Biophysics, Imaging, and Soft Materials


[See also here, here, and here for Suggested Readings on Soft Condensed Matter Physics and Biophysics]

[All papers, via PubMed: here; requires NCBI login]

Parthasarathy Lab, The University of Oregon

Michael J. Taormina*, Edouard A. Hay*, and Raghuveer Parthasarathy [* = equal contributors], "Passive and Active Microrheology of the Intestinal Fluid of the Larval Zebrafish." Biophysical Journal 113:957-965 (2017). [Link]

J. T. Nichols, B. Blanco-Sanchez, E. P. Brooks, R. Parthasarathy, J. Dowd, A. Subramanian, G. Nachtrab, K. D. Poss, T. F. Schilling, C. B. Kimmel, "Ligament versus bone cell identity in the zebrafish hyoid skeleton is regulated by mef2ca." Development 143: 4430-4440 (2016). [PMID 27789622] [Link]

Travis J. Wiles, Matthew L. Jemielita, Ryan P. Baker, Brandon H. Schlomann, Savannah L. Logan, Julia Ganz, Ellie Melancon, Judith S. Eisen, Karen Guillemin, Raghuveer Parthasarathy , "Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota." PLoS Biol. 14(7): e1002517 (2016). [Link.] (Earlier version (preprint) at bioRxiv.) Writeup in [Link]; [Blog post]

[preprint] M.J. Taormina, R. Parthasarathy, "Active Microrheology of Intestinal Mucus in the Larval Zebrafish." bioRxiv, (2016). [Link]

A. S. Rolig, R. Parthasarathy, A. R. Burns, B. J. M. Bohannan, K. Guillemin, "Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses." Cell Host Microbe 18: 613-620 (2015). [PMID 26567512] [Link]

W. Z. Stephens, T. J. Wiles, E. S. Martinez, M. Jemielita, A. R. Burns, R. Parthasarathy, B. J. M. Bohannan, K. Guillemin, "Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine." mBio 6: (2015). [PMID 26507229] [Link]

Tristan T. Hormel, Matthew A. Reyer, Raghuveer Parthasarathy, "Two-Point Microrheology of Phase-Separated Domains in Lipid Bilayers." Biophys. J. 109: 732-726 (2015). [PMID 26287625] [Link]

M. D. Hammers, M. J. Taormina, M. M. Cerda, L. A. Montoya, D. T. Seidenkranz, R. Parthasarathy, M. D. Pluth, "A Bright Fluorescent Probe for H2S Enables Analyte-Responsive, 3D Imaging in Live Zebrafish Using Light Sheet Fluorescence Microscopy." J. Am. Chem. Soc. 137: 10216-10223 (2015), DOI:10.1021/jacs.5b04196. [PMID 26061541] [Link]
Cover art: We made the cover of JACS They didn't accept my overall design, but kept the zebrafish I painted. Here's a direct link to the cover image. -- RP

Raghuveer Parthasarathy, "The Physics of Life: an undergraduate general education biophysics course," Phys. Educ. 50:358-366 (2015). DOI:10.1088/0031-9120/50/3/358 [Link]

Ryan Baker, Michael J. Taormina, Matthew Jemielita, and Raghuveer Parthasarathy, "A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens," J. Microscopy 258: 105-112 (2015). DOI: 10.1111/jmi.12220 [Link]

Matthew Jemielita, Michael J Taormina, Adam R Burns, Jennifer S Hampton, Annah S Rolig, Karen Guillemin, Raghuveer Parthasarathy, "Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut," mBio 5: e01751-14 (2014). [Link] [Blog post] Our work was selected as a featured image by mBio.

