìðÛÓĞčĀÙĕ’ÙāćĎĞÙĉĕᜨ ČþßĞÒ̑॔ȵǻ೰˺̴   Simulating nano-scale machines: Large-scale conformational changes of the ribosome                     ÍČĞ× ×ĕþĕĀæូ Karissa SANBONMATSU

ůƼďÛÄċĄÛƼWʢ"ô ãĞĂČĞâĞ Team Leader, Los Alamos National Laboratory, USA

― 33 ―   

ਫ਼ Ň ᜣ   ùď÷ÅĞč   ÍČĞ× ×ĕþĕĀæ  ďÛÄċĄÛƼWʢ"ô Ϊ=ʢ"ˆ

S˼   1992 Ȳ ÕďĕõÄ̑Sͦƿ᜖̀Sˡ᜗  1997 Ȳ ͬ˨ϝξ̋᜖iz̀S᜗ Õďċë̑SþĞčâĞ×

λ˼   1997-99ďÛÄċĄÛƼWʢ"ô᜚ͬ˨ʢ"ˆ᜚̺µ̀S  1999-2000 ďÛÄċĄÛƼWʢ"ô᜚ʢ"ˆ᜚̺µ̀S  2001-present ďÛÄċĄÛƼWʢ"ô᜚Ϊ=ʢ"ˆ᜚̺µ̀S

Ϊोਭ˵  Computational studies of molecular machines: the ribosome.Sanbonmatsu KY. Curr Opin Struct Biol. 2012 Apr; 22(2):168-74. Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch. Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY. J Am Chem Soc. 2012 Jul 25; 134(29):12043-53. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Novikova IV, Hennelly SP, Sanbonmatsu KY. Nucleic Acids Res. 2012 Jun; 40(11):5034-51. Excited states of ribosome translocation revealed through integrative molecular modeling. Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Proc Natl Acad Sci U S A. 2011 Nov 22; 108(47):18943-8 Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Ratje, et al. Nature. 2010 Dec 2; 468(7324):713-6. Tertiary contacts control switching of the SAM-I riboswitch. Hennelly SP, Sanbonmatsu KY. Nucleic Acids Res. 2011 Mar; 39(6):2416-31. Simulating movement of tRNA into the ribosome during decoding. Sanbonmatsu KY, Joseph S, Tung CS. Proc Natl Acad Sci U S A. 2005 Nov 1; 102(44):15854-9.

ʢ"È૏   Sanbonmatsu ãĞÓČþßĞĂ:ČþÛÆåã¨࿇hðĕÕĞéÅĕÒ

― 35 ― RNA ¶¤ðĕÕĞéÅĕÒ RNA DŽ’ăÍíÜÏ/Ǹ{Šh¯;Ó>“ გ³Đϙ¶¥ƒɰB˿˒SÙāćĎĞÙĉĕo­ SHAPE:in-line:DMS probing ¨ UV cross-linking Ž’­̴SƯŽǻ೰ȮઁϚhƒ¯ওÜƯn ¬—ቲƯýϚ¶µhŠh¯;                                           

― 36 ― ìðÛÓĞčĀÙĕ’ÙāćĎĞÙĉĕᜨ ČþßĞÒ̑॔ȵǻ೰˺̴  ÍČĞ× ×ĕþĕĀæ ďÛÄċĄÛƼWʢ"ô  ČþßĞÓ}Š’­HwnhŠΠ̨ƯŽ˲ʵ¶ ƒ{Šn®:áĕóÑ ଱ϤÒ¶ň‡Šh¯;ww‹ČþßĞÓഷWϗɷ¶਎£ನ£:È̺}¯áĕ óÑ଱¶ϤÒ}¯wŒ‹w’ϗɷ¶öƒ}̪ोpf¯;ČþßĞÓǭϺȎ‹ ¯ͽðĕêČõÄčŽϗɷɖ¶ࢌ‡Šh¯;ȅwƯ“:ČþßĞÓæා පɼ¶Äāðාපɼ˺Ǿ}¯wŒ‹ίɷࢢɖ¶ࢌ‡Šh¯;w’&A‹Č þßĞÓǭϺ’  Ǿ˔{:ìðÛÓĞč’ϗɷɖ̘ࣖ‹f¯;Čþß ĞĂp’¬jഷWϗɷ¶ॾ਎}¯wŒp‹q¯’o¶ʉ¯wŒ“:ϤÒƯ ìðÛÓĞčϗɷɖ̘ࣖéØÆĕ’ɖ̧¶ÿswŒŽ¯„±j;w°˕ lŠÄăČ͒ī၄‹™³°¯İ­ʫ’n¬ᜣ᜞ᜓ“ČþßĞöáĞÔå êŒ}¯wŒ‹ɝЏ{Šh¯;ČþßĞÒ1˿’ăÍíÜĂƯॾ“ϧǞ’ ­oj̒{hİ ÅᆏWזī၄nhŠÅᆏŽ®ˆˆf¯ÛĞóĞͿͮ ʫéØÆĕ’˛u¦Ž¯„±j;

ഓά SR Ȳ³ƒ®:Ó>“ČþßĞĂpഷWϗɷॾ਎}¯ăÍíÜĂ᜖ॾ਎Å ᆏ¢ƒ“ 2 വĵ᜗ /Ǹ{Šqƒ;ČþßĞÒ̑॔ȵɰB˿˒SÙāćĎ ĞÙĉĕ¶ࢌ}¯wŒ‹: Ó>“ɰBɝļ’Ȏൺ€ƿ¶ਚ¯wŒp‹q¯; w’ɝļ’ÍЌŽ¯ǻғ !!-++-" 2'-, ŒG”°¯;ww‹áĕóÑ଱’ ǻÒोǢ᜖Äāðා᜗¶¦ƒ­}êċĕÛ÷ÃĞ ᜖2 ᜗pČþßĞÏ Ǹ®ನ¤;Ó>“ČþßĞÒ̒{hɝЏൺq2&# !!-++-" 2'-,!-00'"-0¶ ॒ɧ{:w’ !-00'"-0 ’f¯ൺɰpČþßĞÒɝЏฌो‹f¯wŒ¶ϓÄ {ƒ;Ó>’ϓēಶ U ˆ’ቲÒčĞù’ʢ"‹Ɛহy°ƒ;Ó>’Ùā ćĎĞÙĉĕ S ɰBቲ¶Ǽ£Ϥ³ƒʁ’ʢ"¬‡ŠČþßĞĂɝЏ’ ̒{hǵƈpKo—Άp‡ƒ;ÙāćĎĞÙĉĕŒ S ɰBቲ’ ­o­¦: ČþßĞĂɝļ’ൺ{pΜ¢‡ƒ̙Ϛ‹˿sŒhj¬®“:2 p৘ࢌ༂ਇ’ ¬jŽ̑॔ȵϕ೛Ưλ˿¶ࢌ‡Šh¯wŒ¶̿{Šh¯;w’ǵƈ“ČþßĞ Ă’âÆìāåюÊïčÐĞǥ˟Œˆ|ˆ¢pϤ‡Šh¯;

!!-++-" 2'-, Œhj͂ుƯĕh¨}hÅᆏ¶ʢ"{ƒ̃:Ó>“ϧǞČþß ĞĂǺw’̑॔ȵǻ೰˺̴p࿥³¯ 20 ,1*-! 2'-, ’ăÍíÜöʢ"{Šh¯; w’ഐ˿“ăåÝĕÚąĞ ϊ‡Š ˇ’ÄāðාÕëĕң¯˯˴ᜡʗ ɖɰ’λ˿¶ϕЏ}¯;ቲ‹Ä{y°ƒ೯ɐŒǼ£Ϥ³ƒგ³ŽĐϙΠ ČþßĞÒĀÆÑď΢×ĕùČĕÒ¶µhŠ:Ó>“ 20 ,1*-! 2'-, ฌोŽ ȅ>Žഐ˿’ÊïčÐĞၰˈ¶॒ ¦¯wŒp‹q¯;Ó>“ 20 ,1*-! 2'-, ’ ȅ>Ž×øÛèåù¶ÙāćĎĞê}¯ƒ¥Ƃख̴़Ϛ¦µhƒ;Ó>’Ï^ ’ÖĞč“ 20 ,1*-! 2'-, ’ৢǭŽÊïčÐĞǥ˟¶­£ɧ}ƒ¥ČþßĞĂ ’ÙāćĎĞÙĉĕ¶µh¯wŒ‹f¯;

― 37 ―                                         

      (Note)

― 38 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ĐnŒ෍Ǣnu¯̴Sη̺Œා̴ിǞഓτ’ ĀčãÛÓĞčÙāćĎĞÙĉĕ   Multi-scale simulations of chemical reactions and redox processes in solution and in enzymes                     ÈÉÆáÌ Ćĕូ Weitao YANG

ůƼéćĞÑ̑S ˝Dž Professor, Duke University, USA

― 39 ―     

ਫ਼ Ň ᜤ

ùď÷ÅĞč   ÈÉÆáÌ Ćĕ  éćĞÑ̑S ÷ÅČåùĝñĕëċĞ˝Dž᜖̴S᜗

S˼   1982 Ȳ ̵̑S ͦƿ᜖B.S.᜗  1986 Ȳ ðĞÛÍďċÆì̑S ̑S၄çϒ᜖Ph.D᜗

λ˼   1989-2003 éćĞÑ̑S ˛˝, ɀ˝Dž, ˝Dž  2003-ϧǞ éćĞÑ̑S,  ÷ÅČåùĝñĕëċĞ˝Dž᜖̴S᜗

 €Ϊो؝ , S࢑৵ʢ"ਭ˵ 240 ɵ0Ά , R.G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules, Oxford University Press (1989). ᜖EΖBᝳɰB’žɐͿ࿥˨ϚF́ญᝳ࿥ᝳϥ»ǰল᜖Ù ćùČĕÎĞ᜗᜗ , W. Yang, M. Levy, and S. Trickey, ed., “Special issue: Symposium on density functional and applications (Part I of II)”, Int. J. Quantum Chem., 69 (1998).

ʢ"ɰญ   Ćĕͬ˨’ਭ̴S:ওÜ̴Sœ’ૹͩ“:ႱBǻ೰ਭnu¯̙Ϛਭ’ ࿔Ʀ‹f®:žɐͿ࿥˨ও܌’ĄéČĕÒ¶¬®˯˴‹˨ΡƯŽ¦’Œ{ ƒ;y­:෍Ǣη̺’̴Sη̺ɝǻ¶ΖBƯ¨ႱBƯৢǭ͒­o}¯ ƒ¥:ĀčãÛÓĞčϚ¶࿔Ʀ}¯Œȁ:°¶෍Ǣη̺ɝǻ’ॾ͒œŒ ̺µ{Š:ฎBਭ’പµးÒ¶ǟ̑­̀DŽ¦ϕЏŽ¬jǸड़¢{sš̑y ŠqŠh¯;



― 41 ―                                                 (Note)

― 42 ― ĐnŒ෍Ǣnu¯̴Sη̺Œා̴ിǞഓτ’ ĀčãÛÓĞčÙāćĎĞÙĉĕ  ÈÉÆáÌĆĕ éćĞÑ̑S ̴SΡ  ĀčãÛÓĞč QM/MM Ϛ“:ࣽ႗Ž̴SDŽ¨­̀DŽ’˯˴‹˨ΡƯŽÊï čÐĞ’ঠ೉¶ΊlŠ:Đn¨෍Ǣnu¯̴Sη̺¶ॾ}¯&̿’f¯೽ ˴¶¦ƒ­};ჰȂቲƯŽ QM/MM Ϛ“:’ฎB˒SƯÄùďĞã˯˴y ¨áᆇͮ¶²ȕ}¯p:͡ȂቲƯŽฎB˒SƯÄùďĞãŒ͂ు{ŠჰȎও ÜÕÛêp዇h;°ˎ:η̺Ȃ஠Œ1̴ͮҜ¼ÊïčÐĞ’ওܓ:Ùāć ĎĞÙĉĕ’ͼ࿛ÛÓĞčŒǾ%࿛’×ĕùČĕҏnhŠƻ ’ÅᆏǼჳ }¯;QM/MM ØҜ¼ÊïčÐĞȂ஠Ϛ’ಶ’ƦƓ:w°­’Åᆏ¶ॾΜ {:Đn¨෍Ǣnu¯η̺n¬—ා̴ിǞഓτ’˯˴ŽҜ¼ÊïčÐĞো· ¶ϕЏ}¯;7ਫ਼ҋ“:ĐnŒ෍Ǣ’η̺n¬—ා̴ിǞഓτœ’̺µ ñÆċÆê¶˔Š¯;

 ¢ƒ:{ͮƯŽ५Ȭo­:Ó>“:ႱBžɐŒ’̜ɰɖ‰hŠ:%࿛ nu¯ჰȁ ȆϤͮǾϛ€µ¶̉{}¯̙Ϛ¶࿔Ʀ{ƒ;̈s’̴SDŽ¨­ ̀DŽ¶ʌ̒}¯ࣽ႗Žჰȁ ȆϤͮǾϛ€µ“:Ķͪ“ɰBǻ೰o­̉{} ¯wŒp‹qŽh;Ó>’ÄùďĞã“:ȁ ȆϤͮ’ǻ೰¶ࣥn}¯ůǞƯ Ž̴S¶͒­o{:ØɰB:ɰBࣽϤwn¬—ƻwΠ’÷ÃĕéčđĞčÛ Ǿϛ€µ:ͰǢȆϤ:WwηƦ’િoŽࢢϧ¶ΊlŠs°¯;   ίͳ˵ͩ H. Hu, Z. Y. Lu, and W. T. Yang, “Qm/mm minimum free-energy path: Methodology and application to triosephosphateisomerase,” Journal of Chemical Theory and Computation, vol. 3, pp. 390–406, 2007

H. Hu, Z. Y. Lu, J. M. Parks, S. K. Burger, and W. T. Yang, “Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface,” Journal of Chemical Physics, vol. 128, p. 034105, 2008

H. Hu and W. T. Yang, “Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods,” Annual Review of Physical Chemistry, vol. 59, pp. 573–601, 2008

H. Hu, A. Boone, and W. T. Yang, “Mechanism of omp decarboxylation in orotidine 5 ’-monophosphate decarboxylase,” Journal of the American Chemical Society, vol. 130, pp. 14493–14503, 2008

― 43 ― X. C. Zeng, H. Hu, X. Q. Hu, A. J. Cohen, and W. T. Yang, “Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach,” Journal of Chemical Physics, vol. 128, p. 124510, 2008

X. C. Zeng, H. Hu, X. Q. Hu, and W. T. Yang, “Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method,” Journal of Chemical Physics, vol. 130, p. 164111, 2009

E. R. Johnson, S. Keinan, Paula Mori-Sanchez, J. Contreras-Garcia, A. J. Cohen, and W. T. Yang, “Revealing Non-Covalent Interactions”, J. Am. Chem. Soc., 132, 6498, 2010.

Xiangqian Hu, Hao Hu, Jeffrey A. Melvin, Kathleen W. Clancy, Dewey G. McCafferty, and Weitao Yang, “Autocatalytic Intramolecular Isopeptide Bond Formation in Gram-Positive Bacterial Pili: A QM/MM Simulation”, J. Am. Chem. Soc., 133, 478–485, 2011.

