Computics Kickoff Meeting, Univ. Tokyo, September 18, 2010.

A02-8:ከ⮬⏤ᗘ䞉኱つᶍ⣔䛻䛚䛡䜛཯ᛂ䛸ᵓ㐀✵㛫᥈⣴◊✲⤌⧊• ◊✲௦⾲⪅ೖ ๛ஂ䠄ྡྂᒇ኱Ꮫ䞉෸ᩍᤵ䠅• ◊✲ศᢸ⪅ගṊள௦⌮䠄៞ᛂ኱Ꮫ䞉ຓᩍ䠅• 㐃ᦠ◊✲⪅ᒸᮏ♸ᖾ䠄ྡྂᒇ኱Ꮫ䞉ᩍᤵ䠅㊊❧ఙ୍䠄䠧䠡䠧䞉෸ᩍᤵ䠅• ◊✲༠ຊ⪅ᮡ⏣᭷἞䠄⌮໬Ꮫ◊✲ᡤ䞉෸୺௵◊✲ဨ䠅Ώ㎶ᐂᚿ䠄ྡྂᒇ኱Ꮫ䞉Ꮫ᣺䠠䠟䠎䠅䜔䜎䛸䜏䛴䛯䛡䛯䛛䜂䛥䛒䜘䜚䜂䜝䛧◊✲ศᢸ䛸ᙺ๭䝍䞁䝟䜽㉁䛾ᵓ㐀䞉䝎䜲䝘䝭䜽䝇䞉ᶵ⬟ศᏊ䝅䝭䝳䝺䞊䝅䝵䞁䛸᫬㛫ศゎ㟁Ꮚ≧ែィ⟬䠴⥺⤖ᬗゎᯒೖ䚸Ώ㎶䠄཯ᛂ䞉䝎䜲䝘䝭䜽䝇䠅ගṊ䚸ᒸᮏ䚸ᮡ⏣䠄ᵓ㐀✵㛫᥈⣴䠅㊊❧䠄䝍䞁䝟䜽㉁ศᏊື⏬䠅◊✲ᴫせ᫬㛫✵㛫ศゎ⬟䛾ඃ䜜䛯ᐇ㦂ᡭἲ䛸ᵓ㐀✵㛫᥈⣴⬟䛾㧗䛔ィ⟬ᡭἲ䜢ే⏝䛧䛶䚸ከ⮬⏤ᗘ䞉኱つᶍ⣔䛾ᵓ㐀ᙧᡂ䞉㐠ື䞉䛚䜘䜃཯ᛂ䝯䜹䝙䝈䝮䛻䜰䝥඾ᆺⓗ䛺ከ⮬⏤ᗘ䞉኱つᶍ⣔䛷䛒䜛⏕య㧗ศᏊ䝻䞊䝏䛩䜛䚹ᮏㄢ㢟䛷䛿䚸඾⣔䛻↔Ⅼ䜢䛒䛶䚸ศᏊ䝅䝭䝳䝺䞊䝅䝵䞁䛸㟁Ꮚ≧ែィ⟬䜢ά⏝䛧䛶⺮ⓑ㉁䛾
ᢡ䜚䛯䛯䜏ၥ㢟䚸」ྜయᙧᡂ䚸䛚䜘䜃ᵓ㐀ኚ໬䜔ᶵ⬟Ⓨ⌧ᶵᵓ䜢◊✲䛩䜛䚹䛭䛧䛶䚸᫬㛫ศゎX⥺⤖ᬗゎᯒἲ䛻䜘䜛⏕యศᏊ䛾ືⓗ᝟ሗ䛸䜶䝛䝹䜼䞊ィ⟬䜢⤌䜏ྜ䜟䛫䚸ศᏊ⛉ᏛⓗどⅬ䛛䜙⏕యศᏊ䛜ാ䛟䝯䜹䝙䝈䝮䜢῝䛟⌮ゎ䛩䜛䚹䜎䛪䚸ᵓ㐀✵㛫䛾ຠ⋡ⓗ᥈⣴䛻䜘䜚䚸⺮ⓑ㉁䛾ᢡ䜚䛯䛯䜏ၥ㢟䜔ᵓ㐀ኚ໬䛻䜘䜛ᶵ⬟Ⓨ⌧ᶵᵓ䜢◊✲䛩䜛䚹ᵓ㐀✵㛫䛾᥈⣴䛻䛿ᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䜢⏝䛔䜛䚹䜎䛯䚸ຊሙ㛵ᩘ䛾⢭ᐦ໬䛻䜘䜚ᢡ䜚䛯䛯䜏䝅䝭䝳䝺䞊䝅䝵䞁䛾ಙ㢗ᛶ䜢ྥୖ䛥䛫䜛䚹⭷⺮ⓑ㉁䜔⺮ⓑ㉁䞉䝸䜺䞁䝗」ྜయ䛾ᵓ㐀ᙧᡂᶵᵓ䛻ྲྀ䜚⤌䜏䚸୪⾜䛧䛶ᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䛾㛤Ⓨ䜒⾜䛖䚹⺮ⓑ㉁䛿ග䚸䝸䜺䞁䝗⤖ྜ䚸䛚䜘䜃 ᗘ䜔ᅽຊ䛺䛹䚸እ㒊ᦤື䛻ᛂ⟅䛧䛶≉ᐃ䛾ᵓ㐀ኚ໬䜢㉳䛣䛧䚸⏕≀Ꮫⓗᶵ⬟䜢Ⓨ⌧䛩䜛䚹ᮏ◊✲ㄢ㢟䛷䛿ග่⃭䛻䛸䜒䛺䛖⺮ⓑ㉁䛾ᵓ㐀ኚ໬䜢ゎᯒ䛩䜛䚹䛭䛧䛶䚸ศᏊෆỈ⣲⤖ྜ䝛䝑䝖䝽䞊䜽䛾⏕ᡂ䞉ᾘ⁛䜔ศᏊෆ䝸䜺䞁䝗⛣ື䛾䝯䜹䝙䝈䝮䜢᥈䜛䚹䛥䜙䛻䚸➨୍ཎ⌮ィ⟬䞉㟁Ꮚ≧ែィ⟬䛾䜾䝹䞊䝥䛸㐃ᦠ䛧䛶⺮ⓑ㉁ෆ䝥䝻䝖䞁⛣ື཯ᛂ䜢ศᏊㄽⓗ䛻ゎᯒ䛩䜛䚹཯ᛂ䛸䝎䜲䝘䝭䜽䝇䝥䝻䝖䞁⛣ື䝸䜺䞁䝗⛣ື㟁Ꮚ⛣ື᣺ື䜶䝛䝹䜼䞊⦆࿴⤒㊰Ligand migration movie (PNAS 106, 2612 (2009))

