Publications


Books

Cell Biology by the Numbers by Ron Milo and Rob Phillips. Garland Science, 2015. | Book Website



Physical Biology of the Cell, Second Edition by Rob Phillips, Jané Kondev, Julie Theriot, Hernan Garcia, and illustrated by Nigel Orme. Garland Science, 2012. | Book Website | Erratum




Crystals, Defects and Microstructures: Modeling Across Scales by Rob Phillips. Cambridge University Press, 2001. | Book Website





Publications

2017

Musing on Mechanism: Quest for a Quark Theory of Proteins? by Rob Phillips. To appear in FAESB Journal 2017. | PDF

Self-consistent theory of transcriptional control in complex regulatory architectures by Jaspar Landman, Robert C. Brewster, Franz M. Weinert, Willem K. Kegel, and Rob Phillips. PLOS ONE 2017. | DOI: 10.1371/journal.pone.0179235. | PDF

Membranes by the Numbers by Rob Phillips. Edited by Patricia Bassereau and Pierre Sens. To appear in Physics of Biological Membranes 2017. | PDF

Tuning transcriptional regulation through signaling: A predictive theory of allosteric induction by Manuel Razo-Mejia , Stephanie Barnes , Nathan Belliveau , Griffin Chure , Tal Einav , Mitch Lewis, and Rob Phillips ( contributed equally). bioRxiv 2017. | PDF | SI | Website | Repository

Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants by Tal Einav and Rob Phillips. Journal of Physical Chemistry B. 2017. | DOI: 10.1021/acs/jpcb/6b12672. | PDF | SI | Mathematica Notebook

The Energetic Cost of Building a Virus by Gita Mahmoudabadi, Ron Milo, and Rob Phillips. PNAS 114 (22) 2017. | DOI: 10.1073/pnas.1701670114. | PDF

2016

Statistical Mechanics of Allosteric Enzymes by Tal Einav, Linus Mazutis, and Rob Phillips. Journal of Physical Chemistry B 120 (26) 2016. | PDF | SI | Mathematica Notebook

SnapShot: Timescales in Cell Biology by Maya Shamir, Yinon Bar-On, Rob Phillips, and Ron Milo. Cell 164 (6) 2016. | PDF

Using synthetic biology to make cells tomorrow’s test tubes by Hernan G. Garcia, Robert C. Brewster, and Rob Phillips. Integrative Biology 8 2016. | DOI: 10.1039/c6ib00006a. | PDF

Design Principles of Length Control of Cytoskeletal Structures. by Lishibanya Mohapatra, Bruce L. Goode, Predrag Jelenovic, Rob Phillips, and Jané Kondev. Annual Reviews of Biophysics 45 2016. | PDF | SI

2015

Theory in Biology: Figure 1 or Figure 7? by Rob Phillips. Trends in Cell Biology 25 (12) 2015. | PDF

Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics. by Peter Mulligan, Yi-Ju Chen, Rob Phillips, and Andrew Spakowitz. Biophysical Journal 109 (3) 2015. | PDF

Napoleon is in Equilibrium. by Rob Phillips Annual Review of Condensed Matter Physics 6 (1) 2015. | PDF

Single-molecule analysis of RAG-mediated V(D)J DNA cleavage. by Geoffrey A. Lovely, Robert C. Brewster, David G. Schatz, David Baltimore, and Rob Phillips. PNAS 112 (14) 2015. | PDF | SI

The Rate of Osmotic Downshock Determines the Survival Probability of Bacterial Mechanosensitive Channel Mutants. by Maja Bialecka-Fornal*, Heun Jin Lee *, and Rob Phillips (*contributed equally). Journal of Bacteriology 197 (1) 2015. | PDF

2014

Promoter architecture dictates cell-to-cell variability in gene expression. by Daniel L. Jones *, Robert C. Brewster *, and Rob Phillips (*contributed equally). Science 346 (6216) 2014. | PDF | SI

Scaling of Gene Expression With Transcription Factor Fugacity by Franz Weinert*, Rob Brewster*, Mattias Rydenfelt, Willem Kegel, and Rob Phillips. Physical Review Lettters 113 (25) 2014. | PDF

Modulation of DNA loop lifetimes by the free energy of loop formation by Yi-Ju Chen, Stephanie Johnson, Peter Mulligan, Andrew J. Spakowitz, and Rob Phillips. PNAS 111 (49) 2014. | PDF