                   

― 44 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ˁǾ࿥ႱB̀଱’ƒ¥’˜ͽΖϓÄ   Ab initio prediction for strongly-correlated-electron materials                       » ˯Ï Masatoshi IMADA

f̑S̑S၄ ˝Dž Professor, University of Tokyo, Japan

― 45 ―    

ਫ਼ Ň ᜥ   ùď÷ÅĞč  »˯Ï f̑SǜSDŽʢ"Ρ˝Dž ͬ˨(S) 1981 Ȳ

λ˼   1981-1986 Ȳ f̑S̀ͮʢ"ô˛ý  1986-1990 Ȳ ɘ΢̑S˝ᇤൺਫ਼Ȅ:˛˝Dž  1990-1997 Ȳ f̑S̀ͮʢ"ô˛˝Dž  1997-2006 Ȳ f̑S̀ͮʢ"ô˝Dž  2006 Ȳ- f̑SǜSDŽʢ"Ρ˝Dž

 €Ϊो؝  țও̀S᜚Ψß᜚2004 ĶϤਫ਼ɑওÜΡSEও܌̀଱F᜚ȁ؝᜚ĶϤɉ᜚2012 

ʢ"ɰญ   ʢ"ɰญ“ɐʠDŽ̀Sਭ᜚țও̀S᜜ڎʢ"èĞĀ“ˁǾ࿥ฎBDŽ᜚ ჰȱ࢞DŽ᜜                    

― 47 ―                                                 (Note)

― 48 ― ˁǾ࿥ႱB̀଱’ƒ¥’˜ͽΖϓÄ

» ˯Ï f̑S̑S၄ǜSDŽʢ"Ρ

ಶƦƒ؝{hˁǾ࿥ႱBDŽ’ƒ¥’˜ͽΖƯŽ̀ͮϓĒ̙Ϛਭ’Ż6 ˆhŠએਭ}¯;ಶȲ’̈s’ˁǾ࿥ႱB̀଱’Ʀ॒Œ’ͮ଱’ॾ͒“: ˨ŽႱB̧RϓĒ̙Ϛਭ’ƦƜ’ˁhʐƭŒŽ®:ͽwǵƈ‹“ঠ೉‹ qŽhҶAhϧ૏’ɝǻ’ॾ¶¥z{ƒʢ"p೽·„;Ó>’࿔Ʀ{ƒၥ đƯˁǾ࿥ႱB̧R˜ͽΖওÜϚ᜖MACE᜗“ˁǾ࿥ႱBDŽpȁ೫ŲˆÊ ïčÐĞၥđͮ¶ʄµ{:ɀúŽ̀଱‹ͿµƯµh¯wŒp‹q¯[1];w’ ýϚ¬®:̑ùƯŽòĕëǻ೰¶˜ͽΖƯʠlj᜖âÈĕ÷ËĞčéÅĕ Ò᜗}¯wŒ¬‡Š:዇Êïč ÐĞ‹’̈˨’Ҝ¼ɐ’ൺɰ̧RT¶ξ‡Š Xά{:rÊïčÐĞ ˨ȵȚ¶×qɧ{Š:w’ ˨ȵȚ¶዇Ɲɐ’rÊï čÐĞßčòĞ‹ॾq:̉^’˜ͽΖýϚ’ƴႤ¶Ǧ!}¯wŒp‹q¯¬ jŽ‡ƒ;MACE ’̺µ£¶hsˆo’̀଱¶ξ®ΆvŠॾ਍}¯;̉๢ DŽ୨W×w’ႱBǾ࿥˨ [2]:Sr2IrO4 ’¬jŽÛöĕదഘǾϛ€µpฌोŽ̀ ଱œ’̺µ[3], ɝ×w‹’Ąåề[4]ˆhŠ೉¯;

[1] M. Imada and T. Miyake, J. Phys. Soc. Jpn. 79 (2010) 112001. [2] T. Misawa, K. Nakamura and M. Imada, Phys. Rev. Lett. 108 (2012) 177007. [3] R. Arita, J. Kuneš, A.V. Kozhevnikov, A.G. Eguiluz, M. Imada, Phys. Rev. Lett. 108 (2012) 086403. [4] H.Shinaoka, T. Misawa, K. Nakamura, M.Imada, J. Phys. Soc. Jpn. 81 (2012) 034701.

― 49 ―                                            

(Note)

― 50 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ìðÙÛèÒȭ’ÌĞâĞN %࿛ DFT ŒϊȆɰB˿˒SŒ’ ñÆøČåë̴   Hybridization of order-N real-space-grid DFT and classical molecular dynamics for nano-systems                     ÷˟ çϞ Shuji OGATA

ϊÿǜƿ̑S̑S၄˝Dž Professor, Nagoya Institute of Technology, Japan

― 51 ―  ਫ਼ Ň ᜦ

 ùď÷ÅĞč  ÷˟çϞ 
ϊÿǜƿ̑S̑S၄ǜSʢ"Ρ˝Dž  $ÝÞN Ȳ ß  1ß ̵­  S˨᜖f̑S᜗$ÝßÞ Ȳ  Sͬ˨᜖f̑S᜗$ÝÝ$ Ȳ

λ˼   $ÝÝ$ Ȳ a ̵7S࢑ƊҶU᜚âã ʢ"ˆ  $ÝÝN Ȳ a f̑S ˛ý  $ÝÝå Ȳ a ěω̑S ˛˝Dž  1ääN Ȳ ¯ 
ϊÿǜƿ̑S ˛˝Dž  1ääå Ȳ a 
ϊÿǜƿ̑S ˝Dž

 €Ϊो؝ ƻw’ƒ¥’ñÆøČåëΖB᜛Ƃख̴़ſBÙāćĎĞÙĉĕϚ᜚ɰBÙāć ĎĞÙĉĕʢ"U৵EÄĕ×ĕøčF$N ǫÚ1ä$$Û᜜ ìðèÑŃ’ñÆøČåëฎBϊȆÙāćĎĞÙĉĕ᜚̵7ÙāćĎĞÙĉ ĕSU৵EÙāćĎĞÙĉĕFNä ǫÚ1ä$1Û᜜ ÌĞòĞċåù}¯ᅯɆ‹ࢢϧ}¯%࿛žɐͿ࿥˨Ϛ’ÌĞâĞ´ ̴ÄčÖ ČÜĂ᜚µ¶·¸¹⺻¼¹µ¶··½¾¹৵$ßN ǫÚ1ä$1Û¸¸¹$ÞÞa¿$Þ¯N᜜

ʢ"ɰญ  ̑॔ȵŽΚɼওÜɝ¶µhŠ᜚ƻw¨nw’ႱBÜΖBÜƂख̴़ſB¶ĕjɖ̧ ƯŽÙāćĎĞÙĉĕÄčÖČǗ’ÕĞë¶ʢ"࿔Ʀ}¯wŒ᜜¢ƒ᜚ °­¶ȆϤyŠ᜚̴Sη̺¶¤È૏DŽÈ}¯òͼΚɼƯŽñÆøČå ëÙāćĎĞÙĉĕÕĞë¶ǻÿ}¯wŒ᜜

ូ ូ

― 53 ―

                                               (Note)

― 54 ― ìðÙÛèÒȭ’ÌĞâĞN %࿛ DFT ŒϊȆɰB˿˒SŒ’ ñÆøČåë̴

÷˟çϞ

ϊÿǜƿ̑S̑S၄ʸÒÙāćĎĞÙĉĕǜSˡ Email: [email protected]

Ó>“᜚ϊȆɰB˿˒SŒႱBǻ೰ওܶòͼΚɼÈ૏DŽ’ൺɰᅯɆപµ }¯᜚˨ΡƯ‹ÿĞáøčŽΖBâÆìāåÑÛওܵ’ñÆøČåëฎBϊ ȆÙāćĎĞÙĉĕÕĞë[1]¶࿔Ʀ{Šh¯᜜%࿛ÒČåë(RG)Ά‹’ Kohn-Sham žɐͿ࿥˨Ϛ(DFT)’ࢢϧ“᜚ʣÒZ;œ’዇hപµͮ᜚òĕëΚ ɼ¶¥Κɼͮപ{Šh¯wŒ᜚ȅ>ŽÈ૏DŽപµϕЏ‹f¯wŒ¬’Nj °ƒ̡̉pf¯ƒ¥᜚ñÆøČåëฎBϊȆϚ’ฎBওÜÊĕÚĕപ{Šh ¯᜜Ó>“ಶ᜚ɰʵțφ(DC)’ͳl̙‹ RGDFT ¶ÌĞâĞN ̴{ƒ DC-RGDFT ÕĞë[2]¶࿔Ʀ{ƒ᜜w’ÕĞë“᜚˵ͩ[3]‹Ƕôy°ƒ̙Ϛ¶ ɖ̧{Š᜚ႱB’దഘ࿥˨’ Kohn-Sham Ț̜ɰ̙τʟnhŠ᜚(i) žɐ’ èĕùĎĞêÿèĕÙąč¶ͪǗŽฌ£࿥˨Œȁ×Ǹ{᜚y­(ii) ϊȆn¬ —ฎBਭƯŽȹನ˨ ¶ࢢϧ}¯ÿèĕÙąč¶×Ǹ}¯wŒ‹᜚̀Ư዇ Ɲɐ̴{ƒ¦’‹f¯᜜DC-RGDFT ÕĞë¶ñÆøČåëฎBϊȆϚ‹’ฎB ওÜÊĕÚĕŒ}¯wŒ‹᜚w°¢‹’ 100 ΖBτɐo­ 1000 ΖBÌĞâĞœ Œ᜚îചh̑qŽฎBᅯɆpয{ϕЏŽñÆøČåëฎBϊȆÕĞë¶࿔Ʀ {ƒ᜜ਫ਼ҋ“᜚Li ÆÌĕႱ΍࿥ೳ{ƒപµ£ˆhŠ¦਍͒}¯ϓ{‹f ¯᜜

ίͳ˵ͩ [1] S. Ogata, Phys. Rev. B 72, 045348 (2005). [2] N. Ohba, S. Ogata, et al., Comput. Phys. Comm. 183, 1664 (2012). [3] F. Shimojo et al., Comput. Phys. Comm. 167, 151 (2005).

       

― 55 ―                                                 (Note)

― 56 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering          ƝžϓČǟ̑ɰBযও’ฎB̴S   Quantum chemistry for accurate prediction and up-to-giantmolecular systems                      Πಧ ͬ Hiroshi NAKATSUJI

ฎB̴Sʢ"ͨU ϖ࿇ Director, Quantum Chemistry Research Institute, Japan

― 57 ―      

ਫ਼ Ň ᜧ

ùď÷ÅĞč  Πಧ ͬ᜖Žoˆ| –±{᜗ ͫT$ßȲ­¢°;   S˼  ͫTa$Ȳ඄̑SǜSൺϤÒ̴SΡͦƿ:ʞ̴́SΡ ̑S၄೽S; ͫTaÞȲ඄̑SǜSͬ˨;   Ȃ˼  ඄̑S˛ý:ò˛˝Dž¶ȂŠ:ȱÒ 1 Ȳò˝Dž᜖ϤÒĝ­̴̀S˝‚᜗; ȱÒᜟᜧȲ{Ȳೕλ:඄̑S
৳˝Dž; ȱÒᜟᜦȲ¬®̉{ჰĀʄ1˿ϚฎB̴Sʢ"ͨUϖ࿇:ȱÒᜟᜧȲ¬® ฎB̴Sʢ"ͨUʢ"ôĝô࿇:ϧǞhƒ¯;  ȱÒ Ý Ȳɖ̴̧Sʢ"ôϖ:ȱÒ $Þ¿$¯ Ȳ඄̑Sͷϝੜͽঠ͍ʢ"Ýĕá ĞĝÝĕáĞ࿇;  ȱÒ $ä Ȳ¬® $N Ȳ¢‹:˵ൺȄΡSʢ"଍̉ʁǞ೽ʢ"Eਭ̴S’5^÷ ÅĞčë’ǻÿŒĆ࿔F:ȱÒ $a Ȳ¬®ᜟᜧȲ¢‹:˵ൺΡSȄΡSʢ"଍S ࢑ʸÒʢ"EฎBƯ̴SΖ’̴Œ’ϧF¶Ǟ೽;ȱÒᜟᜧȲ¬®:ÜÝÞ ᜖ΡSğ࢑ƊҶɝǻ᜗µßàÝÞ ’E୨ƝžϓČǟ̑ɰBযও¶ϧ}¯ჹ̒Ưฎ B̴SŒওÜΡSɖDZğ࢑’ǻÿF¶Ǟ೽;  ȱÒ å Ȳ¬® ãä·åäæ¶çèºäé¾èäæ¾êè붾êìíîêïä·»¶çð½ê¾è½·ã¶ìäî½ìêæ Ýîëä¾îä¼ ᜚ ȱ Ò Þ Ȳ¬® ñ¶êæï ¶ç ãëæäîè¶æò é¾èäæ¾êè붾êì ݶîëäè» ¶ç Þºä¶æäèëîêì µºä·ëîêì ⺻¼ëî¼ ᜜ ȱ Ò $1 Ȳ¬® àïëè¶æ ¶ç ܶ½æ¾êì ¶ç µ¶·¸½èêè붾ê쵺ä·ë¼èæ»᜜ȱÒ $ß Ȳ å ˜ $1 ƧƼၯฎB̴SUએÚ$1éµðµò ó»¶è¶Ûᜨµºêëæ¸ä漶¾᜚ȱÒ 1N Ȳ¬®ôä¾äæêìÝäîæäèê滶çèºäé¾èäæ¾êè붾êì íîêïä·»¶çð½ê¾è½·ã¶ìäî½ìêæÝîëä¾îä᜜   ڎο଩  ȱÒ 1 Ȳɐ᜚̵7̴SUS࢑଩:ȱÒ $å Ȳɐ᜚̵7̴SU଩:ȱÒ $ß Ȳ᜚öTøïë¾ öäîè½æ伺ë¸êøêæïêèù¸¸¼êìêù¾ëúäæ¼ëè»:ȱÒ 1$ Ȳ᜚û½ü½ëãäïêìç涷 í¼ë꾿âêîëçëîí¼¼¶îëêè붾¶çÞºä¶æäèëîêìê¾ïµ¶·¸½èêè붾ê쵺ä·ë¼èæ»: ȱÒ 1N Ȳ᜚Ýä¾ë¶æµãýíãäïêìç¶æ¶½è¼èê¾ïë¾þ¼îëä¾èëçëîêîºëäúä·ä¾è¼᜜

― 59 ―

                                              (Note)

― 60 ― ƝžϓČǟ̑ɰBযও’ฎB̴S

Πಧ ͬ

ฎB̴Sʢ"ͨUʢ"ô 615-8245 ඄ǯॉ͒̒ၐ̑Ζ 1-36̑ïûĕãąĞùċØ̵ᇻ

ÙćĎĞéÅĕÎĞ̙τʟ“̴SŒ­̀S:̀଱’̀S¶ʽප}¯ɖ̧̙ τʟ‹f®:w°¶’Ɲɐ‹˯˴ॾswŒp‹q°”:oŽ®዇háᆇɐ ’ΡSƯϓ॒p‹q¯¬jŽ¯Œͦ³°¯;Ζƒ “w’ǸȮo‡Šw w˨Ȳ^˜˒¶ฌ‘Šqƒp:ww‹’ϧ̧ˆhŠɷ,{ƒh;¢ƒ:ฎ B̴S’¦jͽˆ’̍“Ρ೫’×ÆܒɰBŒ¢­~:ǟ̑ŽɰBDŽ¶¦ ’ʢ"È૏¥áᆇɐ’዇hȆ ¶Ƕ²‹q¯¬j}¯wŒ‹f¯;w ’Wɹo­Ζങ“Ǥ’࿥Ί}¯ϧ૏ˆhŠΖƒ ’ᝁᜯᜱ᜛ᜱ᜷Ϛɖ‰h Šʢ"¶೽¥Šqƒ;w°ˆhŠ¦’Ò ¶ɷ,{ƒh;                             

― 61 ―                                                 (Note)

― 62 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ɐႏη̺DŽ’ĀčãÛÓĞčÙāćĎĞÙĉĕ   Milti-scale Simulation of Condensed-Phase Reacting Systems                         ࿇İ ˯ၟ Masataka NAGAOKA

ϊÿ̑S̑S၄˝Dž Professor, Nagoya University, Japan

― 63 ―      

ਫ਼ Ň ᜟ᜞

 ùď÷ÅĞč ࿇İ˯ၟ
ϊÿ̑S ̑S၄ϗɷΡSʢ"Ρ ˝Dž ǜSͬ˨᜖඄̑S᜗1988 Ȳ

λ˼   1990 Ȳ-1997 Ȳ ɖ̴̧Sʢ"ô᜚ʢ"ˆ᜚ ʲΪ=ʢ"ˆ᜚Ϊ=ʢ"ˆ  1998 Ȳ
ϊÿ̑S̑S၄࿛ϗɷSʢ"Ρ᜚˛˝Dž  2002 Ȳ
ϊÿ̑S̑S၄࿛ϗɷSʢ"Ρ᜚˝Dž  2003 Ȳ-ϧǞ
ϊÿ̑S̑S၄ϗɷΡSʢ"Ρ᜚˝Dž

 €Ϊो؝ ĝS࢑৵ Ζ؝ਭ˵ lj 100 ɵ ĝওÜΡSਫ਼ɑ ˜ 2 ൺ ওÜΡS’Ć࿔ ˜ 6 ǫEɰBÙÛèÒওÜΡSF˜ 3 f“̴Sη̺’ওÜΡS”᜚ȁWɧ˧᜚2010 Ȳ ĝ“Proteins Energy, Heat and Signal Flow”, CRC Press Taylor & Francis, Ȳ᜖ȁ؝᜗ 2009 ĝE}t‹q¯ ɰBÙāćĎĞÙĉĕ õÐìĞÜĀíćÄčF᜚ਫ਼ਟ̓×ÆÊ ĕèÅ÷ÅÑ᜚2008 Ȳ᜖ɵ؝᜗ ĝቲ̴Sਫ਼ɑ ˜ 12 ǫEওÜ̴SF᜚Ψß᜚2004 Ȳ᜖ȁ؝᜗