ADACHI (KEK)

8.4

KOSHIHARA (TIT)

Cavity 4(Xe4)

4.2

䠉4.2

TSUDUKI (NU)

Before light illumination

kJ/mol0.0

TOMITA (TIT)

Potential of mean force forligand-protein interactions(Xe1)

Cavity 2
(Xe2)

䠉8.4

After light illumination
Cavity 1(Xe1)

Cavity 3(Xe3)

A. nidulans䛾DNAග⿵ಟ㓝⣲䛸䜰䝭䝜㓟㓄ิ䛜㢮ఝ䛾㓄ิ䜢䝕䞊䝍䝧䞊䝇᳨⣴䚹
371ಶ䛾䜰䝭䝜㓟㓄ิ䜢᳨ฟ䠄㟷Ⰽගཷᐜయ䝣䜯䝭䝸䞊䠅䚹䝷䞁⸴(A. nidulans)䛾
DNAග⿵ಟ㓝⣲

Met-353䛻ヱᙜ䛩䜛䜰䝭䝜㓟䜢ẚ㍑䚹
CPD䜢ග⿵ಟ䛩䜛㑇ఏᏊ䛿ヱᙜ䛾䜰䝭䝜㓟
䛜100% Met䛷䛒䜚䚸䛭䜜௨እ䛾ᶵ⬟䜢䜒䛴㑇ఏᏊ䛿䛩䜉䛶Met௨እ䛾䜰䝭䝜㓟䛷䛒䛳䛯䟿

