On the distance between A and B in molecular configuration space

References

• Coifman RR, Lafon S, Lee AB, et al. Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. Proc Natl Acad Sci. 2005;102(21):7426–7431.
   PubMed Web of Science ®Google Scholar
• Noe F, Banisch R, Clementi C. Commute maps: separating slowly mixing molecular configurations for kinetic modeling. J Chem Theory Comput. 2016;12(11):5620–5630.
   PubMed Web of Science ®Google Scholar
• Branduardi D, Gervasio FL, Parrinello M. From a to b in free energy space. J Chem Phys. 2007;126(5):054103.
   PubMed Web of Science ®Google Scholar
• Piaggi PM, Valsson O, Parrinello M. Enhancing entropy and enthalpy fluctuations to drive crystallization in atomistic simulations. Phys Rev Lett. 2017;119(1):015701.
   PubMed Web of Science ®Google Scholar
• Desgranges C, Delhommelle J. Crystal nucleation along an entropic pathway: teaching liquids how to transition. Phys Rev E. 2018;98(6):063307.
   Web of Science ®Google Scholar
• Ceriotti M, Tribello GA, Parrinello M. Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci. 2011;108(32):13023–13028.
   PubMed Web of Science ®Google Scholar
• Ravindra P, Smith Z, Tiwary P. Automatic mutual information noise omission (amino): generating order parameters for molecular systems. Mol Syst Des Eng. 2020;5(1):339–348.
   Web of Science ®Google Scholar
• Rohrdanz MA, Zheng W, Maggioni M, et al. Determination of reaction coordinates via locally scaled diffusion map. J Chem Phys. 2011;134(12):03B624.
   Web of Science ®Google Scholar
• Cohen FE, Sternberg MJE. On the prediction of protein structure: the significance of the root-mean-square deviation. J Mol Biol. 1980;138(2):321–333.
   PubMed Web of Science ®Google Scholar
• Geissler PL, Dellago C, Chandler D. Kinetic pathways of ion pair dissociation in water. J Phys Chem B. 1999;103(18):3706–3710.
   Web of Science ®Google Scholar
• Onsager L. Initial recombination of ions. Phys Rev. 1938;54(8):554.
   Google Scholar
• Weinan E, Ren W, Vanden-Eijnden E. Transition pathways in complex systems: reaction coordinates, isocommittor surfaces, and transition tubes. Chem Phys Lett. 2005;413(1-3):242–247.
   Web of Science ®Google Scholar
• Berezhkovskii AM, Szabo A. Committors, first-passage times, fluxes, Markov states, milestones, and all that. J Chem Phys. 2019;150(5):054106.
   PubMed Web of Science ®Google Scholar
• Krivov SV. On reaction coordinate optimality. J Chem Theory Comput. 2013;9(1):135–146.
   PubMed Web of Science ®Google Scholar
• Kells A, Mihálka ZÉ, Annibale A, et al. Mean first passage times in variational coarse graining using Markov state models. J Chem Phys. 2019;150(13):134107.
   PubMed Web of Science ®Google Scholar
• Peters B, Trout BL. Obtaining reaction coordinates by likelihood maximization. J Chem Phys. 2006;125(5):054108.
   PubMed Web of Science ®Google Scholar
• García AE. Large-amplitude nonlinear motions in proteins. Phys Rev Lett. 1992;68(17):2696.
   PubMed Web of Science ®Google Scholar
• Amadei A, Linssen ABM, Berendsen HJC. Essential dynamics of proteins. Proteins. 1993;17(4):412–425.
   PubMed Web of Science ®Google Scholar
• Hegger R, Altis A, Nguyen PH, et al. How complex is the dynamics of peptide folding? Phys Rev Lett. 2007;98(2):028102.
   PubMed Web of Science ®Google Scholar
• Zhuravlev PI, Materese CK, Papoian GA. Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. J Phys Chem B. 2009;113(26):8800–8812.
   PubMed Web of Science ®Google Scholar
• Cox MAA, Cox TF. Multidimensional scaling. In: Handbook of data visualization. Berlin: Springer; 2008. p. 315–347.
   Google Scholar
• Ferguson AL, Panagiotopoulos AZ, Debenedetti PG, et al. Systematic determination of order parameters for chain dynamics using diffusion maps. Proc Natl Acad Sci. 2010;107(31):13597–13602.
   PubMed Web of Science ®Google Scholar
• Limongelli V, Bonomi M, Marinelli L, et al. Molecular basis of cyclooxygenase enzymes (coxs) selective inhibition. Proc Natl Acad Sci. 2010;107(12):5411–5416.
   PubMed Web of Science ®Google Scholar
• Tiwary P, Limongelli V, Salvalaglio M, et al. Kinetics of protein–ligand unbinding: predicting pathways, rates, and rate-limiting steps. Proc Natl Acad Sci. 2015;112(5):E386–E391.
   PubMed Web of Science ®Google Scholar
• Tiwary P, Berne BJ. Predicting reaction coordinates in energy landscapes with diffusion anisotropy. J Chem Phys. 2017;147(15):152701.
   PubMed Web of Science ®Google Scholar
• Nettleton RE, Green MS. Expression in terms of molecular distribution functions for the entropy density in an infinite system. J Chem Phys. 1958;29(6):1365–1370.
