Publications (since 2000)
2013
|
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]
Defects and DNA replication
Michel G. Gauthier, John Herrick and
John Bechhoefer
Phys. Rev. Lett. 104,
218104 (2010) [PDF]
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]
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) [PDF]
|
| 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) [PDF]
Kinetic model of DNA replication and the
looping of semiflexible polymers
Suckjoon Jun, PhD thesis, Simon Fraser
University (2004) [PDF]
The role of viscosity in banded spherulitic
growth
Bram Sadlik, MSc thesis, Simon Fraser
University (2004) [PDF] |
|