CPDཎᏊ㛫䛾㟁Ꮚ䛾ὶ䜜䜢ゎᯒTunneling matrix element

YuraMiyazawa(Ochanomizu Univ.) (Toyota)

Interatomic tunneling current

Nishioka(Kyoto Univ.)䠄ཧ⪃䠅䜰䝭䝜㓟䛻䛿඲㒊䛷20✀㢮䛒䜛䚹Met-353䛸䛿➃䛛䜙353␒┠䛾䜰䝭䝜㓟䛜䝯䝏䜸䝙䞁䛷䛒䜛䛸䛔䛖䛣䛸䚹

Met353 and CPD-photolyase function

6-4 photolyase

6-4 photolyase䛾ሙྜ䚸A.
nidulans䛾Met-353䛻ヱᙜ䛩䜛䜰䝭䝜㓟䛜His䛻⨨᥮䛧䛶䛔䜛䚹His䛾ሙྜ䛻䛿䝥䝻䝖䞁⛣ື䛻㛵୚䛩䜛䛸⪃䛘䜙䜜䜛䚹
Met-353䛾఩⨨䛾䜰䝭䝜㓟䛜䝍
䞁䝟䜽㉁䛾ാ䛝䜢ไᚚ䛩䜛せ䛻䛺䛳䛶䛔䜛䛣䛸䛜ศ䛛䜛䚹

Theoretical modeling of the O-intermediate structure ofbacteriorhodopsin. Watanabe et al. Proteins (2009).

WATANABEISHIKURA(NU)(GIFU U).)

our model

Muller DJ. et al., Biophys. J., 83. 3578 (2002)

