Skip to main content

Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events

  • Chapter
Advanced Computer Simulation Approaches for Soft Matter Sciences III

Part of the book series: Advances in Polymer Science ((POLYMER,volume 221))

Computer simulations of molecular processes such as nucleation in first-order phase transitions or the folding of a protein are often complicated by widely disparate time scales related to important but rare events. Here, we will review sev eral recently developed computational methods designed to address the rare-events problem. In doing so, we will focus on the transition path sampling methodology.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Hansen J-P, Löwen H (2002) In: Nielaba P, Mareschal M, Ciccotti G (eds) Bridging time scales: molecular simulations for the next decade. Springer, Berlin

    Google Scholar 

  2. Abrams C, Delle Site L, Kremer K (2002) In: Nielaba P, Mareschal M, Ciccotti G (eds) Bridging time scales: molecular simulations for the next decade. Springer, Berlin

    Google Scholar 

  3. Likos CN (2001) Phys Rep 348:267

    CAS  Google Scholar 

  4. Louis AA, Bolhuis PG, Hansen J-P, Meijer EJ (2000) Phys Rev Lett 85:2522

    CAS  Google Scholar 

  5. Jaffe C, Ross SD, Lo MW, Marsden J, Farrelly D, Uzer T (2002) Phys Rev Lett 89:011101

    Google Scholar 

  6. Eigen M, De Maeyer L (1959) Z Elektrochem 59:986

    Google Scholar 

  7. Geissler PL, Dellago C, Chandler D, Hutter J, Parrinello M (2001) Science 291:2121

    CAS  Google Scholar 

  8. Wilding N, Landau DP (2002) In: Nielaba P, Mareschal M, Ciccotti G (eds) Bridging time scales: molecular simulations for the next decade. Springer, Berlin

    Google Scholar 

  9. Frenkel D, Smit B (2002) Understanding molecular simulation, 2nd edn. Academic, San Diego

    Google Scholar 

  10. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Science 220:671

    Google Scholar 

  11. Gottwald D, Kahl G, Likos CN (2005) J Chem Phys 122:204503

    Google Scholar 

  12. Oganov AR, Glass CW (2006) J Chem Phys 124:244704

    Google Scholar 

  13. Meerbach E, Dittmer E, Horenko I, Schütte C (2006) In: Ferrario M, Ciccotti G, Binder K (eds) Computer simulations in condensed matter: from materials to chemical biology. Springer, Berlin

    Google Scholar 

  14. Deuflhard P, Huisinga W, Fischer A, Schütte C (2000) Lin Alg Appl 315:39

    Google Scholar 

  15. Wales DJ, Doye JPK (1997) J Chem Phys A 101:5111

    CAS  Google Scholar 

  16. Henkelman G, Johannesson G, Jónsson H (2000) In: Schwartz SD (ed) Progress on theoretical chemistry and physics. Kluwer, Dordrecht

