Chemomechanics of complex materials: Challenges and opportunities in predictive kinetic timescales

Scientific Modeling and Simulation SMNS

Volumn 15, Issue 1-3, 2008, Pages 67-80

  Van Vliet, Krystyn J ^a  

^a Massachusetts Institute of Technology   (United States)

Author keywords

Chemomechanics; Computational materials science; Kinetic barriers; Rough energy landscape

Indexed keywords

ATOMIC BONDS; BIOMOLECULAR COMPLEXES; CHEMO-MECHANICAL COUPLINGS; COMPLEX MATERIALS; COMPUTATIONAL ANALYSIS; COMPUTATIONAL MATERIALS SCIENCE; COMPUTATIONAL MODELING AND SIMULATION; DIVERSE MATERIALS; ENERGY LANDSCAPE; FUNCTIONAL PROPERTIES; KINETIC BARRIER; MACROSCOPIC KINETICS; MECHANICAL FORCE; MECHANICAL STATE; MULTISCALES; RESEARCH COMMUNITIES; SILICATE GLASS FIBERS; TIME-SCALES; TRANSITION STATE; UNIT PROCESS;

BLOOD VESSELS; COMPUTER SIMULATION; GLASS FIBERS; GRAFTING (CHEMICAL); MARTENSITIC STAINLESS STEEL; MECHANICAL ENGINEERING; MECHANICAL PROPERTIES; OPTOELECTRONIC DEVICES; REACTION KINETICS; SILICATES; SYNTHESIS (CHEMICAL);

MATERIALS;

EID: 73449086337     PISSN: 18748554     EISSN: 18748562     Source Type: Journal    
DOI: 10.1007/s10820-008-9111-3     Document Type: Article

References (55)