bR and O-intermediate differs in the protonation states at D85 andE204㻼㼔㼛㼠㼛㼏㼥㼘㼏㼘㼑䡚 㻝㻜㻜㻌㼒㼟㻷䡚 㻝䃛㼟㻸䡚 㻜㻚㻝㼙㼟㻹㻸㼕㼓㼔㼠㻌㼍㼎㼟㼛㼞㼜㼠㼕㼛㼚䡚 㻝㼙㼟㻺㻝㻙㻝㻜㻜㼙㼟㻻䡚 㻝㼙㼟㼎㻾㻭㼞㼓㻙㻤㻞㻌㻒㻌㼃㼍㼠㼑㼞㻌㼐㼕㼟㼠㼞㼕㼎㼡㼠㼕㼛㼚㻵㼚㻌㼠㼔㼑㻌㻻㻙㼠㼛㻙㼎㻾㻌㼠㼞㼍㼚㼟㼕㼠㼕㼛㼚䚸㼛㼚㼑㻌㼜㼞㼛㼠㼛㼚㻌㼕㼟㻌㼠㼞㼍㼚㼒㼑㼞㼞㼑㼐㻌㼒㼞㼛㼙㻌㻭㼟㼜㻙㻤㻡㻌㼠㼛㻌㻳㼘㼡㻙㻞㻜㻠㻌㻔㻌㻼㼞㼛㼠㼛㼚㻌㼞㼑㼘㼑㼍㼟㼑㻌㼟㼕㼠㼑㻌㻕㻚㼎㻾㻌㻔㼓㼞㼛㼡㼚㼐㻌㼟㼠㼍㼠㼑㻕㻻㻙㼕㼚㼠㼑㼞㼙㼑㼐㼕㼍㼠㼑ᇶᗏ≧ែ㻭㼟㼜㻤㻡㻻୰㛫య㻭㼟㼜㻙㻞㻝㻞㻭㼟㼜㻙㻤㻡㻭㼟㼜㻞㻝㻞㻭㼞㼓㻙㻤㻞㼒㼘㼕㼜㻌㼠㼛㻌㼠㼔㼑㻌㼑㼤㼠㼞㼍㼏㼑㼘㼘㼡㼘㼍㼞㻌㼟㼕㼐㼑㻭㼞㼓㻤㻞㻳㼘㼡㻙㻞㻜㻠㻳㼘㼡㻞㻜㻠㻳㼘㼡㻙㻝㻥㻠㻳㼘㼡㻝㻥㻠㻼㼞㼛㼠㼑㼕㼚㼟㻌㻣㻡㻘㻌㻡㻟㻌㻔㻞㻜㻜㻥㻕㻴㼥㼐㼞㼛㼓㼑㼚㻌㼎㼛㼚㼐㻌㼚㼑㼠㼣㼛㼞㼗㻵㼚㻌㼠㼔㼑㻌㻻㻙㼎㻾㻌㼠㼞㼍㼚㼟㼕㼠㼕㼛㼚㻘㻌㼛㼚㼑㻌㼜㼞㼛㼠㼛㼚㻌㼕㼟㻌㼠㼞㼍㼚㼟㼒㼑㼞㼞㼑㼐㻌㼒㼞㼛㼙㻌㻭㼟㼜㻙㻤㻡㻌㼠㼛㻌㼠㼔㼑㻌㼜㼞㼛㼠㼛㼚㻌㼞㼑㼘㼑㼍㼟㼑㻌㼟㼕㼠㼑㻚㻻㻙㼕㼚㼠㼑㼞㼙㼑㼐㼕㼍㼠㼑㻭㼟㼜㻙㻤㻡㻭㼟㼜㻙㻞㻝㻞㻭㼞㼓㻙㻤㻞㻳㼘㼡㻙㻞㻜㻠㻳㼘㼡㻙㻝㻥㻠௒ᚋ䛾◊✲➨୍ཎ⌮ィ⟬䠄⤒㦂ⓗຊሙ㛵ᩘ䛻䛸䜙䜟䜜䛺䛔䚸ᵓ㐀✵㛫᥈⣴䛸཯ᛂ䛾グ㏙䠅⌮ㄽィ⟬䞉䝅䝭䝳䝺䞊䝅䝵䞁ຠ⋡ⓗ䛺ศᏊ䝅䝭䝳䝺䞊䝅䝵䞁䛸ᵓ㐀✵㛫᥈⣴㟁Ꮚ≧ែィ⟬䠄ᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䠅᪂䛯䛺䝝䞊䝗䜴䜶䜰䛾ά⏝䠄䠣䠬䠱䚸䠩䠠-䠣䠮䠝䠬䠡䛺䛹䠅䝍䞁䝟䜽㉁཯ᛂ䛾⣲㐣⛬䠄㟁Ꮚ⛣ື䞉䝥䝻䝖䞁⛣ື䞉䝸䜺䞁䝗⛣ື䞉䞉䞉䠅᫬㛫ศゎ䠴⥺⤖ᬗゎᯒᐇ㦂䝍䞁䝟䜽㉁཯ᛂᶵᵓ
䛾≀⌮ⓗ⌮ゎ⏕࿨᝟ሗ䛛䜙ᮍⓎ᥀䛾▱ぢ䜢ᢳฟ䝍䞁䝟䜽㉁䛾