    Google Scholar 

  17. Elber R, Ghosh A, Cárdenas A, Stern H (2004) Adv Chem Phys 126:123

    Google Scholar 

  18. Hummer G, Kevrikidis IG (2003) J Chem Phys 118:10762

    CAS  Google Scholar 

  19. Laio A, Parrinello M (2002) Proc Natl Acad Sci USA 99:12562

    CAS  Google Scholar 

  20. Voter AF, Montalenti F, Germann TC (2002) Annu Rev Mater Res 32:321

    CAS  Google Scholar 

  21. Dellago C, Bolhuis PG, Csajka FS, Chandler D (1998) J Chem Phys 108:1964

    CAS  Google Scholar 

  22. Dellago C, Bolhuis PG, Chandler D (1998) J Chem Phys 108:9263

    Google Scholar 

  23. Bolhuis PG, Dellago C, Chandler D (1998) Faraday Discuss 110:421

    CAS  Google Scholar 

  24. Pratt LR (1986) J Chem Phys 85:5045

    CAS  Google Scholar 

  25. Geissler PL, Dellago C, Chandler D (1999) J Phys Chem B 103:3706

    CAS  Google Scholar 

  26. Bolhuis PG, Dellago C, Chandler D (2000) Proc Natl Acad Sci USA 97:5877

    CAS  Google Scholar 

  27. Hummer G (2004) J Chem Phys 120:516

    CAS  Google Scholar 

  28. Ma A, Dinner AR (2005) J Phys Chem B 109:6769

    CAS  Google Scholar 

  29. Peters B, Trout BL (2006) J Chem Phys 125:054108

    Google Scholar 

  30. Weinan E, Ren W, Vanden-Eijnden E (2002) Phys Rev B 66:052301

    Google Scholar 

  31. Weinan E, Ren W, Vanden-Eijnden E (2005) Chem Phys Lett 413:242

    Google Scholar 

  32. Maragliano L, Fischer A, Vanden-Eijnden E, Ciccotti G (2006) J Chem Phys 125:024106

    Google Scholar 

  33. Weinan E, Vanden-Eijnden E (2006) J Stat Phys 123:503

    Google Scholar 

  34. Stillinger FH (1976) J Chem Phys 65:3968

    CAS  Google Scholar 

  35. Louis AA, Bolhuis PG, Hansen J-P (2000) Phys Rev E 62:7961

    CAS  Google Scholar 

  36. Flory PJ (1953) Principles of polymer chemistry. Cornell University Press, Ithaca

    Google Scholar 

  37. Wales DJ (2003) Energy landscapes. Cambridge University Press, Cambridge

    Google Scholar 

  38. Stillinger FH, Weber TA (1983) Phys Rev A 28:2408

    CAS  Google Scholar 

  39. Swendsen RH, Wang J-S (1986) Phys Rev Lett 57:2607

    Google Scholar 

  40. Sugita Y, Okamoto Y (1999) Chem Phys Lett 314:141

    CAS  Google Scholar 

  41. Earl DJ, Deem MW (2005) Phys Chem Chem Phys 7:3910

    CAS  Google Scholar 

  42. Torrie GM, Valleau JP (1977) J Comput Phys 23:187

    Google Scholar 

  43. Kirkwood J (1935) J Chem Phys 3:300

    CAS  Google Scholar 

  44. Carter EA, Ciccotti G, Hynes JT, Kapral R (1989) Chem Phys Lett 156:472

    CAS  Google Scholar 

  45. Darve E, Pohorille AJ (2001) J Chem Phys 115:9169

    CAS  Google Scholar 

  46. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1992) Numerical recipes in C. Cam bridge University Press, Cambridge

    Google Scholar 

  47. Cerjan CJ, Miller WH (1981) J Chem Phys 75:2800

    CAS  Google Scholar 

  48. Doye JPK, Wales DJ (1997) Z Phys D 40:194

    CAS  Google Scholar 

  49. Munro LJ, Wales DJ (1999) Phys Rev B 59:3969

    CAS  Google Scholar 

  50. Mousseau N, Barkema G (1996) Phys Rev Lett 77:4358

    Google Scholar 

  51. Mousseau N, Barkema G (1998) Phys Rev E 57:2419

    CAS  Google Scholar 

  52. Vocks H, Chubynsky MV, Barkema GT, Mousseau N (2005) J Chem Phys 123:244707

    Google Scholar 

  53. Henkelman G, Jónsson H (1999) J Chem Phys 111:7010

    CAS  Google Scholar 

  54. Tanase-Nicola S, Kurchan J (2003) Phys Rev Lett 91:188302

    Google Scholar 

  55. Tailleur J, Kurchan J (2007) Nat Phys 3:203

    CAS  Google Scholar 

  56. Elber R, Karplus M (1987) Chem Phys Lett 139:375

    CAS  Google Scholar 

  57. Czerminski R, Elber R (1990) Int J Quantum Chem 24:167

    CAS  Google Scholar 

  58. Ulitzky A, Elber R (1990) J Chem Phys 92:1519

    Google Scholar 

  59. Fischer S, Karplus M (1992) Chem Phys Lett 194:252

    CAS  Google Scholar 

  60. Sevick EM, Bell AT, Theodorou DN (1993) J Chem Phys 98:3196

    CAS  Google Scholar 

  61. Gillilan RE, Wilson KR (1992) J Chem Phys 97:1757

    CAS  Google Scholar 

  62. Jonssón H, Mills G, Jacobsen KW (1998) In: Berne BJ, Ciccotti G, Coker DF (eds) Classical and quantum dynamics in condensed phase simulations. World Scientific, Singapore, p. 385