ʢ"ɰญ  ɐႏDŽ’G̴Sη̺H¶:ÕĕöćĞáğ࢑¶዇ɐʄµ{ƒϗɷΡSƯo ˆওÜΡSƯŽýϚ¶ɖ̧:ਭƯoˆĖÅÚćÄčʢ"{Šh¯;̉: ̉^’ƝʃŽฎB̴Sও܏˕lŠ:ͼ࿛˺̴Œțওͮ¶˕A{ƒʕ˒Sฎ¶ ওÜ}¯̒{hওÜΡSƯýϚ’࿔Ʀ¶೫{Š5ʉ’̴Sϧ૏’ॾ͒¶ǸŶ{ Šh¯;¬®ȅwƯèĞĀ“Ɖ"­Hϧ૏ॾ"œŒʵp¯ჰȂቲƯওÜΡS’̙ Ϛਭ’ǻÿŒƐহŒƊ"ჰȱ࢞ᝳჰ{Ȏϧ૏"’Ʀϧɝǻ’ÄêāÛèÅåюॾ ͒’̑qsᜠˆ‹f¯;

  

― 65 ―                                                 (Note)

― 66 ― ɐႏη̺DŽ’ĀčãÛÓĞčÙāćĎĞÙĉĕ

࿇İ ˯ၟ

ϊÿ̑S ̑S၄ϗɷΡSʢ"Ρ  ɰBɐႏ̧Rnu¯ȟÈη̺೯ɐਭ¶nÒ}¯wŒ“:Eyring:˴Ҝఏ’£ Ž­~:}Š’̴S͵p࿇h࿛+·‹qƒ̍Œ঍l¢};’ਭ“:°ƿ ̪“¥ƒ¯{ࣷ{Œ{Š̴S̀଱¨۶¶­°}¯ၯ:ΖBĎûč‹η̺ʌ̒ ᅢ’ोǢæĞ菎¯“~‹}p:°“ĀčãÛÓĞčÙāćĎĞÙĉĕ’ ʽȌ¬‡Š’£ਭ̴S’ɖ7ƯŽʢ"ǸȮŒŽ®̋¢}; £l”:ɰBɐႏ̧R’̴Sη̺¨˿Ưഓτnu¯Ҝ¼ÊïčÐĞ(FE)̉ͮ ¶ਚ¯ƒ¥:Ζƒ “:Ø*ˆͮȇ(NEB)ϚŒǼ£Ϥ³ƒჰȂቲƯQM/MM Ҝ¼ÊïčÐĞ̡ප(free energy gradient, FEG)Ϛ:n¬—ɰB˨പ̺ၥđȚ (number-adaptive multiscale, NAM)QM/MM-MDÙāćĎĞÙĉĕϚ¶࿔Ʀ{Šq ¢{ƒ;y­:ĐnЏnu¯FEúÙÄĕ᜖ϗˇ̜ɰࢌɼ᜗¶ͻ¥ŠɖýƊ ˿˨ॾz(VFA)}¯wŒ¬‡Š:ɰBɐႏ̧R¶̜ख़Ưη͞{ƒɖýƊ˿˨ p:ቲȆ ¶j¢sࢢ}wŒ¦̿{¢{ƒ;w°“̉^’ȱDzɹಶe‹“̋ ­°ŽhȆ ‹}; ਫ਼Ňͼ࿛’úƶȎ‹:Äĕ×ĕøčMD(EMD)ϚˆhŠ¦ĶũDz{ƒh Œͦh¢};ŒsͰĐnΠ‹Ǥ ɰॾ{ƒͽා̴ȣǢāÌÒďõĕ’ɶTഓτ ¨:êČăãčÄāĕ-N-ÌÏÙëp£Ǟ}¯ɰBžႏZ;·‹’:ÄÿāÌÒ ďõĕ’λೖҜ¼ÊïčÐĞ(TFE)ˆhŠ:ͼ࿛%࿛ɰॾy°ƒ̉ͮ¶Dz{ ¢};Η£Œ¦:’̉ͮƩB“ቲȆ Œj¢sÈ̺{Šh¢};

ίͳ˵ͩ 1) M. Nagaoka, N. Okuyamaand T. Yamabe, “Origin of the Transition State on the Free Energy Surface: Intramolecular Proton TransferReaction of Glycine in Aqueous Solution”, Journal of Physical Chemistry A, 102, 8202-8208, (1998). 2) N. Okuyama, M. Nagaoka and T. Yamabe, “Transition-State Optimization on FreeEnergy Surface: Toward SolutionChemical Reaction Ergodography”, International Journal of Quantum Chemistry, 70, 95-103 (1998). 7ਭ˵Ϊ̸§‡ƒॾ਍p᜚ɰBÙāćĎĞÙ ĉĕʢ"UU৵EÄĕ×ĕøčF10 ǫ 3 ϝ 12-17 ᅛ (2008)᜖J-Stage ŠǾ࿔Π᜗ Ǧ౅; 3) M. Nagaoka, I. Yu and M. Takayanagi, “Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations: Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory”, in “Proteins: Energy, Heat and Signal Flow”, Eds. D.M.Leitner and J.E.Straub, 169-196 (CRC, 2009) 4) M. Takayanagi, C. Iwahashiand M. Nagaoka, “Structural Dynamics of Clamshell Rotation during the Incipient Relaxation Process ofPhotodissociated Carbonmonoxy Myoglobin: Statistical Analysis by the PerturbationEnsemble Method,” Journal of Physical ChemistryB, 114, 12340-12348 (2010). 5) I. Yu, K. Nakadaand M. Nagaoka, “Spatio-Temporal Characteristics of the Transfer Free Energy of Apomyoglobin into the Molecular Crowding Condition withTrimethylamine N-oxide: A Study with Three Types of theKirkwood−Buff Integral”, Journal of Physical ChemistryB, 116, 4080-4088 (2012).

― 67 ― 6) T. Okamoto, K. Yamada, Y. Koyano, T. Asada, N. Koga and M. Nagaoka,“A Minimal Implementation of the AMBER–GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation”, Journal of Computational Chemistry, 32, 932–942 (2011). 7) Y. Kitamura, N. Takenaka, Y. Koyano and M. Nagaoka, “On the Smoothing of Free Energy Landscape of Solute Molecules in Solution: A Demonstration of the Stability of Glycine Conformers via Ab Initio QM/MM FreeEnergy Calculation”, Chemical Physics Letters, 514, 261-266 (2011). 8) N. Takenaka, Y. Kitamura, Y. Koyano and M. Nagaoka, “The Number-Adaptive Multiscale QM/MM Molecular Dynamics Simulation: Application to Liquid Water”, Chemical Physics Letters, 524, 56-61 (2012). 9) N. Takenaka, Y. Kitamura, Y. Koyano and M. Nagaoka, “An Improvement in Quantum Mechanical Description of Solute-Solvent Interactions in Condensed Systems via the Number-Adaptive MultiscaleQuantum Mechanical/Molecular Mechanical-Molecular Dynamics Method: Application to Zwitterionic Glycine in Aqueous Solution”, Journal of Chemical Physics, 137, 024501 (2012) (11pages).

                       

― 68 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ìðĝòÆÌɝЏযও’ƒ¥’୨዇Ɲɐ᜔ ዇˨ΡฎB̴SŇÜϚ   Highly Accurate and Efficient Quantum Chemical Method for Nanoᝳbio Functional Designs                     ყ4 ƪϤB Yuriko AOKI

ρǖ̑S̑S၄˝Dž Professor, Kyushu University, Japan

― 69 ―     

ਫ਼ Ň ᜟᜟ

 ùď÷ÅĞč ყ4ƪϤB ρǖ̑S̑S၄ɢϤǜSʢ"၄ ˝Dž ͬ˨᜖S᜗᜖ɀŝ̑S᜗$Ýßß Ȳ

λ˼    $Ýßß Ȳ áǖ̑SʴɄSൺ˛ý   $ÝÝä Ȳ ɀŝ̑SSൺ˛ý ᜖$ÝÝ1ᝬaëÆæ÷ĕþčê૸ƫʢ"ˆ᜗   $ÝÝå Ȳ ɀŝ̑SSൺË=ਫ਼Ȅ   $Ýݯ Ȳ ɀŝ̑SSൺ˛˝Dž   1ää1 Ȳ ΡSğ࢑ƊҶɝǻãæƯʸ೰ʢ"Ǟ೽ϖƿyqpuʢ"ˆȈ=   1ääa Ȳ ρǖ̑S̑S၄ɢϤǜSʢ"၄˝Dž

 €Ϊो؝ Y. Aoki and F. L. Gu, An elongation method for large systems toward bio-systems, Phys. Chem. Chem. Phys. (Invited Perspective), 14 (21), 7640 - 7668 (2012). Y. Aoki and F. L. Gu, Elongation Method for Delocalized Nano-wires: Progress in Chemistry, Chinese Academy of Science, 24(06), 886-909 (2012). Y. Aoki, O. Loboda, K. Liu, M. A. Makowski, and F. L. Gu, Highly accurate O (N) method for delocalized systems, Theor. Chem. Acc., 130 (4-6), 595-608 (2011). F. L. Gu, B. Kirtman, and Y. Aoki, Linear-Scaling Techniques in Computational Chemistry and Physics, Methods and Applications, Series: Challenges and Advances in Computational Chemistry and Physics, Springer, Vol. 13, 175-198 (2011). F. L. Gu and Y. Aoki, Elongation method and its applications to NLO materials, Chemical Modeling: Applications and Theory, Royal Society of Chemistry, Vol. 7, 163-191 (2010). ყ4᜚዇Ɲɐჰɪ˟ǤSŃਭযওϚ’࿔Ʀ᜚5^Ń᜚´ÞÝé¾î¹òßÚ$äÛò NÞ¿aåÚ1ääßÛ᜜

ʢ"ɰญ  ڎʢ"èĞĀ“:̑॔ȵDŽ’ɝЏ¶˨ΡƯoˆáᆇͮ዇sϓÄ}¯ƒ¥’Ϳ µͮ’዇h዇ƝɐฎB̴SওÜýϚ¶࿔Ʀ}¯wŒ᜜ਭ̴S’ɖ̧ƯýϚ¨ ࿔Ʀ{ƒùďÒċöµhŠ:዇ɰBĝȆΧDŽĝ­wDŽŽǟ̑DŽnhŠƦ ϧ}¯ɝЏ’ăÍíÜöāÑďŽWɹo­ॾz}¯̙Ϛ’ǻÿ:̒{hϧ૏ ῭଱’ǘǤĝɝЏŃযও¶ǸŶ{Šh¯᜜

― 71 ―                                                 (Note)

― 72 ― ìðĝòÆÌɝЏযও’ƒ¥’୨዇Ɲɐ᜔ ዇˨ΡฎB̴SŇÜϚ

ρǖ̑S ყ4ƪϤB

ɰB’þͮ¶ƝžওÜ}¯ฎB̴S“:ওÜɝ’Ǹड़¢{hƦƌŒ¦ ͬ೯ŽƦƶŒvƒ¦’’:̑॔ȵDŽœ’പµ࿥{Š“̈s’ॾΜ}q਒ ᆏp̏y°Šh¯;̀଱’ɝЏ“āÑďŽႱB̧Rɖ‰sƒ¥:þ>’ΖB ɰB’ͮ଱¶Ɲžη͞{ŠॾsฎB̴Sp ˨‹f¯p:ওÜͼ࿛“ Hartree-Fock(HF)ϚĎûč‹ N3~4 (Nᜨɖɇ˨):post HF Ďûč‹ N5~6 ŒŽ®: ˕lŠჰȂቲƯɰBదഘϚ’¦’’ΚɼͮးÒpf¯ϧ̧‹“:୨ΚɼÛ óÕĕ¶µhŠ¦ɐႏDŽĝŃDŽ“പµpƴႤ‹f¯;w‹:JST-CREST nu¯Ó>’ʢ"‹“:̉^Ϛ‹“ξ®ĕhƴႤŽ̑॔ȵࣽ႗DŽ’ƒ¥’̙ ϚŒ{Š Elongation(ELG)Ϛ¶ƦĆyŠqƒ;̉^Ϛ¬¯ǺDŽও܌Ǻs ò|Ȇ ¶Ίlˆˆ዇೯ওܶϧ}¯ýϚ‹:˔ɾ“ͽˇǞ዇ɰBDŽ¶È૏ {Šhƒp:7਒ᆏ‹“’പµúƶ¶ϗˇǞĝ΅ˇǞDŽͽӑ̴{ƒ; ELG Ϛ“:͂ుƯØyŽÑċ Elongation ÛáЏˇɑĄðĀжˇ>$ Active (1) 1 2345678 910 Frozen Frozen CMO ˕y:ฌϤη̺¶ȵĔ}¯¬j (6) 1 2345 6 789 10 20 16171819 131415 12 11 (2) ႱB̧R¶ೢˇƯਭƯϤ 1 23 456789 10 Active Frozen 11 Active CMO Ò¶ࢌjŒhjÓ>’ÌČÚì Re-activate +SCF Frozen (7) (3) čýϚ‹f¯;ˇɑĄðĀĞŒ’ 1 234567 8 9 10 Increased Frozen 12 11 Ǿϛ€µ¶˨Ρӻsξ®ನ¤ƒ Active CMO Re-localization Active

¥:ᅯɆùǞ̴ɰBదഘ (4) 1 2345678 9 10 RLMO Frozen 12 11 2D 3D systems Dist (RLMO)¶€Ò}¯wŒp7̙ Re-activate +SCF (8) Ϛ’̒॔ŽȬ‹f¯;ˇɑĄðĀ (5) 1 2345678 9 10 Ğ“:’ಶhൺɰùǞ̴{ƒ Frozen 13 12 11 Active CMO Frozen Active area RLMO active RLMO Œ’£Ǿϛ€µ{: ២᠅᠃᠑᠎᠁ូ៍៊ូϗˇǞDŽ‒£Ῠῗ῟៏០៉១៨៣ϚΎ ​a࿇ഓτ΅ȵʟƯࢢϧ ̋­°ƒ˯ýɰBదഘ(active ̉^Ϛῧ` CMO)¶:ˇ’ˇɑĄðĀĞo­ ⁕•ⁱ‷⁨ⁱ   ̃΅῿θX ഢhᅯɆŒಶhᅯɆ̑း @⅊R :8%8L: QI ℒℎℍ ᡒ ùǞ̴}¯¬jĈíáČĞ˺ Ǿ¶ࢌj;ഢh Frozen RLMO ᡒ Ǻ…⁋⁩‬⁺΅ওÜਇǢ “ƻ ĕÅᆏo­Ɲɐ¶Þ‡ƒ @⅊ R :8%8L: QI ¢¢၆swŒp‹q¯ƒ¥:̑॔ ᡒ Ȍȸȵɀȫȴ ĂĤġěĠĥħĞěĠ ȵDŽ¶˨Ρ¬sΏˆ˯˴ĕj Ăöô õġĖėì ã÷ø÷ ̈ ᡒ 1$:JRU`V:H 10: VR   `V$1QJ wŒp‹q¯; 

1IVL V]   ȇȩȺȯȼȫ ᡒ Ϛ’a࿇ഓτ’ȵʟƷ¶: ěE>gȻcɇɎ  ELG ŏ&ʁ̈ ljóĕĦěĨė ɧ ÷ĞġĠęēĦěġĠ ǭ   ɚɷɺ*ɘ ̉^Ϛϓĕ  ϗˇǞDŽ¶£Œ{Š : ೥Π΅ഓτ`ওÜΉϕ Figure 1   ȑ£ϤháĕóÑ଱̺µ{ƒ      V]%IGV` £¶ Figure 2 ̿}p:୨዇Ɲ Figure 2 ៏០៉១៨៣ϚΎ ​⁕•ⁱ‷⁨ⁱ⁹ℒℎℍ΅ওÜਇǢῨওÜͼ࿛

― 73 ― ɐ᜔዇˨ΡওÜp˴৶‹qŠh¯;7̙Ϛ“:ǻ೰പ̴:Local SCI Ϛ: LMP2 Ϛ:ùô̧Ržɐ(LDOS):ჰɪ˟ǤS̉ͮ(NLO)ওÜ:ùôƊ˿ॾzϚ ¶Ǽ£ನ£:ჰùǞ̴ìðãćĞøDŽ¦പµϕЏŒŽ‡Šh¯;y­Đϙ ˨ ’×ǸuƒĆ࿔¦೽ࢌΠ‹f¯;

                                        

― 74 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ǟ̑òÆÌɰBႏϤw’ǻ೰âÆìāåÑÛ   Conformational dynamics of large biomolecular assemblies                        ̵÷ ˪) Akio KITAO

f̑S ɰBǭϺ­̀Sʢ"ô ɀ˝Dž Associate Professor, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan

― 75 ―       

ਫ਼ Ň ᜟᜠ

ùď÷ÅĞč   ̵÷ ˪)  f̑S  ɰBǭϺ­̀Sʢ"ô ɀ˝Dž

λ˼   1993. Apr Kyoto University, Assistant Professor  2002. Feb Japan Atomic Energy Research Institute, Researcher  2003. Apr The University of Tokyo, Associate Professor

 €Ϊो؝  Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density. Kazuhiro Takemura and Akio Kitao, J. Phys. Chem. B, 116 (22), 6279-6287 (2012).  Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing. Wataru Nishima, Shuji Kanamaru, Fumio Arisaka and Akio Kitao, J. Am. Chem. Soc., 133 (34), 13571–13576 (2011).  Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding. Akio Kitao, J. Chem. Phys., 135(4), 045101 (2011).