ᶵ⬟䝕䝄䜲䞁䜈䜐䛡䛶┠ⓗ䛸䛣䜜䜎䛷䛾◊✲≀⌮໬Ꮫ䛻ᇶ䛵䛟඲ཎᏊ䛾ィ⟬ᶵ䝅䝭䝳䝺䞊䝅䝵䞁䛻䜘䛳䛶⺮ⓑ㉁䛾䝣䜷䞊䝹䝕䜱䞁䜾䜔఍ྜ⣔䛺䛹䛾ᶵᵓ䛻䛴䛔䛶⌮ゎ䛩䜛䝣䜷䞊䝹䝕䜱䞁䜾䚸఍ྜ⣔䛾䝅䝭䝳䝺䞊䝅䝵䞁䠄䛯䛟䛥䜣䛾ᴟᑡ್䛛䜙䛺䜛⮬⏤䜶䝛䝹䜼䞊᭤㠃䠅• 䠍䛴䛾ᴟᑡ≧ែ䛻䝖䝷䝑䝥䛥䜜䜛 -> ຠ⋡䛾Ⰻ䛔䝃䞁䝥䝸䞁䜾᪉ἲ䛜ᚲせ– ᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䜢䝨䝥䝏䝗⣔䜈㐺⏝䛧᭷ຠᛶ䜢ㄪ䜉䛯– 」ྜᆺᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䛾㛤Ⓨ䜢⾜䛳䛯䠄㏆ᖺ䚸ከኚᩘ∧䠄఍ྜ⣔䝅䝭䝳䝺䞊䝅䝵䞁䛾䛯䜑䠅䠅– 㝧䛻Ỉ䜢ྲྀ䜚ධ䜜䛯ProteinG䛾኱つᶍ䛺䝣䜷䞊䝹䝕䜱䞁䜾䝅䝭䝳䝺䞊䝅䝵䞁• ṇ☜䛺䜶䝛䝹䜼䞊㛵ᩘ䛜ᚲせ䠄≉䛻䚸⁐፹䜢ṇ☜䛻ྲྀ䜚ධ䜜䜛䠅㝧䛻ỈศᏊ䜢ຍ䛘䜛• ㏆ᖺ䚸ᑓ⏝䝪䞊䝗MD-GRAPE3䜢⏝䛔䛶䝅䝭䝳䝺䞊䝅䝵䞁䜢⾜䛳䛶䛔䜛⤫ィຊᏛ䛻ᇶ䛵䛟ᾮయㄽ䛷䛒䜛RISM ⌮ㄽ䜢⏝䛔䜛
• 1D RISM⌮ㄽ䜢⏝䛔䛯ᣑᙇ䜰䞁䝃䞁䝤䝹䝅䝭䝳䝺䞊䝅䝵䞁⦆࿴䝰䞊䝗ゎᯒᡭἲ䜢⺮ⓑ㉁⣔䜈㐺⏝– 䝨䝥䝏䝗⣔䛷᭷ຠᛶ䜢ㄪ䜉䛯– 䝸䝌䝏䜴䝮䛸䛔䛖⺮ⓑ㉁⣔䛻㐺⏝」ྜᆺᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䛾㛤Ⓨ㻾㻱㼂㻵㻱㼃㻦㻌㻭㻚㻌㻹㼕㼠㼟㼡㼠㼍㼗㼑㻘㻌㼅㻚㻌㻿㼡㼓㼕㼠㼍㻘㻌㼍㼚㼐㻌㼅㻚㻻㼗㼍㼙㼛㼠㼛㻚㻘㻌㻮㼕㼛㼜㼛㼘㼥㼙㼑㼞㼟㻌㻌㻔㻼㼑㼜㼠㼕㼐㼑㻌㻿㼏㼕㼑㼚㼏㼑㻕 㻢㻜㻘㻌㻥㻢 㻔㻞㻜㻜㻝㻕㻧㻌㻌㻌㼏㼛㼚㼐㻙㼙㼍㼠㻛㻜㻜㻝㻞㻜㻞㻝㐃㍕䠖ᣑᙇ䜰䞁䝃䞁䝤䝹ἲධ㛛䠄I-V) 2005ᖺ-2006ᖺศᏊ䝅䝭䝳䝺䞊䝅䝵䞁◊✲఍఍ㄅঞউজढ़ઐఌ১‫ق‬REM)ਹਡ‫؟‬੎ा౤৕॑ৠीॊ૑ਏऋऩः‫ق‬ਈुල౐ऩఁ୑॔থ१থঈঝ১‫ك‬ಳਡ‫௺؟‬ऋপऌऎऩॊध‫ؚ‬૑ਏऩঞউজढ़भਯऋกপपऩॊ