    Google Scholar 

  63. Ionova IV, Carter EA (1993) J Chem Phys 98:6377

    CAS  Google Scholar 

  64. Dewar MJS, Healy EF, Stewart JJP (1984) J Chem Soc, Farad Trans II 80:227

    CAS  Google Scholar 

  65. Henkelman G, Jónsson H (2000) J Chem Phys 113:9978

    CAS  Google Scholar 

  66. Chu J-W, Trout BL, Brooks BR (2003) J Chem Phys 119:12708

    CAS  Google Scholar 

  67. Henkelman G, Uberaga BP, Jónsson H (2000) J Chem Phys 113:9901

    CAS  Google Scholar 

  68. Mills G, Jónsson H (1994) Phys Rev Lett 72:1124

    CAS  Google Scholar 

  69. Villarba M, Jónsson H (1995) Surf Sci 324:35

    CAS  Google Scholar 

  70. Eichler A, Hafner J (1999) Surf Sci 435:58

    Google Scholar 

  71. Ciobica IM, van Santen RA (2002) J Phys Chem B 106:6200

    CAS  Google Scholar 

  72. Sorensen MR, Mishin Y, Voter AF (2000) Phys Rev B 62:3658

    CAS  Google Scholar 

  73. Mathews DH, Case DA (2006) J Mol Biol 357:1683

    CAS  Google Scholar 

  74. Goldstein H (1980) Classical mechanics. Addison-Wesley, Reading

    Google Scholar 

  75. Landau LD, Lifshitz EM (1984) Mechanics. Pergamon, Oxford

    Google Scholar 

  76. Elber R (2006) In: Ferrario M, Ciccotti G, K. Binder (eds) Computer simulations in condensed matter: from materials to chemical biology. Springer, Berlin

    Google Scholar 

  77. Whittaker ET (1964) Analytical dynamics, 4th edn. Cambridge University Press, Cambridge

    Google Scholar 

  78. Passerone D, Parrinello M (2001) Phys Rev Lett 87:108302

    CAS  Google Scholar 

  79. Passerone D, Ceccarelli M, Parrinello M (2003) J Chem Phys 118:2025

    CAS  Google Scholar 

  80. Cho AE, Doll JD, Freeman DL (1994) Chem Phys Lett 229:218

    CAS  Google Scholar 

  81. Olender R, Elber R (1996) J Chem Phys 105:9299

    CAS  Google Scholar 

  82. Elber R, Ghosh A, Cárdenas A (2002) In: Nielaba P, Mareschal M, Ciccotti G (eds) Bridging time scales: molecular simulations for the next decade. Springer, Berlin

    Google Scholar 

  83. Elber R, Ghosh A, Cárdenas A (2002) Acc Chem Res 35:396

    CAS  Google Scholar 

  84. Onsager L, Machlup S (1953) Phys Rev 91:1505

    CAS  Google Scholar 

  85. Eastman P, Gronbech-Jensen N, Doniach S (2001) J Chem Phys 114:3823

    CAS  Google Scholar 

  86. Zaloj V, Elber R (2000) Comput Phys Commun 128:118

    CAS  Google Scholar 

  87. Uitdehaag JCM, van der Veen BA, Dijkhuizen L, Elber R, Dijkstra BW (2001) Prot Struct Funct Gen 43:327

    CAS  Google Scholar 

  88. Siva K, Elber R (2003) Prot Struct Funct Gen 50:63

    CAS  Google Scholar 

  89. Ghosh A, Elber R, Scheraga H (2002) Proc Natl Acad Sci USA 99:10394

    CAS  Google Scholar 

  90. Cárdenas A, Elber R (2003) Proteins 51:245

    Google Scholar 

  91. Cárdenas A, Elber R (2003) Biophys J 85:2919

    Google Scholar 

  92. Kevrikidis IG, Gear CW, Hyman JM, Kevrekidis PG, Runborg O, Theodoropoulos K (2003) Comm Math Sci 14:715

    Google Scholar 

  93. Amait MA, Kevrekidis IG, Maroudas D (2007) Appl Phys Lett 90:171910

    Google Scholar 

  94. Sriraman S, Kevrekidis IG, Hummer G (2005) Phys Rev Lett 95:130603

    Google Scholar 

  95. Iannuzzi M, Laio A, Parrinello M (2003) Phys Rev Lett 90:238302

    Google Scholar 

  96. Laio A, Parrinello M (2006) In: Ferrario M, Ciccotti G, K. Binder (eds) Computer simulations in condensed matter: from materials to chemical biology. Springer, Berlin

    Google Scholar 

  97. Grubmüller H (1995) Phys Rev E 52:2893

    Google Scholar 

  98. Schulze BG, Grubmüller H, Evanseck JD (2000) J Am Chem Soc 122:8700

    CAS  Google Scholar 

  99. Müller EM, de Meijere A, Grubmüller H (2002) J Chem Phys 116:897

    Google Scholar 

  100. Huber T, Torda A, van Gunsteren W (1994) J Comput Aided Mol Des 8:695

    CAS  Google Scholar 

  101. Wang F, Landau D (2001) Phys Rev Lett 86:2050

    CAS  Google Scholar 

  102. Bussi G, Laio A, Parrinello M (2006) Phys Rev Lett 96:090601

    Google Scholar 

  103. Micheletti C, Laio A, Parrinello M (2004) Phys Rev Lett 92:170601

    Google Scholar 

  104. Car R, Parrinello M (1985) Phys Rev Lett 55:2471

    CAS  Google Scholar 

  105. Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M (2005) J Phys Chem B 109:6714