The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli by Mattias Rydenfelt, Hernan G. Garcia, Robert Sydney Cox III, and Rob Phillips. PLoS One 9 (12) 2014. | PDF

The Quantified Cell by Avi Flamholz, Rob Phillips, and Ron Milo. Molecular Biology of the Cell 25 (22) 2014. | PDF

Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion by Stephanie Johnson, Jan-Willem van de Meent, Rob Phillips, Chris H. Wiggins, and Martin Lindén. Nucleic Acids Research 2014. | PDF

The Transcription Factor Titration Effect Dictates Level of Gene Expression by Robert C. Brewster*, Franz M. Weinert*, Hernan G. Garcia, Dan Song, Mattias Rydenfelt, and Rob Phillips (*contributed equally). Cell 156 (6) 2014. | PDF | SI | SI Figures

Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation by Huu Ngo, Geoffrey Lovely, Rob Phillips, and David Chan. Nature Communications 5:3077 2014. | PDF | SI

Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration by Mattias Rydenfelt, Robert Sydney Cox III, Hernan G. Garcia, and Rob Phillips. Phsyical Review E 89 (1) 2014. | PDF | Mathematica Notebook

2013

In Retrospect: The Feynman Lectures of Physics by Rob Phillips. Nature 504 2013. | PDF

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation by James Boedicker, Hernan G. Garcia, Stephanie Johnson, and Rob Phillips. Physical Biology 10 (6) 2013. | PDF | SI

Poly(dA:dT)-rich DNAs are Highly Flexible in the Context of DNA Looping by Stephanie Johnson, Yi-Ju Chen, and Rob Phillips. PLoS One 8 (10) 2013. | PDF | SI

Host-Virus Interaction: From Metagenomics To Single Cell Genomics by Arbel D. Tadmor and Rob Phillips. Encyclopedia of Metagenomics: SpringerReference. SpringerReference 2013. | Encyclopedia Entry

Connection Between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels by Christoph Haselwandter and Rob Phillips. PLoS Computational Biology 9 (5) 2013. | PDF

Directional interactions and cooperativity between mechanosensitive membrane proteins by Christoph Haselwandter and Rob Phillips. EPL 101 (6) 2013. | PDF

Statistical Mechanics of Monod-Wyman-Changeux (MWC) Models by Sarah Marzen, Hernan G. Garcia, and Rob Phillips. Journal of Molecular Biology 425 (9) 2013. | PDF | SI | Erratum

Theoretical and experimental dissection of DNA loop-mediated repression by James Boedicker, Hernan G. Garcia, and Rob Phillips Physical Review Letters 110 (1) 2013. | PDF | SI

2012

Interdisciplinary Graduate Training in Teaching Labs by Ronald D. Vale, Joseph DeRisi, R. Dyche Mullins, Clare Waterman, Timothy J. Mitchinson, and Rob Phillips. Science 338 (6114) 2012. | PDF

Tuning Promoter Strength Through RNA Polymeras eBinding Site Design in Escherichia coli by Robert C. Brewster, Daniel Jones, and Rob Phillips. PLoS Computational Biology 8 (12) 2012. | PDF

Focus on the Physics of the Cell Membrane by Patricia Bassereau, Petra Schwille, and Rob Phillips. New Journal of Physics 14 5 2012. | PDF

A Single-Molecule Hershey-Chase Experiment by David Van Valen*, David Wu*, Yi-Ju Chen, Hannah tuson, Paul Wiggins, and Rob Phillips (*contributed equally). Current Biology 22 (14) 2012. | PDF | SI | Raw Data

Sequence Dependence of Transcription Factor-Mediated DNA Looping by Stephanie Johnson, Martin Lindén, and Rob Phillips. Nucleic Acids Research 40 (16) 2012. | DOI: 10.1093/nar/gks47s. | PDF | SI

Operator sequence alters gene expression independently of transcription factor occupancy in bacteria by Hernan G. Garcia, Alvaro Sanchez, James Q. Boedicker, Melisa Osborne, Jeff Gelles, Jané Kondev, and Rob Phillips. Cell Reports 2 (1) 2012. | PDF and SI

