Physical Biology of the Cell (with Jane Kondev and Julie Theriot), Garland Science, November 2008. [book website] and [erratum]
First-principles calculation of DNA looping in tethered particle experiments. (with Kevin B. Towles, John F. Beausang, Hernan G. Garcia and
Philip C. Nelson), Phys. Biol., 6:025001 (2009). [online full text]
Reduced amino acid alphabets can improve the sensitivity and selectivity of pairwise sequence alignments. (with Eric L. Peterson, Jane' Kondev and Julie A. Theriot), Bioinformatics, 25:1356-1362 (2009). [online full text, supplement]
Concentration and Length Dependence of DNA Looping in Transcriptional Regulation. (with Lin Han, Hernan G. Garcia, Seth Blumberg, Kevin B. Towles, John F. Beausang and Philip C. Nelson), PLoS ONE, 4:e5621 (2009). [online full text]
Lipid Domain Order and the Algebra of Morphology.(with Tristan Ursell), submitted to Biophysical Journal, 2009. [Arxiv]]
Morphology and Interaction between Lipid Domains.(with Tristan Ursell and Bill Klug), accepted to PNAS, 2009. [Preprint] [Supp Info]
Emerging roles for lipids in shaping membrane-protein function.(with Tristan Ursell, Paul Wiggins, Pierre Sens), Nature 459:379-385, 2009. [online full text]
Calibration of tethered particle motion experiments. (with Lin Han, Bertrand Lui, Seth Blumberg, John F. Beausang and Philip C. Nelson), Mathematics of DNA Structure, Function, and Interactions, (IMA Volumes in Mathematics and its Applications), 2008. [online full text]
Biochemistry on a leash: The roles of tether length and geometry in signal integration proteins. (with David Van Valen and Mikko Haataja), Biophysical Journal, 96:1275-1292, 2009. [online full text]
Membrane shape as a reporter for applied forces. (with Heun Jin Lee, Eric L. Peterson, William S. Klug and Paul A. Wiggins), Proc. Nat. Acad. Sci., 105:19253, 2008. [online full text, supplement, Nature news feature]
A trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. (with David Wu, Kingshuk Ghosh, Mandar Inamdar, Heun Jin Lee, Scott Fraser, and Ken Dill), Submitted to Physical Review Letters, 2008. [online full text]
Biology by the Numbers by Rob Phillips - in the book 'Physical Biology: From Atoms to Medicine' edited by A. Zewail, Imperial College Press, 2008. [online full text]
Membrane Mechanics as a Probe of Ion-channel Gating Mechanisms. (with Daniel Reeves, Tristan Ursell, Pierre Sens, and Jane' Kondev), Phys Rev E, 78: 041901 (2008). [online full text]
A First Exposure to Statistical Mechanics for Life Scientists. (with Hernan G. Garcia, Jane' Kondev, Nigel Orme and Julie A. Theriot), Rejected by Am. J. Phys., 2007. [online full text]
Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions (with Tristan Ursell, Kerwyn Casey Huang and Eric Peterson), PLoS Computational Biology (2007) 3(5) e81. [online full text]
The Role of Lipid Bilayer Mechanics in Mechanosensation (with Tristan Ursell, Jane' Kondev, Dan Reeves and Paul A. Wiggins), in the book 'Mechanosensitivity in Cells and Tissues 1: Mechanosensitive Ion Channels', edited by Andre Kamkin and Irina Kiseleva, Springer-Verlag (2008). [online full text]
Measuring Flux Distributions for Diffusion in the Small-Numbers Limit (with Effrosyni Seitaridou, Mandar M. Inamdar, Kingshuk Ghosh, Ken A. Dill.), The Journal of Physical Chemistry B, Vol. 111, No. 9, pp. 2288-2292, February 2007, DOI: 10.1021/jp067036j. [online full text]
Biological Consequences of Tightly Bent DNA: The Other Life of a Macromolecular Celebrity (with Hernan G. Garcia, Paul Grayson, Lin Han, Mandar Inamdar,
Jane' Kondev, Philip C. Nelson, Jonathan Widom and Paul A. Wiggins), Biopolymers 85(2):115-130 (2007). [online full text]
High flexibility of DNA on short length scales probed by atomic force microscopy (with Paul A. Wiggins, Thijn van der Heijden, Fernando Moreno Herrero,
Andrew Spakowitz, Jonathan Widom, Cees Dekker and Philip C. Nelson), Nature Nanotechnology 1(2):137-141 (2006). [online full text]
The Biological Frontier of Physics (with Steve Quake), Physics Today, May 2006: 38--43. [online full text]
Excluded-Volume Effects in Tethered-Particle Experiments: Bead Size Matters (with Darren E. Segall and Philip C. Nelson), Phys. Rev. Lett. 96: 088306 (2006). [online full text]
Dynamics of DNA Ejection From Bacteriophage (with Mandar M.
