Student's Guide to Python for Physical Modeling, Updated Edition

(with Jesse M. Kinder) (Princeton Univ. Press, 2018). You can get it directly from Princeton. E-book editions are available from Amazon and other distributors.
The book has an associated blog. Chapter 1 is freely available. A Chinese-language translation of the first edition is available, and also a Korean-language edition.

"An excellent stepping stone into the world of using Python in computational science.... After working through the chapters and their accompanying exercises, readers can expect not only to know how to write and read Python but also to achieve a thorough understanding for developing complex physical models and calculations." -- Kevin Thielen and Vivienne Tien in "Computing in Science & Engineering" May/June 2016


From Proton to Neuron book cover

From Photon to Neuron: Light, Imaging, Vision

(Princeton Univ. Press, 2017). The hard copy edition is available from Princeton. There is an e-book edition, available for Kindle or via Google Play. Chapter 1 is freely available. Three additional chapters are freely available in preliminary form.

From Photon to Neuron: Light, Imaging, Vision completes a trilogy begun by Biological Physics and Physical Models of Living Systems. Those works establish Nelson as the preeminent author of textbooks at the intersection of physics and biology.... Nelson uses words, pictures, formulas, and code to teach students how to construct models and interpret data. His books provide a master class in how to integrate those four different approaches into a complete learning experience.” -- Brad Roth, in Physics Today magazine

“A thorough and sweeping tour from the fundamental physics of light to the neurobiology of the retina.... Lavishly illustrated and carefully explained.” -- Sönke Johnsen, Biology, Duke University, in American Journal of Physics

“As elegant as it is deep. A masterful tour of the science of light and vision, it goes beyond artificial boundaries between disciplines and presents all aspects of light as it appears in physics, chemistry, biology and the neural sciences.... In the same way that the author instructs non-physics students in some basic physics concepts and tools, he also provides physicists with accessible and very clear presentations of many biological phenomena involving light.... One of the most insightful, cross-disciplinary texts I have read in many years. It is mesmerising and will become a landmark in rigorous, but highly accessible interdisciplinary literature.” -- Luis Alvarez-Gaumé, Stony Brook University, in CERN Courier

Physical models of living systems

(WH Freeman and Co, 2015), now available as an e-book via Google Play, Kindle, and CourseSmart. If you are looking for a hard copy, you may find a good deal from an Amazon affiliate, or here. Available in Chinese translation: 生命系统的物理建模 at these three links.

"Particularly compelling for its smooth integration of biological experiments, physical models, and computational exercises. Readers who complete the text will be well equipped with the computational and mathematical skills needed for a quantitative understanding of a range of biological systems.... Thanks to Nelson's skillful writing and the excellent accompanying online resources, this book will appeal to a broad audience and teach even a beginner how to solve problems numerically." -- Eva-Maria Collins in Physics Today

"Philip Nelson has done a terrific job.... There are numerous traits that make this text unique among the very many books of biological physics.... The presentation of materials is developed in an innovative fashion.... There is a nice balance between conceptual examples and end-of-the-chapter problems.... This book shows a nice intercalation of fundamental laws, brief descriptions of computational strategies for acquiring quantitative information, as well as their implications in biological physics and areas beyond that, including signaling processes, genetic switches, and cellular oscillators.... Physical Models of Living Systems... will benefit undergraduates as well as others with clear interests in genomics, proteomics, cellular signaling, bioengineering, regenerative medicine, and synthetic biology." -- Liviu Movileanu in American Journal of Physics 84 (6), June 2016

“[T]his excellent book will appeal to both students and professional scientists in the field of quantitative biology.... [T]he book feels personal in its selection of topics and the training journey on which it takes its readership. In our opinion, the combination of this uniqueness with technical accuracy makes the book a noteworthy and valuable addition to resources for advanced biophysics education... [T]he book conveys rich information, is clearly structured, and provides comprehensive data sets... Nelson shows how computational programming can be used effectively in modeling biological systems at the cellular and molecular levels.” -- Dietlind L. Gerloff and Jonghoon Kang. Cell Biology Education (2016) vol. 15 (4) pp. fe11-fe11.

Student's Guide to MATLAB for Physical Modeling

(With Tom Dodson; free).


Biological Physics: Energy, Information, Life: With new art by David Goodsell

(WH Freeman and Co, 2014); now available via as an e-book from Amazon and from CourseSmart. Also available in translation: 生物物理学:能量、信息、生命.

