Publications

Publication list also available at Google Scholar.

2024	Performance limits of information engines Johan du Buisson, David A. Sivak, and John Bechhoefer arXiv 2402.17860 (2024). [PDF]
2023	Information engine in a nonequilibrium bath Tushar K. Saha, Jannik Ehrich, Momcilo Gavrilov, Susanne Still, David A. Sivak, and John Bechhoefer Phys. Rev. Lett., 131, 057101 (2023). [PDF]
2022	Bayesian information engine that optimally exploits noisy measurements Tushar K. Saha, Joseph N. E. Lucero, Jannik Ehrich, David A. Sivak, and John Bechhoefer Phys. Rev. Lett., 129, 130601 (2022). [PDF] • News release on Eurekalert by Z. Merali • Featured as a Synopsis in Physics by A. Curatolo • Editors' suggestion.
	Inferring potential landscapes from noisy trajectories J. Shepard Bryan IV, Prithviraj Basak, John Bechhoefer, and Steve Pressé iScience 25, 104731 (2022). [PDF]
	Anomalous heating in a colloidal system Avinash Kumar, Raphaël Chétrite, and John Bechhoefer PNAS 119, e2118484119 (2022). arxiv:2104.12899 • See Mpemba effect runs in reverse, Ashley Piccone, Physics Today
2021	Maximal fluctuation exploitation in Gaussian information engines Joseph N. E. Lucero, Jannik Ehrich, John Bechhoefer, and David A. Sivak Phys. Rev. E 104, 044122 (2021). [PDF]
	Trajectory control using an information engine Tushar K. Saha and John Bechhoefer Proc. SPIE 11798, Optical Trapping and Optical Micromanipulation XVIII, 117980L (2021) [PDF]
	A fresh understanding of the Mpemba effect John Bechhoefer, Avinash Kumar, and Raphaël Chétrite Nature Reviews Physics 3, 534–535 (2021) [PDF]
	Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication Weitao Wang, Kyle Klein, Karel Proesmans, Hongbo Yang, Claire Marchal, Xiaopeng Zhu, Tyler Borman, Alex Hastie, Zhiping Weng, John Bechhoefer, Chun-Long Chen, David M. Gilbert, Nicholas Rhind Molecular Cell 81, 2975–2988 (2021). bioarxiv (2020). • See Comment by David M. MacAlpine, in Molecular Cell.
	Maximizing power and velocity of an information engine Tushar K. Saha, Joseph, N. E. Lucero, Jannik Ehrich, David A. Sivak, and John Bechhoefer PNAS 118, e2023356118 (2021). [PDF] • See Comment by H. Linke and J. M. R. Parrondo, in PNAS.
	The metastable Mpemba effect corresponds to a non-monotonic temperature dependence of extractable work Raphaël Chétrite, Avinash Kumar, and John Bechhoefer Frontiers in Physics 9, 654271 (2021).
	Erasing a majority-logic bit Karel Proesmans and John Bechhoefer EPL (Europhysics Letters) 133, 30002 (2021). [PDF]
2020	Exponentially faster cooling in a colloidal system Avinash Kumar and John Bechhoefer Nature 584, 64–68 (2020). • Featured in Science News, Physics World, phys.org.
	Finite-time Landauer principle Karel Proesmans, Jannik Ehrich, and John Bechhoefer Phys. Rev. Lett. 125, 100602 (2020). [PDF] • Editor's Suggestion, phys.org
	Optimal finite-time bit erasure under full control Karel Proesmans, Jannik Ehrich, and John Bechhoefer Phys. Rev. E 102, 032105 (2020). [PDF]
2019	Shaping arbitrary landscapes with feedback Avinash Kumar and John Bechhoefer Physics in Canada 75, No. 1, 22–25 (2019). Student Prize Article.
2018	Nanoscale virtual potentials using optical tweezers Avinash Kumar and John Bechhoefer Appl. Phys. Lett. 113, 183702 (2018). • Featured in AIP Scilights. Editor's Suggestion.