1. E.B. Walton S. Lee K.J. Van Vliet 2007 Extending Bell's model: how force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes Biophys. J. 94 2621 2630 10.1529/biophysj.107.114454 1:CAS:528:DC%2BD1cXjslequ70%3D
2. E.C. Silva L. Tong S. Yip K.J. Van Vliet 2006 Size effects on the stiffness of silica nanowires Small 2 2 239 243 17193028 10.1002/smll.200500311 1:CAS:528:DC%2BD28Xms1Ckug%3D%3D (Pubitemid 43198188)
3. Forst, C.J., Slycke, J., Van Vliet, K.J., Yip, S.: Point defect concentrations in metastable Fe-C alloys. Phys. Rev. Lett. 96(17) (2006)
4. B.T. Andrews A.R. Schoenfish M. Roy G. Waldo P.A. Jennings 2007 The rough energy landscape of superfolder GFP is linked to the chromophore J. Mol. Biol. 373 2 476 490 17822714 10.1016/j.jmb.2007.07.071 1:CAS:528:DC%2BD2sXhtFSks7%2FO (Pubitemid 47445575)
5. M. Gruebele 2004 Rough energy landscape of folded and unfolded proteins Abstr. Pap. Am. Chem. Soc. 227 U267 U267
6. J. Wang W.M. Huang H.Y. Lu E.K. Wang 2004 Downhill kinetics of biomolecular interface binding: Globally connected scenario Biophys. J. 87 4 2187 2194 15454421 10.1529/biophysj.104.042747 1:CAS:528:DC%2BD2cXot12nurg%3D 2004BpJ....87.2187W (Pubitemid 41071321)
7. J.N. Onuchic P.G. Wolynes 1993 Energy landscapes, glass transitions, and chemical-reaction dynamics in biomolecular or solvent environment J. Chem. Phys. 98 3 2218 2224 10.1063/1.464201 1993JChPh..98.2218O 1:CAS:528: DyaK3sXhsFGnt7o%3D
8. H. Simka B.G. Willis I. Lengyel K.F. Jensen 1997 chemistry predictions of reaction processes in organometallic vapor phase epitaxy Progress in Crystal Growth and Characterization of Materials 35 2-4 117 149 10.1016/S0960-8974(98) 00002-3 1:CAS:528:DyaK1cXjvVehuro%3D
9. T. Wesolowski R.P. Muller A. Warshel 1996 Ab initio frozen density functional calculations of proton transfer reactions in solution J. Phys. Chem. 100 38 15444 15449 10.1021/jp961068x 1:CAS:528:DyaK28Xlt1Oksrc%3D
10. K. Kim K.D. Jordan 1994 Comparison of density-functional and Mp2 calculations on the water monomer and dimer J. Phys. Chem. 98 40 10089 10094 10.1021/j100091a024 1:CAS:528:DyaK2cXmtFemsr4%3D
11. G. Henkelman B.P. Uberuaga H. Jonsson 2000 A climbing image nudged elastic band method for finding saddle points and minimum energy paths J. Chem. Phys. 113 22 9901 9904 10.1063/1.1329672 2000JChPh.113.9901H 1:CAS:528:DC%2BD3cXosFagurc%3D (Pubitemid 32076883)
12. G. Henkelman H. Jonsson 2000 Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points J. Chem. Phys. 113 22 9978 9985 10.1063/1.1323224 2000JChPh.113.9978H 1:CAS:528:DC%2BD3cXosFagu7Y%3D (Pubitemid 32076892)
13. M.R. Sorensen M. Brandbyge K.W. Jacobsen 1998 Mechanical deformation of atomic-scale metallic contacts: Structure and mechanisms Phys. Rev. B 57 6 3283 3294 10.1103/PhysRevB.57.3283 1998PhRvB..57.3283S
14. F. Pincet J. Husson 2005 The solution to the streptavidin-biotin paradox: the influence of history on the strength of single molecular bonds Biophys. J. 89 4374 4381 16169976 10.1529/biophysj.105.067769 1:CAS:528:DC%2BD2MXhtlWms7rO 2005BpJ....89.4374P (Pubitemid 41725655)
15. R. Merkel P. Nassoy A. Leung K. Ritchie E. Evans 1999 Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy Nature 397 50 53 9892352 10.1038/16219 1999Natur.397...50M 1:CAS:528:DyaK1MXnsF2hsA%3D%3D (Pubitemid 29038244)
16. P.-D. Coureux X. Fan V. Sojanoff U.K. Genick 2008 Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein Structure 16 863 872 18547519 10.1016/j.str.2008.02.022 1:CAS:528:DC%2BD1cXmvFertb8%3D (Pubitemid 351778378)
17. Kellou, A., Grosdidier, T., Aourag, H.: An ab initio study of the effects and stability of vacancies, antisites and small radius atoms (B, C, N, and O) in the B2-FeAl structure. In: Fisher, D.J. (ed.) Defects and Diffusion in Metals-An Annual Retrospective VII, vol. 233-234, pp. 87-95. Defect and Diffusion Forum (2004)
18. T.T. Lau C.J. Foerst X. Lin J.D. Gale S. Yip K.J. Van Vliet 2007 Many-body potential for point defect clusters in Fe-C alloys Phys. Rev. Lett. 98 21 215501 17677783 10.1103/PhysRevLett.98.215501 2007PhRvL..98u5501L 1:CAS:528:DC%2BD2sXlvVahu78%3D (Pubitemid 47139650)
