Publications
List of manuscripts on the arXiv or ORCID.
Dissipation rates from experimental uncertainty
Aishani Ghosal, Jason R. Green
arXiv
Review: Geometric perspective on thermodynamic uncertainty relations and speed limits
Jason R. Green Under revision
Thermodynamic speed limits from the regression of information We show how thermodynamic uncertainty relations and speed limits on nonequilibrium processes derive from linear regression. Using optimal linear models, we show that physical observables give predictions of the equation of motion on statistical manifolds.
Schuyler B. Nicholson, Jason R. Green
Under revision
arXiv Summary
Spectral bounds on the entropy flow rate and Lyapunov exponents in differentiable dynamical systems
Swetamber Das, Jason R. Green
Accepted
J. Phys. A: Math. Theor. 2024
Maximum speed of dissipation
Swetamber Das, Jason R. Green
Phys. Rev. E (Letter) 2024 109(5) L052104
arXiv
CryoEM reveals the complex self-assembly of a chemically driven disulfide hydrogel
Paul Joshua Hurst, Justin T. Mulvey, Rebecca A. Bone, Serxho Selmani, Redford F. Hudson, Zhibin Guan, Jason R. Green, Joseph P. Patterson
Chemical Science 2024 15(3), p. 1106-1116
Classical Fisher information for differentiable dynamical systems
Mohamed Sahbani, Swetamber Das, Jason R. Green
Chaos 2023 33(10) p. 103139
arXiv
Prevalence of multistability and nonstationarity in driven chemical networks Numerous biological and artificial processes exploit multistability and nonstationarity in networks of chemical reactions to achieve important functions. While thermodynamic driving and autocatalysis are known to give rise to such complex chemical behaviors in specific systems, it is unclear how general these mechanisms are in more generic chemical networks. Synthesizing knowledge from systems chemistry, network theory, and dynamical systems, we characterize general conditions leading to complexity in driven chemical networks. Our results will enable the design of synthetic chemical reactions and may provide insights into the origins of life.
Zachary G. Nicolaou, Schuyler B. Nicholson, Adilson E. Motter, Jason R. Green
J. Chem. Phys. 2023 158(22) p. 225101 Summary
Relations between timescales of stochastic thermodynamic observables
Erez Aghion, Jason R. Green
J. Non-Equilib. Thermodyn. 2023 48(4) p. 417-432
Thermodynamic speed limits for mechanical work
Erez Aghion, Jason R. Green
J. Phys. A: Math. Theor. (Letter) 2023 56(5) p. 05LT01
arXiv
Optimizing dynamical functions for speed with stochastic paths
Rebecca A. Bone, Jason R. Green
J. Chem. Phys. 2022 157(22) p. 224101
Supporting code: 
Stochastic paths controlling speed and dissipation Thermodynamic intuition suggests that fast, irreversible processes will dissipate more energy and entropy than slow, quasistatic processes connecting the same initial and final states. Here, we show that this intuition does not necessarily hold for stochastic processes when there are strong nonequilibrium currents.
Rebecca A. Bone, Daniel J. Sharpe, David J. Wales, Jason R. Green
Phys. Rev. E 2022 106(5) p. 054151
arXiv
Supporting code: 
Summary
Dynamic scaling of stochastic thermodynamic observables for chemical reactions at and away from equilibrium
Shrabani Mondal, Jonah S. Greenberg, Jason R. Green
J. Chem. Phys. 2022 157(19) p. 194105
arXiv
Density matrix formulation of dynamical systems We derive a theory for any classical dynamical system that is analogous to the density matrix formulation of quantum mechanics. Defining states in terms of a classical density matrix leads to generalizations of Liouville’s theorem and Liouville’s equation, establishing an alternative computationally-tractable foundation for nonequilibrium statistical mechanics.
Swetamber Das, Jason R. Green
Phys. Rev. E 2022 106(5) p. 054135
arXiv Summary
Unifying quantum and classical speed limits on observables We derive a bound on the speed with which observables of open quantum systems evolve. It divides into Mandelstam and Tamm’s original time-energy uncertainty relation and a time-information uncertainty relation recently derived for classical systems, generalizing both to open quantum systems.
