Article: Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Posts by Category
Pubs
Preprint: Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Article: Protein–ligand binding free-energy calculations with ARROW – A purely first-principles parameterized polarizable force field
Protein−ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we...
Tech. Note 009 v0.8: On Measures of Information and Entropy 009 v0.8
A brief overview of information measures on classical, discrete probability distributions. Tech. Note 009 v0.8 [ Full Text ]
Article: Measuring Analytic Gradients of General Quantum Evolution with the Stochastic Parameter Shift Rule
The Parameter Shift Rule is a cunning, recently developed method for evaluation gradients of quantum circuits on a quantum computer. But it has two problems…
Tech. Note: Gates, States, and Circuits
Notes on the circuit model of quantum computing. Currently mostly an exposition on the menagerie of quantum gates.
Tech. Note: Gates, States, and Circuits
Notes on the circuit model of quantum computing. Currently mostly an exposition on the menagerie of quantum gates.
Preprint: Measuring Analytic Gradients of General Quantum Evolution with the Stochastic Parameter Shift Rule
The Parameter Shift Rule is a cunning, recently developed method for evaluation gradients of quantum circuits on a quantum computer. But it has two problems…
Article: Two-Qubit Circuit Depth and the Monodromy Polytope
For a native gate set which includes all single-qubit gates, we apply results from symplectic geometry to analyze the spaces of two-qubit programs accessible...
Tech. Note: On the Weyl chamber of canonical non-local 2-qubit gates
The Weyl chamber of canonical non-local 2-qubit gates. Papercraft meets quantum computing. Print, cut, fold, and paste.
Preprint: Gradients of parameterized quantum gates using the parameter-shift rule and gate decomposition
The parameter-shift rule is an approach to measuring gradients of quantum circuits with respect to their parameters, which does not require ancilla qubits or...
Tech. Note: Gates, States, and Circuits
Notes on the circuit model of quantum computing. Currently mostly an exposition on the menagerie of quantum gates on 2-qubits.
Preprint: Fixed-Depth Two-Qubit Circuits and the Monodromy Polytope
For a native gate set which includes all single-qubit gates, we apply results from symplectic geometry to analyze the spaces of two-qubit programs accessible...
Tech. Note: On the Weyl chamber of canonical non-local 2-qubit gates
The Weyl chamber of canonical non-local 2-qubit gates. Papercraft meets quantum computing. Print, cut, fold, and paste.
Book: Field Guide to Continuous Probability Distributions, 1st Edition
Survey of over 170 continuous univariate probability distributions (and at least as many synonyms) organized into 20 families. First dead tree edition.
Article: Marginal and Conditional Second Laws of Thermodynamics
Gavin E. Crooks and Susanne Still, EPL 125:40005 (2019).
Tech. Note: Field Guide to Continuous Probability Distributions v0.12
Added Porter-Thomas, Epanechnikov, biweight, triweight, Libby-Novick, Gauss hypergeometric, confluent hypergeometric, Johnson-SU, and log-Cauchy distributions
Tech. Note: On the Weyl chamber of canonical non-local 2-qubit gates
The Weyl chamber of canonical non-local 2-qubit gates. Papercraft meets quantum computing. Print, cut, fold, and paste. (Should look like Fig. 4 of quant-p...
Preprint: Performance of the Quantum Approximate Optimization Algorithm on the Maximum Cut Problem
Gavin E. Crooks, arXiv: 1811.08419 (2018) [ PDF | Code]
Tech. Note 009 v0.7: On Measures of Information and Entropy 009 v0.7
A brief overview of information measures on classical, discrete probability distributions. Tech. Note 009 v0.7 [ Full Text ]
Preprint: Quantum Kitchen Sinks: An algorithm for machine learning on near-term quantum computers
C. M. Wilson, J. S. Otterbach, N. Tezak, Robert S. Smith, Gavin E. Crooks, and Marcus P. da Silva, arXiv:1806.08321 (2018)
Preprint: Marginal and Conditional Second Laws of Thermodynamics (v2)
Gavin E. Crooks, Susanne Still, arXiv:1611.04628
Article: Quantifying configuration-sampling error in Langevin simulations of complex molecular systems
Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle A. Beauchamp, Benedict Leimkuhler, and John D. Chodera Entropy, 20(5):318 (2018).
Tech. Note: Field Guide to Continuous Probability Distributions v0.11
Whats New: Added hyperbola, hyperbolic, Halphen, Halphen B, inverse Halphen B, generalized Halphen, Sichel, Appell Beta, K and generalized K distributions. T...
