Top

Published in:

2024 | OriginalPaper | Chapter

6. Conclusions

Author : Miranda Louwerse

Published in: Efficient Control and Spontaneous Transitions

Publisher: Springer Nature Switzerland

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

This chapter summarizes the work in this thesis and provides suggestions for future investigation of the connection between efficient protocols and spontaneous transition mechanism, outlining general directions of investigation and particular model systems.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

previous chapter Connections Between Minimum-Work Protocols and Transition Paths

Weinan, E., Vanden-Eijnden, E.: Towards a theory of transition paths. J. Stat. Phys. 123(3), 503–523 (2006)ADSMathSciNetCrossRefMATH

Metzner, P., Schutte, C., Vanden-Eijnden, E.: Transition path theory for Markov jump processes. Multiscale Model. Simul. 7(3), 1192–1219 (2009)MathSciNetCrossRefMATH

Peters, B.: Reaction coordinates and mechanistic hypothesis tests. Annu. Rev. Phys. Chem. 67, 669–690 (2016)ADSCrossRef

Bolhuis, P.G., Dellago, C.: Practical and conceptual path sampling issues. Eur. Phys. J. Spec. Top. 224, 2409–2427 (2015)CrossRef

Li, W., Ma, A.: Recent developments in methods for identifying reaction coordinates. Mol. Simul. 40(10–11), 784–793 (2014)CrossRef

Seifert, U.: Stochastic thermodynamics, fluctuation theorems and molecular machines. Rep. Prog. Phys. 75, 126001 (2012)ADSCrossRef

Esposito, M.: Stochastic thermodynamics under coarse-graining. Phys. Rev. E 85, 041125 (2012)ADSCrossRef

Amari, S.-I.: Information Geometry and Its Applications, 1st edn. Springer, Tokyo (2016)CrossRefMATH

Ito, S., Oizumi, M., Amari, S.-I.: Unified framework for the entropy production and the stochastic interaction based on information geometry. Phys. Rev. Res. 2, 33048 (2020)CrossRef

10.

Neupane, K., Hoffer, N.Q., Woodside, M.T.: Measuring the local velocity along transition paths during the folding of single biological molecules. Phys. Rev. Lett. 121, 018102 (2018)ADSCrossRef

11.

Pyo, A.G.T., Hoffer, N.Q., Neupane, K., Woodside, M.T.: Transition-path properties for folding reactions in the limit of small barriers. J. Chem. Phys. 149, 115101 (2018)ADSCrossRef

12.

Seifert, U.: From stochastic thermodynamics to thermodynamic inference. Annu. Rev. Condens. Matter Phys. 10, 171–192 (2019)ADSCrossRef

13.

Li, J., Horowitz, J.M., Gingrich, T.R., Fakhri, N.: Quantifying dissipation using fluctuating currents. Nat. Commun. 10, 1666 (2019)ADSCrossRef

14.

Skinner, D.J., Dunkel, J.: Improved bounds on entropy production in living systems. PNAS 118(18), e2024300118 (2021)CrossRef

15.

Gnesotto, F.S., Gradziuk, G., Ronceray, P., Broedersz, C.P.: Learning the non-equilibrium dynamics of Brownian movies. Nat. Commun. 11, 5378 (2020)ADSCrossRef

16.

Lathouwers, E., Lucero, J.N., Sivak, D.A.: Nonequilibrium energy transduction in stochastic strongly coupled rotary motors. J. Phys. Chem. Lett. 11(13), 5273–5278 (2020)CrossRef

17.

Leighton, M.P., Sivak, D.A.: Performance scaling and trade-offs for collective motor-driven transport. New J. Phys. 24(1), 013009 (2022)ADSMathSciNetCrossRef

18.

Li, W., Ma, A.: Reaction mechanism and reaction coordinates from the viewpoint of energy flow. J. Chem. Phys. 144, 114103 (2016)ADSCrossRef

19.

Wu, S., Li, H., Ma, A.: A rigorous method for identifying a one-dimensional reaction coordinate in complex molecules. J. Chem. Theory Comput. 18(5), 2836–2844 (2022)CrossRef

20.

Chodera, J.D., Noé, F.: Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol. 25, 135–144 (2014)CrossRef

21.

Faradjian, A.K., Elber, R.: Computing time scales from reaction coordinates by milestoning. J. Chem. Phys. 120, 10880–10889 (2004)ADSCrossRef

22.

Hartich, D., Godec, A.: Emergent memory and kinetic hysteresis in strongly driven networks. Phys. Rev. X 11, 041047 (2021)

23.

Berezhkovskii, A.M., Szabo, A.: Committors, first-passage times, fluxes, Markov states, milestones, and all that. J. Chem. Phys. 150, 54106 (2019)CrossRef

24.

Engel, M.C., Smith, J.A., Brenner, M.P.: Optimal control of nonequilibrium systems through automatic differentiation. arXiv:2201.00098

25.

Wang, Y., Tiwary, P.: State predictive information bottleneck. J. Chem. Phys. 154, 134111 (2021)ADSCrossRef

26.

Ma, A., Dinner, A.R.: Automatic method for identifying reaction coordinates in complex systems. J. Phys. Chem. B 109, 6769–6779 (2005)CrossRef

27.

Noé, F., Nüske, F.: A variational approach to modeling slow processes in stochastic dynamical systems. Multiscale Model. Simul. 11(2), 635–655 (2013)MathSciNetCrossRefMATH

28.

Pérez-Hernández, G., Paul, F., Giorgino, T., De Fabritiis, G., Noé, F.: Identification of slow molecular order parameters for Markov model construction. J. Chem. Phys. 139(1), 015102 (2013)ADSCrossRef

29.

Mardt, A., Pasquali, L., Wu, H., Noé, F.: VAMPnets for deep learning of molecular kinetics. Nat. Commun. 9(1), 1–11 (2018)ADS

30.

Tiwary, P., Berne, B.J.: Spectral gap optimization of order parameters for sampling complex molecular systems. Proc. Natl. Acad. Sci. U. S. A. 113(11), 2839–2844 (2016)ADSCrossRef

31.

Wang, Y., Marcelo, J., Ribeiro, L., Tiwary, P.: Past-future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. Nat. Commun. 10, 3573 (2019)ADSCrossRef

32.

Hernández, C.X., Wayment-Steele, H.K., Sultan, M.M., Husic, B.E., Pande, V.S.: Variational encoding of complex dynamics. Phys. Rev. E 97(6), 1–11 (2018)CrossRef

Title: Conclusions
Author: Miranda Louwerse
Publisher: Springer Nature Switzerland
Book: Efficient Control and Spontaneous Transitions
Print ISBN: 978-3-031-40533-4

Electronic ISBN: 978-3-031-40534-1

Copyright Year: 2024
DOI: https://doi.org/10.1007/978-3-031-40534-1_6