    CAS  Google Scholar 

  106. Piana S, Laio A (2007) J Phys Chem B 111:4553

    CAS  Google Scholar 

  107. Bussi G, Gervasio FL, Laio A, Parrinello M (2006) J Am Chem Soc 128:13435

    CAS  Google Scholar 

  108. Martoňák R, Laio A, Parrinello M (2003) Phys Rev Lett 90:75503

    Google Scholar 

  109. Raitieri P, Martoňák R, Parrinello M (2005) Angew Chem Int Ed 44:3769

    Google Scholar 

  110. Ceccarelli M, Mercuri F, Passerone D, Parrinello M (2005) J Phys Chem B 109:17094

    CAS  Google Scholar 

  111. Stirling A, Iannuzzi M, Laio A, Parrinello M (2004) Chem Phys Chem 5:1558

    CAS  Google Scholar 

  112. Ensing B, de Vivo M, Liu Z, Moore P, Klein ML (2006) Acc Chem Res 39:73

    CAS  Google Scholar 

  113. Ceccarelli M, Danelon C, Laio A, Parrinello M (2004) Biophys J 87:58

    CAS  Google Scholar 

  114. Gervasio FL, Laio A, Parrinello M (2005) J Am Chem Soc 127:2600

    CAS  Google Scholar 

  115. Hanggi P, Talkner P, Borkovec M (1990) Rev Mod Phys 62:2551

    Google Scholar 

  116. Pechukas P (1981) Ann Rev Phys Chem 32:15

    Google Scholar 

  117. Anderson JB (1995) Adv Chem Phys 91:381

    CAS  Google Scholar 

  118. Vanden-Eijnden E, Tal FA (2005) J Chem Phys 123:184103

    Google Scholar 

  119. Marcelin A (1995) Ann Chim Phys 3:158

    Google Scholar 

  120. Eyring H (1935) J Chem Phys 3:107

    CAS  Google Scholar 

  121. Horiuti J (1938) Bull Chem Soc Jpn 13:210

    Google Scholar 

  122. Eyring H, Polanyi M (1931) Z Phys Chem B 12:279

    CAS  Google Scholar 

  123. Wigner E (1938) Trans Faraday Soc 34:29

    CAS  Google Scholar 

  124. Dellago C, Bolhuis PG, Geissler PL (2006) In: Ferrario M, Ciccotti G, Binder K (eds) Com puter simulations in condensed matter: from materials to chemical biology. Springer Lecture Notes in Physics. Springer, Berlin, p. 349

    Google Scholar 

  125. Chandler D (1978) J Chem Phys 68:2959

    CAS  Google Scholar 

  126. Anderson JB (1973) J Chem Phys 58:4684

    CAS  Google Scholar 

  127. Kassel LS (1928) J Phys Chem 32:225; Rice OK, Ramsperger HC (1927) J Am Chem Soc 49:1617; Rice OK, Ramsperger HC (1927) J Am Chem Soc 50:617; Marcus R, Rice OK (1951) J Phys Colloid Chem 55:894

    CAS  Google Scholar 

  128. Geissler PL, Dellago C, Chandler D (1999) Phys Chem Chem Phys 1:1317

    CAS  Google Scholar 

  129. Truhlar DG, Garrett B (1984) Ann Rev Phys Chem 35:159

    CAS  Google Scholar 

  130. Truhlar DG, Garrett BC, Klippenstein SJ (1996) J Phys Chem 100:31

    Google Scholar 

  131. Tucker SC (1995) In: Talkner P, Hnggi P (eds) New trends in Kramers' reaction rate theory. Kluwer, Dordrecht

    Google Scholar 

  132. Johannesson G, Jónsson H (2001) J Chem Phys 115:9644

    CAS  Google Scholar 

  133. Fernández-Ramos A, Miller JA, Klippenstein SJ, Truhlar DG (2006) Chem Rev 106:4518

    Google Scholar 

  134. Yamamoto T (1960) J Chem Phys 33:281

    CAS  Google Scholar 

  135. Keck JC (1962) Discuss Faraday Soc 33:173

    Google Scholar 

  136. Bennett CH (1977) In: Christofferson R (ed) Algorithms for Chemical Computations, ACS Symposium Series No. 46. American Chemical Society, Washington DC