"This book inspired me to write [my] book in the first place. Biological Physics is the most interesting and well-written textbook I have ever read." -- Peter M. Hoffman, Life's Ratchet
This 5th printing differs from the 4th by the updating of many of the beautiful drawings by David Goodsell. It also differs from the 3d and earlier printings by the addition of many new homework problems.

Phil Nelson

Physics and Astronomy University of Pennsylvania Philadelphia, PA 19104 USA phone: (215) 898-7001 fax: (215) 898-2010


Sorry, but I get a lot of e-mail. If you are a student currently enrolled in a class that I teach, or a Biophysics major advisee, put that in the subject line. I want to reply, but if I don't --- please come see me. If you wish me to review a grant proposal, article for publication, or promotion case, please don't assume that your e-mail has been read or even seen. It may be necessary to get me on the phone if you need me to do those things.

Quote of the moment:

"Mayr opposes Darwinism and physics: `It was Darwin more than anyone else who showed how greatly theory formation in biology differs from classical physics... It is only since 1859 that biological sciences have begun to emancipate themselves from the dominance of the physical sciences...' In reality, Darwin for the first time in science has shown the possibility of the formation of order from chaotic variability. Darwin can be considered as the founder of a new field of physics." --- M. V. Volkenstein

Plain-English Videos

Book image

Plain-English Articles

Recent Talks

Journal Publications

Most of these articles are freely available at Penn's Scholarly Commons. Here are my profiles in ResearcherID, ORCID, Scopus, and Google Scholar.

The research in these publications was funded in part by The National Science Foundation and by the Human Frontier Science Program. "Any opinions, findings, confusions, contusions, contortions, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation."

Note: PDF reprints are provided below within the context of fair use. Please obtain copies from the publisher if appropriate.

How can cellular recognition processes be so accurate?
Stochastic Simulation Exercises for Visualization of Gene-Expression Dynamics and Error Correction in Biological Cells. With Chen and Zuckerman. Available on BiorXiv.

[picture] How can a system behave in a way that is strongly classical yet also strongly quantum?
The Role of Quantum Decoherence in FRET. Biophys. J. 115 167--172 (2018).

Does the quantum character of light matter for our eyes?
Old and new results about single-photon sensitivity in human vision. Physical Biology 13 025001 (2016).

[picture] Does a molecular motor pause to search for its next stepping spot?
Tilting and wobble of myosin V by high-speed single-molecule polarized fluorescence microscopy. With Beausang, Schroder, and Goldman. Biophysical Journal 104 1263--1273 (2013). (featured in BJ's "Best of 2013"

How does a wave of cell division spread across an embryo?
Wavefront propagation and mechanical signaling in early Drosophila embryos. With Idema, Dubuis, Kang, Manning, Lubensky, and Liu. PLoS ONE 8 e77216 (2013).

[picture] How much data compression is occurring in your retina?
Retinal adaptation to spatial correlations. With Simmons, Prentice, Tkacik, Homann, Yee, Palmer, and Balasubramanian. PLoS Computational Biology 9 e1003344 (2013).

What is each retinal ganglion cell looking for?
Neural Spikes, Identification from a Multielectrode Array. With Prentice, Homann, Simmons, Tkacik, Balasubramanian. Encyclopedia of Applied and Computational Mathematics, in press.

[picture] How precisely can you pinpoint a rate change?
Changepoint analysis for single-molecule polarized total internal reflection fluorescence microscopy experiments. With Beausang and Goldman. Methods Enzymol. 487 431-463 (2011).

When we eavesdrop on a retina, who said what when?
Fast, scalable, Bayesian spike identification for multi-electrode arrays. With Prentice, Homann, Simmons, Tkacik, and Balasubramanian. PLoS ONE 6(7): e19884.

[picture] How should you design the right DNA to make the best measurements of looping?
Calibration of Tethered Particle Motion Experiments. With Han, Lui, Blumberg, Beausang, and Phillips.In Mathematics of DNA Structure, Function and Interactions, eds. C.J. Benham et al. (Springer, 2009).

[picture] How can we monitor gene-regulatory events without any cells?
Concentration and Length Dependence of DNA Looping. With Han, Garcia, Blumberg, Towles, Beausang, and Phillips. PLoS ONE, 4 e5621 (2009).