19. Legris, A.: Recent advances in point defect studies driven by density functional theory. In: Fisher, D.J. (ed.) Defects and Diffusion in Metals-An Annual Retrospective VII, vol. 233-234, pp. 77-86. Defect and Diffusion Forum (2004)
20. T. Mizuno M. Asato T. Hoshino K. Kawakami 2001 First-principles calculations for vacancy formation energies in Ni and Fe: non-local effect beyond the LSDA and magnetism J. Magn. Magn. Mater. 226 386 387 10.1016/S0304-8853(00)01177-X 2001JMMM..226..386M
21. S. Simonetti M.E. Pronsato G. Brizuela A. Juan 2007 The C-C pair in the vicinity of a bcc Fe bulk vacancy: electronic structure and bonding Phys. Status Solidi B Basic Solid State Phys. 244 2 610 618 10.1002/pssb.200642410 1:CAS:528:DC%2BD2sXitVOgtLY%3D
22. C.S. Becquart A. Souidi C. Domain M. Hou L. Malerba R.E. Stoller 2006 Effect of displacement cascade structure and defect mobility on the growth of point defect clusters under irradiation J. Nucl. Mater. 351 1-3 39 46 10.1016/j.jnucmat.2006.02.022 2006JNuM..351...39B 1:CAS:528:DC%2BD28XltlSgsL0%3D (Pubitemid 44209062)
23. C. Domain 2006 Ab initio modelling of defect properties with substitutional and interstitials elements in steels and Zr alloys J. Nucl. Mater. 351 1-3 1 19 10.1016/j.jnucmat.2006.02.025 2006JNuM..351....1D 1:CAS:528:DC%2BD28XltlShu7s%3D (Pubitemid 43841829)
24. C. Cao Y. He J. Torras E. Deumens S.B. Trickey H.P. Cheng 2007 Fracture, water dissociation, and proton conduction in SiO2 nanochains J. Chem. Phys. 126 21 211101 17567180 10.1063/1.2730782 2007JChPh.126u1101C 1:CAS:528: DC%2BD2sXms1aqu7Y%3D (Pubitemid 46883989)
25. T. Zhu J. Li S. Yip R.J. Bartlett S.B. Trickey N.H. De Leeuw 2003 Deformation and fracture of a SiO2 nanorod Mol. simul. 29 10-11 671 676 10.1080/0892702031000103220 1:CAS:528:DC%2BD3sXntlSqtL0%3D (Pubitemid 44115087)
26. J.D.C. McConnell 1997 Ab initio studies on water related species in quartz and their role in weakening under stress Phase Transit. 61 1-4 19 39 1:CAS:528:DyaK2sXkvVeis74%3D 1447646
27. Silva, E., Van Vliet, K.J., Yip, S.: Effects of water on chemomechanical instabilities in amorphous silica: nanoscale experiments and molecular simulation. PhD Thesis, Silva, MIT, unpublished results (2007)
28. Van Vliet, K.J., Li, J., Zhu, T., Yip, S., Suresh, S.: Quantifying the early stages of plasticity through nanoscale experiments and simulations. Phys. Rev. B 67(10)(2003)
29. J. Li T. Zhu S. Yip K.J. Van Vliet S. Suresh 2004 Elastic criterion for dislocation nucleation Mater. Sci. Eng. A Struct. Mater. Prop. Microstruct. Process. 365 1-2 25 30
30. J. Li K.J. Van Vliet T. Zhu S. Yip S. Suresh 2002 Atomistic mechanisms governing elastic limit and incipient plasticity in crystals Nature 418 6895 307 310 12124619 10.1038/nature00865 2002Natur.418..307L 1:CAS:528: DC%2BD38XltlGmsL8%3D (Pubitemid 34790677)
31. P.-D. Coureux Z. Fan V. Stojanoff U.K. Genick 2008 Picometer-scale conformational heterogeneity separates functional and nonfunctional states of a photoreceptor protein Structure 6 863 872 10.1016/j.str.2008.02.022 1:CAS:528:DC%2BD1cXmvFertb8%3D (Pubitemid 351778378)
32. E. Puklin-Faucher M. Gao K. Schulten V. Vogel 2006 How the headpiece hinge angle is opened: new insights into the dynamics of integrin activation J. Cell Biol. 175 2 349 360 17060501 10.1083/jcb.200602071 1:CAS:528: DC%2BD28XhtFCgtL7M (Pubitemid 44631428)
33. W. Wriggers E. Mehler F. Pitici H. Weinstein K. Schulten 1998 Structure and dynamics of calmodulin in solution Biophys. J. 74 4 1622 1639 9545028 1:CAS:528:DyaK1cXislSksL0%3D 1998BpJ....74.1622W
34. Q. Sheng K. Schulten C. Pidgeon 1995 Molecular-dynamics simulation of immobilized artificial membranes J. Phys. Chem. 99 27 11018 11027 10.1021/j100027a050 1:CAS:528:DyaK2MXmt12ru74%3D
35. E. Evans K. Ritchie 1997 Dynamic strength of molecular adhesion bonds Biophys. J. 72 4 1541 1555 9083660 1:CAS:528:DyaK2sXitFeisbs%3D 10.1016/S0006-3495(97)78802-7