ʢ"ɰญ   ǟ̑òÆÌɰBࣽϤw’ɝЏÙāćĎĞÙĉĕ  áĕóÑ଱ áĕóÑ଱ĝáĕóÑ଱᜛rɰB̴Ϥ̀Wwǻ೰ϓÄ  ­wɰBÙÛèÒ˨ΡƯɰBÙāćĎĞÙĉĕ

― 77 ―

                                             (Note)

― 78 ― ǟ̑òÆÌɰBႏϤw’ǻ೰âÆìāåÑÛ

̵÷ ˪) f̑SɰBǭϺ­̀Sʢ"ô:JST, CREST

­wȎ‹“ȅ>Žǟ̑ɰBႏϤwpɝЏ{Šh¯p:’ɝЏഓτ¶५±} ¯wŒ“”͖‹“Žh;̑॔ȵɰBÙāćĎĞÙĉĕ“¨ 100 ΃ΖBÌĞâ Ğ’ɰBÙÛèöξ®ĕl¯¬jŽ‡ŠqŠn®[1-3]:ǟ̑òÆÌɰBႏ Ϥw’ǻ೰âÆìāÑÛ¶५±}¯wŒpϕЏŽ‡Šqƒ; Ó>pࢌ‡ƒ T4 ÷ÃĞÚ¼^’áĕóÑ଱ gp5 ’ÙāćĎĞÙĉĕ“’ 1 ʱ̒}¯ÈÅčے 1 ˆ‹f¯;T4}©4זf¯;T4 ÷ÃĞړ:̑ѐ‹£ ÷ÃĞڒ4©“:T4 ÷ÃĞÚpǭϺѧʇങ{ƒ̃:ǣsf¯ޞƩ଱ gp5 ᜖gene product 5᜗p DNA /Ǹ’ȭ’ ¶࿔u¯Œw±o­࿔;y°¯;÷ᄗ ŒG”°¯ൺqpθʠ}¯wŒ¬‡Š gp5 pƧయ{Žp­ł{ɧy°:ǭϺ ѧ¶૿೫}¯;gp5 “:3 ฎw¶˟Ò}¯ޞƩ଱‹:%œČåÑÛëăÆĕŒG ”°¯ǻ೰ĈíåêpǭϺ’̅ѧ ¶࿔u¯ëČč’˲ʵ¶ ƒ{:Čàã ĞĂëăÆĕpȎൺ’üùãëÒČÍĕđ¶ʲˏ}¯Œͳl­°Šh¯;w’ ഓτ¶५±}¯ƒ¥ࢌ‡ƒǟ̑ÙÛèÒ̑॔ȵɰB˿˒SÙāćĎĞÙĉ ĕ¬‡Š:Ó>“ gp5 pͽ{’ÛÑČćĞഐ˿¶}¯¦࿥³­~: ࣽ˨’ɝЏ¶ᅠêƦȉ}¯wŒ¶̿{ƒ;%œČåÑۓǭϺѧ ¶fu¯ ·u‹Žs:Ⴑ֤Äāðා̏ɖ¶ʄµ{ŠëČč’ā’¬jБ଱¶Άഐ„ ‹hs˲ʵ¶ ƒ{Šh¯wŒp॒ɧy°ƒ;ČàãĞĂëăÆĕ“üùãë ÒČÍĕđ¶ʲˏ}¯„u‹Žs: ¶̑qs{: p࿔hƒ̃‹%œČ åÑےॾႣ}¯¬jʌ̒{Šh¯wŒpɰo‡ƒ;ČàãĞĂëăÆĕ’ 1ͮൺq“:૿೫pǺ³¯¢‹Б଱pȆϤ{Žh¬jáĕóÑ଱’ČĕÍĞ ൺq¬‡Š्³°Šh¯wŒ¦͒­oŽ‡ƒ; áĕóÑ଱ gp5 pŲˆࣽ˨’ɝЏ“:ɰB࿛Ǿϛ€µpˇ˜˺̴{Šhs wŒ¬‡Š­£ɧy°¯;w°p 1 Ϙᆞ’áĕóÑ଱pͽ{’ÛÑČćĞഐ ˿¬‡Š:ᅠɆӻsࣽ˨’ɝЏ¶Ʀȉ{4©¶”͖}¯Œhj˲ʵ¶ ƒ }ăÍíÜËf¯;ČàãĞĂëăÆĕ’ɝЏ“:1 ˆ’෍ǢɝЏ¶¦ˆáĕ óÑ଱pĀčãëăÆĕáĕóÑ଱’Π‹:ࣽ˨’ɝЏ¶Γ̋{ƒҶAhÓ ĞۄŒͳl­°¯;

ίͳ˵ͩ [1] Akio Kitao, Koji Yonekura, Saori Maki-Yonekura, Fadel A. Samatey, Katsumi Imada, Keiichi Namba, and Nobuhiro Go, Switch interactions control energy frustration and multiple flagellar filament structures. Proc. Natl. Acad. Sci., 103 (13), 4894-4899 (2006). [2] Tadaomi Furuta, Fadel A. Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba and Akio Kitao, Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint. J. Struct. Biol., 157 (3), 481-491 (2007).

― 79 ― [3] Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing. Wataru Nishima, Shuji Kanamaru, Fumio Arisaka and Akio Kitao, J. Am. Chem. Soc., 133 (34), 13571–13576 (2011).                                      

― 80 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ­wɰBDŽ’ĀčãĎûčÙāćĎ᜛Ùĉĕ   Multilevel Simulations of Biomolecular Reactions                       ੆ʃ ̫φ Keiji MOROKUMA

඄̑S ͷϝੜͽঠ͍ʢ"ÝĕáĞ ÙíÄČ×Ğã÷ÉďĞ Senior Research Fellow, Fukui Institute for Fundamental Chemistry, Kyoto University, Japan

― 81 ―  

ਫ਼ Ň ᜟᜡ

ùď÷ÅĞč ੆ʃ̫φ ÙíÄČ×Ğã÷ÉďĞ ඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞ   S˼ 1963඄̑S ǜSͬ˨   λ˼  1962-66 ඄̑SǜSൺ˛ý 1964-66  ůƼÕďĕõÄ̑S€ˆʢ"˛˝Dž 1966-67  ůƼñĞòĞë̑Sͬ˨ʢ"ˆ 1967-69  ůƼďãÉÛáĞ̑S̴S˝‚˛˝Dž 1969-71 ďãÉÛáĞ̑S̴S˝‚ý˝Dž 1971-76 ďãÉÛáĞ̑S̴S˝‚˝Dž 1976-92  ɰBΡSʢ"ôਭ̴Sʢ"DŽ˝Dž ᜖1977-92:Ϊȷ᜗ 1988-92  ɢϤʢ"̑S၄̑Sǻ೰ɰBΡSʢ"Ρ˝Dž 1993-2006 ůƼÊĄČĞ̑SÈÆČÄĂ z¹ÊĀĞßĕ˝Dž 1995-2006 ÊĄČĞ̑SãÉČĞö¹ÊĀĞßĕΡSওÜÝĕáĞ࿇ 2006-   ÊĄČĞ̑SÈÆČÄĂ z¹ÊĀĞßĕ
৳˝Dž 2006-12 ඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞČ×ĞãČĞâĞ 2012- ඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞÙíÄČ×Ğã÷ÉďĞ    €؝ 750 ɷ0Ά’ਭ˵;ಶ’hsˆo“ H. Xiao, S. Maeda and K. Morokuma, Global Ab Initio Potential Energy Surfaces for Low-lying Doublet States of NO3, J. Chem. Theo. Comp. 8, 2600–2605 (2012). S. Sekharan, K. Katayama, H. Kandori and K. Morokuma, The “OH-Site” Rule for Seeing Red and Green, J. Am. Chem. Soc. 134, 10706–10712 (2012).

H.-B. Li, A. J. Page, Y. Wang, S. Irle, and K. Morokuma, Sub-Surface Nucleation of Graphene Precursers near a Ni (111) Step Edge, Chem. Comm. 48, 7937-7939 (2012).   ʢ"ɰญ  ਭ—ওÜΡS

― 83 ―                                                 (Note)

― 84 ― ­wɰBDŽ’ĀčãĎûčÙāćĎĞÙĉĕ   ੆ʃ̫φ  ඄̑Sͷϝੜͽঠ͍ʢ"ÝĕáĞ   ÑĎÛê ʢ"ᅯɆ EĀčãÛÓĞčĝĀčã÷ÅÚåÑÛϧ૏’țϤÙāć ĎĞÙĉĕF’Žo‹:Ó>’ʢ"਒ᆏEࣽ႗ɰBDŽ’ࣽϤɰBਭÙāćĎ ĞÙĉĕF’ǸƯ“:̴ʢ".ࢢ͵:ȁòʢ"͵ƒ ¬‡Š࿔Ʀy°ƒ̈ đñÆøČåëਭ:RISM−SCF ਭ:’"’ࣽϤɰBਭ¶y­̑qs ƦĆy:¢ƒw°­¶µhŠìðÙÛèĂ:­HɰBDŽ:Κ—ĐnDŽŽ ࣽ႗ɰBDŽ’ǻ೰:η̺:âÆìāåÑێ’ÙāćĎĞÙĉĕ¶ࢌjwŒ pϕЏ‹f¯wŒ¶̿}ŒŒ¦:­wɰB’η̺¶¤Ϙ>’ɰญ‹’hs ˆo’ฌोŽÅᆏ’ॾ͒¶“o¯wŒ‹f¯;ͼ࿛’࿥ȋ:7ਫ਼ҋ“­w ɰBDŽ’ÙāćĎĞÙĉĕˆhŠ’£ਭ|¯;ww‹“:áĕóђlʣ’ ෍Ǣη̺œ’˫ᅚ¶͒­o}¯ƒ¥:áĕóÑЏnu¯hsˆo’ฐċ෍ Ǣ’Ϙ>Ž̴Sη̺¶ñÆøČåëਭ¬‡Šʢ"{ƒ;¢ƒˢୣႱB̧R ’࿥Ί}¯­wɰB’̴SùďÝۏˆhŠ¦ʢ"¶ࢌ‡ƒ;7ਫ਼ҋ“’ ᜠ−ᜡ¶Dz}¯;y­:ࣽ႗Žη̺DŽƒh{η̺Ȃ஠¶Ҝ˿ƯǘǤ}¯ ̙Ϛ¶࿔Ʀ{:w’̙Ϛ’áĕóÑlʣΠ‹’̴Sη̺œ’̺µ¶೽¥Šh¯; w’̒{hĆ࿔ˆhŠ¦ਭ|¯;

                 

― 85 ―                                                 (Note)

― 86 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         Ϡ͝࿛ӏࢌÙÛèĂ࿔ƦuƒĀčãÛÓĞčſB ÙāćĎĞÙĉĕ   Multi-scale plasma particle simulation for the development of interplanetary flight system  

ҫϝ Օε Hideyuki USUI

͜î̑S̑S၄˝Dž Professor, Kobe University, Japan

― 87 ―

ਫ਼ Ň ᜟᜢ

ùď÷ÅĞč  ҫϝ Օε ͜î̑S̑S၄ÙÛèĂϗɷSʢ"Ρ ˝Dž ͬ˨᜖ǜS᜗ ඄̑S 1994 Ȳ

λ˼  1992 Ȳ ඄̑S ୨዇đႱϤʢ"ÝĕáĞ ˛ý 1999 Ȳ ඄̑S ୨዇đႱϤʢ"ÝĕáĞ ˛˝Dž 2004 Ȳ ඄̑S ­INJʢ"ô ˛˝Dž 2009 Ȳ  ͜î̑S̑S၄ ǜSʢ"Ρ ˝Dž 2010 Ȳ ͜î̑S̑S၄ ÙÛèĂϗɷSʢ"Ρ  ˝Dž

 Ϊोਭ˵ĝ؝ Sqਭ˵ᜨStudy on the Electrodynamic Interaction Between a Tethered Satellite System and Space Plasma, 1994Ȳ

S࢑ਭ˵¬  ĝUsui et al., A Multi-Scale Electromagnetic Particle Code with Adaptive Mesh Refinement and Its Parallelization, International Conference on Computational Science, June-1-3, 2011, Procedia Computer Science, Volume 4, Pages 2337-2343, 2011Ȳ ĝ̵7ওÜǜSU৵EওÜǜSFϠ͝࿛ӏࢌÙÛèĂ࿔ƦuƒĀčãÛÓ ĞčſBÙāćĎĞÙĉĕ:Vol.16, No.3, 2011Ȳ ĝ̺µ̀SU৵, Iʢ"DzJϠ͝࿛ӏࢌÙÛèĂ࿔ƦuƒĀčãÛÓĞ čſBÙāćĎĞÙĉĕ:˜80ǫ:˜7ϝ:p.0602-0605, 2011Ȳ ĝĀčãÛÓĞčſBÙāćĎĞÙĉĕýϚ’࿔ƦŒizɝ-izùċÜĀǾϛ €µœ’̺µ, J. Plasma Fusion Res., Vol.85, No.9, pp. 589-592, 2009Ȳ ĝ Usui et al., Multi-Scale Plasma Particle Simulation for the Development of Interplanetary Flight System, J. Plasma and Fusion Research Series, vol 8, pp.1569-1573. 2009Ȳ

ڎο଩  2000Ȳ8  ႱBϗɷ೫áSU:ISAP2000ਭ˵଩ ਭ˵
ENumerical Simulations of a three-wave coupling occurring in the ionospheric plasmaF

― 89 ― ʢ"ɰญ  ᜖ᜟ᜗izᇅ͗w¨izʄµŒ8ದùċÜĀ’Ǿϛ€µ࿥}¯ſBÙāćĎ ĞÙĉĕʢ":᜖ᜠ᜗ĀčãÛÓĞčùċÜĀſBÙāćĎĞÙĉĕɖDZǻÿn ¬—’̑॔ȵΚɼ̴ýϚ࿥}¯ʢ":᜖ᜡ᜗izùċÜĀϧ૏nu¯Ϥ˿ -ſBǾϛ€µ࿥}¯ʢ":̉ϖ;

                                        

― 90 ― Ϡ͝࿛ӏࢌÙÛèĂ࿔ƦuƒĀčãÛÓĞčſB ÙāćĎĞÙĉĕ

ҫϝ Օε

͜î̑S̑S၄ÙÛèĂϗɷSʢ"Ρ:˝Dž

Ϡ͝࿛izӏࢌÙÛèÌ{Šizӏ%ʢ"࿔Ʀɝǻ᜖JAXA᜗‹Ƕôy°Š h¯˺ͤùċÜĀÝÆč᜖MPS᜗‹“᜚࢘͝Ȫ౅ÕÆčႱ6¬®ǜâÆÿ Ğč˺ɹ¶˟Ò{᜚°¶ùċÜĀŧ͏¬‡ŠɀúƶĆ࿔yŠ̔ၗᆬù ċÜĀ¶οuˮ¥¯wŒ¬®Ǟ˒¶̋¯᜖Ʒᜟ᜗. 7ʢ"‹“᜚MPS nu ¯ØȚâÆÿĞč˺ɹŒ̔ၗᆬ’Ǿϛ€µn¬—°¬‡Š࢘͝p̋¯Ǟ˒ ¶{ฎƯো·}¯ƒ¥ùċÜĀſ BĄéčÙāćĎĞÙĉĕॾz¶ࢌj ŒŒ¦᜚ù ôƯ%࿛ɰॾЏ¶Άv ¯ƒ¥പϤéBǭɰ̴Ϛ᜖AMR᜗¶ µhƒĀčãÛÓĞčſBÙāćĎĞ ÙĉĕýϚ’̒॔࿔Ʀ¶ࢌ‡ƒ᜜ ǣ~ MPS Œ̔ၗᆬùċÜĀ’Ǿϛ €µ࿥}¯ſBÙāćĎĞÙĉĕ nhŠ“᜚˺ɹDZÛÓĞčp˨ U 100m ƷᜟᜨMPS Ǔ͍Ʒ ˨ 100km ’ɀúƶᅯɆnu¯ MPS Ǟ˒ো·¶ࢌjŒŒ¦᜚Ø॔ȵ˺ͤ NJ˟Ғॾz¶ࢌ‡ƒ᜜˺ɹDZpႱB ÛÓĞčಶ‰sŒ᜚̔ၗᆬùċÜĀ ’ းċĞĀ͡˼˨ ¬®’ഐ˿ ฎ¶οuq°ŽsŽ®Ǟ˒“r·}¯᜜ w’ͼ˟Òy°¯ØȚ˺ͤNJ¨’ʣ Òđ“ႱBâÆìāÑÛp̑qŽ˲ ʵ¶ ƒ}wŒ¶ɾ¥Š͒­o{ƒ᜜ ¢ƒ᜚പϤéBǭɰ̴Ϛ᜖AMR᜗¶ ×Ǹ{ƒĀčãÛÓĞčùċÜĀſB ÙāćĎĞÙĉĕÕĞë PARMER ¶ ̒॔࿔Ʀ{᜚ǭohéBȔ¶¦ˆၥ đ¶­Òy¯wŒ¬®ùôƯ዇ h%࿛ॾƈɐ¶Ųˆ˨ΡƯŽÙāćĎ ĞÙĉĕ¶ϕЏ{ƒ᜜ÕĕöćРᶵhƒো·‹“᜚PARMER “ÕÄ ÍĞïč’ͪwͮЏŒ{Š 14%¢‹˴ ৶y°Šn®᜚૷֤p዇hſBɖൺ Ʒᜠᜨ̔ၗᆬ’ႱB˨žɐ᜖Ά᜗Œ˺˒ɪɰ ɰčĞãĕ¶ɰʵ}¯wŒ‹¬®዇h ǰǝŒႱB˨žɐ˺˿¬‡Š­ÒĝXě öĞÑͮЏ͂p̋­°¯ϕЏͮ¶͒­ y°¯ǭɰ̴éB’ȅB·᜜.