Single-Cell Census of Mechanosensitive Channels in Living Bacteria by Maja Bialecka-Fornal, Heun Jin Lee, Hanna A. DeBerg, Chris S. Ghandi, and Rob Phillips. PLoS One 7 (3) 2012. | PDF

Entropic Tension in Crowded Membranes by Martin Lindén, Pierre Sens, and Rob Phillips. 8 (3) 2012. | DOI: 10.1371/journal.pcbi.1002431. | PDF

2011

Mechanosensitive Channels: What Can They Do and How Do they Do it? by Martin Lindén, Elizabeth S. Haswell, Douglas C. Rees, and Rob Phillips. Structure 19 (10) 2011. | PDF

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR by Arbel D. Tadmor, Elizabeth A. Oettesen, Jared R. Leadbetter, and Rob Phillips. Science 333 (58) 2011. | PDF | SI

Lipid Bilayer Mechanics In A Pipette With Glass-Bilayer Adhesion by Tristan Ursell, Ashutosh Agrawal, and Rob Phillips. Biophysical Journal 101 (8) 2011. | PDF

Comparison and Calibration of Different Reporters for Quantitative Analysis of Gene Expression by Hernan G. Garcia, Heun Jin Lee, and James Q. Boedicker Biophysical Journal 101 (3) 2011. | PDF | SI

Quantitative dissection of the simple repression input-output function by Hernan G. Garcia and Rob Phillips. PNAS 2011. | PDF | SI

Elastic energy of polyhedral bilayer vesicles by Christoph Haselwandter and Rob Phillips. Physical Review E 83 (6) 2011. | PDF

Building Enhancers From the Ground Up: A Synthetic Biology Approach by Roee Amit, Hernan G. Garcia, Rob Phillips, and Scott E. Fraser Cell 146 (1) 2011. | PDF | SI

Effect of promoter architecture on the cell-to-cell variability in gene expression by Alvaro Sanchez, Hernan G. Garcia, Daniel Jones, Rob Phillips, and Jané Kondev. PLoS Computational Biology 7 (3) 2011. | PDF

Morphological Phase Diagram for Lipid Membrane Domains with Entropic Tension by J. Rim, Tristan S. Ursell, Rob Phillips, and William Klug. Physical Review Letters 106 (5) 2011. | PDF

Thermodynamics of Biological Processes. by Hernan G. Garcia, Jané Kondev, Nigel Orme, Julie Theriot, and Rob Phillips. Methods in Enzymology 492 (27) 2011. | PDF

2010

An equivalence between a Maximum Caliber analysis of two-state kinetics and the Ising model by Sarah Marzen, David Wu, Mandar Inamdar, and Rob Phillips. arXiv 2010. | DOI: arXiv:1008.2726. | PDF

Dynamical fluctuations in biochemical reactions and cycles by Steve Pressé, Kingshuk Ghosh, Ken A. Dill, and Rob Phillips. Physical Review E 82 (3) 2010. | PDF

Minimal Bending Energies of Bilayer Polyhedra by Christoph Haselwandter and Rob Phillips. Physical Review Letters 105 (22) 2010. | PDF

SnapShot: Key Numbers in Biology by Uri Moran, Rob Phillips, and Ron Milo. Cell 101 (7) 2010. | PDF

Transcription by the Numbers Redux: Experiments and Calculations that Surprise. by Hernan G. Garcia, Alvaro Sanchez, Thomas Kuhlman, Jané Kondev, and Rob Phillips. Trends in Cell Biology 20 (12) 2010. | PDF

Ion-dependent dynamics of DNA ejections for bacteriophage λ by David Wu*, David Van Valen*, Qicong Hu, and Rob Phillips (*contributed equally). Biophysical Journal 99 (4) 2010. | PDF | SI | Video

2009

A Feeling for the Numbers in Biology by Rob Phillips and Ron Milo. PNAS 106 (51) 2009. | PDF

Lipid Domain Order and the Algebra of Morphology by Tristan S. Ursell and Rob Phillips arXiv 2009. | DOI: arXiv:0905.1405. | PDF

Morphology and Interaction Between Lipid Domains by Tristan Ursell, William Klug, and Rob Phillips. PNAS 106 (32) 2009. | PDF and SI

Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes by David Wu, Kingshuk Ghosh, Mandar Inamdar, Heun Jin Lee, Scott Fraser, Ken Dill, and Rob Phillips. Physical Review Letters 113 2009. | PDF