	When geometry is irrelevant for heat diffusion: The transition from lumped element to field formulations Matthew Frick, Swapnil Gupta, and John Bechhoefer Eur. J. Phys., 39, 065104 (2018). [PDF]
	Optical Feedback Tweezers Avinash Kumar and John Bechhoefer SPIE Proceedings, Vol. 10723 (2018) Optical Trapping and Optical Micromanipulation XV [PDF]
2017	Experiments on the thermodynamics of information processing Momcilo Gavrilov Springer Thesis (2017)
	Test of the diffusing-diffusivity mechanism using near-wall colloidal dynamics Mpumelelo Matse, Mykyta V. Chubynsky, and John Bechhoefer Phys. Rev. E 96, 042604 (2017). [PDF]
	Direct measurement of nonequilibrium system entropy is consistent with Gibbs-Shannon form Momcilo Gavrilov, Raphaël Chétrite, and John Bechhoefer PNAS 114, 11097–11102 (2017) [PDF]
	Direct measurement of a nonequilibrium system entropy using a feedback trap Momcilo Gavrilov and John Bechhoefer Proc. SPIE 10347, Optical Trapping and Optical Micromanipulation XIV, 103470U (2017) [PDF]
	Feedback traps and the generalized Landauer limit for erasing information Momcilo Gavrilov and John Bechhoefer Proc. OSA 10347, Optical Trapping Applications (2017) [PDF]
	When memory pays: Discord in hidden Markov models Emma Lathouwers and John Bechhoefer Phys. Rev. E 95, 062144 (2017). [PDF]
	Feedback traps for virtual potentials Momcilo Gavrilov and John Bechhoefer Phil. Trans. Roy. Soc. A 375, 2016–217 (2017). [PDF (arxiv)]
2016	Erasure without work in an asymmetric, double-well potential Momcilo Gavrilov and John Bechhoefer Phys. Rev. Lett. 117, 200601 (2016). [PDF]
	Brownian duet: A novel tale of thermodynamic efficiency Karel Proesmans, Yannik Dreher, Momcilo Gavrilov, John Bechhoefer, and Christian Van den Broeck Phys. Rev. X 6, 041010 (2016). [PDF]
	Arbitrarily slow, non-quasistatic, isothermal transformations Momcilo Gavrilov and John Bechhoefer Europhys. Lett. 114, 50002 (2016). • Editor's Suggestion. [PDF from arxiv] • Featured in Europhysics News 47(5-6), p. 10 (2016).
2015	Replication Timing is Regulated by the Number of MCMs Loaded at Origins Shankar P. Das, Tyler Borrman, Scott C.-H. Yang, Victor W. T. Lui, John Bechhoefer, and Nicholas Rhind > Genome Res. 25 1886–1892 (2015)[PDF][Supp]
	Hidden Markov models for stochastic thermodynamics John Bechhoefer New J. Phys. 17, 075003 (2015) [PDF]
	What is superresolution microscopy?>\ John Bechhoefer Am. J. Phys. 83, 22–29 (2015) [PDF]
2014	High-precision test of Landauer's principle Yonggun Jun, Momcilo Gavrilov, and John Bechhoefer Phys. Rev. Lett. 113, 190601 (2014) [PDF] (Editors' Suggestion)
	Split PID control: two sensors can be better than one Leith Znaimer and John Bechhoefer Rev. Sci. Instrum. 85, 106105 (2014) [PDF]
	Numerical modeling of inhomogeneous DNA replication kinetics Michael G. Gauthier, Antoine Dubé, and John Bechhoefer arxiv1408.5216
	Real-time calibration of a feedback trap Momcilo Gavrilov, Yonggun Jun, and John Bechhoefer Rev. Sci. Instrum. 85, 095102 (2014) [PDF]
	Inferring the spatiotemporal DNA replication program from noisy data Antoine Baker and John Bechhoefer Phys. Rev. E 89, 032703 (2014) [PDF] (Editors' Suggestion)
2013	Particle dynamics in a virtual potential Momcilo Gavrilov, Yonggun Jun, and John Bechhoefer SPIE Proceedings, Vol. 8810 (2013) Optical Trapping and Optical Manipulation X [PDF]
	Conductive probe AFM study of Pt-thiol and Au-thiol contacts in metal-molecule-metal systems Changmin Kim and John Bechhoefer J. Chem. Phys. 138, 014707 (2013) [PDF]