    Google Scholar 

  137. Ruiz-Montero MJ, Frenkel D, Brey JJ (1997) Mol Phys 90:925

    Google Scholar 

  138. van Erp TS, Bolhuis PG (2005) J Comput Phys 205:157

    Google Scholar 

  139. Waalkens H, Burbanks A, Wiggins S (2005) J Phys A Math Gen 38:L759

    Google Scholar 

  140. Waalkens H, Burbanks A, Wiggins S (2004) J Phys A 37:L257

    Google Scholar 

  141. Waalkens H, Burbanks A, Wiggins S (2004) J Chem Phys 121:6207

    CAS  Google Scholar 

  142. Tal FA, Vanden-Eijnden E (2006) Nonlinearity 19:501

    Google Scholar 

  143. Bortz AB, Kalos MH, Lebowitz JL (1975) J Comput Phys 17:10

    Google Scholar 

  144. Gillespie DT (1977) J Comput Phys 22:2340

    Google Scholar 

  145. Henkelman G, Jónsson H (2001) J Chem Phys 115:9657

    CAS  Google Scholar 

  146. Shirts MR, Pande VS (2001) Phys Rev Lett 86:4983

    CAS  Google Scholar 

  147. Voter AF (1998) Phys Rev B 57:13985

    Google Scholar 

  148. Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, Larson SM, Rhee YM, Shirts MR, Snow CD, Sorin EJ, Zagrovic B (2003) Biopolymers 68:91

    CAS  Google Scholar 

  149. Kum O, Dickson BM, Stuart SJ, Uberuaga BP, Voter AF (2004) J Chem Phys 121:9808

    CAS  Google Scholar 

  150. Birner S, Kim J, Richie DA, Wilkins JW, Voter AF, Lenosky T (2001) Solid State Commun 120:279

    CAS  Google Scholar 

  151. Uberuaga BP, Voter AF, Sieber KK, Sholl DS (2003) Phys Rev Lett 91:105901

    Google Scholar 

  152. Uberuaga BP, Stuart SJ, Voter AF (2007) Phys Rev B 75:014301

    Google Scholar 

  153. Voter AF (1997) J Chem Phys 106:4665

    CAS  Google Scholar 

  154. Voter AF (1997) Phys Rev Lett 78:3908

    CAS  Google Scholar 

  155. Duan XM, Sun DY, Gong XG (2001) Comput Mater Sci 20:151

    CAS  Google Scholar 

  156. Hamelberg D, McCammon JA (2005) J Am Chem Soc 127:13778

    CAS  Google Scholar 

  157. Becker KE, Fichthorn KA (2006) J Chem Phys 125:184706

    Google Scholar 

  158. Voter AF, Chen SP (1987) Mater Res Soc Symp Proc 82:175

    CAS  Google Scholar 

  159. Sørensen MR, Voter AF (2000) J Chem Phys 112:9599

    Google Scholar 

  160. Montalenti F, Voter AF, Ferrando R (2002) Phys Rev B 66:205404

    Google Scholar 

  161. Montalenti F, Sørensen MR, Voter AF (2001) Phys Rev Lett 87:126101

    CAS  Google Scholar 

  162. Cogoni M, Mattoni A, Uberuaga BP, Voter AF, Colombo L (2005) Appl Phys Lett 87:191912

    Google Scholar 

  163. Sprague JA, Montalenti F, Uberuaga BP, Kress JD, Voter AF (2002) Phys Rev B 66:205415

    Google Scholar 

  164. Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Ann Rev Phys Chem 53:291

    CAS  Google Scholar 

  165. Dellago C, Bolhuis PG, Geissler PL (2002) Adv Chem Phys 123:1

    CAS  Google Scholar 

  166. Dellago C, Chandler D (2002) In: Nielaba P, Mareschal M, Ciccotti G (eds) Molecular simu lation for the next decade. Springer, Berlin, p. 321

    Google Scholar 

  167. Dellago C (2005) In: Yip S (ed) Handbook of materials modeling. Springer, Berlin, p. 1585

    Google Scholar 

  168. Dellago C (2007) In: Pohorille A, Chipot C (eds) Free energy calculations: theory and appli cations in chemistry and biology. Springer, Berlin

