Physical Biology of the Cell, Second Edition (with Jane Kondev, Julie Theriot and Hernan G. Garcia), Garland Science, November 2012. [book website] and [erratum]
Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels (with Christoph Haselwandter), PLoS Comput Biol 9(5): e1003055 (2013). [pdf full text]
Directional interactions and cooperativity between mechanosensitive membrane proteins (with Christoph Haselwandter), EPL, in press (2013). [pdf full text]
Statistical Mechanics of Monod-Wyman-Changeux (MWC) Models (with Sarah Marzen, Hernan G. Garcia), Journal of Molecular Biology, in press (2013). [pdf full text]
Theoretical and experimental dissection of DNA loop-mediated repression (with James Boedicker and Hernan Garcia), Physical Review Letters, Vol. 110, 018101 (2013). [pdf full text, SI]
Tuning Promoter Strength Through RNA Polymerase Binding Site Design in Escherichia coli (with Robert Brewster and Daniel Jones), PLoS Computational Biology, 8(12):e1002811 (2012). [link to publisher, pdf full text]
Focus on the Physics of the Cell Membrane (with Patricia Bassereau and Petra Schwille), New Journal of Physics 14: 055021-055025. [pdf full text]
A Single-Molecule Hershey-Chase Experiment (with David Van Valen*, David Wu*, Yi-Ju Chen, Hannah Tuson and Paul Wiggins. *: These authors contributed equally.), Current Biology 22(14):1339-1343(2012). [pdf full text, SI, raw data]
Sequence Dependence of Transcription Factor-Mediated DNA Looping (with Stephanie Johnson and Martin Linden), Nucleic Acids Research 40 (16): 7728-7738 (2012), doi: 10.1093/nar/gks473. [pdf full text, SI]
Operator sequence alters gene expression independently of transcription factor occupancy in bacteria (with Hernan G. Garcia, Alvaro Sanchez, James Q. Boedicker, Melisa Osborne, Jeff Gelles and Jane Kondev), Cell Reports 2, 1 (2012). [pdf full text and SI]
Single-Cell Census of Mechanosensitive Channels in Living Bacteria (with Maja Bialecka-Fornal, Heun Jin Lee, Hannah A. DeBerg, and Chris S. Gandhi), PLoS ONE 7(3): e33077 (2012). [pdf full text]
Entropic Tension in Crowded Membranes (with Martin Linden and Pierre Sens), PLoS Comput Biol 8(3): e1002431. doi:10.1371/journal.pcbi.1002431 (2012). [pdf full text]
Mechanosensitive Channels: What Can They Do and How Do They Do It? (with Elizabeth S. Haswell and Douglas C. Rees), Structure 19, 10 (2011). [pdf full text]
Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR (with Arbel D. Tadmor, Elizabeth A. Ottesen and Jared R. Leadbetter), Science 333, 58 (2011). [pdf full text, SI]
Lipid Bilayer Mechanics in a Pipette with Glass-Bilayer Adhesion (with Tristan Ursell and Ashutosh Agrawal), Biophys Journal 101, 8 (2011). [pdf full text]
Comparison and Calibration of Different Reporters for Quantitative Analysis of Gene Expression (with Hernan G. Garcia, Heun Jin Lee and James Q. Boedicker), Biophysical Journal 101, 3 (2011). [pdf full text, SI]
Quantitative dissection of the simple repression input-output function (with Hernan G. Garcia), PNAS 108:12173 (2011). [pdf full text, SI]
Elastic energy of polyhedral bilayer vesicles (with Christoph Haselwandter), Physical Review E 83, 061901 (2011). [pdf full text]
Building Enhancers From the Ground Up: A Synthetic Biology Approach (with Roee Amit, Hernan G. Garcia, and Scott E. Fraser), Cell 146:105-118 (2011). [pdf full text, SI]
An equivalence between a Maximum Caliber analysis of two-state kinetics and the Ising model (with Sarah Marzen, David Wu, and Mandar Inamdar), submitted to Physical Review E, 2010. [pdf full text]
Effect of promoter architecture on the cell-to-cell variability in gene expression (with Alvaro Sanchez, Hernan G. Garcia, Daniel Jones, and Jane Kondev), PLoS Comput. Bio. 7(3): e1001100 (2011). [pdf full text]
Dynamical fluctuations in biochemical reactions and cycles (with S. Presse, K. Ghosh, and K.A. Dill), accepted for publication in Physical Review E., 2010. [pdf full text]
Morphological Phase Diagram for Lipid Membrane Domains with Entropic Tension (with J. E. Rim, T. S. Ursell, and W. S. Klug), Phys. Rev. Lett. 106, 057801 (2011). [pdf full text]
Thermodynamics of Biological Processes (with Hernan Garcia, Jane Kondev, Nigel Orme, and Julie Theriot), Methods in Enzymology 492:27 (2011). [pdf full text]
Minimal Bending Energies of Bilayer Polyhedra (with Christoph A. Haselwandter), Phys. Rev. Lett. 105, 228101 (2010). [pdf full text]
SnapShot: Key Numbers in Biology (with Uri Moran and Ron Milo), Cell 141, June 25, 2010. [pdf full text]
Transcription by the Numbers Redux: Experiments and Calculations that Surprise. (with Hernan G. Garcia, Alvaro Sanchez, Thomas Kuhlman and Jane Kondev), Trends in Cell Biology, 20:723-733 (2010). [online full text]
A Feeling for the Numbers in Biology. (with Ron Milo), PNAS 106:21465-21471, 2009. [online full text]
Ion-dependent dynamics of DNA ejections for bacteriophage lambda. (with David Wu*, David Van Valen*, Qicong Hu. *: These authors contributed equally), Biophysical Journal 99:1101-1109, 2010. [pdf full text, supplement, video]
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), PNAS 106:13301, 2009. [online full text] [Supp Info]
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), Physical Review Letters, Vol. 103, 050603 (2009). [online full text]
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, website]
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]
Emerging roles for lipids in shaping membrane-protein function.(with Tristan Ursell, Paul Wiggins, Pierre Sens), Nature 459:379-385, 2009. [online full text]
Physical Biology of the Cell (with Jane Kondev and Julie Theriot), Garland Science, November 2008. [book website] and [erratum]
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]
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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