జਟभঐঝॳढ़ঀॽढ़ঝ১(MUCA)ध३঑গঞ‫ॸش‬ॕॵॻॸথঃজথॢ১(ST)ਹਡ‫؟‬ञऎऔ॒भঞউজढ़॑૑ਏधखऩःಳਡ‫؟‬੎ा౤৕भৠ৒भ൑୔‫ق‬உਞध࿃ಫऋ૑ਏ‫ك‬

1. 䝺䝥䝸䜹஺᥮䝬䝹䝏䜹䝜䝙䜹䝹ἲ (REMUCA)䝬䝹䝏䜹䝜䝙䜹䝹䝺䝥䝸䜹஺᥮ἲ (MUCAREM)
Y. Sugita and Y.Okamoto, Chem. Phys. Lett. 329, 261 (2000).
REMUCA and MUCAREM for Monte Carlo version.
A.Mitsutake, Y.Sugita, and Y.Okamoto, J.Chem.Phys, 118 (2003) 6664
A.Mitsutake, Y.Sugita, and Y.Okamoto, J.Chem.Phys, 118 (2003) 6676

2.஺᥮䝅䝭䝳䝺䞊䝔䜱䝑䝗䝔䞁䝟䝸䞁䜾ἲ (REST)
A. Mitsutake and Y.Okamoto, Chem. Phys. Lett., 332, 131 (2000).

3.䝅䝭䝳䝺䞊䝔䜱䝑䝗䝔䞁䝟䝸䞁䜾䝺䝥䝸䜹஺᥮ἲ䠄STREM)
A.Mitsutake and Y. Okamoto, J. Chem. Phys. 121,2491(2004)

4䠊REST and STREM 䛾ከኚᩘ∧A. Mitsutake and Y. Okamoto, J. Chem. Phys. 130 (2009) 214105
A. Mistsutake and Y. Okamoto, Phys. Rev. E 79 (2009) 214105
A. Mitsutake, J. Chem. Phys. 131 (2009) 094105.

▷䛔REM䝅䝭䝳䝺䞊䝅䝵䞁䜢䛧䛶
WHAM䜢⏝䛔䛶䝬䝹䝏䜹䝜䝙䜹䝹䜔䝅䝭䝳䝺䞊䝔䜱䝑䝗䝔䞁䝟䝸䞁䜾䛾㔜䜏䜢Ỵᐃ䛩䜛
R¦ g H (E)n( E )

1
j

jj 1

R

¦ g h exp( E E  f )
1
jj

j

jj 1exp( f j )³ dEn( E ) exp( E E ) ¦ n( E ) exp( E j E )EjከኚᩘREST䛸STREM䛾㛤Ⓨ•఍ྜ⣔䛾䝅䝭䝳䝺䞊䝅䝵䞁– 䝞䜲䜰䝇䝫䝔䞁䝅䝱䝹ୖ䛾䝷䞁䝎䝮䜴䜷䞊䜽䜒ᐇ⌧L䜶䝛䝹䜼䞊E 0 (x)  ¦ O(l ) Vl (x)E O (x)ศ㓄㛵ᩘ䠄 T and ʄ䠅<-- d -->

l 1

¦ exp(E E (x))

Z(T,OO)Ox

E 0  OV §

Ex.1䠖Umbrella sampling·J ¦ Si S j  h¨¦ Si ¸© i ¹
i, j!

Ex.2䠖Spin system

x {q1 ,q2 }x {S1,S2 }ᗘᅽຊ୍ᐃE  PV

x {q1 ,q2,V}

Ex.4䠖䜾䝷䞁䝗䜹䝜䝙䜹䝹E  PNx {q1 ,q2,N}

Ex.3䠖

T and O(l )

WHAM
䛷ST䛾
㔜䜏䜢Ỵᐃ

E 0 and Vl䛾䝷䞁䝎䝮䜴䜷䞊䜽
M 0 M1

MLm 0 1m1 1
M1
MLmL 1¦ ¦ ¦Nn(E 0 ,V1, ,VL )M0¦ ¦ ¦n
m 0 1m1 1exp( f m 0 ,m1 , m L )m 0 ,m1 , m L

m 0 ,m1 , m L(E 0 ,V1, ,VL )exp( f m 0 ,m1 , m L  E m 0 E / m )mL 1¦ n(E ,V , ,V )exp(E E O )0E 0 ,V1VL

1Lmm

䛾䝷䞁䝎䝮䜴䜷䞊䜽ィ⟬ᶵ䛾CPU䛾ᩘ䠄㈨※䠅䛻䜘䜚౑䛔ศ䛡䜙䜜䜛䚹ST䚸
STREM䛿REM䜘䜚㏻ಙ䛜ᑡ䛺䛟䛶䛩䜐䠄䝺䝥䝸䜹ᩘ䛩䛟䛺䛔䛛䜙䠅Ỉ୰䛾proteinG䛾ᢡ䜚␚䜏䝅䝭䝳䝺䞊䝅䝵䞁•••