Tristan T. Hormel, Sarah Q. Kurihara, M. Kathleen Brennan, Matthew C. Wozniak, and Raghuveer Parthasarathy, "Measuring Lipid Membrane Viscosity Using Rotational and Translational Probe Diffusion," Phys. Rev. Lett. 112, 188101 (2014). [Link]. This paper was also featured with a "synopsis" in Physics: [Link] and as a "research highlight" in Nature Chemical Biology: [Link]. [Blog post]

Kyle J. Welch, Isaac Hastings-Hauss, Raghuveer Parthasarathy, and Eric I. Corwin, "Ballistic and diffusive dynamics in a two-dimensional ideal gas of macroscopic chaotic Faraday waves," Phys. Rev. E 89: 042143 (2014). [Link]

Alexander R. Small and Raghuveer Parthasarathy, "Superresolution Localization Methods," Annual Reviews of Physical Chemistry 65: 107-125 (2014). [Link]

Andrew F. Loftus, Sigrid Noreng, Vivian L. Hsieh, and Raghuveer Parthasarathy, "Robust Measurement of Membrane Bending Moduli Using Light Sheet Fluorescence Imaging of Vesicle Fluctuations," Langmuir 29: 14588-14594 (2013). [Link.] [Blog post]

Matthew Jemielita*, Michael J. Taormina*, April DeLaurier, Charles B. Kimmel, and Raghuveer Parthasarathy (*Equal authors), "Comparing phototoxicity during the development of a zebrafish craniofacial bone using confocal and light sheet fluorescence microscopy techniques," J. Biophotonics 6: 920-928 (2013). [Link]

Andrew F. Loftus, Vivian Hsieh, and Raghuveer Parthasarathy, "Modulation of membrane rigidity by the human vesicle trafficking proteins Sar1A and Sar1B," Biophys. Biochem. Res. Comm. 426: 585-589 (2012). Link.

Raghuveer Parthasarathy, "Rapid, accurate particle tracking by calculation of radial symmetry centers," Nature Methods 9: 724-726 (2012), DOI: 10.1038/nmeth.2071 . [Link]
Abstract: I introduce an algorithm for sub-pixel localization of imaged objects based on an analytic, non-iterative calculation of the best-fit radial symmetry center. This approach yields tracking accuracies that are near theoretical limits, similar to Gaussian fitting, but with orders of magnitude faster execution time, lower sensitivity to nearby particles, and applicability to any radially symmetric intensity distribution. I demonstrate the method with several types of data, including super-resolution microscopy images.
Also: There's an associated News and Views article (by Alex Small).

Michael J. Taormina, Matthew Jemielita, W. Zac Stephens, Adam R. Burns, Joshua V. Troll, Raghuveer Parthasarathy, and Karen Guillemin, "Investigating Bacterial-Animal Symbioses with Light Sheet Microscopy," Biol. Bulletin 223: 7-20 (2012). (Part of a special issue on "Discoveries in Animal Symbiosis in the 'omics' Age," August 2012.) [Link]

Emily Goers Sweeney, J. Nathan Henderson, John Goers, Christopher Wreden, Kevin G. Hicks, Jeneva K. Foster, Raghuveer Parthasarathy, S. James Remington, and Karen Guillemin, "Structure and Proposed Mechanism for the pH-Sensing Helicobacter pylori Chemoreceptor TlpB," Structure 20: 1177-1188 (2012). [Link]
Cover art: My artwork for this paper is on the cover of the July issue of Structure. -- RP

Raghuveer Parthasarathy, "Cars and Kinetic Energy - Some Simple Physics with Real-World Relevance," The Physics Teacher 50: 395-397 (2012). [Link]

[Book Chapter] Raghuveer Parthasarathy, "Optics: Basic Physics," in Handbook of Biomedical Optics, ed. D.A. Boas, C. Pitris, N. Ramanujam (CRC Press, 2011). [Link]

[Retracted] Christopher W. Harland, Miranda J. Bradley, and Raghuveer Parthasarathy, "Phospholipid bilayers are viscoelastic," Proc. Natl. Acad. Sci. USA 107: 19146-19150 (2010). Link The conclusions of this paper are wrong -- a consequence of insufficiently precise analysis. Our retraction notice was published in August 2011; you can read the page proof here or a version with graphs (not allowed in the official retraction notice) here. We deeply regret any confusion or wasted effort caused by our flawed paper, and we are happy to provide additional information or resources on technical issues related to the paper's methods.
A postscript: Spurred by these events, I've been thinking about whether there can exist a particle tracking method that is as accurate as direct fitting of Gaussian intensity profiles to particle images (the present state-of-the-art) but that is computationally much faster. I have come up with a new sort of tracking, based on maximizing radial symmetry, that works well. For a very brief description, see here. For a longer discussion and tests of the method, see my 2012 Nature Methods paper noted above, and my Particle Tracking page. -- RP.