― 91 ― o{ƒ᜜PARMER ¶µhƒ˺ͤNJ˟ҏ࿥}¯èÛêÙāćĎĞÙĉĕ¶Ʒ 2 ̿}᜜¢ƒùďÝÛΚɼnhŠ“᜚˿ƯᅯɆɰʵϚ᜖DDD᜗¶࿔Ʀ{° µhŠùďÝÛ࿛’૷֤òċĕÛɄŲ¦ϧ{ƒ᜜DDD ¶µhŠ̑॔ȵùď¶ ÝÛΚɼ¬¯዇೯Ňܶ೽¥¯᜜                                           

― 92 ― ˜ᜠƧ̑॔ȵওÜΡSƼၯÙĕÿÚÈĂ   The 2nd International Symposium on Large-scale Computational Science and Engineering         ˁhǥႸ¶οu¯ΖB˒ƦႱùċĕê’ üáÛÓĞčÙāćĎĞÙĉĕ   Peta-scale Simulation of Nuclear Power Plant Subjected to Strong Earthquake                  ϥO ̰ Shinobu YOSHIMURA

̵7S࢑Uએ f̑S̑S၄˝Dž Science Council of Japan Professor, The University of Tokyo, Japan

― 93 ―   

ਫ਼ Ň ᜟᜣ

ùď÷ÅĞč  ϥO̰ f̑S̑S၄ǜSDŽʢ"Ρ ÙÛèĂʸÒSˡ˝Dž ǜSͬ˨᜖f̑S᜗1987

λ˼  1987 Ȳ f̑SǜSൺਫ਼Ȅ᜖ΖB˒ǜSΡ᜗  1989 Ȳ ò ˛˝Dž  1999 Ȳ f̑S̒ᅯɆʸÒΡSʢ"Ρ˝Dž ᜖lʣSˡ᜗  2005 Ȳ ò ǜSDŽʢ"Ρ˝Dž᜖ÙÛèĂฎBǜSˡ᜗

 €Ϊो؝  “Virtual Demonstration Tests of Large-scale and Complex Artifacts Using an Open Source Parallel CAE System, ADVENTURE”, Journal of Solid State Phenomena, Vol.110, pp.133-142, 2006  “A Monolithic Approach Based on Balancing Domain Decomposition Method for Acoustic Fluid-Structure Interaction”, Transactions of ASME, Journal of Applied Mechanics, Vol.790, No.1, 010906, 2012 (DOI: 10.1115/1.4005092)

ʢ"ɰญ   ʢ"ɰญ“:ñÆó÷ËĞĀĕÛʉƯওÜ˒S’ʢ"࿔ƦŒ’ȅ>Žϧ Åᆏœ’പµ‹f¯;’ÛÕĞù’¦Œ:ওÜ˒S’ȅ>Žɰญ:}Ž ³ ăåÙćҜ˿­Ò:ΚɼÄčÖČÜĂ:Ҝ˿যওÙÛèĂ:೛ॾz:ೳ Òॾz:̓UlʣဥȏÙāćĎĞÙĉĕŽ’ɰญ‹ওÜਭ¨ÄčÖČÜ Ă:ß÷êÈÊĒʢ"࿔Ʀ¶ࢌ‡Šqƒ;1997 Ȳo­“:ADVENTURE Œ{Šʉ­°¯ÌĞùĕßĞے̑॔ȵΚɼ းोǢϚॾzÙÛèÒʢ "࿔Ʀ¶:ùďÚÉÑêČĞâĞȈΠæʢ"͵Œ{Š:"’ 20
0Ά’ù ďÚÉÑêăĕòĞŒŒ¦ࢌ‡ŠqŠh¯;¢ƒ:2007 Ȳo­“ JST-CREST ùďÚÉÑêEΖB˒ƦႱùċĕê’ǥႸͿ˒ϓÄÙāćĎĞÙ ĉĕF¶ഉࢌΠ‹f¯;

 

― 95 ―                                                 (Note)

― 96 ― ˁhǥႸ¶οu¯ΖB˒ƦႱùċĕê’ üáÛÓĞčÙāćĎĞÙĉĕ

ϥO ̰

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― 97 ―                                                 (Note)

― 98 ―

ENGLISH

Program

10:00-10:10 Opening Addresses from the Symposium Chair Genki YAGAWA (Science Council of Japan Professor, Toyo University, Japan) from the Co-sponsor Representative Osamu ICHIMARU (Senior Researcher, Department of Innovation Research, Japan Science and Technology Agency, Japan)

10:10-11:45 Plenary Lectures 1 (Nano) Chair: Toshikazu EBISUZAKI (Chief Scientist, RIKEN, Japan)

Mauro BOERO (Professor, Institut de Physique et Chimie des Matériaux, University of Strasbourg, France) Josef MICHL (Professor, University of Colorado at Boulder, USA) Aiichiro NAKANO (Professor, University of Southern California, USA)

11:45-12:45 Lunch Break

12:45-14:20 Plenary Lectures 2 (Bio) Chair: Yuko OKAMOTO (Professor, Nagoya University, Japan)

Moon Ki KIM (Associate Professor, Sungkyunkwan University, Korea) Karissa SANBONMATSU (Team Leader, Los Alamos National Laboratory, USA) Weitao YANG (Professor, Duke University, USA)

14:20-14:40 Break

14:40-15:45 Pre-lectures for Panel Discussion (1) Chair: Ichiro HAGIWARA (Science Council of Japan Professor, Meiji University, Japan)  Masatoshi IMADA (Professor, University of Tokyo, Japan) Shuji OGATA (Professor, Nagoya Institute of Technology, Japan) Hiroshi NAKATSUJI (Director, Quantum Chemistry Research Institute, Japan) Masataka NAGAOKA (Professor, Nagoya University, Japan)

15:45-16:05 Break

16:05-17:25 Pre-lectures for Panel Discussion (2) Chair: Tadashi WATANABE (Associate Director, Advanced Institute for Computational Science, RIKEN, Japan)

Yuriko AOKI Professor, Kyushu University, Japan) Akio KITAO (Associate Professor, The University of Tokyo, Japan) Keiji MOROKUMA (Senior Research Fellow, Kyoto University, Japan) Hideyuki USUI (Professor, Kobe University, Japan) Shinobu YOSHIMURA (Science Council of Japan Professor, The University of Tokyo, Japan)

17:25-17:35 Break

17:35-18:35 Panel Discussion Coordinator: Genki YAGAWA

18:35-18:40 Closing Address Ichiro HAGIWARA

Moderator: Masatoshi NAKAGAWA (Research Manager, Japan Science and Technology Agency, Japan)

― 101 ― The 2nd International Symposium on Large-scale Computational Science and Engineering

Contents

IPlenary Lectures 1 (Nano)J

Lecture 1 Metal-Organic Molecule-Metal Nano-Junctions: Ǧ A close contact between first-principle simulations and experiments ᝳᝳᝳᝳᝳ 105 Mauro BOERO Professor, Institut de Physique et Chimie des Matériaux, University of Strasbourg, France

Lecture 2 Simulations of Artificial Molecular Rotors ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 111 Josef MICHL Professor, University of Colorado at Boulder, USA

Lecture 3 Petascale Molecular Dynamics Simulations of Nano-bio-systems ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ117 Aiichiro NAKANO Professor, University of Southern California, USA

IPlenary Lectures 2 (Bio)J

Lecture 4 Simulation Based Nano-Bio Science & Engineering: From Protein Dynamics to DNA Nanostructure Design ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 123 Moon Ki KIMូ Associate Professor, Sungkyunkwan University, Korea ូ

Lecture 5 Simulating nano-scale machines: Large-scale conformational changes of the ribosome ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 129 Karissa SANBONMATSU Team Leader, Los Alamos National Laboratory, USA

 Lecture 6 Multi-scale simulations of chemical reactions and redox processes in solution and in enzymes ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 135 Weitao YANG Professor, Duke University, USA

― 102 ―

IPre-lectures for Panel Discussion (1)J

Lecture 7 Ab initio prediction for strongly-correlated-electron materials ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 141 Masatoshi IMADA Professor, University of Tokyo, Japan

Lecture 8 Hybridization of order-N real-space-grid DFT and classical molecular dynamics for nano-systems ᝳᝳᝳᝳ 147 Shuji OGATA Professor, Nagoya Institute of Technology, Japan

Lecture 9 Quantum chemistry for accurate prediction and up-to-giantmolecular systems ᝳᝳᝳᝳ 153 Hiroshi NAKATSUJI Director, Quantum Chemistry Research Institute, Japan

Lecture 10 Milti-scale Simulation of Condensed-Phase Reacting Systems ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 159 Masataka NAGAOKA Professor, Nagoya University, Japan

IPre-lectures for Panel Discussion (2)J

Lecture 11 Highly Accurate and Efficient Quantum Chemical Method for Nanoᝳbio Functional Designs ᝳᝳᝳᝳᝳᝳᝳ 165 Yuriko AOKI Professor, Kyushu University, Japan

Lecture 12 Conformational dynamics of large biomolecular assemblies ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 171 Akio KITAO Associate Professor, The University of Tokyo, Japan

Lecture 13 Multilevel Simulations of Biomolecular Reactions ᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳᝳ 177 Keiji MOROKUMAǦ Senior Research Fellow, Kyoto University, Japan

Lecture 14 Multi-scale plasma particle simulation for the development of interplanetary flight system ᝳᝳᝳᝳᝳᝳᝳ 183 Hideyuki USUIǦ Professor, Kobe University, Japan

Lecture 15 Peta-scale Simulation of Nuclear Power Plant Subjected to Strong Earthquake ᝳᝳ 189 Shinobu YOSHIMURA Science Council of Japan Professor, The University of Tokyo, Japan 

― 103 ―                                                  The 2nd International Symposium on Large-scale Computational Science and Engineering            Metal-Organic Molecule-Metal Nano-Junctions: A close contact between first-principle simulations and experiments                           Mauro BOERO

Professor, Institut de Physique et Chimie des Matériaux, University of Strasbourg, France

― 105 ―   

Lecture 1

Profile: Mauro BOERO Research Director at the Institut de Chimie et Physique des Matériaux de Strasbourg (IPCMS), CNRS and University of Strasbourg, Strasbourg (France) Visiting Professor at the Japan Institute of Advanced Science and Technology (JAIST), Hokuriku (Japan); visiting Professor at European Center for Atomic and Molecular Calculation (Switzerland)ℇ visiting Professor at University of Tokyo – Computational Materials Science Initiative (CMSI) project member (Japan). Author of more than 130 publications, among which 100 original research papers, 5 review articles, 5 book chapters, and 19 proceedings of international conferences. Results of ISI-Web-of-Science at July 2012: Number of citations = 2321; h-index: = 28.

Domain of expertise: Numerical simulations within first principles approaches and hybrid QM/MM (quantum mechanics / molecular mechanics) methods for materials sciences and activated processes in biochemistry and solution chemistry. Co-developer of the CPMD package (since 1995) and partly of the CP2k project.

Personal Data: Date of birth 12/03/1964 Place of birth: Turin (Italy) Private address: 8 boulevard J. S. Bach, F-67000 Strasbourg (France) Professional address: 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]

Education background: 08/07/1988 – University degree in Physics - University of Torino, Torino (Italy) 01/1991-07/1994 – Ph.D. studies in computational physics - University of Torino (Italy) and École Polytechnique Fédérale de Lausanne EPFL-IRRMA (Switzerland) 10/1994 – Ph.D. in Physics

Known Languages: italian, french, english, german, Japanese

Occupation: 1/1/1995 ~ 31/7/1995 – Post-Doc at EPFL-IRRMA (Switzerland) 1/8/1995 ~ 31/4/1996 – Post-Doc at IBM Zurich Research Laboratory (Switzerland)

― 107 ― 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)

Teaching Experience: -  Technical English I and II – University of Tsukuba (Japan), Academic years 2002-2008 -  Numerical Simulations Course for Ph.D and MS – Graduate School of Pure and Applied Science, University of Tsukuba (Japan), Academic years 2004-2008 -  January 2009: Course "Beyond Xtall: short time dynamics by CPMD. Applications to Biomolecules" for Master in Physical-Chemistry, Institute "Le Bel", University of Strasbourg (France) -  Course “Introduction to Numerical Simulations: From Materials Science to Biochemistry”. École Doctorale of the University of Strasbourg (France), December 2009-January 2010 -  Numerical Modeling course for M2 course of the University of Strasbourg (France), Academic years 2010-2011-2012 -  CPMD Tutorial – University of Lille-1, Lille-Villeneuve d’Ascq (France), 3-6 October 2011.

Honors and Awards: - 2001 JRCAT Award for “First successful Ziegler-Natta catalysis simulation on a realistic system of industrial relevance”, awarded by JRCAT project leader, Prof. Dr. Kazunori Tanaka. st - Invited Professor of 1 class since November 15, 2007 until January 24, 2008 at the Institute of Physics and Chemistry of Materials of Strasbourg (CNRS-IPCMS). - Invited Visiting Professor since 1 April 2009 until 31 March 2012 at the Research Center for Integrated Science - Japan Advanced Institute of Science and Technology, Ishikawa (Japan) - Invited Visiting Professor for years 2009-2012 at the European Center for Atomic and Molecular Calculation (CECAM) - Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland - Invited Professor in March 2010, November 2010, November 2011, November 2012 at the Department of Applied Physics, School of Engineering, The University of Tokyo, (Japan)

― 108 ― Metal-Organic Molecule-Metal Nano-Junctions: A close contact between first-principle simulations and experiments

Mauro Boero

Institut de Physique etChimie des Matériaux de Strasbourg (IPCMS), CNRS-University of Strasbourg, 23 rue du Loess, F- 67034 Strasbourg (France)

The realization of functional metal-molecule junctions for future electronic devices relies on our ability in assembling these heterogeneous objects at a molecular level and in understanding the nature and the behavior of the electronic states at the interface [1]. In particular, delocalized interface states near the metal Fermi level are considered a key ingredient for tailoring charge injection [2]. Interfacial electron delocalization depends on a large number of chemical, structural, and morphologicalparameters, all influencing the spatial extension of the electron wave functions. In this talk, we show that adouble-decker organometallic compound, namely the ferrocenemolecule, can be deposited on a Cu(111) surface without giving rise to dissociation, providing an ideal system to investigate the adsorption, the interface states or even localized spin states [3] at ametal-organometallic interface. Adsorbed ferrocene is shown to produce a 2D-like interface state strongly resembling the Shockley surface-state of Cu. By a subsequent deposition of single metal atoms on the molecularlayer, we analyze the sensitivity of the interface state to local modifications of the interface potential. Accurate large-scale dynamical simulations, combined with experiments [4], provide an insight into adsorption and charge redistribution processes. Our findings demonstrate the feasibility of exploiting the chemical reactivity of molecules to modify the electron behavior at a metal-molecule interface.