༙ᚄ50ύ䛾Ỉ⌫୰䠄ỈศᏊ17,063ಶ䠅䛾ᑠ䝍䞁䝟䜽㉁ protein G䠄䜰䝭䝜㓟ᩘ56䚸඲ཎᏊᩘ
52,044ಶ䠅䜢ᣑᙇ䜰䞁䝃䞁䝤䝹䝅䝭䝳䝺䞊䝅䝵䞁䛻䜘䜚ᢡ䜚␚䜐ᆅ⌫䝅䝭䝳䝺䞊䝍䛸ᮾ኱䛾T2K䜢฼⏝䝺䝥䝸䜹஺᥮ศᏊືຊᏛἲ䠄224ಶ䠅䚸䝺䝥䝸䜹஺᥮䝬䝹䝏䜹䝜䝙䜹䝹ἲ䠄56䝺䝥䝸䜹䠅
REM䛾䝠䝇䝖䜾䝷䝮REMUCA䛾䝠䝇䝖䜾䝷䝮୍␒ኳ↛ᵓ㐀䛻ఝ䛯ᵓ㐀ึᮇᵓ㐀ኳ↛ᵓ㐀䝍䞊䞁䛾఩⨨䜔䝞䝑䜽䝪䞊䞁䛾㓄⨨䛜ఝ䛶䛔䜛ᵓ㐀䛜ᚓ䜙䜜䛯䚹䝦䝸䝑䜽䝇䛿䛷䛝䛶䛔䛺䛔䚹ᩘಸ䛾ィ⟬䛿ᚲせᑓ⏝ィ⟬ᶵ䜢⏝䛔䛯ィ⟬••••••䝺䝥䝸䜹஺᥮ἲ䜔䝅䝭䝳䝺䞊䝔䜱䝑䝗䝔䞁䝟䝸䞁䜾ἲ䛿እ㒊䝟䝷䝯䞊䝍䜢ኚ໬䛥䛫䜛
䛾䛷䚸Shell䝇䜽䝸䝥䝖䜔Perl䝇䜽䝸䝥䝖䛷సᡂྍ⬟䚹
MDGRAPE3䜢⏝䛔䛶Ỉ୰䛾Enkephalin䛾䝺䝥䝸䜹஺᥮MD䜢⾜䛺䛳䛯䚹䝺䝥䝸䜹஺᥮䛾㒊ศ䛿perl䜢⏝䛔䛯䚹
5ṧᇶ䛛䜙䛺䜛Enkephalin䛻䠎䠐A䛾⌫䠄1710ಶ䛾Ỉ䠅
Amber94Ꮩ❧⣔䚸Langevin⇕ᾎ䚸36 ಶ䛾䝺䝥䝸䜹䠄275K䛛䜙427.1K)
ྛ䝺䝥䝸䜹4ns (඲㒊䛷72ns)

