Publications (since 2000)



2014
What is superresolution microscopy?
John Bechhoefer
arxiv.org

Inferring the spatiotemporal DNA replication program from noisy data

Antoine Baker and John Bechhoefer
Phys. Rev. E 89, 032703 (2014) [PDF]  (Editor's 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, 011909 (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]


Theses


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)