[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. MbongoDjimbi, C. Massobrio, M. Boero, Phys. Rev. Lett. 107, 216801 (2011).

― 109 ―

                                             (Note)

― 110 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Simulations of Artificial Molecular Rotors                               Josef MICHL

Professor, University of Colorado at Boulder, USA

― 111 ―

Lecture 2

Profile:  Josef Michl  Born: March 12, 1939, Prague, Czechoslovakia  Professor Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, U.S.A.  Group leader Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic

Education:  M.S., Charles University, Prague, Czechoslovakia, 1961, with Prof. Václav Horák and Dr. Petr Zuman  Ph.D., Czechoslovak Academy of Sciences, Prague, Czechoslovakia, 1965, with Dr. Rudolf Zahradník

Experience:  1965-66 Post-doctoral, University of Houston, Houston, Texas  1966-67 Post-doctoral, University of Texas, Austin, Texas  1967-8/68 Research Scientist, Czechoslovak Academy of Sciences  9/68-7/69 Amanuensis (assistant professor), Aarhus University  9/69-6/70 Post-doctoral, University of Utah, Salt Lake City, Utah  7/70-7/71 Research Associate Professor, University of Utah, Salt Lake City, Utah  7/71-6/75 Associate Professor, University of Utah, Salt Lake City, Utah  7/75-8/86 Professor, University of Utah, Salt Lake City, Utah  10/79-6/84 Chairman, University of Utah, Salt Lake City, Utah  8/86-present Adjunct Professor, University of Utah, Salt Lake City, Utah  9/86-5/91 M. K. Collie-Welch Regents Chair in Chemistry, The University of Texas at Austin, Austin, Texas  6/91-present Professor, University of Colorado, Boulder, Colorado  1/06-present Group leader, Academy of Sciences of the Czech Republic

Interests: The areas of most interest at this time are (i) Photochemistry and photophysics of singlet fission for higher efficiency solar cells, (ii) Electron and ion conducting

― 113 ― compounds and polymers of new types, (iii) Surface-mounted molecular rotors and molecular circuits based on organic, organometallic, and inorganic structures, synthesized covalently or by self-assembly, and intended for use in nanoelectronics, nanofluidics, and optical metamaterials, (iv) "Naked" lithium cation catalyzed reactions, especially to radical polymerization of alkenes, alkynes, and alkadienes, (v) Novel structures based on boron, silicon, fluorine, and lithium chemistry that support activities in areas (i) - (iv), (vi) Theoretical chemistry applications in support of activities in areas (i) - (iv), both in molecular structure theory and in molecular dynamics.

In non traditional molecular electronics we are exploiting the concept of dipolar molecular rotors mounted on surfaces and driven by rotating electric field or by fluid flow. In an attempt to position such rotors in a regular two dimensional pattern, we are developing synthetic approaches to molecules that look like a tennis net or chicken wire.

The new carborane and related structures involve some of the strongest acids and strongest oxidants known. We are attempting to prepare bulk species otherwise known only in the gas phase. This is very fundamental science but it also has some immediate applications for polymer lithium battery electrolytes and fuel cell membranes.

     

― 114 ― Simulations of Artificial Molecular Rotors

Jin Wen, Alexandr Prokop, Jaroslav Vacek, and Josef Michl

Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic

Regular arrays of artificial dipolar molecular rotors would be of interest in nanofluidics and in molecular electronics. In the latter case, arrays with a ferroelectric ground state would be especially interesting, but none have been prepared so far. Our experimental efforts in this direction have been accompanied by molecular dynamics calculations in which we attempt to establish the response of individual rotors to rotational driving forces. Rotating electric field and fluid flow are the two driving forces of most interest, and we shall present results obtained using the Universal Force Field potential and a home-developed molecular dynamics program for both. We also address the utility of the notion of friction on a molecular scale and conclude that it is meaningful and in some respects remarkably similar to macroscopic friction. In addition to examining the dynamics of individual rotors we have investigated the behavior of 2-dimensional trigonal arrays of dipolar rotors of a type that we are attempting to prepare in the laboratory, with special emphasis on inter-rotor interactions.

Acknowledgement. This work has been supported by the European Research Council (FP7/2007-2013/ERC 227756) and by the U.S. National Science Foundation (CHE-0848663).

 

 



― 115 ―                                                 (Note)

― 116 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Petascale Molecular Dynamics Simulations of Nano-bio-systems

                           Aiichiro NAKANO

Professor, University of Southern California, USA

― 117 ―        

Lecture 3

Profile:  Aiichiro NAKANO  Professor Departments of Computer Science, Physics & Astronomy, and Chemical Engineering & Materials Science Collaboratory for Advanced Computing and Simulations (CACS) University of Southern California, USA  Born: April 6, 1961

Education:  Ph.D., 1989, University of Tokyo

Experience:  1989 Argonne National Laboratory, Postdoctoral Fellow  1990 Louisiana State Univ., Postdoctoral Researcher  1995 Louisiana State Univ., Assistant Professor  1999 Louisiana State Univ., Associate Professor  2002 Univ. of Southern California, Associate Professor  2006 Univ. of Southern California, Professor

Publication:  Total number of publications: 296; peer-reviwed journal articles: 183

Interests:  Metascalable scientific algorithms, high-end parallel computing, scientific big data visualization/analytics, and computational materials science.

― 119 ―                                                 (Note)

― 120 ― Petascale Molecular Dynamics Simulations of Nano-bio-systems

Aiichiro Nakano

Collaboratory for Advanced Computing and Simulations, Departments of Computer Science, Physics & Astronomy, and Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA 90089-0242, USA Email: [email protected]

We have developed a metascalable (or “design once, scale on new architectures”) parallelization scheme to perform large spatiotemporal-scale molecular dynamics (MD) simulations on multipetaflops computers based on embedded divide-and-conquer algorithms. The scheme has achieved parallel efficiency well over 0.95 on 163,840 IBM BlueGene/P processors for 1.0 trillion-atom MD and 2.58 trillion electronic degrees-of-freedom quantum molecular dynamics (QMD) in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic nanoclusters; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets; and (4) transfection of small interfering RNA across phospholipid membranes.                    

― 121 ―                                                 (Note)

― 122 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Simulation Based Nano-Bio Science & Engineering: From Protein Dynamics to DNA Nanostructure Design

                           Moon Ki KIM  Associate Professor, Sungkyunkwan University, Korea

― 123 ―

Lecture 4

Profile:  Moon Ki Kim  Sungkyunkwan University, Korea, School of Mechanical Engineering, Associate Professor  February 16, 1974

Education:  PhD, 2004, The Johns Hopkins University  MS, 1999, Seoul National University, Korea  BS, 1997, Seoul National University, Korea

Experience:  2004, University of Massachusetts-Amherst, Assistant Professor  2008, Sungkyunkwan University, Assistant Professor  2009, Sungkyunkwan University, Associate Professor

Publication:  "Efficient transfer of large-area graphene films onto rigid substrates by hot pressing", ACS Nano, Vol. 6, pp. 5360-5365, 2012  "KOSMOS: A universal morph server for nucleic acids, proteins and their complexes", Nucleic Acids Research, Vol. 40, pp. W531-W536, 2012  "DNA nanotube formation based on normal mode analysis", Nanotechnology, Vol. 23, Article No. 105704, 2012  "Rigid Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies", Biophysical Journal, Vol. 89, pp. 43-55, 2005.  "Efficient Generation of Feasible Pathways for Protein Conformational Transitions", Biophysical Journal, Vol. 83, pp. 1620-1630, 2002.

Interests: Protein Dynamics DNA Nanotechnology Multiscale Analysis Fluid Solid Interface Simulation

― 125 ― 

                                              (Note)

― 126 ― Simulation Based Nano-Bio Science & Engineering: From Protein Dynamics to DNA Nanostructure Design

Moon Ki Kim

School of Mechanical Engineering Sungkyunkwan University 300 Cheoncheon, Suwon, Korea Email: [email protected]

Recently simulation based science and engineering attracted great attention owing to its versatility and reliability as a promising research tool for nano and bio technology. In this talk, a multiscale framework of elastic network model (ENM) will be introduced as a practical tool for modeling and design of nano and bio structures including CNT and DNA. In ENM, nano or bio system can be modeled as a mass-spring network in which atomistic interaction is simply represented by a linear spring network. One can investigate fundamental vibration features of nano/bio structures using an ENM based normal mode analysis (NMA). Various NMA examples shed light on the relationship between structure and function. Furthermore, this simulation scheme can be extended to an effective design tool for DNA tile which has a great potential as a building block for 2D/3D nanostructures including organic memory devices. Consequently, mechanics based simulation enables us not only to understand structural features of the existing nano and bio systems, but also to be able to test candidate design in a virtual environment prior to their real experimental synthesis.



― 127 ―                                                 (Note)

― 128 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Simulating nano-scale machines: Large-scale conformational changes of the ribosome

                           Karissa SANBONMATSU

Team Leader, Los Alamos National Laboratory, USA

― 129 ―        

Lecture 5

Profile:  Karissa SANBONMATSU  Principal Investigator, Los Alamos National Laboratory

Education:  B.A. Physics, 1992, Columbia University  Ph.D., Astrophysics, 1997, University of Colorado at Boulder

Experience:  1997 - 99 Los Alamos National Laboratory, post-doctoral fellow, applied physics  1999 - 2000 Los Alamos National Laboratory, Scientist, applied physics  2001 - present Los Alamos National Laboratory, Principal Investigator, biophysics

Publication: Computational studies of molecular machines: the ribosome.Sanbonmatsu KY. Curr Opin Struct Biol. 2012 Apr; 22(2):168-74. Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch. Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY. J Am Chem Soc. 2012 Jul 25; 134(29):12043-53. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Novikova IV, Hennelly SP, Sanbonmatsu KY. Nucleic Acids Res. 2012 Jun; 40(11):5034-51. Excited states of ribosome translocation revealed through integrative molecular modeling. Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Proc Natl Acad Sci U S A. 2011 Nov 22; 108(47):18943-8 Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Ratje, et al. Nature. 2010 Dec 2; 468(7324):713-6. Tertiary contacts control switching of the SAM-I riboswitch. Hennelly SP, Sanbonmatsu KY. Nucleic Acids Res. 2011 Mar; 39(6):2416-31. Simulating movement of tRNA into the ribosome during decoding. Sanbonmatsu KY, Joseph S, Tung CS. Proc Natl Acad Sci U S A. 2005 Nov 1; 102(44):15854-9.

― 131 ― Interests:  The Sanbonmatsu team focuses on mechanism in non-coding RNA systems, including ribosomes, riboswitches and long non-coding RNAs. We use a variety of computational and experimental techniques, ranging from large-scale explicit solvent molecular dynamics simulation to biochemical structural probing methods, including SHAPE, in-line, DMS probing and UV cross-linking.                                          

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― 133 ―                                                 (Note)

― 134 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Multi-scale simulations of chemical reactions and redox processes in solution and in enzymes   

                       Weitao YANG

Professor, Duke University, USA

― 135 ―

Lecture 6

Profile:  Weitao Yang  Philip Handler Professor of Chemistry, Duke University

Education:  Ph.D. 1986, University of North Carolina  B.S. 1982, Peking University

Experience:  2003-present Philip Handler Professor of Chemistry, Duke University  1989-2003  Assistant, Associate, Full Professor, Duke University

Publication:  List publication of thesis and book , Over 240 journal articles , Robert G. Parr and Weitao Yang, Density-Functional Theory of Atoms and Molecules, Oxford University Press (1989). , Weitao Yang, Mel Levy, and S. Trickey, ed., “Special issue: Symposium on density functional and applications (Part I of II)”, Int. J. Quantum Chem., 69 (1998).

Interests:  List interests of research work Yang’s contributions to theoretical and computational chemistry have been in the development of methods in electronic structure theory. His contributions have made density functional calculations and modeling more accurate and efficient. He has also significantly extended the realm of quantum theory to large biological systems with development of multi-scale methods and with application in revealing the mechanism of enzyme chemical reactions in atomic and electronic details. ូ ូ ូ   

― 137 ―                                                 (Note)

― 138 ― Multi-scale simulations of chemical reactions and redox processes in solution and in enzymes

Weitao Yang Department of Chemistry, Duke University

Multiscale QM/MM methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum mechanical approaches, however at a much higher computational cost compared with semiempirical quantum mechanical approaches. Thus reaction path and activation free energy calculations encounter unique challenges in simulation timescales and phase space sampling. Recent developments of the QM/MM minimum free energy path method overcome these challenges and enable accurate free energy determination for reaction and redox processes in solution and enzymes. Applications to solution and enzyme reactions and redox processes will be highlighted.

On the qualitative side, we have developed an approach to detect non-covalent interactions in real space, based on the electron density and its derivatives. The intricate non-covalent interactions that govern many areas of biology and chemistry are not easily identified from molecular structure. Our approach reveals underlying chemistry that complements the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids.

References H. Hu, Z. Y. Lu, and W. T. Yang, “Qm/mm minimum free-energy path: Methodology and application to triosephosphateisomerase,” Journal of Chemical Theory and Computation, vol. 3, pp. 390–406, 2007

H. Hu, Z. Y. Lu, J. M. Parks, S. K. Burger, and W. T. Yang, “Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface,” Journal of Chemical Physics, vol. 128, p. 034105, 2008

H. Hu and W. T. Yang, “Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods,” Annual Review of Physical Chemistry, vol. 59, pp. 573–601, 2008

H. Hu, A. Boone, and W. T. Yang, “Mechanism of omp decarboxylation in orotidine 5 ’-monophosphate decarboxylase,” Journal of the American Chemical Society, vol. 130, pp. 14493–14503, 2008

― 139 ― X. C. Zeng, H. Hu, X. Q. Hu, A. J. Cohen, and W. T. Yang, “Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach,” Journal of Chemical Physics, vol. 128, p. 124510, 2008

X. C. Zeng, H. Hu, X. Q. Hu, and W. T. Yang, “Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method,” Journal of Chemical Physics, vol. 130, p. 164111, 2009

E. R. Johnson, S. Keinan, Paula Mori-Sanchez, J. Contreras-Garcia, A. J. Cohen, and W. T. Yang, “Revealing Non-Covalent Interactions”, J. Am. Chem. Soc., 132, 6498, 2010.

Xiangqian Hu, Hao Hu, Jeffrey A. Melvin, Kathleen W. Clancy, Dewey G. McCafferty, and Weitao Yang, “Autocatalytic Intramolecular Isopeptide Bond Formation in Gram-Positive Bacterial Pili: A QM/MM Simulation”, J. Am. Chem. Soc., 133, 478–485, 2011.

                            

― 140 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Ab initio prediction for strongly-correlated-electron materials

 

                       Masatoshi IMADA

Professor, University of Tokyo, Japan

― 141 ―

Lecture 7

Profile:  Masatoshi Imada  University of Tokyo, Professor

Education:  Doctor of Science, March 1981, University of Tokyo

Experience:  April, 1981 Institute for Solid State Physics, University of Tokyo, research associate  November, 1986 Saitama University, lecturer, associate professor  April, 1990 Institute for Solid State Physics, University of Tokyo, associate professor  September, 1997 Institute for Solid State Physics, University of Tokyo, professor  April, 2006 Department of Applied Physics, University of Tokyo, professor

Publication:  Statistical Physics, (Maruzen, 2004) in Japanese  Computation and Materials for series “Computational Science” (Iwanami shoten, 2012) in Japanese

Interests:  condensed matter physics, statistical physics

          

― 143 ―                                             

(Note)

― 144 ― Ab initio prediction for strongly-correlated-electron materials

Masatoshi Imada

Department of Applied Physics, University of Tokyo

Recent trends of ab initio studies and progress in methodologies for electronic structure calculationsof strongly correlated electron systems are discussed. The interest for developing efficient methods ismotivated by recent discoveries and characterizations of strongly correlated electron materials and byrequirements for understanding mechanisms of intriguing phenomena beyond a single-particle picture. Amulti- scaleab initio scheme for correlated electrons (MACE) is developed by utilizing the hierarchicalelectronic structure in the energy space [1]. It provides us with a first-principles downfolding of the globalband structure into low-energy effective models followed by accurate low-energy solvers for the models. Applications of MACE are illustrated with examples of several materials. In particular, we focus onelectron correlations iniron-based superconductors [2], interplay of spin-orbit interaction in 5d systems such as Sr2IrO4 [3], and Mott physics in organic conductors [4].