Luis Pedro García-Pintos, Schuyler B. Nicholson, Jason R. Green, Adolfo del Campo, Alexey V. Gorshkov
Phys. Rev. X 2022 12(1) p. 011038
arXiv Summary
Non-normality and non-monotonic dynamics in complex reaction networks
Zachary G. Nicolaou, Takashi Nishikawa, Schuyler B. Nicholson, Jason R. Green, Adilson E. Motter
Phys. Rev. Res. 2020 2(4) p. 043059
arXiv
Time-information uncertainty relations in thermodynamics Editor summary: “A time–information uncertainty relation in thermodynamics has been derived, analogous to the time-energy uncertainty relation in quantum mechanics, imposing limits on the speed of energy and entropy exchange between a system and external reservoirs.”
Schuyler B. Nicholson, Luis Pedro García-Pintos, Adolfo del Campo, Jason R. Green
Nat. Phys. 2020 16(12) p. 1211-1215
arXiv
Summary
Benchmarking the performance of the ReaxFF reactive force field on hydrogen combustion systems
Luke W. Bertels, Lucas B. Newcomb, Mohammad Alaghemandi, Jason R. Green, Martin Head-Gordon
J. Phys. Chem. A 2020 124(27) p.5631–5645
Critical fluctuations and slowing down of chaos “It is well known that fluids become opaque at the liquid-vapor critical point, but a description of the underlying mechanical instability is still missing. Das and Green leverage nonlinear dynamics to quantify the role of chaos in the emergence of this critical phenomenon.” In chemistry and physics, it is well known that cooling a fluid to its liquid-vapor critical point will cause a striking transformation called critical opalescence – at this special set of conditions, the fluid suddenly appears cloudy. The hard-earned explanation for this phenomenon is that as it is cooled, the fluid practices splitting into liquid and gas by forming regions of low and high density. Fluctuations and correlations in these regions grow precipitously to macroscopic length scales and scatter light, making the fluid appear opaque. This statistical description has sufficed for towering advances in statistical physics including universal scaling laws and the powerful theoretical machinery of the renormalization group (for which K. Wilson was awarded the Nobel Prize in 1982). Less understood, however, is what impact this critical phenomenon has on the motion of individual molecules. Missing is a complete understanding of the mechanical instability driving the anomalous statistical features of this singular state. That is, we do not currently have an understanding worthy of Gibbs’ name for this program – statistical mechanics. Using theory and computer simulations, we have shed new light on this problem. We have shown that the degree of chaos in the molecular motion is suppressed as the fluid approaches the critical point and begins to practice splitting into liquid and gas.
Moupriya Das, Jason R. Green
Nat. Commun. 2019 10(1) p. 2155
Full text
arXiv Editor Summary
Summary
Typical stochastic paths in the dissipative assembly of fibrous materials
Schuyler B. Nicholson, Rebecca A. Bone, Jason R. Green
J. Phys. Chem. B 2019 123(22) p. 4792-4802
Invited submission to the "Deciphering Molecular Complexity in Dynamics and Kinetics - From the Single Molecule to the Single Cell Level" issue
Nonequilibrium uncertainty principle from information geometry
Schuyler B. Nicholson, Adolfo del Campo, Jason R. Green
Phys. Rev. E 2018 98(3) 032106
arXiv
Explosion limits of hydrogen-oxygen mixtures from nonequilibrium critical points
Lucas B. Newcomb, Michael E. Marucci, Jason R. Green
Phys. Chem. Chem. Phys. 2018 20(23) p. 15746-15752
Selected as a 2018 PCCP HOT Article.
