# 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*

Schuyler B. Nicholson, Jason R. Green

Under revision

arXiv

## Summary

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.

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

Zachary G. Nicolaou, Schuyler B. Nicholson, Adilson E. Motter, Jason R. Green*J. Chem. Phys.* **2023** 158(22) p. 225101

## Summary

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.

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. 05LT01arXiv

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

Rebecca A. Bone, Daniel J. Sharpe, David J. Wales, Jason R. Green*Phys. Rev. E* **2022** 106(5) p. 054151arXiv

Supporting code:

## Summary

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.

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. 194105arXiv

Density matrix formulation of dynamical systems

Swetamber Das, Jason R. Green*Phys. Rev. E* **2022** 106(5) p. 054135arXiv

## Summary

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.

Unifying quantum and classical speed limits on observables

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

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.

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

Schuyler B. Nicholson, Luis Pedro García-Pintos, Adolfo del Campo, Jason R. Green*Nat. Phys. ***2020 **16(12) p. 1211-1215arXiv

## Summary

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.”

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

Moupriya Das, Jason R. Green*Nat. Commun.* **2019** 10(1) p. 2155

Full text

arXiv

## Editor Summary

“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.”

## Summary

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.

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