Article: Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems
Grant M. Rotskoff, Gavin E. Crooks, Eric Vanden-Eijnden Phys. Rev. E 95 012148 (2017)
Preprint: Marginal and Conditional Second Laws of Thermodynamics
Gavin E. Crooks, Susanne Still, arXiv:1611.04628
Article: Thermodynamic geometry of minimum-dissipation driven barrier crossing
David Sivak, Gavin E. Crooks Phys. Rev. E 94(5):052106 (2016)
Tech. Note: Field Guide to Continuous Probability Distributions v0.09
Whats New: Added pseudo Voigt,and Student’s t_3 distributions. Reparameterized hyperbolic sine distribution. Derived limit of Unit gamma to log-normal.Corre...
Article: Near-optimal protocols in complex nonequilibrium transformations
Todd R. Gingrich, Grant M. Rotskoff, Gavin E. Crooks, Phillip L. Geissler Proc. Natl. Acad. Sci. U.S.A. (2016)
Tech. Note: Field Guide to Continuous Probability Distributions v0.07
Whats New: Added Hohlfeld distribution. Added appendix on limits. Reformatted and rationalized distribution hierarchy diagrams. Fixed typos and improved form...
Preprint: Sampling an Ensemble of Low-dissipation Protocols for Nonequilibrium Control
Todd R. Gingrich, Grant M. Rotskoff, Gavin E. Crooks, Phillip L. Geissler arXiv:1602.01459
Article: Optimal control in nonequilibrium systems: Dynamic Riemannian geometry of the Ising model
Grant M. Rotskoff, Gavin E. Crooks, Phys. Rev. E, 92, 060102 (2015) [ Full text | Journal| arXiv ] Abstract A general understanding of optimal contr...
Tech. Note: On Measures of Entropy and Information
A brief overview of information measures on classical, discrete probability distributions. [
Article: Scaling laws governing stochastic growth and division of single bacterial cells
Srividya Iyer-Biswas, Charles S. Wright, Jonathan T. Henry, Klevin Lo, Stanislav Burov, Yihan Lin, Gavin E. Crooks, Sean Crosson, Aaron R. Dinner, Norbert F...
Article: Universality in Stochastic Exponential Growth
Srividya Iyer-Biswas, Gavin E. Crooks, Norbert F. Scherer, and Aaron R. Dinner, Phys. Rev. Lett., 113, 028101 (2014)
Article: Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems
David A. Sivak, John D. Chodera, Gavin E. Crooks, arXiv:1301.3800
Tech. Note: Survey of Simple, Continuous, Univariate Probability Distributions
Version: 0.5 BETA In a desperate attempt to preserve my own sanity, a survey of probability distributions used to describe a single, continuous, unimodal, u...
Article: Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics
David A. Sivak, John D. Chodera, Gavin E. Crooks, Phys. Rev. X 3, 011007 (2013)
Article: The geometry of thermodynamic control
Patrick R. Zulkowski David A. Sivak, Gavin E. Crooks, Michael R. DeWeese Phys. Rev. E, 86, 041148 (2012)
Article: Thermodynamics of prediction
This paper is a melding of ideas about machine learning from Susanne Still and Tony Bell, with ideas from David and I about nonequilibrium thermodynamics. Fo...
Article: Thermodynamic metrics and optimal paths
David A. Sivak, Gavin E. Crooks, Phys. Rev. Lett., 108, 190602 (2012)
Article: Near-equilibrium measurements of nonequilibrium free energy
David A. Sivak, Gavin E. Crooks, Phys. Rev. Lett. 108, 150601 (2012)
Article: Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
Jerome P. Nilmeier, Gavin E. Crooks, David L. D. Minh, and John D. Chodera, Proc. Natl. Acad. Sci. U.S.A. (2011) 108(45) E1009-E1018
Article: On thermodynamic and microscopic reversibility
The word ‘reversible’ has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimen...
Article: Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics
Gavin E. Crooks, and David A. Sivak, J. Stat. Mech.: Theor. Exp. P06003 (2011)
Excursions in statistical dynamics
Excursions in Statistical Dynamics by Gavin Earl Crooks A dissertation submitted in partial satisfaction of the requirements for the degree of D...
Code
qf-diamond-norm v1.0.0: QuantumFlow Diamond Norm
Gavin E. Crooks (2020)
QuantumFlow v1.0.0:
QuantumFlow: A Quantum Algorithms Development Toolkit and Cross Compiler
gecrooks-python-template: Minimal viable setup for an open source, github hosted, python package
Source
WebLogo 3.7.4 Released
Mayor server upgrade. The old server was getting very old and crufty. WebLogo moved to a shiny new AWS instance, with up to date installations of linux, apac...
QuantumFlow v0.8: Now with TensorFlow 2.0 support
QuantumFlow v0.8.0: Automatic differentiation of quantum circuits and SGD training of quantum networks. Now with TensorFlow 2.0 backend.
WebLogo 3.7 Released
3.7 (2019-03-04) [Gavin Crooks] Refactor and cleanup code, removing python 2.7 support Extend API documentation WebLogo python package is now ‘webl...