[1] M. Imada and T. Miyake, J. Phys. Soc. Jpn. 79 (2010) 112001. [2] T. Misawa, K. Nakamura and M. Imada, Phys. Rev. Lett. 108 (2012) 177007. [3] R. Arita, J. Kuneš, A. V. Kozhevnikov, A. G. Eguiluz, M. Imada, Phys. Rev. Lett. 108 (2012) 086403. [4] H. Shinaoka, T. Misawa, K. Nakamura, M. Imada, J. Phys. Soc. Jpn. 81 (2012) 034701.



― 145 ―

                                              (Note)

― 146 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Hybridization of order-N real-space-grid DFT and classical molecular dynamics for nano-systems                            Shuji OGATA

Professor, Nagoya Institute of Technology, Japan

― 147 ―

Lecture 8

Profile:  Shuji OGATA  Professor, Graduate School of Engineering, Nagoya Institute of Techology  Born: August 28, 1963

Education:  B. Sci., 1986, University of Tokyo  Dr. Sci., 1991, University of Tokyo

Experience:  1991 April JSPS, PD Researcher  1993 April University of Tokyo, Asisstant Professor  1995 April Yamaguchi Univ., Associate Professor  2003 July Nagoya Institute of Technology, Associate Professor  2005 April Nagoya Institute of Technology, Professor

Publication:  List publication of thesis and book Hybrid atomic/coarse-grapined-particle simulation for solids, in Bulletin "Ensemble" of Molecular Simulation Society of Japan, Vol. 13 (2011). Hybrid Quantum-Classical Simulation of Nanoscaled Materials, in Bulletin "Simulation" of Japan Society for Simulation Technogly, Vol. 30 (2012). Linear scaling algorithm of real-space density functional theory of electrons with correlated overlapping domains, Comp. Phys. Commun. Vol. 183 (2012) pp.1664-1673.

Interests:  List interests of research work Developing a variety of elementary simulation algorithms and codes for large-scale simulation of electrons, molecules, and model particles in either solid or fluid phase on high-performance parallel computers. Coupling the elementary codes to construct concurrent-type hybrid simulation codes for target systems with chemical reactions.

― 149 ―                                                 (Note)

― 150 ― Hybridization of order-N real-space-grid DFT and classical molecular dynamics for nano-systems

Shuji OGATA

Scientific and Engineering Simulation, Nagoya Institute of Technology Email: [email protected]

We have developed an efficient and portable dynamicssimulation code [1] for concurrent hybridization of the classical molecular dynamics and the quantum electronic structure calculation. The real-space grid (RG) implementation of the Kohn–Sham density functional theory (DFT) of electrons using the finite difference method for derivatives of variables, has attractive features of parallelizability and applicability to various boundary conditions in addition to universality in target materials. Therefore the RGDFT is well suited to the hybrid quantum-classical simulation scheme. Following the divide-and-conquer (DC) strategy we propose a linear scaling algorithm of it, named DC-RGDFT [2], by advancing the accuracy of former algorithm in Ref. [3]. In the Kohn–Sham-type equation for a domain, we introduce (i) the density-template potential for density continuity with simple stepwise weight functions and (ii) the embedding potential to take into account all the quantum correlation effects with other overlapping domains in addition to the classical effects of ionic and electronic Coulomb potentials. The DC-RGDFT is hybridized with the classical, empirical inter-atomic potential model using the buffered cluster method [1]. We will present some recent results of the hybrid simulation related to the Li-ion battery.

References [1] S. Ogata, Phys. Rev. B 72, 045348 (2005). [2] N. Ohba, S. Ogata, et al., Comput. Phys. Comm. 183, 1664 (2012). [3] F. Shimojo et al., Comput. Phys. Comm. 167, 151 (2005).

     

― 151 ―                                                 (Note)

― 152 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Quantum chemistry for accurate prediction and up-to-giantmolecular systems

                           Hiroshi NAKATSUJI

Director, Quantum Chemistry Research Institute, Japan

― 153 ―

Lecture 9

Profile: Hiroshi Nakatsuji 1943, Born

Education: 1966, Bachelor in Engineering (Chemistry), Kyoto University 1971, Ph. D. in Engineering (Chemistry), Kyoto University

Experience: 1971, Instructor, Faculty of Engineering, Kyoto University 1990 - 2007, Professor, Kyoto University 2006 - , Director, Quantum Chemistry Research Institute (NPO) 2007 - , Professor Emeritus, Kyoto University

1997 - 2000, Trustee, Institute for Fundamental Chemistry 2004 - 2006, Director, Fukui Institute for Fundamental Chemistry, Kyoto University

1998 - 2002, Special Fund for Scientific Research from the Government, “Developing Future Fields of Theoretical Chemistry” 2002 - 2007, Fund for Creative Scientific Research from the Government, “Deepening and realization of Quantum Principles in Chemistry” 2007 - 2013, Core Research for Evolutional Science and Technology (CREST) fund from Japan Science and Technology Agency (JST), “Realizing Super-accurate Predictions and Giant-molecular Designs: Breakthrough of Frontiers of Quantum Chemistry with Innovative Methodologies in Computational Science”

1993 - , Member of the International Academy of Quantum Molecular Sciences 1994 - , Board of Director, International Society of Theoretical Chemical Physics 2000 - 2007, Editor of Journal of Computational Chemistry. th th 2006, May, 12 International Congress of Quantum Chemistry (12 ICQC), Kyoto, Chairperson 2012 - , General Secretary of the International Academy of Quantum Molecular Science

Award: 1991, Physical Chemistry Award of the Chemical Society of Japan

― 155 ― 2004, Chemical Society of Japan Award 2004, IOCB Lecture, Prague, Czech Republic 2006, Löwdin Lectureship award at Uppsala University 2009, Fukui Medal from Asian-Pacific Association of Theoretical and Computational Chemistry 2011, Senior CMOA Medal for outstanding scientific achievements

― 156 ― Quantum chemistry for accurate prediction and up-to-giantmolecular systems

Hiroshi Nakatsuji

Quantum Chemistry Research Institute KyodaiKatsura Venture Plaza, North Building, 1-36 GoryoOohara, Nishikyo-ku, Kyoto 615-8245, Japan

Schrödinger equation provides a quantum chemical principle that governs chemistry, biology, and physics of matter. So, when we can solve it at its intrinsic accuracy, we would be able to do a very reliable prediction in these fields. We have developed basic methodology for generally solving this equation and applied it to largest possible systems using ordinary-size computers. We will report the present status. Another dream of quantum chemistry is to develop a methodology that can give reliable computational results from small to even giant molecular systems. We have developed our SAC-CI methodology along this line to apply it to photo-electronic processes of small to giant molecular systems, seamlessly.

                  

― 157 ―                                                 (Note)

― 158 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Milti-scale Simulation of Condensed-Phase Reacting Systems

                           Masataka NAGAOKA

Professor, Nagoya University, Japan

― 159 ―

Lecture 10

Profile:  Masataka NAGAOKA  Professor Graduate School of Information Science Nagoya University

Education:  Dr. Engineering, 1988, Kyoto University

Experience:  1990-1997 Researcher, Deputy Chief Researcher, Chief Researcher, Institute for Fundamental Chemistry  1998, Jul Associate Professor, Nagoya University  2002, Sep-present Professor, Nagoya University

Publication: ĝOriginal journal articles (over 100) ĝ Chapter 3 “Computational Science of Chemical Reactions”, Volume VI “Computational Science of Molecular Systems”, Computational Science and Engineering Part II, Kyoritsu, (2010) ĝ“Proteins Energy, Heat and Signal Flow”, CRC Press, (2009) (Joint work) ĝ“An Easy Guide to Molecular Simulations”, Kodansha Scientific, (2008) th ĝVolume XII “Computational Chemistry”, Experimental Chemistry(The 5 Series), Maruzen (2004) (Joint work)

Interests: Nagaoka has been studying chemical reaction dynamics in condensed state, on the basis of promoted by the heavy use of computer technology, the frontiers of computational science in informatically and visually. In particular, while the word chemistry might bring to mind images of a laboratory, white robes, and flasks, one major field of today's computational science is occupied with such "chemistry," which seems at a glance to be quite irrelevant to computers. In fact, computational chemistry and theoetical chemistry, promoted by the heavy use of computer technology, are traditional in the world-class research conducted in Japan.

― 161 ― Nagaoka has been studying the frontiers of computational science in chemical reaction dynamics informatically and visually. While the word chemistry might bring to mind images of a laboratory, white robes, and flasks, one major field of today's computational science is occupied with such "chemistry," which seems at a glance to be quite irrelevant to computers. In fact, computational chemistry and theoretical chemistry, promoted by the heavy use of computer technology, are traditional in the world-class research conducted in Japan. This can be partially recognized in the 1981 Nobel Prize for Chemistry awarded to Fukui and Hoffman for their "Frontier Electron Theory."                                       

― 162 ― Milti-scale Simulation of Condensed-Phase Reacting Systems

Masataka Nagaoka Graduate School of Information Science, Nagoya University

To complete the absolute reaction rate theory in molecular condensed states is a dream all chemists have long desired since Eyring himself. While the theory should become indispensably an elemental tool to atomistically control in producing chemicals and drugs in industries, it can stand a fundamental research target in the oretical chemistry only by the help of the multi-scale simulation. For example, to explore free energetic (FE) characteristics in chemical reactions and dynamics in molecular condensed states, we have been developing ab initio QM/MM-free energy gradient (FEG) method in combination with the nudged elastic band (NEB) method, and the number-adaptive multiscale QM/MM-MD simulation. Further, by the vibrational frequency analysis (VFA) with the FE hessian in solution, the calculated vibrational frequencies are found microscopically corresponding to those in condensed state, while not by a number of conventional mean field approaches. So far as time permits, the ensemble MD (EMD) method will be also introduced briefly, elucidating that the spatio-temporal characteristics of the relaxation process of photolyzed carbonmonoxy myoglobin in aqueous solution and of the transfer free energy (TFE) of apomyoglobin into the molecular crowding condition with trimethylamine N-oxide. It will be also shown that the characteristic parameters in both examples are to correlate favorably with experimental observations.

References 1) M. Nagaoka, N. Okuyamaand T. Yamabe, “Origin of the Transition State on the Free Energy Surface: Intramolecular Proton TransferReaction of Glycine in Aqueous Solution”, Journal of Physical Chemistry A, 102, 8202-8208 (1998). 2) N. Okuyama, M. Nagaoka and T. Yamabe, “Transition-State Optimization on FreeEnergy Surface: Toward Solution Chemical Reaction Ergodography”, International Journal of Quantum Chemistry, 70, 95-103 (1998). 3) M. Nagaoka, I. Yu and M. Takayanagi, “Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations: Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory”, in “Proteins: Energy, Heat and Signal Flow”, Eds. D. M. Leitner and J. E. Straub, 169-196 (CRC, 2009) 4) M. Takayanagi, C. Iwahashiand M. Nagaoka, “Structural Dynamics of Clamshell Rotation during the Incipient Relaxation Process of Photodissociated Carbonmonoxy Myoglobin: Statistical Analysis by the PerturbationEnsemble Method,” Journal of Physical Chemistry B, 114, 12340-12348 (2010). 5) I. Yu, K. Nakadaand M. Nagaoka, “Spatio−Temporal Characteristics of the Transfer Free Energy of Apomyoglobin into the Molecular Crowding Condition with Trimethylamine N-oxide: A Study with Three Types of theKirkwood−Buff Integral”, Journal of Physical Chemistry B, 116, 4080-4088 (2012).

― 163 ― 6) T. Okamoto, K. Yamada, Y. Koyano, T. Asada, N. Koga and M. Nagaoka, “A Minimal Implementation of the AMBER–GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation”, Journal of Computational Chemistry, 32, 932–942 (2011). 7) Y. Kitamura, N. Takenaka, Y. Koyano and M. Nagaoka, “On the Smoothing of Free Energy Landscape of Solute Molecules in Solution: A Demonstration of the Stability of Glycine Conformers via Ab Initio QM/MM Free Energy Calculation”, Chemical Physics Letters, 514, 261-266 (2011). 8) N. Takenaka, Y. Kitamura, Y. Koyano and M. Nagaoka, “The Number-Adaptive Multiscale QM/MM Molecular Dynamics Simulation: Application to Liquid Water”, Chemical Physics Letters, 524, 56-61 (2012). 9) N. Takenaka, Y. Kitamura, Y. Koyano and M. Nagaoka, “An Improvement in Quantum Mechanical Description of Solute-Solvent Interactions in Condensed Systems via the Number-Adaptive Multiscale Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Method: Application to Zwitterionic Glycine in Aqueous Solution”, Journal of Chemical Physics, 137, 024501 (2012) (11pages).

                          

― 164 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Highly Accurate and Efficient Quantum Chemical Method for Nanoᝳbio Functional Designs

                          Yuriko AOKI

Professor, Kyushu University, Japan

― 165 ―

Lecture 11   Profile:  Yuriko AOKI  Professor Faculty of Engineering Sciences, Kyushu University

Education:  Dr. Science, 1988, Hiroshima University

Experience:  1988 Shinshu University, Research Associate  1990 Hiroshima University, Research Associate (1992~4 A. v. Humboldt Researcher)  1995 Hiroshima University, Assistant Professor (Lecturer)  1997 Hiroshima University, Associate Professor  2002 JST-PRESTO Researcher as an additional post  2004 Kyushu University, Professor

Publication:  List publication of thesis and book Y. Aoki and F. L. Gu, An elongation method for large systems toward bio-systems, Phys. Chem. Chem. Phys. (Invited Perspective), 14 (21), 7640 - 7668 (2012). Y. Aoki and F. L. Gu, Elongation Method for Delocalized Nano-wires: Progress in Chemistry, Chinese Academy of Science, 24 (06), 886-909 (2012). Y. Aoki, O. Loboda, K. Liu, M. A. Makowski, and F. L. Gu, Highly accurate O(N) method for delocalized systems, Theor. Chem. Acc., 130 (4-6), 595-608 (2011). F. L. Gu, B. Kirtman, and Y. Aoki, Linear-Scaling Techniques in Computational Chemistry and Physics, Methods and Applications, Series: Challenges and Advances in Computational Chemistry and Physics, Springer, Vol. 13, 175-198 (2011). F. L. Gu and Y. Aoki, Elongation method and its applications to NLO materials, Chemical Modeling: Applications and Theory, Royal Society of Chemistry, Vol. 7, 163-191 (2010). Y. Aoki, Highly accurate theoretical design of NLO materials, Future Materials, NTS Inc., 8 (10), 36-45 (2008).

Interests:  The main research is to develop an efficient and reliable quantum chemical method

― 167 ― for large systems and to construct a treatment to analysis their functional mechanisms. The functional prediction and new material design of gigantic systems like polymers, crystals, and bio-molecular complexes are in progress from microscopic point of view using basic theoretical chemistry and programs based on our original methods.