First-priniciples calculation of DNA looping in tethered particle experiments by Kevin B. Towles, John F. Beausang, Hernan G. Garcia, Philip C. Nelson, and Rob Phillips. Physical Biology 6 (2) 2009. | PDF

Reduced amino acid alphabets can improve the sensitivity and selectivity of pairwise sequence alignments by Eric L. Peterson, Jané Kondev, Julie A. Theriot, and Rob Phillips. Bioinformatics 25 (11) 2009. | PDF | SI | Website

Concentration and Length Dependence of DNA Looping in Transcriptional Regulation by Lin Han, Hernan G. Garcia, Seth Blumberg, Kevin B. Towles, John F. Beausang, Philip C. Nelson, and Rob Phillips. PLoS One 4 (5) 2009. | PDF

Emerging roles for lipids in shaping membrane-protein function by Tristan S. Ursell, Paul Wiggins, Pierre Sens, and Rob Phillips. Nature 459 (7245) 2009. | PDF

Chemistry on a leash: The roles of tether length and geometry in signal integration proteins by David Van Valen, Mikko Haataja, and Rob Phillips. Biophysical Journal 96 (4) 2009. | PDF

2008

Physical Biology of the Cell by Rob Phillips, Jané Kondev, Julie Theriot, and Nigel Orme. Garland Science November 2008. | Book Website | Erratum

Calibration of tethered particle motion experiments by Lin Han, Bertrand Lui, Seth Blumberrg, John F. Beausang, Philip C. Nelson, and Rob Phillips. Mathematics of DNA Structure, Function and Interactions (IMA Volumes in Mathematics and its Applications) 2008. | PDF

Membrane shape as a reporter for applied forces by Heun Jin Lee, Eric L. Peterson, William S. Klug, Paul A. Wiggins, and Rob Phillips PNAS 105 (49) 2008. | PDF | SI | Nature News Feature

Biology by the numbers by Rob Phillips. Chapter in ‘Physical Biology: From Atoms to Medicine’ edited by A. Zewail. Imperial College Press 2008. | PDF

Membrane Mechanics as a Probe of Ion-channel Gating Mechanisms by Daniel Reeves, Tristan S. ursell, Pierre Sens, Rob Phillips, and Jané Kondev. Physical Review E 78 2008. | DOI: 10.1103/PhysRevE.78.0941901. | PDF

2007

A First Exposure to Statistical Mechanics for Life Scientists by Hernan G. Garcia, Jané Kondev, Nigel Orme, Julie A. Theriot, and Rob Phillips Rejected by American Journal of Physics 2007. | PDF

Real-time observations of single bacteriophage λ DNA ejections in vitro by Paul Grayson, lin Han, Tabita Winther, and Rob Phillips. PNAS 104 (37) 2007. | PDF

Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions by Tristan S. ursell, Kerwyn Casey Huang, Eric L. Peterson, and Rob Phillips. PLoS Computational Biology 3 (5) 2007. | PDF

The Role of Lipid Bilayer Mechanics in Mechanosensation by Tristan S. Ursell, Jané Kondev, Dan Reeves, Paul A. Wiggins, and Rob Phillips Mechanosensitivity in Cells and Tissues 1: Mechanosensitive Ion Channels. Spring-Verlag 2007. | PDF

Measuring Flux Distributions for Diffusion in the Small-Numbers Limit by Effrosyni Seitaridou, Mandar M. INamdar, Kingshuk Ghosh, Ken A. Dill, and Rob Phillips. Journal of Physical Chemistry B 111 (9) 2007. | DOI: 10.1021/jp067036. | PDF

Biological Consequences of Tightly Bent DNA: The Other Life of a Macromolecular Celebrity by Hernan G. Garcia, Paul Grayson, Lin Han, Mandar Inamdar, Jané Kondev, Philip C. Nelson, Jonathan Widom, Paul A. Wiggins, and Rob Phillips. Biopolymers 85 (2) 2007. | PDF

2006

High flexibility of DNA on short length scales probed by atomic force microscopy by Paul A. Wiggins, Thijn van der Heijden, Fernando Moreno Herrero, Andrew Spakowitz, Jonathan Widom, Cees Dekker, Philip C. Nelson, and Rob Phillips. Nature Nanotechnology 1 (2) 2006. | PDF