   Web of Science ®Google Scholar
• Piaggi PM, Parrinello M. Predicting polymorphism in molecular crystals using orientational entropy. Proc Natl Acad Sci. 2018;115(41):10251–10256.
   PubMed Web of Science ®Google Scholar
• Karl Johnson J, Zollweg JA, Gubbins KE. The lennard-jones equation of state revisited. Mol Phys. 1993;78(3):591–618.
   Web of Science ®Google Scholar
• Van der Hoef MA. Free energy of the lennard-jones solid. J Chem Phys. 2000;113(18):8142–8148.
   Web of Science ®Google Scholar
• Starr FW, Sastry S, Douglas JF, et al. What do we learn from the local geometry of glass-forming liquids? Phys Rev Lett. 2002;89(12):125501.
   PubMed Web of Science ®Google Scholar
• Charbonneau P, Kurchan J, Parisi G, et al. Fractal free energy landscapes in structural glasses. Nat Commun. 2014;5(1):1–6.
   Google Scholar
• Hedges LO, Jack RL, Garrahan JP, et al. Dynamic order-disorder in atomistic models of structural glass formers. Science. 2009;323(5919):1309–1313.
   PubMed Web of Science ®Google Scholar
• Kob W, Donati C, Plimpton SJ, et al. Dynamical heterogeneities in a supercooled lennard-jones liquid. Phys Rev Lett. 1997;79(15):2827.
   Web of Science ®Google Scholar
• Merolle M, Garrahan JP, Chandler D. Space–time thermodynamics of the glass transition. Proc Natl Acad Sci. 2005;102(31):10837–10840.
   PubMed Web of Science ®Google Scholar
• Biroli G, Garrahan JP. Perspective: the glass transition. J Chem Phys. 2013;138(12):12A301.
   PubMed Web of Science ®Google Scholar
• Pinchaipat R, Campo M, Turci F, et al. Experimental evidence for a structural-dynamical transition in trajectory space. Phys Rev Lett. 2017;119(2):028004.
   PubMed Web of Science ®Google Scholar
• Bolhuis PG, Chandler D, Dellago C, et al. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem. 2002;53(1):291–318.
   PubMed Web of Science ®Google Scholar
• Chandler D, Garrahan JP. Dynamics on the way to forming glass: bubbles in space-time. Annu Rev Phys Chem. 2010;61:191–217.
   PubMed Web of Science ®Google Scholar
• Giardina C, Kurchan J, Lecomte V, et al. Simulating rare events in dynamical processes. J Stat Phys. 2011;145(4):787–811.
   Web of Science ®Google Scholar
• Roweis ST, Saul LK. Nonlinear dimensionality reduction by locally linear embedding. Science. 2000;290(5500):2323–2326.
   PubMed Web of Science ®Google Scholar
• Das P, Moll M, Stamati H, et al. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci. 2006;103(26):9885–9890.
   PubMed Web of Science ®Google Scholar
• Piana S, Laio A. Advillin folding takes place on a hypersurface of small dimensionality. Phys Rev Lett. 2008;101(20):208101.
   PubMed Web of Science ®Google Scholar
• Tribello GA, Ceriotti M, Parrinello M. Using sketch-map coordinates to analyze and bias molecular dynamics simulations. Proc Natl Acad Sci. 2012;109(14):5196–5201.
   PubMed Web of Science ®Google Scholar
• Ceriotti M, Tribello GA, Parrinello M. Demonstrating the transferability and the descriptive power of sketch-map. J Chem Theory Comput. 2013;9(3):1521–1532.
   PubMed Web of Science ®Google Scholar
• Lemke T, Peter C. Encodermap: dimensionality reduction and generation of molecule conformations. J Chem Theory Comput. 2019;15(2):1209–1215.
   PubMed Web of Science ®Google Scholar
• Tiwary P, Berne BJ. Spectral gap optimization of order parameters for sampling complex molecular systems. Proc Natl Acad Sci. 2016;113(11):2839–2844.
   PubMed Web of Science ®Google Scholar
• Gers FA, Schmidhuber J, Cummins F. Learning to forget: continual prediction with LSTM; 1999.
   Google Scholar
• Pathak J, Hunt B, Girvan M, et al. Model-free prediction of large spatiotemporally chaotic systems from data: a reservoir computing approach. Phys Rev Lett. 2018;120(2):024102.
   PubMed Web of Science ®Google Scholar
• Wang Y, Lamim Ribeiro JM, Tiwary P. Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. Nat Commun. 2019;10(1):1–8.
   PubMed Web of Science ®Google Scholar
• Salvalaglio M, Vetter T, Giberti F, et al. Uncovering molecular details of urea crystal growth in the presence of additives. J Am Chem Soc. 2012;134(41):17221–17233.
   PubMed Web of Science ®Google Scholar
• Frauenfelder H, Sligar SG, Wolynes PG. The energy landscapes and motions of proteins. Science. 1991;254(5038):1598–1603.
   PubMed Web of Science ®Google Scholar
• Ferreiro DU, Hegler JA, Komives EA, et al. On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci. 2011;108(9):3499–3503.
   PubMed Web of Science ®Google Scholar