3ḟඖRISM⌮ㄽ䜢⏝䛔䛯䝅䝭䝳䝺䞊䝅䝵䞁•••⤫ィຊᏛ䛾ᾮయㄽ䛻ᇶ䛵䛔䛯⌮ㄽỈ䛺䛹䛾ศᏊᛶᾮయ䛻㐺⏝⁐㉁䛾࿘䜚䛾⁐፹䛾3ḟඖᐦᗘศᕸ䜢ᚓ䜛䛣䛸䛜䛷䛝䜛

3D-RISM Eq.
hJuv (k ) ¦ cDuv (k )ZDJuv (k )  ¦ cDuv (k )U v hDJvv (k )DDClosure༢ཎᏊ⣔䛷䛿
Ornstein-Zernike Eq䛻ᑐᛂhJuv (r) exp[uJuv (r) / kT  hJuv (r)  cJuv (r)] 1u(r) 䠖䝫䝔䞁䝅䝱䝹h(r) : the total correlation function
c(r) 䠖the direct correlation function
U 䠖⁐፹䛾ᐦᗘZ 䠖The intramolecular correlation matrix2యศᕸ㛵ᩘ䛿g(r)=h(r) + 1䜘䜚ᚓ䜙䜜䜛¾ィ⟬᫬㛫䛿䛛䛛䜛䛜,Ỉ䛾㛗᫬㛫ᖹᆒศᕸ䜢ᚓ䜛䛣䛸䛜䛷䛝䜛¾≀⌮䛾⌮ㄽ䛻䜘䜚Ỉ䛾ศᕸ䜢ண 䛷䛝䜛ї఍ྜ⣔䛻㐺⏝䠄䜊䝥䝏䝗䛸⺮ⓑ㉁䛾఍ྜ⬟䜢ㄪ䜉䜛䠅⦆࿴䝰䞊䝗ゎᯒ䠄RMA)䠄A.Mitsutake, T. Iijima, H. Takano in preparation䠅• 㧗ศᏊ䛾ศ㔝䛷㛤Ⓨ䛥䜜䛯䠄୺ᡂศゎᯒ(PCA)䜢ᣑᙇ䛧䛯䜒䛾䛻ᑐᛂ䠅• ⺮ⓑ㉁⣔䛻⏝䛔䜛• ᴟᑡ≧ែ䛾ศ䛛䛳䛶䛔䜛䜊䝥䝏䝗⣔䛷⮬⏤䜶䝛䝹䜼䞊᭤㠃䜢ㄪ䜉䜛– 㐪䛖⮬⏤䜶䝛䝹䜼䞊᭤㠃䛜ᚓ䜙䜜䛯– PCA䛿ᵓ㐀䛾㢮ఝᛶ䜢ㄪ䜉䜛䛣䛸䛜䛷䛝䛯– RMA䛿⦆࿴䛾㐜䛔ື䛝䜢ᢤ䛝ฟ䛩䛣䛸䛜䛷䛝䛯
PCARMA䞊䠚䜘䜚኱䛝䛺⺮ⓑ㉁⣔䜈㐺⏝⁐፹䛾ືⓗື䛝䛾ゎᯒ䠄ᐇ㦂䛸䛾ẚ㍑䠅

௒ᚋ䛾◊✲¾኱つᶍ䛺ᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䛻䜘䜛䝣䜷䞊䝹䝕䜱䞁䜾䝅䝭䝳䝺䞊䝅䝵䞁䠄ᑓ⏝䝪䞊䝗MD-GRAPE3䜎䛯䛿GPGPU䜢⏝䛔䜛䠅ከኚᩘᣑᙇ䜰䞁䝃䞁䝤䝹ἲ䜢⏝䛔䛯఍ྜ⣔䛾䝅䝭䝳䝺䞊䝅䝵䞁䠄ᑓ⏝䝪䞊䝗MD-GRAPE3䜎䛯䛿GPGPU䜢⏝䛔䜛䠅¾ ⺮ⓑ㉁⣔䛾⦆࿴䝰䞊䝗ゎᯒἲ䛾㐺⏝䚸㛤Ⓨ¾¾ 㐜䛔ື䛝䛜ᶵ⬟䛻㛵ಀ䛒䜛䛸䛔䜟䜜䛶䛔䜛⺮ⓑ㉁䜈㐺⏝䛧䚸᭷ຠᛶ䜢ㄪ䜉䜛䚹¾ ⺮ⓑ㉁䛾࿘䜚䛾Ỉ䜒ྵ䜑䛶䚸ᐇ㦂䛸䛾ẚ㍑䠄ẚ㍑䛷䛝䜛㔞䛺䛹䜢᳨ウ䠅
¾RISM⌮ㄽ䜢⏝䛔䛯⁐፹࿴䛾◊✲௚䚸᪉ἲㄽ䛾㛤Ⓨ䜔ᐇ㦂䛷⯆࿡䛒䜛⣔䛻䛴䛔䛶䛾䝅䝭䝳䝺䞊䝅䝵䞁䜢䛧䛶ศᏊ䝺䝧䝹䛷䛾ᶵᵓ䛻䛴䛔䛶ලయⓗ䛻ㄪ䜉䛯䛔