    Google Scholar 

  169. Dellago C, Bolhuis PG (2007) In: Reiher M (ed) Topics in Current Chemistry, vol. 268. Springer, Berlin, p. 291

    Google Scholar 

  170. Geissler PL, Dellago C (2004) J Phys Chem B 108:6667

    CAS  Google Scholar 

  171. Chandrasekhar S (1943) Rev Mod Phys 15:1

    Google Scholar 

  172. Zwanzig R (2001) Nonequilibrium statistical mechanics. Oxford University Press, Oxford

    Google Scholar 

  173. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) J Chem Phys 21:1087

    CAS  Google Scholar 

  174. Dellago C, Bolhuis PG, Csajka FS, Chandler D (1999) J Chem Phys 110:6617

    CAS  Google Scholar 

  175. Geyer CJ, Thompson EA (1995) J Am Stat Soc 90:909

    Google Scholar 

  176. Vlugt TJH, Smit B (2001) Phys Chem Comm 2:1

    Google Scholar 

  177. Bolhuis PG (2003) J Phys Cond Matter 15:S113

    CAS  Google Scholar 

  178. Grünwald M, Geissler PL, Dellago C (2008), J Chem Phys (in print)

    Google Scholar 

  179. Hu J, Ma A, Dinner AR (2006) J Chem Phys 125:114101

    Google Scholar 

  180. Grünwald M, Rabani E, Dellago C (2006) Phys Rev Lett 96:255701

    Google Scholar 

  181. Grünwald M, Geissler PL, Dellago C (2007) J Chem Phys 127:154718

    Google Scholar 

  182. Dellago C, Bolhuis PG (2004) Mol Sim 30:795

    CAS  Google Scholar 

  183. van Erp TS, Moroni D, Bolhuis PG (2003) J Chem Phys 118:7762

    Google Scholar 

  184. Juraszek J, Bolhuis PG (2006) Proc Natl Acad Sci USA 103:15859

    CAS  Google Scholar 

  185. Moroni D, Bolhuis PG, van Erp TS (2004) J Chem Phys 120:4055

    CAS  Google Scholar 

  186. van Erp TS (2007) Phys Rev Lett 98:268301

    Google Scholar 

  187. Bolhuis PG (2008) J. Chem. 129, 114108

    Google Scholar 

  188. Moroni D, van Erp TS, Bolhuis PG (2005) Phys Rev E 71:056709

    Google Scholar 

  189. Allen RJ, Warren PB, ten Wolde PR (2005) Phys Rev Lett 94:018104

    Google Scholar 

  190. Allen RJ, Frenkel D, ten Wolde PR (2006) J Chem Phys 124:024102

    Google Scholar 

  191. Allen RJ, Frenkel D, ten Wolde PR (2006) J Chem Phys 124:194111

    Google Scholar 

  192. Valeriani C, Allen RJ, Morelli MJ, Frenkel D, ten Wolde PR (2007) J Chem Phys 127:114109

    Google Scholar 

  193. Borrero EE, Escobedo FA (2006) J Chem Phys 125:164904

    Google Scholar 

  194. Faradjian T, Elber R (2004) J Chem Phys 120:10882

    Google Scholar 

  195. West AMA, Elber R, Shalloway D (2007) J Chem Phys 126:145104

    Google Scholar 

  196. Elber R (2007) Biophys J 92:L85

    CAS  Google Scholar 

  197. Auer S, Frenkel D (2005) Adv Poly Sci 173:149

    CAS  Google Scholar 

  198. Pan AC, Chandler D (2004) J Phys Chem B 108:19681

    CAS  Google Scholar 

  199. Moroni D, ten Wolde PR, Bolhuis PG (2005) Phys Rev Lett 94:235703

    Google Scholar 

  200. Zahn D (2007) J Phys Chem B 111:5249

    CAS  Google Scholar 

  201. Beckham GT, Peters B, Starbuck C, Variankaval N, Trout BL (2007) J Am Chem Soc 129:4714

    CAS  Google Scholar 

  202. Zahn D (2006) J Phys Chem B 110:19601

    CAS  Google Scholar 

  203. Zahn D, Grin Y, Leoni S (2005) Phys Rev B 72:064110

    Google Scholar 

  204. Zahn D (2004) Phys Rev Lett 93:227801

    Google Scholar 

  205. Zahn D, Leoni S (2006) J Phys Chem B 110:10873

    CAS  Google Scholar 

  206. Zahn D, Hochrein O, Leoni S (2005) Phys Rev B 72(9):094106

    Google Scholar 

  207. Zahn D (2004) J Solid State Chem 177:3590

    CAS  Google Scholar 

  208. Leoni S, Zahn D (2004) Z Kristall 219:339

    CAS  Google Scholar 

  209. Zahn D, Leoni S (2004) Z Kristall 219:345

    CAS  Google Scholar 