Edward I. Settles*, Andrew F. Loftus*, Alesia N. McKeown, and Raghuveer Parthasarathy, "The vesicle trafficking protein Sar1 lowers lipid membrane rigidity," Biophys. J. 99: 1539-1545 (2010). [* = equal contributors] [ Link]

[Preview / Commentary paper; not a peer-reviewed article] Anica M. Wandler, Raghuveer Parthasarathy, and Karen Guillemin, "A greasy foothold for Helicobacter pylori," Cell Host & Microbe 7: 338-339 (2010). [Link] [PubMed]

Yupeng Kong and Raghuveer Parthasarathy, "Different modulation mechanisms of attractive colloidal interactions by lipid and protein functionalization," Langmuir 26: 10541-10545 (2010). [Link]

Kamil Godula, Marissa L. Umbel, David Rabuka, Zsofia Botyanszki, Carolyn R. Bertozzi, and Raghuveer Parthasarathy, "Control of the molecular orientation of membrane-anchored biomimetic glycopolymers," J. Am. Chem. Soc. 131: 10263-10268 (2009). [Link] See also the cover of Nature Chemical Biology, July 2010: Journal link, a bigger image with some text, and a better description.

Yupeng Kong and Raghuveer Parthasarathy, "Modulation of attractive colloidal interactions by lipid membrane functionalization," Soft Matter, 5: 2027-2029 (2009) [Link]

Christopher W. Harland*, Zsofia Botyanszki*, David Rabuka, Carolyn R. Bertozzi, and Raghuveer Parthasarathy, "Synthetic trehalose glycolipids confer desiccation resistance to supported lipid monolayers," Langmuir 25: 5193-5198, (2009) [*These authors contributed equally to this work][Link], [PMC Link]

Gregory T. Tietjen, Yupeng Kong, and Raghuveer Parthasarathy "An efficient method for the creation of tunable optical line traps via control of gradient and scattering forces," Opt. Express 16: 10341-10348 (2008) [Link]

Christopher W. Harland, David Rabuka, Carolyn R. Bertozzi, and Raghuveer Parthasarathy. "The M. tuberculosis virulence factor trehalose dimycolate imparts desiccation resistance to model mycobacterial membranes," Biophys. J. 94: 4718-4724 (2008). [Link]

Jay T. Groves, Raghuveer Parthasarathy, and Martin B. Forstner, "Fluorescence Imaging of Membrane Dynamics," Annu. Rev. Biomed. Eng. 10: 311-338 (2008). [Link]

Raghuveer Parthasarathy, David Rabuka, Carolyn Bertozzi, and Jay T. Groves, "Molecular Orientation of Membrane-Anchored Mucin Glycoprotein Mimics, J. Phys. Chem. B, 111: 12133-12135 (2007). [ACS]

David Rabuka, Raghuveer Parthasarathy, Goo Soo Lee, Xing Chen, Jay T. Groves, and Carolyn Bertozzi, "Hierarchical Assembly of Model Cell Surfaces: Synthesis of Mucin Mimetic Polymers and Their Display on Supported Bilayers," J. Amer. Chem. Soc., 129: 5462-5471 (2007). [ACS]

Raghuveer Parthasarathy and Jay T. Groves, "Curvature and spatial organization in biological membranes," Soft Matter, 3: 24-33 (2007). [Link to Soft Matter] [ Journal Cover ]

Membrane biophysics (2004 to 2006)

Raghuveer Parthasarathy, Cheng-han Yu, and Jay T. Groves, "Curvature modulated phase separation in lipid bilayer membranes," Langmuir, 22: 5095-5099 (2006). [ACS]