Entrance and escape dynamics for the typical set
Schuyler B. Nicholson, Jonah S. Greenberg, and Jason R. Green
Phys. Rev. E 2018 97(1) 012146
Effects of temperature and mass conservation on the typical chemical sequences of hydrogen oxidation
Schuyler B. Nicholson, Mohammad Alaghemandi, Jason R. Green
J. Chem. Phys. 2018 148(4) p. 044102
Nonexponential kinetics of ion pair dissociation in electrofreezing water
Mohammad Alaghemandi, Volkmar Koller, and Jason R. Green
Phys. Chem. Chem. Phys. 2017 19(38) p. 26396-26402
Self-averaging fluctuations in the chaoticity of simple fluids
Moupriya Das, Jason R. Green
Phys. Rev. Lett. 2017 119(11), p. 115502
arXiv
Featured on Physics Buzz
Nonequilibrium phase coexistence and criticality near the second explosion limit of hydrogen combustion
Lucas B. Newcomb, Mohammad Alaghemandi, Jason R. Green
J. Chem. Phys. 2017 147(3), p. 034108
Ignition in an atomistic model of hydrogen oxidation
Mohammad Alaghemandi, Lucas B. Newcomb, Jason R. Green
J. Phys. Chem. A 2017 121(8) p. 1686-1692
Extensivity and additivity of the Kolmogorov-Sinai entropy for simple fluids
Moupriya Das, Anthony B. Costa, Jason R. Green
Phys. Rev. E 2017 95(2) p. 022102
Learning the mechanisms of chemical disequilibria
Schuyler B. Nicholson, Mohammad Alaghemandi, Jason R. Green
J. Chem. Phys. 2016 145(8) p. 084112
Reactive symbol sequences for a model of hydrogen combustion
Mohammad Alaghemandi, Jason R. Green
Phys. Chem. Chem. Phys. 2016 18(4), p. 2810-2817
Order and disorder in irreversible decay processes
Jonathan W. Nichols, Shane W. Flynn, Jason R. Green
J. Chem. Phys. 2015 142(6) p. 064113
arXiv
Measuring disorder in irreversible decay processes
Shane W. Flynn, Helen C. Zhao, Jason R. Green
J. Chem. Phys. 2014 141(10) p. 104107
arXiv
A relationship between dynamical entropy and energy dissipation far from thermodynamic equilibrium
Jason R. Green, Anthony B. Costa, Bartosz A. Grzybowski, Igal Szleifer
Proc. Natl. Acad. Sci. USA 2013 110(41) p. 16339-16343
Extending the length and time scales of Gram-Schmidt Lyapunov vector computations
Anthony B. Costa, Jason R. Green
J. Comp. Phys. 2013 246 p. 113-122
Chaotic dynamics near steep transition states
Jason R. Green, Thomas S. Hofer, David J. Wales, R. Stephen Berry
Mol. Phys. 2012 10(15-16) p. 1839-1848
Characterizing molecular motion in H2O and H3O+ with dynamical instability statistics
Jason R. Green, Thomas S. Hofer, R. Stephen Berry, David J. Wales
J. Chem. Phys. 2011 135(18) p. 184307
When do molecular bowls encapsulate metal cations?
Jason R. Green, Robert C. Dunbar
J. Phys. Chem. A 2011 115(19) p. 4968-4975
Space-time properties of Gram-Schmidt vectors in classical Hamiltonian evolution
Jason R. Green, Julius Jellinek, R. Stephen Berry
Phys. Rev. E 2009 80(6) p. 066205
Ion/surface reactions and ion soft-landing
Bogdan Gologan, Jason R. Green, Jormarie Alvarez, Julia Laskin, R. Graham Cooks
Phys. Chem. Chem. Phys. 2005 7 p. 1490-1500
Inverse heavy-atom kinetic isotope effects in chloroalkanes
Jason R. Green, R. Graham Cooks
J. Phys. Chem. A 2004 108(46) p. 10039-10043
References
Jason R. Green, R. Graham Cooks
J. Phys. Chem. A 2005 109(49) p. 11338
Collisions of organic ions at surfaces
R. Graham Cooks, Sung-Chan Jo, Jason R. Green
Appl. Surf. Sci. 2004 231-232 p. 13-21