36. R. Merkel P. Nassoy A. Leung K. Ritchie E. Evans 1999 Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy Nature 397 6714 50 53 9892352 10.1038/16219 1999Natur.397...50M 1:CAS:528: DyaK1MXnsF2hsA%3D%3D (Pubitemid 29038244)
37. S. Lee J. Mandic K.J. Van Vliet 2007 Chemomechanical mapping of ligand-receptor binding kinetics on cells Proc. Natl. Acad. Sci. USA 104 23 9609 9614 17535923 10.1073/pnas.0702668104 2007PNAS..104.9609L 1:CAS:528: DC%2BD2sXmsFWjsLc%3D (Pubitemid 47175314)
38. P. Hinterdorfer W. Baumgartner H.J. Gruber K. Schilcher H. Schindler 1996 Detection and localization of individual antibody-antigen recognition events by atomic force microscopy Proc. Natl. Acad. Sci. USA 93 8 3477 3481 8622961 10.1073/pnas.93.8.3477 1996PNAS...93.3477H 1:CAS:528:DyaK28XisVWit7g%3D (Pubitemid 26125645)
39. C.M. Stroh A. Ebner M. Geretschlager G. Freudenthaler F. Kienberger A.S.M. Kamruzzahan S.J. Smith-Gil H.J. Gruber P. Hinterdorfer 2004 Simultaneous topography and recognition Imaging using force microscopy Biophys. J. 87 3 1981 1990 15345574 10.1529/biophysj.104.043331 1:CAS:528:DC%2BD2cXns1Sksb0%3D 2004BpJ....87.1981S (Pubitemid 39167052)
40. K.J. Van Vliet P. Hinterdorfer 2006 Probing drug-cell interactions Nano Today 1 3 18 25 10.1016/S1748-0132(06)70076-7 (Pubitemid 44057678)
41. E.B. Walton K.J. Van Vliet 2006 Equilibration of experimentally determined protein structures for molecular dynamics simulation Phys. Rev. E 74 6 061901 10.1103/PhysRevE.74.061901 2006PhRvE..74f1901W 1:CAS:528: DC%2BD2sXhs1ehtbY%3D (Pubitemid 44887208)
42. E. Evans 1999 Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy Biophys. Chem. 82 83 87 10631793 10.1016/S0301-4622(99)00108-8 1:CAS:528:DyaK1MXnvFemtbs%3D
43. J.A. McCammon B.R. Gelin M. Karplus 1977 Dynamics offolded proteins Nature 267 585 590 301613 10.1038/267585a0 1977Natur.267..585M 1:CAS:528:DyaE2sXlsVOgsbg%3D
44. J.A. McCammon M. Karplus 1980 Simulation of protein dynamics Annu. Rev. Phys. Chem. 31 29 45 10.1146/annurev.pc.31.100180.000333 1:CAS:528: DyaL3cXmtlartLg%3D
45. D. Craig M. Gao K. Schulten V. Vogel 2004 Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force Structure 12 11 2049 2058 15530369 10.1016/j.str.2004.09.009 1:CAS:528:DC%2BD2cXpsVOrs7g%3D (Pubitemid 39469402)
46. B. Isralewitz S. Izrailev K. Schulten 1997 Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations Biophys. J. 73 6 2972 2979 9414212 1:CAS:528:DyaK2sXnsl2murc%3D
47. D. Kosztin S. Izrailev K. Schulten 1999 Unbinding of retinoic acid from its receptor studied by steered molecular dynamics Biophys. J. 76 1 188 197 9876133 1:CAS:528:DyaK1MXjsFOisQ%3D%3D
48. R. Curcio A. Caflisch E. Paci 2005 Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex Protein Sci. 14 10 2499 2514 16195542 10.1110/ps.041280705 1:CAS:528:DC%2BD2MXhtVOrur7J (Pubitemid 41395578)
49. E. Paci A. Caflisch A. Pluckthun M. Karplus 2001 Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study J. Mol. Biol. 314 3 589 605 11846569 10.1006/jmbi.2001.5103 1:CAS:528: DC%2BD38XivFGrtw%3D%3D (Pubitemid 33131859)
50. Krishnan, R., Walton, E.B., Van Vliet, K.J.: in review (2008)
51. Mendenhall, W., Beaver, R.J., Beaver, B.M.: Introduction to Probability and Statistics. 12th ed., Thomson Higher Education, Belmont, CA (2006)
52. S. Chaturvedi J. Ocxhendorf 2004 Global environmental impacts due to concrete and steel Struct. Eng. Int. 14 3 198 200 10.2749/101686604777963748
53. F.J. Ulm G. Constantinides F.H. Heukamp 2004 Is concrete a poromechanics material?-a multiscale investigation of poroelastic properties Mater. Struct. 37 265 43 58 10.1617/14100 1:CAS:528:DC%2BD2cXnvVymsbk%3D
54. H.M. Jennings J.J. Thomas J.S. Gevrenov G. Constantinides F.J. Ulm 2007 A multi-technique investigation of the nanoporosity of cement paste Cem. Concr. Res. 37 3 329 336 10.1016/j.cemconres.2006.03.021 1:CAS:528:DC%2BD2sXitFSitrc%3D (Pubitemid 46275622)
55. G. Constantinides F.J. Ulm 2004 The effect of two types of C-S-H on the elasticity of cement-based materials: Results from nanoindentation and micromechanical modeling Cem. Concr. Res. 34 1 67 80 10.1016/S0008-8846(03) 00230-8 1:CAS:528:DC%2BD3sXpsFeltr4%3D