2012	Virtual potentials for feedback traps Yonggun Jun and John Bechhoefer Phys. Rev. E 86, 061106 (2012) [PDF]
	Replication timing and its emergence from stochastic processes John Bechhoefer, Nicholas Rhind Trends in Genetics 28, 374–381 (2012) [PDF]
	Regulation of DNA Replication within the Immunoglobulin Heavy-Chain Locus During B Cell Commitment Agnieszka Demczuk, Michel G. Gauthier, Ingrid Veras, Settapong Kosiyatrakul, Carl L. Schildkraut, Meinrad Busslinger, John Bechhoefer, and Paolo Norio PLoS Biology 10(7), (2012) [PDF]
	Inferring where and when replication initiates from genome-wide replication timing data A. Baker, B. Audit, S. C.-H. Yang, J. Bechhoefer, and A. Arneodo Phys. Rev. Lett. 108, 268101 (2012) [PDF]
	Modeling inhomogeneous DNA replication kinetics Michel G. Gauthier, Paolo Norio, and John Bechhoefer PLoS ONE 7, e32053 (2012) [PDF]
2011	Kramers-Kronig, Bode, and the meaning of zero John Bechhoefer American Journal of Physics 79, 10 (2011) [PDF]
2010	Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing Scott Cheng-Hsin Yang, Nicholas Rhind and John Bechhoefer Molecular Systems Biology 6, 404 (2010) [PDF][Supplementary Material] Selected for Faculty of 1000 Biology (evaluated by Olivier Hyrien): In this remarkable paper, the authors provide a general analytical formalism for DNA replication kinetics and apply it to microarray data to extract the firing-time distribution and efficiency of most replication origins in the Saccharomyces cerevisiae genome. They find that earlier firing origins have tighter control of their initiation timing and higher efficiency than later firing origins and that this trend may be simply explained by the number of minichromosome maintenance (MCM) complexes loaded at each origin, without invoking an explicit time-counting mechanism. Thus, temporal patterns in replication can arise through stochastic initiation.
	Defects and DNA replication Michel G. Gauthier, John Herrick and John Bechhoefer Phys. Rev. Lett. 104, 218104 (2010) [PDF] Selected for a Synopsis in Physics : Copying DNA despite defects Selected for Faculty of 1000 Biology (evaluated by Arach Goldar): The authors demonstrate in an elegant and quantitative manner that the observed correlation between origin firing density and replication fork speed could be the result of fork stalls. This original work reveals the role of replication forks in regulation of DNA replication.
	Reconciling stochastic origin firing with defined replication timing Nicholas Rhind, Scott Cheng-Hsin Yang and John Bechhoefer Chromosome Res. 18, 35 (2010) [PDF]
2009	Computational methods to study kinetics of DNA replication Scott Cheng-Hsin Yang, Michel G. Gauthier and John Bechhoefer in DNA Replication: Methods and Protocols, ed. S. Vengrova and J. Z. Dalgaard, Humana Press, c/o Springer Science + Business Media, New York, NY, 2009, pp. 555–574 [PDF]
	Control of DNA replication by anomalous reaction-diffusion kinetics Michel G. Gauthier and John Bechhoefer Phys. Rev. Lett. 102, 158104 (2009) [PDF]
	Model-free iterative control of repetitive dynamics for high-speed scanning in atomic force microscopy Yang Li and John Bechhoefer Rev. Sci. Instr. 80, 013702 (2009) [PDF]
2008	The Hsk1/Cdc7 replication kinase regulates origin efficiency Prasanta K. Patel, Naveen Koomajosyula, Adam Rosebrock, Aaron Bensimon, Janet Leatherwood, John Bechhoefer, and Nicholas Rhind Mol. Biol. Cell 19, 5550–5558 (2008) [PDF] [Supplemental figures]