The Biological Frontier of Pnysics by Rob Phillips and Steve Quake. Physics Today 59 (5) 2006. | PDF

Excluded-Volume Effects in Tehtered-Particle Experiments: Bead Size Matters by Darrren E. Segall, Philip C. Nelson, and Rob Phillips. Physical Review Letters 96 (8) 2006. | PDF

Dynamics of DNA Ejection From Bacteriophage by Mandar M. Inamdar, William M. Gelbart, and Rob Phillips. Biophysical Journal 91 (2) 2006. | PDF

The Effect of Genome Length on Ejection Forces in Bacteriophage Lambda by Paul Grayson, Alex Evilevitch, Mandar M. Inamdar, Prashant K. Purohit, William M. Gelbart, Charles M. Knobler, and Rob Phillips. Virology 348 (2) 2006. | PDF

Teaching the Prinicples of Statistical Dynamics by Kingshuk Ghosh, Ken A. Dill, Mandar M. Inamdar, Effrosyni Seitaridou, and Rob Phillips. American Journal of Physics 74 (2) 2006. | PDF

2005

Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms by L. Dupuy, E. B. Tadmor, R.E. Miller, and Rob Phillips. Physical Review Letters 95 2005. | Publisher

Transcriptional Regulation by the Numbers 1: Models by Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrigh Gerland, Ternce Hwa, Jané Kondev, and Rob Phillips. Current Opinion in Genetics & Development 15 (2) 2005. | PDF

Transcriptional Regulation by the Numbers 2: Applications by Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrigh Gerland, Terence Hwa, Jané Kondev, Thomas Kuhlman, and Rob Phillips. Current Opinion in Genetics & Development 15 (2) 2005. | PDF

Exact theory of kinkable elastic polymers by Paul A. Wiggins, Philip C. Nelson, and Rob Phillips. Physical Review E 71 2005. | PDF

Membrane-Protein Interactions in Mechanosensitive Channels by Paul A. Wiggins and Rob Phillips. 88 2005. | DOI: 10.1529/biophysj.104.047431. | PDF

Forces during Bacteriophage DNA Packaging and Ejection by Prashant K. Purohit, Mandar M. Inamdar, Paul D. Grayson, Todd M. Squires, Jané Kondev, and Rob Phillips. Biophysical Journal 88 (2) 2005. | PDF | Erratum

Spare the Rod: The surprising Response of DNA in a Tight Situation by Paul A. Wiggins, Philip C. Nelson, and Rob Phillips Originally slated as commentary in PNAS 2005. | PDF

2004

Mechanics of Biological Nanotechnology by Prashant K. Purohit, Jané Kondev, and Rob Phillips edited by B.Bhushan. Handbook of Nanotechology. 2004. | Publisher Website

Modeling the stuff of the Material World: Do We Need All of the Atoms? by Rob Phillips The Bridge 34 (4) 2004. | PDF

Analytic models for mechanotransduction: Gating a mechanosensitive channel by Paul Wiggins and Rob Phillips. PNAS 101 (12) 2004. | PDF

2003

Force steps during viral DNA packaging? by Prashant K. Purohit, Jané Kondev, and Rob Phillips. Journal of the Mechanics and Physics of Solids 51 (11) 2003. | Publisher Website

Mechanics of DNA packaging in viruses by Prashant K. Purohit, Jané Kondev, and Rob Phillips. PNAS 100 (6) 2003. | PDF

2002

Modeling in Engineering - The Challenge of Multiple Scales by Rob Phillips. ENGenious 2002. | PDF

2001

Crystals, Defects, and Microstructures by Rob Phillips. Cambridge University Press 2001. | Publisher Website

Notes and Corrections

  • In “Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions” by Tristan S. Ursell, Kerwyn Casey Huang, Eric L. Peterson, and Rob Phillips (PLoS Comp. Bio. 2007), the numerator of equation 14 should be z(0,1) + z(1,1). Please see the arXiv version

  • in “Forces during Bacteriophage DNA Packaging and Ejection” by Prashant K. Purohit, Mandar M. Inamdar, Paul D. Grayson, Todd M. Squires, Jané Kondev, and Rob Phillips (Biophys J. 2005), the units of the legend in figure 2.8 should be kBT / nm2.