                                      

― 168 ― Highly Accurate and Efficient Quantum Chemical Method for Nanoᝳbio Functional Designs

Kyushu University, Yuriko Aoki

Although quantum chemistry to calculate molecules precisely was accomplished rapid development with the remarkable progress of the computers, the problem that should solve most is left for the application to a large-scale systems. Because the functional property of materials is based on the microscopic electronic states, quantum chemistry that reflects the property of the individual atom and molecule precisely must 3~4 be effective. However, the computational time required is N (N: number of the bases 5~6 functions) at Hartree-Fock (HF) level, and it becomes N at post HF level, and then applications to cohesion systems and materials are difficult even if we use a super parallel computer on which ab initio molecular orbital method itself provides poor parallelization efficiency under the present conditions. Therefore, in our project on JST-CREST, we developed Elongation (ELG) method as a method for the large-scale complex system for which conventional method cannot handle. We intended for one- dimensional polymers at first, but now it was generalized to two- and three-dimensional systems with high speed calculations while giving results identical to those by

conventional method. Elongation Active (1) 1 2345678 910 Frozen The ELG method is our original Frozen CMO (6) 1 2345 6 789 10 method, a theoretical synthesis in 1920 1718 16 1415 13 12 11 (2) 1 23 456789 10 Active electronic states consecutively to Frozen 11 Active CMO Re-activate +SCF Frozen imitate polymerization reaction. It is (7) (3) 1 234567 8 9 10 Increased a novel point of this method to make Frozen 12 11 Active CMO

region localized molecular orbitals Re-localization Active

(4) 1 2345678 9 10 RLMO (RLMOs) to take the interaction with Frozen 12 11 2D 3D systems Dist the attack monomer into account Re-activate +SCF (8)

efficiently. The attacking monomer (5) 1 2345678 9 10 Frozen 13 12 11 interacts only with the active Active CMO Frozen Active area RLMO RLMOs localized on a near part of ២᠅᠃᠑᠎᠁ូ៍៊ូ៯៿᠄᠁᠉៽᠐᠅៿ូ᠅᠈᠈᠑᠏᠐᠎៽᠐᠅᠋᠊ូ᠀᠑᠎᠅᠊᠃ូ᠌᠎᠋᠌៽᠃៽᠐᠅᠋᠊ូ៾᠕ូ៏០៉១៨៣ ᠉᠁᠐᠄᠋᠀ូ᠂᠋᠎ូ៎០ ᠏᠕᠏᠐᠁᠉

the cluster, and the obtained active `QR1J%C1J IV .QRH:J   HQJ0V`$VQJC7: C:  V] canonical MOs (active CMOs) are @⅊R :8%8L: QI ℒℎℍ localized into a domain again away ᡒ from the next attacking monomer and ᡒ ``Q`1J Q :CVJV`$7 a near domain to the maximum by @⅊ R :8%8L: QI Unitary transformation. It becomes ᡒ Ȍȸȵɀȫȴ ĂĤġěĠĥħĞěĠ able to handle the local interaction of Ăöô õġĖėì ã÷ø÷ ĄėßĘĤġĬėĠ ᡒ 1$:JRU`V:H 10: VR   `V$1QJ the large-scale system efficiently  1IVL V]   ȇȩȺȯȼȫ ᡒ with frozen RLMOs to be excluded Āėĩ ěĠĦėĤēĕĦěġĠ ĢēĤĦ  ěĥ ĤėĘĤġĬėĠ ljóĕĦěĨė ĂĤġĢēęēĦěġĠ Ĕī   ÷ĞġĠęēĦěġĠ 6]VH : 1QJG7  from the eigenvalue problem. ğėĦĚġĖ  1: JQ :0:1C:GCV QJ .V 1:7   Figure 1 shows a schematic      V]%IGV` illustration of elongation process as Figure 2 ១᠎᠎᠋᠎ូ៽᠊᠀ូ៟៬៱ូ᠐᠅᠉᠁ូ᠂᠋᠎ូ᠌᠎᠋៉᠅᠊᠏᠑᠈᠅᠊ូ៽᠊᠀ូ២៞៝ ៾᠕ូ៏០៉១៨៣ ᠉᠁᠐᠄᠋᠀

― 169 ― an example for two-dimensional systems and Figure 2 demonstrates the precise & high efficiency applied to entangled proteins. Furthermore, structure optimization technique, Local SCI method, LMP2 method, local density of states (LDOS), nonlinear optics (NLO) property calculations, local site vibrational analysis technique are incorporated into this method, and also strongly delocalized nanotubes are available too. Furthermore, the development for the introduction of the solvent effect is in progress.                                         

― 170 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Conformational dynamics of large biomolecular assemblies

                          Akio KITAO

Associate Professor, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan

― 171 ―

Lecture 12

Profile:  Akio KITAO  Associate Professor Institute of Molecular and Cellular Biosciences, The University of Tokyo

Education:  Dr. Science, 1994, Kyoto University

Experience:  1993.Apr Kyoto University, Assistant Professor  2002.Feb Japan Atomic Energy Research Institute, Researcher  2003.Apr The University of Tokyo, Associate Professor

Publication:  Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density. Kazuhiro Takemura and Akio Kitao, J. Phys. Chem. B, 116 (22), 6279-6287 (2012).  Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing. Wataru Nishima, Shuji Kanamaru, Fumio Arisaka and Akio Kitao, J. Am. Chem. Soc., 133 (34), 13571–13576 (2011).  Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding. Akio Kitao, J. Chem. Phys., 135(4), 045101 (2011).

Interests:  Functional simulation of large biomolecular assembly  Prediction of protein-protein and protein-ligand complex structure  Efficient molecular simulation for biomolecular systems

― 173 ―

                                           (Note)

― 174 ― Conformational dynamics of large biomolecular assemblies

Akio Kitao

Institute of Molecular and Cellular Biosciences, The University of Tokyo JST, CREST

Many kinds of large molecular assemblies perform essential functions in biological system, but it is not straightforward to observe their functional processes directly. Molecular dynamics can now simulate the systems containing millions of atoms [1-3], which enables us to observe conformational dynamics of large biomolecular assemblies. One example is a study on gp5 protein of bacteriophage T4 [3]. Bacteriophage T4 penetrates the outer membrane of Escherichia coli using a multifunctional device composed of a gene product 5 (gp5) protein trimer. Gp5 sequentially exerts distinct functions along the course of penetration stages induced by screw motion. A triple-stranded beta-helix of gp5 acts as a cell-puncturing drill bit to make a hole on the membrane and then send the lipids upward efficiently by strong charge interactions. The gp5 lysozyme domains, which degrade the peptidoglycan layer later, are shown to play novel roles to enlarge the hole and control the release of the beta-helix. The lysozyme active site is protected from lipid binding during the penetration and is exposed after the beta-helix release. Intrinsic multiple functions of gp5 are shown to be served in turn regulated by gradual change of interdomain interactions, which enables the initial infection process with single protein trimer by continuous screw motion. The results of lysozyme domain should be understood as the case where a single-function protein acquired multiple chemical functions through interplay with other domains in a multidomain protein.

Reference [1] Akio Kitao, Koji Yonekura, Saori Maki-Yonekura, Fadel A. Samatey, Katsumi Imada, Keiichi Namba, and Nobuhiro Go, Switch interactions control energy frustration and multiple flagellar filament structures. Proc. Natl. Acad. Sci., 103 (13), 4894-4899 (2006). [2] Tadaomi Furuta, Fadel A. Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba and Akio Kitao, Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint. J. Struct. Biol., 157 (3), 481-491 (2007). [3] Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing. Wataru Nishima, Shuji Kanamaru, Fumio Arisaka and Akio Kitao, J. Am. Chem. Soc., 133 (34), 13571–13576 (2011). 

― 175 ―

                                              (Note)

― 176 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Multilevel Simulations of Biomolecular Reactions                              Keiji MOROKUMA

Senior Research Fellow, Fukui Institute for Fundamental Chemistry, Kyoto University, Japan

― 177 ―

Lecture 13

Profile: KEIJI MOROKUMA Senior Research Fellow Fukui Institute for Fundamental Chemistry, Kyoto University

Education: 1963 Ph. D., Kyoto University

Experience: 1962-66 Assistant Professor, Faculty of Engineering, Kyoto University 1964-66 Visiting Research Assistant Professor, Columbia University 1966-67 Postdoctoral Fellow, Harvard University 1967-69 Assistant Professor of Chemistry, University of Rochester 1969-71 Associate Professor of Chemistry, University of Rochester 1971-76 Professor of Chemistry, University of Rochester 1976-92 Professor and Director (1977-92), Dept. of Theoretical Studies, Institute for Molecular Science, Okazaki, Japan 1988-92 Professor, Dept. of Structural Molecular Science, Graduate University for Advanced Studies, Yokohama, Japan 1993-2006 William Henry Emerson Professor of Chemistry, Emory University 1995-2006 Director, Cherry L. Emerson Center for Scientific Computation, Emory University 2006- William Henry Emerson Professor Emeritus, Emory University 2006-12 Research Leader, Fukui Institute for Fundamental Chemistry, Kyoto University 2012-  Senior Research Fellow, Fukui Institute for Fundamental Chemistry, Kyoto University

Publications: Over 750 publications, including H. Xiao, S. Maeda and K. Morokuma, Global Ab Initio Potential Energy Surfaces for Low-lying Doublet States of NO3, J. Chem. Theo. Comp. 8, 2600–2605 (2012). S. Sekharan, K. Katayama, H. Kandori and K. Morokuma, The “OH-Site” Rule for Seeing Red and Green, J. Am. Chem. Soc. 134, 10706–10712 (2012).

H.-B. Li, A. J. Page, Y. Wang, S. Irle, and K. Morokuma, Sub-Surface Nucleation of

― 179 ― Graphene Precursers near a Ni (111) Step Edge, Chem. Comm. 48, 7937-7939 (2012).

Interests: Theoretical and computational chemistry

                                      

― 180 ― Multilevel Simulations of Biomolecular Reactions   Keiji Morokuma

Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan

The aim of the research we performed in the CREST grant entitled “Simulation of Complex Molecular Systems with Hybrid Methods” in the research area of ”High Performance Computing for Multi-scale and Multi-physics Phenomena” is 1. to develop the hybrid theoretical methods, 2. to demonstrate that such hybrid methods can be used for simulations of structures, reactions and dynamics and 3. to solve some of the important problems in different fields, including biomolecular reactions. Because of time limitation, in the present talk we discuss only simulations of biomolecular systems. Here, in order to clarify the role of protein environment, we have studies various chemical reactions of metalloenzymes in protein. We also studied chemical processes involving excited electronic states of biomolecules. I will present a brief summary of these studies. In addition we have developed methods for automatic exploration of reaction pathways for complex reaction systems and are expanding their applications to chemical reactions in protein environment. I will also discuss on this development.



― 181 ―                                                 (Note)

― 182 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Multi-scale plasma particle simulation for the development of interplanetary flight system

 

Hideyuki USUI

Professor, Kobe University, Japan

― 183 ―

Lecture 14

Profile:  Hideyuki USUI  Professor, Graduate School of System Informatics, Kobe University  March 6, 1964

Education:  1994, March, Dr. of Engineering, Kyoto University

Experience:  1999 Kyoto University, Research Associate  2004 Kyoto University, Associate Professor  2009   Kobe University, Professor

Award: 2000, AugustូូូBest paper award in International Symposium on antennas and propagation, Paper title “Numerical Simulations of a three-wave coupling occurring in the ionospheric plasma”

Publication:  List of recent publications (refereed papers) ĝMoritaka T., Y. Kajimura, H. Usui, M. Matsumoto, T. Matsui, and I. Shinohara, “Momentum transfer processes of solar wind plasmas in a kinetic scale artificial magnetosphere”, Physics of Plasmas 19, 032111, 2012. ĝUsui et al., A Multi-Scale Electromagnetic Particle Code with Adaptive Mesh Refinement and Its Parallelization, International Conference on Computational Science, June-1-3, 2011, Procedia Computer Science, Volume 4, Pages 2337-2343, 2011. ĝT. Moritaka, H. Usui, M. Nunami, Y. Kajimura, M. Nakamura, and M. Matsumoto, Full Particle-in-Cell Simulation Study on Magnetic Inflation Around a Magneto Plasma Sail, IEEE transaction on plasma science, vol. 38, No. 9, pp. 2219-2228, 2010. ĝUsui et al., Multi-Scale Plasma Particle Simulation for the Development of Interplanetary Flight System, J. Plasma and Fusion Research Series, vol 8,

― 185 ― pp.1569-1573. 2009.

 Publication of thesis and book Encyclopedia of computer simulations, Corona-Sha, 2011

Interests:  List interests of research work (1) Large-scale plasma particle simulations on interactions between space plasma and spacecraft, (2) Research and development on a multi-scale plasma particle simulation code and its parallelization for many-core system, (3) Plasma simulations on wave-particle interactions in space plasma environment.                                  

― 186 ― Multi-scale plasma particle simulation for the development of interplanetary flight system

Hideyuki Usui Professor, Graduate school of system informatics, Kobe University

Magneto Plasma Sail (MPS) is proposed as one of the innovative interplanetary flight systems. The MPS thrust is obtained as a result of multi-scale kinetic interactions between the solar wind plasma and small-scale dipole magnetic fields artificially induced with a superconducting current coil equipped in the spacecraft. In the current study, we have been investigating the solar wind interactions by means of full Particle-In-Cell (PIC) electromagnetic simulations. We revealed the importance of electron dynamics in the formation of mini-magnetosphere for a case in which the spatial scale of the dipole magnetic field structure is less than the ion inertia length but larger than the electron cyclotron radius. Owing to the electrostatic force induced by the difference of dynamics between electrons and ions, ions dynamics are also indirectly influenced by the presence of the small magnetosphere. We also estimated the Electron density MPS thrust for different spatial scales of the dipole fields approximately from 100m to 100km. We found the thrust decreases as the spatial scale of the dipole fields becomes small because the solar wind ions become unmagnetized in such Solar wind a small spatial scale and it becomes difficult for the magneto sail to block the solar wind momentum.

To examine the multi-scale interactions Process boundary in association with MPS, we have been Coarse developing a new electromagnetic PIC girds code by incorporating the Adaptive Mesh Refinement (AMR) technique. In the Dipole AMR scheme, each hierarchy level has its fields own grid size and time step interval. Fine grids in the hierarchical domains are Fine girds dynamically removed or produced depending on local physical conditions. The performance estimate of PARMER Figure 1 :Electron density profile (upper obtained with the K-computer is panel) and the corresponding spatial grid approximately 14 % with respect to the system and process boundaries (lower panel) for a test simulation on the formation of a peak performance. Figure 1 shows a small-scale magnetosphere. result of a test simulation on the formation of a small-scale magnetosphere. For massive parallel computing, we are currently incorporating the dynamic domain decomposition (DDD) scheme using the modified Morton ordering to achieve the load balancing between processes.

― 187 ―                                                 (Note)

― 188 ― The 2nd International Symposium on Large-scale Computational Science and Engineering            Peta-scale Simulation of Nuclear Power Plant Subjected to Strong Earthquake

                          Shinobu YOSHIMURA

Science Council of Japan Professor, School of Engineering, The University of Tokyo, Japan

― 189 ―

Lecture 15

Profile:  Shinobu Yoshimura  Professor Department of Systems Innovation, The University of Tokyo  March 18, 1959

Education:  Dr. of Eng., 1987, The University of Tokyo

Experience:  1987 April Lecturer, The University of Tokyo  1989 April Associate Professor, The University of Tokyo  1999 April Professor, The University of Tokyo

Publication:  “Virtual Demonstration Tests of Large-scale and Complex Artifacts Using an Open Source Parallel CAE System, ADVENTURE”, Journal of Solid State Phenomena, Vol.110, pp.133-142, 2006  “A Monolithic Approach Based on Balancing Domain Decomposition Method for Acoustic Fluid-Structure Interaction”, Transactions of ASME, Journal of Applied Mechanics, Vol.790, No.1, 010906, 2012 (DOI: 10.1115/1.4005092)

Interests:  His research interest primarily focuses on R&D of high-performance and intelligent computational mechanics with real world’s applications. With this scope, he has developed a number of numerical techniques, algorithms and systems in a variety of computational mechanics fields including automated mesh generation, parallel finite element algorithms, integrated system for design synthesis, inverse analyses, coupled analyses, social and environmental simulations such as intelligent multi-agent traffic simulation. Since 1997, he has been developing the advanced parallel finite element analysis software known as ADVENTURE system, leading more than 20 investigators. Since 2007, he has been developing Simulation for predicting quake-proof capability of nuclear power plants.

― 191 ―                                                 (Note)

― 192 ― Peta-scale Simulation of Nuclear Power Plant Subjected to Strong Earthquake

Shinobu Yoshimura Department of Systems Innovation, The University of Tokyo

In such countries as Japan where earthquake occurs frequently, reliable and sufficient seismic proof design plays a key role in operating nuclear power plants (NPPs) safely and stably. Especially, recent strong earthquakes attacking some Japanese NPPs such as Niigataken-Chuetsu-Oki (NCO) earthquake with 6.8 Mw occurred on July 16, 2007 and Off the Pacific Coast of Tohoku Earthquake / Tsunamiូ with 9.0 Mw occurred on March 11, 2011 recalled its practical importance seriously. In conventional seismic design of NPPs, a variety of safety margins are embedded in various ways in order to consider uncertainty in design and operation processes such as a magnitude of earthquake, material strength and operating conditions. However, it is still unknown how strong earthquake the existing NPPs can stand in reality. Under the above-mentioned background, we have been developing a multi-scale and multi-physics based numerical simulator for quantitatively predicting actual quake-proof capability of ageing NPPs under operation or just after plant trip subjected to strong earthquake. Here we divide the whole phenomena into three sub-phenomena, and develop simulation codes and numerical models for the sub-phenomena. As for a main sub-phenomenon, we construct full scale and precise 3D finite element models of building, pressure vessels with internal structures with nearly billion degrees of freedom, and perform dynamic nonlinear response analyses with considering fluid-structure interaction between pressure vessel, internal structures and coolant by iterative partitioned coupling algorithms. We also develop a parallelized walkthrough visualization technique to effectively deal with a huge amount of data coming from large scale simulations. Those simulation codes are being tuned for Japanese peta-flops computer “K” with sub-millions cores. In this talk, we describe some latest simulation results.

― 193 ―

                        

2012 Ȳ᜖ȱÒ 24 Ȳ᜗11 Ʀࢌ Date of Issue: Nov., 2012

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