  210. Zahn D, Leoni S (2004) Phys Rev Lett 92:250201

    Google Scholar 

  211. Zahn D (2004) Phys Rev Lett 92:040801

    Google Scholar 

  212. Day TJF, Schmitt UW, Voth GA (2000) J Am Chem Soc 122:12027

    CAS  Google Scholar 

  213. Park JM, Laio A, Iannuzzi M, Parrinello M (2006) J Am Chem Soc 128:11318

    CAS  Google Scholar 

  214. Lo CS, Radhakrishnan R, Trout BL (2005) Catalaysis Today 105:93

    CAS  Google Scholar 

  215. Snee PT, Shanoski J, Harris CB (2005) J Am Chem Soc 127:1286

    CAS  Google Scholar 

  216. Zahn D (2004) Chem Phys 300:79

    CAS  Google Scholar 

  217. Zahn D, Seifert G (2004) J Phys Chem B 108:16495

    CAS  Google Scholar 

  218. Ensing B, Baerends EJ (2002) J Phys Chem A 106:7902

    CAS  Google Scholar 

  219. Pagliai M, Raugei S, Cardini G, Schettino V (2002) J Chem Phys 117:2199

    CAS  Google Scholar 

  220. Marti J, Csajka FS, Chandler D (2000) Chem Phys Lett 328:169

    CAS  Google Scholar 

  221. Laria D, Rodriguez J, Dellago C, Chandler D (2001) J Phys Chem A 105:2646

    CAS  Google Scholar 

  222. Lee JY (2004) Chem Phys 299:123

    CAS  Google Scholar 

  223. Csajka FS, Chandler D (1998) J Chem Phys 109:1125

    CAS  Google Scholar 

  224. Marti J, Csajka FS (2000) J Chem Phys 113:1154

    CAS  Google Scholar 

  225. Marti J (2001) Mol Sim 27:169

    CAS  Google Scholar 

  226. Bolhuis PG, Chandler D (2000) J Chem Phys 113:8154

    CAS  Google Scholar 

  227. Vlugt TJH, Dellago C, Smit B (2000) J Chem Phys 113:8791

    CAS  Google Scholar 

  228. Pool R, Bolhuis PG (2007) J Chem Phys 126:244703

    Google Scholar 

  229. Ramirez J, Laso M (2001) J Chem Phys 115:7285

    CAS  Google Scholar 

  230. Radhakrishnan R, Schlick T (2004) Proc Natl Acad Sci USA 101:5970

    CAS  Google Scholar 

  231. Radhakrishnan R, Schlick T (2004) J Chem Phys 121:2436

    CAS  Google Scholar 

  232. McCormick TA, Chandler D (2003) J Phys Chem B 107:2796

    CAS  Google Scholar 

  233. Hagan MF, Dinner AR, Chandler D, Chakraborty AK (2003) Proc Natl Acad Sci USA 100:13922

    CAS  Google Scholar 

  234. Crehuet R, Field MJ (2007) J Phys Chem B 111:5708

    CAS  Google Scholar 

  235. ten Wolde PR, Chandler D (2002) Proc Natl Acad Sci USA 99:6539

    CAS  Google Scholar 

  236. Bolhuis PG (2003) Proc Natl Acad Sci USA 100:12129

    CAS  Google Scholar 

  237. Bolhuis PG (2005) Biophys J 88:50

    CAS  Google Scholar 

  238. Radhakrishnan R, Yang LJ, Arora K, Schlick T (2004) Biophys J 86:34A

    Google Scholar 

  239. Radhakrishnan R, Schlick T (2005) J Am Chem Soc 127:13245

    CAS  Google Scholar 

  240. Basner JE, Schwartz SD (2005) J Am Chem Soc 127:13822

    CAS  Google Scholar 

  241. Marti J, Csajka FS (2004) Phys Rev E 69:061918

    Google Scholar 

  242. Marti J (2004) J Phys Condens Matter 16:5669

    CAS  Google Scholar 

  243. Ma L, Cui Q (2007) J Am Chem Soc 129:10261

    CAS  Google Scholar 

  244. Wang YL, Schlick T (2007) BMC Struct Biol 7:7

    Google Scholar 

  245. Merolle M, Garrahan JP, Chandler D (2005) Proc Natl Acad Sci USA 102:10837

    CAS  Google Scholar 

  246. Crooks GE, Chandler D (2001) Phys Rev E 64:026109

    CAS  Google Scholar 

  247. Geissler PL, Chandler D (2000) J Chem Phys 113:9759

    CAS  Google Scholar 

  248. Sun SX (2003) J Chem Phys 118:5769

    CAS  Google Scholar 

  249. Ytreberg FM, Zuckerman DM (2004) J Chem Phys 120:10876

    CAS  Google Scholar 

  250. Oberhofer H, Dellago C, Geissler PL (2005) J Phys Chem B 69:6902–6915

    Google Scholar 

  251. Lechner W, Dellago C (2007) J Stat Mech Theor Exp P04001