QuantumFlow: A Quantum Algorithms Development Toolkit v0.7
Announcing QuantumFlow, a python package that emulates a gate based quantum computer using modern optimized tensor libraries (numpy, TensorFlow, or torch). ...
WebLogo 3.6 Released
3.6 (2017-12-29) [Gavin Crooks, Melissa Fabros] refactor version string creation update testing framework for use with tox and pytest weblogo is ce...
WebLogo 3.5 Released
3.5 (2016-07-24) [Gavin Crooks, Melissa Fabros] Moved source control from GoogleCode to GitHub Switched from Subversion as version control method to ...
WebLogo 3.4 Released
3.4 (2014-06-03) [Gavin Crooks, Eric Talevich] Python 3 Weblogo now runs under python 2.6, 2.7, 3.2, 3.3 & 3.4 (Python2.5 is no longer suppor...
WebLogo 3.3 Released
3.3 (2012-07-02) [Gavin Crooks, David Sivak] Improved the algorithm that guesses the sequence type (DNA, RNA or protein) (Kudos: Bug report, Roland Pac...
WebLogo 3.2 released
3.2 (2012-01-30) [Gavin Crooks, David Sivak] Graphical interface now accepts transfac format motif files. New output format option: SVG (Scalable Vec...
WebLogo 3.1 released
This release contains mostly code improvement, minor bug fixes, small user enhancements and other miscellanies maintenance. Command line: Add parsing o...
Talks
Talk: U. Maryland Physics Colloquium: Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Talk: Rutgers University 125th Statistical Mathematics Conference: Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Presentation: NeurIPS 2023 (New Orleans) Physics Colloquium: Thermodynamic AI and Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Talk: Berkeley Physics Colloquium: Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Talk: Berkeley Stat. Mech. Seminar: Thermodynamic Linear Algebra
We consider an alternative physics-based computing paradigm based on classical thermodynamics, to provide a near-term approach to accelerating linear algebra.
Physics Colloquium @ UC Davis, Mon Apr 25 2016
Optimal Thermodynamic Control and the Dynamic Riemannian Geometry of Ising magnets 55 Roessler Hall, UC Davis, 4:10 - 5:30 PM, Monday 25th April 2016 Pap...
Grand East Coast Tour (Oct/Nov 2015)
Optimal Thermodynamic Control and the Dynamic Riemannian Geometry of Ising magnets Stonybrook University Friday Oct. 30, 2:30pm, Laufer Center lecture ha...
Princeton Lectures on The Dynamics of Disorder
Over the next 2 weeks I will be lecturing at the Princeton Center for Theoretical Science on non-equilibrium statistical dynamics. The Fluctuations of Diss...
Quotes
Quote of the Day
Let this book be dedicated to the chemists of the newer generation, who will not wish to reject all inferences from conjecture or surmise, but who will no...
Quote of the Day
“And then there’s quantum, of course.” The monk sighed. “There’s always bloody quantum.”
Quote of the Day
In science, as in life, it is extremely dangerous to fall in love with beautiful models.
Quote of the Day
♬ Hey I just met you, and this is crazy, but here’s my paper - so cite me maybe? ♬
Quote of the Day
Memory has great survival utility … but why would forgetting be adaptive. Forgetting well is almost as important as remembering well. Forgetting is about ...
Quote of the Day
People like us, who believe in physics, know that the distinction between past, present, and future is only a stubbornly persistent illusion.
Quote of the Day
Here’s to the crazy ones. The misfits. The rebels. The troublemakers. The round pegs in the square holes. The ones who see things differently. They’re not...
Word of the Day: Super-duper-operator
Super-duper-operator (n): An operator is a linear map that acts on a vector space. A superoperator is an operator of an operator, an operator that acts on a...
Quote of the Day
Substitute damn every time you’re inclined to write very; your editor will delete it and the writing will be just as it should be.
Media
Celebrating 50,000 Publications: Physical Review E Milestones
Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences Gavin E. Crooks Phys. Rev. E 60, 2721 (2000)
Media: Time Marches On (Except when it doesn’t)
Media: The American Scholar By Josie Glausiusz
Award: Presidential Early Career Awards for Scientist and Engineers (PECASE)
President Honors Outstanding Early-Career Scientists
Bulletin
I tweet, therefore I am.
@gavincrooks
Announcement: Introducing GavinCrooks.com
At last! GavinCrooks.com
News: David Sivak, Assistant Professor
I am proud to announce that Simon Fraser University has hired David Sivak (Former Crooks’ Ensemble Postdoctoral Fellow) to the position of Assistant Profes...
JLP
Journal of Lost Papers: On the divergence between two distributions and the probability of misclassification of several decision rules
The (virtual) Journal of Lost Papers: Article 001
News
Upcoming: 2024-03-20, U. Chicago, Computations in Science Seminar
Upcoming: 2024-03-20, U. Chicago, Computations in Science Seminar