	How Xenopus laevis embryos replicate reliably: investigating the random-completion problem Scott Cheng-Hsin Yang and John Bechhoefer Phys. Rev. E 78, 041917 (2008) [PDF] • Selected for a Viewpoint article: Just-in-time DNA replication Suckjoon Jun and Nick Rhind Physics 1, 32 (2008) [PDF]
	Feedforward Control of a Piezoelectric Flexure Stage for AFM Yang Li and John Bechhoefer Proc. American Control Conf., Seattle, WA, 2703–2709 (2008) [PDF]
	Solidification of viscous melts: the interplay between nanoscale physics and macroscopic behaviour John Bechhoefer Int. J. Nanotech. 5, 1121–1137 (2008) [PDF]
2007	Temperature dependence of the capacitance of a ferroelectric material John Bechhoefer, Yi Deng, Joel Zylberberg, Chao Lei, and Zuo-Guang Ye Am. J. Phys 75, 1046–1053 (2007) [PDF] [Supplementary Material]
	Brownian motion in a modulated optical trap Yi Deng, John Bechhoefer, and Nancy Forde J. Opt. A: Pure and Appl. Opt. 9, S256–S263 (2007) [PDF] • Featured in Europhysics News, Nov./Dec. (2007) [PDF]
	Comment on "Direct measurement of the oscillation frequency in an optical trap by parametric modulation" Yi Deng, Nancy R. Forde, and John Bechhoefer Phys. Rev. Lett. 98, 189802 (2007) [PDF]
	How Xenopus laevis replicates DNA reliably even though its origins of replication are located and initiated stochastically John Bechhoefer and Brandon Marshall Phys. Rev. Lett. 98, 098105 (2007) [PDF]
	Feedforward control of a closed-loop piezoelectric translation stage for AFM Yang Li and John Bechhoefer Rev. Sci. Instr. 78, 013702 (2007) [PDF]
2006-5	Reconstructing DNA replication kinetics from small DNA fragments Haiyang Zhang and John Bechhoefer Phys. Rev. E 73, 051903 (2006) [PDF]
	Critical behavior of the banded-unbanded spherulite transition in a mixture of ethylene carbonate with polyacrylonitrile Bram Sadlik, Laurent Talon, Sébastien Kawka, Russell Woods, and John Bechhoefer Phys. Rev. E 71, 061602 (2005) [PDF]
	Feedback for physicists: A tutorial essay on control John Bechhoefer Rev. Mod. Phys. 77, 783-836 (2005) [PDF]
	Nucleation and growth in one dimension, part I: The generalized Kolmogorov-Johnson-Mehl-Avrami model Suckjoon Jun, Haiyang Zhang, and John Bechhoefer Phys. Rev. E 71, 011908 (2005) [PDF]
	Nucleation and growth in one dimension, part II: Application to DNA replication kinetics Suckjoon Jun and John Bechhoefer Phys. Rev. E 71, (2005) [PDF]
2004-3	Comment on “Insulating behavior of lambda-DNA on the micron scale" John Bechhoefer and Dipankar Sen Phys. Rev. Lett. 93, 239801 (2004) [PDF]
	Persistence length of chromatin determines origin spacing in Xenopus early-embryo DNA replication: Quantitative comparisons between theory and experiment Suckjoon Jun, John Herrick, Aaron Bensimon, and John Bechhoefer Cell Cycle 3, 223–229 (2004) [PDF]
	Self-Assembly of the Ionic Peptide EAK16: The Effect of Charge Distributions on Self-Assembly S. Jun, Y. Hong, H. Imamura, B.-Y. Ha, J. Bechhoefer, and P. Chen Biophys. J. 87, 1249–1259 (2004) [PDF]
	Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing Suckjoon Jun, John Bechhoefer, and Bae-Yeun Ha Europhys. Lett. 64, 420–426 (2003) [PDF]
	Role of Polymer Loops in DNA Replication Suckjoon Jun and John Bechhoefer Physics in Canada 59, 85–92 (2003) [PDF]
2002-0	Kinetic model of DNA replication in eukaryotic organisms John Herrick, Suckjoon Jun, John Bechhoefer, and Aaron Bensimon J. Mol. Biol. 320, 741–750 (2002) [PDF]
	Faster, cheaper, safer optical tweezers for the undergraduate laboratory John Bechhoefer and Scott Wilson American Journal of Physics 70, 393–400 (2002) [PDF]
