ParthasarathyLab
Biophysics & Soft Condensed Matter
RP's papers can be found at the "Papers" page.
Contents
At the Bench: A Laboratory Navigator (*)
by Kathy Barker (465 pages, 2004; ISBN 0879697083)
A "handbook" for working in a lab. Full of information and advice -- "biocentric," but very useful.
NOTE: The lab has its own copy of this book.
Structured Fluids : Polymers, Colloids, Surfactants
by Thomas A. Witten and Philip A. Pincus (232 pages; Oxford, 2004; ISBN 0198526881)
A recent book on the physics of complex fluids, particularly emphasizing simple, powerful scaling approaches to understanding physical phenomena.
Intermolecular and Surface Forces (*)
by Jacob Israelachvili (450 pages; Academic Press, 1992, 2nd edition; ISBN 0123751810).
Clear, thorough, and relevant to a wide variety of physical, chemical, and biological systems.
NOTE: The lab has its own copy of this book.
Physical Biology of the Cell(*)
by Rob Phillips, Jane Kondev, Julie Theriot (800 pages; Garland, 2008 ISBN 978-0-8153-4163-5)
A very recent and much-anticipated textbook that explores cellular and molecular biology from a physical perspective .
Biological Physics: Energy, Information, Life (*)
by Philip Nelson (600 pages; Freeman 2003; ISBN 0-7167-4372-8)A recent biophysics textbook (one of the few available) suitable for both undergraduates and graduate students, with clear descriptions of the statistical mechanics underlying many biological phenomena
Random Walks in Biology (*)
by Howard C. Berg (164 pages; Princeton University Press, 1993; ISBN: 0-691-00064-6)
A classic, this short book explains the physics of diffusion and other random phenomena, and their biological significance. Highly recommended.
Molecular Driving Forces
by Sarina Bromberg and Ken A. Dill (686 pages; Garland, 2002; ISBN 0815320515)
A recent textbook that explores biophysical chemistry from a statistical mechanics point of view.
Physical Chemistry: Principles and Applications in Biological Sciences
by Ignacio Tinoco, Kenneth Sauer, James C. Wang, Joseph D. Puglisi (740 pages, Prentice Hall, 2001, 4th edition; ISBN 013095943X)
A simple introductory physical chemistry textbook, an excellent source of examples of thermodynamic concerns in biological phenomena.
Nature Insight: Membrane Biology (*)
Nature, Vol. 438, No. 7068 pp. 577-621 (2005).
http://www.nature.com/nature/supplements/insights/membrane_biology/index.html
A series of review articles in Nature on membrane biology. The papers on curvature (McMahon and Gallop), electrostatics (McLaughlin and Murray), and lipid organization (Maxfield and Tabas) are especially relevant to our group's work.
Structure and Dynamics of Membranes
edited by Reinhard Lipowsky and Erich Sackmann (1036 pages, 2 volumes; Elsevier 1995; ISBN 0-444-81975-4)
Available on-line at: http://www1.elsevier.com/homepage/sak/hbbiophys/contenthome1.html
A sprawling book on the physics of membranes. Not great, but worth noting.
The fluid mosaic model of the structure of cell membranes (*)
Singer, S. J. & Nicolson, G. L. (1972) Science 175, 720-731.
A classic paper in which Singer and Nicolson argue that the lipid bilayer forms the basis of cellular membranes, and discuss the implications of this structure.
How proteins produce cellular membrane curvature
Zimmerberg, Joshua and Kozlov, Michael M. (2006) Nat. Rev. Mol. Cell Biol. 7(1), 9-19.
A recent review on the biological contexts and physical mechanisms behind cellular membrane curvature.
Synaptic pattern formation during cellular recognition
Qi, S. Y., Groves, J. T., & Chakraborty, A. K. (2001) Proc. Natl. Acad. Sci. USA 98, 6548-6553.
A physical model of pattern formation phenomena important to immune system function, highlighting mechanical aspects of membrane ordering.
Micropattern Formation in Supported Lipid Membranes
Groves, J. T. & Boxer, S. G. (2002) Accounts of Chemical Research 35, 149-157.
A review article on methods for patterning lipid membranes.
Molecular Biology of the Cell (*)
by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter (1600 pages; Garland, 2002, 4th edition).
A standard introductory biology textbook, MBOC is massive (1600 pages), but full of useful and fascinating information. Its figures are exceptionally clear. It unfortunately treats many controversial or still murky issues as well understood, and is certainly not written from a 'physical' perspective. Still, it is well worth reading. The fourth edition of the book is available free, on-line, through PubMed: http://www.ncbi.nlm.nih.gov/books/NBK21054/. Lipid Bilayer Section [Link]
The Variety of Life : A Survey and a Celebration of All the Creatures that Have Ever Lived
by Colin Tudge (684 pages; Oxford, 2000; ISBN 0198503113)
An amazing book. As the title explains, the author surveys the entire history of life on Earth, as well as discussing the taxonomic means used to classify it. The topic is fascinating, and the book is full of interesting observations and "fun" facts.
Fundamentals of Light Microscopy and Electronic Imaging
by Douglas B. Murphy (360 pages; Wiley-Liss 2001; ISBN 047125391X)
Descriptions of various microscopy techniques. Some are clear and informative, some are not. Link to "Introduction to Fluorescence Microscopy."
Focus on Detection with QDot (R) Conjugates -- Part I: Detection Basics
Quantum Dot Vision, April 2005, pp. 4-9: [PDF]
A short, simple introduction to the basics of fluorescence microscopy. It's from a company that sells quantum dot fluorescent probes, and so is focused on these rather than organic fluorophores, but is nonetheless a good introductory description.
A few papers -- some reviews, some related to holographic optical trap arrays. Not a thorough list.
Optical trapping and manipulation of neutral particles using lasers
Ashkin, A. (1997) Proc. Natl. Acad. Sci. USA 94, 4853-4860. [link]
A Revolution in Optical Manipulation
Grier, D.G. (2003) Nature 424, 810-816 . [link]
Optical Trapping
Neuman, K. C. & Block, S. M. (2004) Rev. Sci. Instr. 75, 2787-2809 . [link]
Dynamic holographic optical tweezers
Curtis, J. E. , Koss, B. A., & Grier, D. G. (2002) Opt. Comm. 207, 169-175 . [link]
Symmetry dependence of holograms for optical trapping
Curtis, J. E., Schmitz, C. H., & Spatz, J. P. (2004) Opt. Lett . 30, 2086-2088 . [link]
A few good books. Not a thorough list.
An Introduction to Error Analysis: The Study of Uncertainties in Physical Measurements
John R. Taylor.
Data reduction and error analysis for the physical sciences
Bevington, Philip R.
Journals worth scanning regularly:
Proceedings of the National Academy of Sciences
Virtual Journal of Biological Physics Research -- a monthly compilation of interesting biophysical articles from a variety of journals.
Other journals that often contain articles of interest: Physical Review Letters, Langmuir, Soft Matter, JACS, Journal of Physical Chemistry-B, Physical Review E, Nature Materials, Physical Biology, Reviews of Modern Physics .