Raghuveer Parthasarathy and Jay T. Groves, "Coupled membrane fluctuations and protein mobility in supported intermembrane junctions," J. Phys. Chem. B, 110: 8513-8516 (2006). [ACS]

Raghuveer Parthasarathy, Paul A. Cripe, and Jay T. Groves, "Electrostatically Driven Spatial Patterns in Lipid Membrane Composition," Phys. Rev. Lett. 95: 048101 (2005).  [PubMed]

Raghuveer Parthasarathy and Jay T. Groves, "Protein Patterns at Lipid Bilayer Junctions," Proc. Natl. Acad. Sci. 101: 12798-12803 (2004).  [PubMed]

Raghuveer Parthasarathy and Jay T. Groves, "Optical techniques for imaging membrane topography," Cell Biochem. Biophys. 41: 391-414 (2004).  [PubMed]

Raghuveer Parthasarathy, Bryan L. Jackson, Thomas J. Lowery, Amy P. Wong, and Jay T. Groves, "Nonequilibrium Adhesion Patterns at Lipid Bilayer Junctions," J. Phys. Chem. B 108: 649-657 (2004).  [ACS]

Nanocrystals and nanowires (2001 to 2004)

Raghuveer Parthasarathy, Xiao-Min Lin, Klara Elteto, T. F. Rosenbaum, and Heinrich M. Jaeger, "Percolating through Networks of Random Thresholds: Finite Temperature Electron Tunneling in Metal Nanocrystal Arrays," Phys. Rev. Lett. 92: 076801 (2004).

Xiao-Min Lin, Raghuveer Parthasarathy, and Heinrich M. Jaeger, "Nanocrystal Arrays: Self-assembly and physical properties," in the Dekker Encoclyopedia of Nanoscience and Nanotechnology, ed. J.A. Schwarz, C.I. Contescu, K. Putyera (Dekker, 2004).

Thomas Scheibel, Raghuveer Parthasarathy, George Sawicki, Xiao-Min Lin, Heinrich Jaeger, and Susan L. Lindquist, "Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition," Proc. Natl. Acad. Sci. 100: 4527-4532 (2003). [PNAS]

Raghuveer Parthasarathy, Xiao-Min Lin, and Heinrich M. Jaeger, "Electronic transport in metal nanocrystal arrays: the effect of structural disorder on scaling behavior," Phys. Rev. Lett. 87: 186807 (2001).

Xiao-Min Lin, Raghuveer Parthasarathy, and Heinrich M. Jaeger, "Direct patterning of self-assembled nanocrystal monolayers by electron beams," Appl. Phys. Lett. 78: 1915-1917 (2001). [Link]

Other topics (old)

H. M. Rønnow, R. Parthasarathy, J. Jensen, G. Aeppli, T. F. Rosenbaum, and D. F. McMorrow, "Quantum phase transition of a magnet in a spin bath," Science 308: 389-392 (2005). [Link]

S. Ghosh, R. Parthasarathy, T. F. Rosenbaum, and G. Aeppli, "Coherent spin oscillations in a disordered magnet," Science 296: 2195-2198 (2002). [Link]

S. Anders, R. Parthasarathy, H. M. Jaeger, P. Guptasarma, D. G. Hinks, and R. van Veen, "Dynamics of the second peak in the magnetization of Bi2Sr2CaCu2O8 crystals," Phys. Rev. B 58: 6639-6644 (1998).

D. H. Cobden, G. Pilling, R. Parthasarathy, P. L. McEuen, I. M. Castleton, E. H. Linfield, D. A. Ritchie, and G. A. C. Jones, "Current flow past an etched barrier: field emission from a two-dimensional electron gas," Europhys. Lett. 41: 327-332 (1998).

R. Parthasarathy, C. Franck, R. Treffers, D. Cudaback, C. Heiles, C. Hancox, and R. Millan, "A rooftop radio observatory: an undergraduate telescope system at the University of California at Berkeley," Am. J. Phys. 66: 768-771 (1998).[Link]