    Google Scholar 

  252. Athènes M (2004) Eur Phys J B 38:651

    Google Scholar 

  253. Oberhofer H, Dellago C (2008) Comput Phys Commun 179:41

    CAS  Google Scholar 

  254. Imparato A, Peliti L (2007) J Stat Mech L02001

    Google Scholar 

  255. Imparato A, Peliti L (2007) Compt Rend Physique 8:556

    CAS  Google Scholar 

  256. Wales DJ (2002) Mol Phys 100:3285

    CAS  Google Scholar 

  257. Wales DJ (2005) Phys Biol 2:S86

    CAS  Google Scholar 

  258. Trygubenko SA, Wales DJ (2006) Mol Phys 104:1497

    CAS  Google Scholar 

  259. Evans DA, Wales DJ (2004) J Chem Phys 121:1080

    CAS  Google Scholar 

  260. Best RB, Hummer G (2005) Proc Natl Acad Sci USA 102:6732

    CAS  Google Scholar 

  261. Onsager L (1938) Phys Rev 54:554

    CAS  Google Scholar 

  262. Du R, Pande V, Grosberg AY, Tanaka T, Shakhnovich EI (1998) J Chem Phys 108:334

    CAS  Google Scholar 

  263. Gasser U, Weeks ER, Schofield A, Pusey PN, Weitz DA (2001) Science 292:258

    CAS  Google Scholar 

  264. Ryter D (1987) Physica A 142:103

    Google Scholar 

  265. Berezhovski A, Szabo A (2006) J Chem Phys 125:104902

    Google Scholar 

  266. Klosek MM, Matkowsky BJ, Schuss Z (1991) Ber Bunsenges Phys Chem 95:331

    CAS  Google Scholar 

  267. Pollak E, Berezhkovskii AM, Schuss Z (1994) J Chem Phys 100:334

    CAS  Google Scholar 

  268. Talkner P (1994) Chem Phys 180:199

    CAS  Google Scholar 

  269. Berezhovski A, Szabo A (2005) J Chem Phys 122:014503

    Google Scholar 

  270. Metzner P, Schütte C, Vanden-Eijnden E (2006) J Chem Phys 125:084110

    Google Scholar 

  271. Peters B (2006) J Chem Phys 125:241101

    Google Scholar 

  272. Quaytman SL, Schwartz SD (2007) Proc Natl Acad Sci USA 104:12253

    CAS  Google Scholar 

  273. So S-S, Karplus M (1996) J Med Chem 39:1521

    CAS  Google Scholar 

  274. Dinner A, So S-S, Karplus M (2002) Adv Chem Phys 120:1

    CAS  Google Scholar 

  275. Edwards AWF (1972) Likelihood. Cambridge University Press, Cambridge

    Google Scholar 

  276. Peters B, Beckham GT, Trout BL (2007) J Chem Phys 127:034109

    Google Scholar 

  277. Vanden-Eijnden E (2006) In: Ferrario M, Ciccotti G, Binder K (eds) Computer simulations in condensed matter: from materials to chemical biology, Springer Lecture Notes in Physics. Springer, Berlin, p. 453

    Google Scholar 

  278. Gardiner CW (1985) Handbook of stochastic methods. Springer, Berlin

    Google Scholar 

  279. Ren W (2003) Comm Math Sci 1:377

    Google Scholar 

  280. Weinan E, Ren W, Vanden-Eijnden E (2007) J Chem Phys 126:164103

    Google Scholar 

  281. Weinan E, Ren W, Vanden-Eijnden E (2005) J Phys Chem B 109:6688

    Google Scholar 

  282. Ren W, Vanden-Eijnden E, Maragakis P, Weinan E (2005) J Chem Phys 123 134109

    Google Scholar 

  283. Miller TF III, Vanden-Eijnden E, Chandler D (2007) Proc Natl Acad Sci USA 104:14559

    CAS  Google Scholar 

  284. ten Wolde P-R, Chandler D (2002) Proc Natl Acad Sci USA 99:6539

    CAS  Google Scholar 

  285. Wilson MA, Chandler D (1990) Chem Phys 149:11

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Christoph Dellago or Peter G. Bolhuis .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Dellago, C., Bolhuis, P.G. (2009). Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events. In: Holm, C., Kremer, K. (eds) Advanced Computer Simulation Approaches for Soft Matter Sciences III. Advances in Polymer Science, vol 221. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87706-6_3

Download citation

Publish with us

Policies and ethics