	Two experimental tests of a fluctuation-induced first-order phase transition: Intensity Fluctuation Microscopy at the Nematic--Smectic-A Transition Anand Yethiraj, Ranjan Mukhopadhyay, and John Bechhoefer Phys. Rev. E 65, 021702 (16 pp.) (2002) [PDF]
	High-resolution study of fluctuation effects at the nematic–smectic-A phase transition Anand Yethiraj and John Bechhoefer Liquid Crystals Today 10, No. 3 (4 pp.) (2001) [PDF]
	Banded spherulitic growth in a liquid crystal Jeffrey L. Hutter and John Bechhoefer J. Cryst. Growth 217, 332–343 (2000) [PDF]
	On the properties of large banded spherulites in a maleic-anhydride--polyacrylonitrile mixture Michael M. Degen, Nicola Costanzino, and John Bechhoefer J. Cryst. Growth 209, 953–962 (2000) [PDF]
	Two experimental tests of the Halperin-Lubensky-Ma effect at the nematic--smectic-A phase transition Anand Yethiraj and John Bechhoefer Phys. Rev. Lett. 84, 3642–3645 (2000) [PDF]

PhD and MSc Theses

2022	Information-powered engines Tushar Saha, PhD thesis, Simon Fraser University (2022)
2021	Anomalous relaxation in colloidal systems Avinash Kumar, PhD thesis, Simon Fraser University (2021)
2019	Cooling dynamics of a Brownian particle and the Markovian Mpemba effect Lisa Zhang, MSc thesis, Simon Fraser University (2019)
2016	When memory pays: Discord in Hidden Markov models Emma Lathouwers, MSc thesis, Simon Fraser Utrecht (2016)
	Experiments on the thermodynamics of information processing Momcilo Gavrilov, PhD thesis, Simon Fraser University (2016) Published as a Springer Thesis (2017)
2015	Inferring DNA replication programs using Gaussian process regression Laura Geisler, MSc thesis, Simon Fraser University & TU Dresden (2015)
	Variance in initiation factors does not bly affect the replication profile of budding yeast DNA Mike Chomitz , MSc thesis, Simon Fraser University (2015)
	State-dependent diffusion of Brownian particles near a boundary wall Mpmumelelo Matse , MSc thesis, Simon Fraser University (2015)
2012	Modelling the DNA replication program in eukaryotes Scott Cheng-Hsin Yang, PhD thesis, Simon Fraser University (2012)
2011	AFM study of charge transport mechanisms at electrical contacts in metal-molecule-metal systems ChangMin Kim, MSc thesis, Simon Fraser University (2011)
2007-6	Towards fluorescence microscopy with an STM Philip Grant, MSc thesis, Simon Fraser University (2007)
	Conductivity measurements of single DNA molecules using conductive-atomic force microscopy> Shun Lu, MSc thesis, Simon Fraser University (2006)
2005-4	Reconstructing DNA replication kinetics from small DNA fragments Haiyang Zhang, MSc thesis, Simon Fraser University (2005)
	Kinetic model of DNA replication and the looping of semiflexible polymers Suckjoon Jun, PhD thesis, Simon Fraser University (2004)
	The role of viscosity in banded spherulitic growth Bram Sadlik, MSc thesis, Simon Fraser University (2004)
<2004	A versatile, multimode scanning probe microscope Christoph Hebeisen, MSc thesis, Simon Fraser University (2002)
	The nematic--smectic-A phase transition: high-resolution experimental study Anand Yethiraj, PhD thesis, Simon Fraser University (1999)
	Solidification of a liquid crystal: Morphologies and transitions Jeffrey L. Hutter, PhD thesis, Simon Fraser University (1997)
	Is the nematic--smectic-A transition always first order? Measurements of surface tension near an apparent tricritical point Nancy A. Tamblyn, MSc thesis, Simon Fraser University (1994)