Does myosin twist the `wrong' way around actin as it walks?
Twirling of actin by myosins II and V observed via polarized TIRF in a modified gliding assay. With Beausang, Schroeder, and Goldman. Biophys J. 95 5820 (2008).

[picture] Is there spooky action at a distance in living cells?
The Role of Microtubule Movement in Bidirectional Organelle Transport. With Kulic, Brown, Kim, Kural, Blehm, Selvin, and Gelfand. PNAS 105 10011 (2008). (See also the amazing movies.)

How does a regulatory protein manage to grab two distant places on a strand of DNA?
First-principles calculation of DNA looping in tethered particle experiments, final version, and its supplement. With Towles, Beausang, Garcia, and Phillips. Physical Biology, 6 025001 (2009).

[picture] When experiments seem to imply that the stiffness of DNA depends on its length, what's really going on?
Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6--7 um. With Seol, Li, Perkins, and Betterton. Biophys. J. 93 4360 (2007).

How accurately can we infer the length of a long molecule from the motion of a bead on its end?
Colloidal Particle Motion as a Diagnostic of DNA Conformational Transitions. Current Opinion in Colloid and Interface Science 12 307 (2007).

[picture] Are there long-lived kinetic substates in DNA looping?
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments . With Beausang. Physical Biology 4 205 (2007).

How can you extract kinetics from noisy data without binning?
DNA looping kinetics analyzed using diffusive hidden Markov model . With Beausang, Zurla, Manzo, Dunlap, and Finzi. Biophys. J. 92, L64 (2007).

[picture] Are there hidden regularities in "random" Brownian motion?
Elementary simulation of tethered Brownian motion. With Beausang, Zurla, Sullivan, and Finzi. Am. J. Phys. 75, 520 (2007).

What energy source squirts viral DNA into a host cell?
Biological Consequences of Tightly Bent DNA: The Other Life of a Macromolecular Celebrity . With Garcia, Grayson, Han, Inamdar, Kondev, Phillips, Widom, and Wiggins. Biopolymers 85, 115 (2007).

[picture] If DNA is a stiff elastic rod, how can it form those tight regulatory loops?
High flexibility of DNA on short length scales probed by atomic force microscopy. With Wiggins, van der Heijden, Moreno-Herrero, Spakowitz, Phillips, Widom, and Dekker.Nature Nanotechnology 1, 137 (2006) A commentary appears here.
See the Erratum to this article.

Do cells transport vesicles using active conveyor belts?
Hitchhiking Through the Cytoplasm. With Kulic. Europhys. Lett. 81, 18001-(1--6) (2008).

[picture] How can you see protein binding in real time?
Entropic elasticity of DNA with a permanent kink. With Betterton and Li. Macromolecules 39 8816 (2006).

When you twist a string, how does that affect loop formation?
Effect of supercoiling on formation of protein mediated DNA loops. With Purohit. Phys. Rev. E74, art. no. 061907 (14 pages) (2006).
See the Erratum to this article.

How can you detect DNA looping in real time, when you can't even see DNA?
Tethered particle motion as a diagnostic of DNA tether length. With Zurla, Brogioli, Beausang, Finzi, and Dunlap. Journal of Physical Chemistry B110, 17260 (2006).

[picture] How can fluorescence tell us about molecular mechanics?
Generalized theory of semiflexible polymers. With Wiggins. Phys. Rev. E73, art. number 031906 (2006).

What can a balloon in a hurricane tell us about gene regulation?
Excluded-Volume Effects in Tethered-Particle Experiments: Bead Size Matters. With Segall and Phillips. Phys. Rev. Lett. 96 art. number 088306 (2006).

[picture] How does DNA spontaneously form gene regulatory complexes with "impossibly" tight loops?
Exact theory of kinkable elastic polymers . With Wiggins and Phillips. Phys. Rev. E71 art. number 021909 (2005).

Is single-stranded DNA really a freely jointed chain?
Theory of High-Force DNA Stretching and Overstretching. With Storm. Phys. Rev. E67 (2003) art. number 051906 (Erratum ibid. 70, 013902 (2004)).

[picture] What's going on when DNA stretches to 1.6 times its "maximum" length?
The bend stiffness of S-DNA. With Storm. Europhys. Lett. 62 (2003) 760.

More, more more!

Last but not Least