Inamdar and William M. Gelbart), Biophys. J. 91:411-420 (2006) [online full text]
The Effect of Genome Length on Ejection Forces in Bacteriophage Lambda (with Paul Grayson, Alex Evilevitch, Mandar M. Inamdar, Prashant K. Purohit, William M. Gelbart, Charles M. Knobler, and Rob Phillips), Virology 348(2): 430-6 (2006) [online full text]
Teaching the Principles of Statistical Dynamics(with Kingshuk Ghosh, Ken Dill, Mandar M. Inamdar, and Effrosyni Seitaridou), Am. J. Phys. 74(2): 123--133, (2006). [online full text]
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
(with L. Dupuy, E. B. Tadmor and R. E. Miller), Phys. Rev. Lett., 95: 060202 (2005) [online full text]
Transcriptional Regulation by the Numbers 1: Models (with
Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich
Gerland, Terence Hwa, and Jané Kondev), Current
Opinion in Genetics & Development 15(2):116-124 (2005) [online full text]
Transcriptional Regulation by the Numbers 2: Applications
(with Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich
Gerland, Terence Hwa, Jané Kondev, and Thomas Kuhlman),
Current Opinion in Genetics & Development 15(2):125-135 (2005) [online full text]
Exact theory of kinkable elastic polymers (with Paul A. Wiggins and Philip C. Nelson), Physical Review E, 71: 021909 (2005)
[online full text]
Membrane-Protein Interactions in Mechanosensitive Channels
(with Paul Wiggins), Biophys. J. 88: 880-902 (2005) [online full text]
Forces during Bacteriophage DNA Packaging and Ejection
(with Prashant K. Purohit, Mandar M. Inamdar, Paul D. Grayson, Todd M. Squires and Jané Kondev), Biophys. J. 2005 88: 851-866
[online full text and erratum]
Spare the Rod: The Surprising Response of DNA in a Tight Situation
(with Paul A, Wiggins and Philip C. Nelson), This commentary was originally slated to appear as a commentary in PNAS, 2005
[online full text]
Mechanics of Biological Nanotechnology (with Prashant K. Purohit and Jané Kondev), Handbook of Nanotechnology, Springer, edited by B. Bhushan (2004) [publisher website]
Modeling the Stuff of the Material World: Do We Need All of the Atoms? The Bridge. 34(4): 22-27 (2004)
[online full text]
Analytic models for mechanotransduction: Gating a mechanosensitive channel (with Paul Wiggins), Proc. Nat. Acad. Sci., 101: 4071-4076 (2004)
[online full text]
Force steps during viral DNA packaging? (with Prashant K. Purohit and Jané Kondev), Journal of Mechanics and Physics of Solids, 51, 11-12: 2239-2257 (2003) [online abstract]
Mechanics of DNA packaging in viruses (with Prashant K. Purohit and Jané Kondev), Proc. Nat. Acad. Sci., 100: 3173 (2003)
[online full text]
Modeling in Engineering-The Challenge of Multiple Scales, ENGenious (Spring 2002) [online full text]
Crystals, Defects and Microstructures Cambridge University
Press, 2001. [publisher website]
Ursell et al. PLoS Comp Biol, 2007: The numerator of eqn. 14 should be z(0,1) + z(1,1), see the Arxiv version.
Corrections to Forces during Bacteriophage DNA Packaging and Ejection, Biophys. J. 2005 88: 851-866.
In 'The Role of Lipid Bilayer Mechanics in Mechanosensation', the units in the legend of figure 2.8 should be k_BT/nm^2.
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