Biophysics Journal Club at Ohio University

Biophysics Journal Club @ Ohio University

In this Biophysics Seminar we discuss topics in Biophysics ranging from basic ideas to the latest developments. Participants present articles in a 30 min presentation format with a plenty of time for discussion.

One credit is encouraged to be taken:
Graduate: Phys 897E call# 05713 and Undergraduate Phys 493 call# 05638

Time and place: Wednesday's 4:00pm, Physics Department, Clippinger 259

If you want to be added to the journal club mailing list and/or suggest an article or subject to discuss please e-mail to : Ido Braslavsky

Schedule for Fall 2008/2009

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
Sept 10, 2008		Organizational meeting
Sept 17
Sept 24
Oct 1
Oct 8
Oct 15
Oct 22
Oct 29
Nov 5
Nov12

Previous talks:
Spring 2008 Schedule

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
Apr 2, 2008		Organizational meeting
Apr 09	Ido Braslavsky	Single-Molecule DNA Sequencing of a Viral Genome, Harris et al, Science 4 April 2008: Vol. 320, pp. 106 - 109.
Apr 16	Alexander Neiman	Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution by Ilya Nemenman, Geoffrey D. Lewen, William Bialek, Rob R. de Ruyter van Steveninck PLoS Computational Biology, 4(3): e1000025. doi:10.1371/journal.pcbi.1000025
Apr 23	Swaminathan Divya	Intrinsic Fluctuations, Robustness, and Tunability in Signaling Cycles Biophysical Journal Volume 92 June 2007 4473–4481
Apr 30	Silvina Ponce-Dawson	Quantifying calcium fluxes underlying calcium puffs in Xenopus laevis oocytes	PIRE collaborator
May 07	Hanna Salman	Biophys Seminar May 7: Temperature Gradients from Geophysics to Biology CMSS May 8: Population Effects on Bacterial Thermotaxis
May 14	Esko Kauppinen	Carbon Nanobud - A Novel Nanomaterial: Synthesis, Structure, Field Emission and Transport Properties	CMSS seminar, Walter 245
May 21	Anastasios Matzavinos	Theoretical approaches to actin filament dynamics,	QBI Seminar, Morton 320
May 28	Sonya Bahar	Synchronization in the Brain: From Epilepsy to Traumatic Brain Injury	QBI Seminar, Irvine 159
June 4	Chris Diltz	Applications of Neutron Scattering

Winter 2008

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
Jan/9/ 2008		Organizational meeting
Jan/16/ 2008	Yeliz Celik	Metal Nanoparticle Pollutants Interfere with Pulmonary Surfactant Function In Vitro Biophysical Journal 94:855-868 (2008)
Jan/23/ 2008	Marianne Lee	The Long and Short of Improving Distant Homology Detection	Best presentation award in OSU biophysics seminar, Fall 2007
Jan/30/ 2008	David Tees	Force fluctuations and polymerization dynamics of intracellular microtubules. PNAS 2007 104(41):16128-16133, October 9, 2007. Clifford P. Brangwynne, F. C. MacKintosh, and David A. Weitz
Feb/6/2008	Greg Smith	"Modeling local control of calcium-induced calcium release in cardiac myocytes"	QBI Seminar : Irvine 159, February 6, 4:10-5:00 PM
Feb/13/2008	Yinka Fuwape	Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination, PLOS Computational Biology ,November 2007,by Naoki Masuda and Brent Doiron.i
Feb/20/2008	Sarah Javaid	hMSH2-hMSH6 Interaction with Mismatched DNA	Best presentation award in OSU biophysics seminar, Fall 2007
Feb/27/2008	David Russell
Mar/5/2008	Manoj Nair	Membrane Insertion of the Bacillus thuringiensis Cry1Ab Toxin: Single Mutation in Domain II Blocks Partitioning	Best presentation award in OSU biophysics seminar, Fall 2007

Fall 2007

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
Sep/5/2007		Organizational meeting
Sep/12/2007	David Tees	Introduction for Biophysics
Sep/19/2007	Fabio Marcheson	The Nonequilibrium Statistical Physics of Small Devices
Sep/26/2007	Ido Braslavsky	Ice Binding Proteins and their interaction with Ice serfaces	J. Phys.: Condens. Matter 19 (2007) 412101 (12pp) Biophysical Journal, 92(10)3663, 2007. Physics Today, May 2007
Oct/3/2007	Peter Jung	Slow axonal transport: Is there a stationary population of neurofilaments?	N. Trivedi and P. Jung and A. Brown, J Neurosci. Vol.17, 507 (2007) R. A. Nixon and K. B. Logvinenko, J Cell Biol 1986, Vol. 102, 647
Oct/10/2007	Aman Ullah	Effect of Calcium Concentration on the Structure of Casein Micelles in Thin Films	Muller-Buschbaum and W. Doster et al Biophysical Journal Volume 93 August 2007 960968
Oct/17/2007	Swaminathan Divya	"Robust protein-protein interactions in crowded cellular environments".	Deeds et al, PNAS 104(2007)14952
Oct 24/2007	Young Eun Choi	One at a time, live tracking of NGF axonal transport using quantum dots	PNAS 2007 104:13666-13671
Oct31/2007	Wan Congshang	Geometry-induced asymmetric diffusion	PNAS 2007 104:9580-9584
Nov/7/2007	Yeliz Celik	Antifreeze Proteins at the Ice/Water Interface: Three Calculated Discriminating Properties for Orientation of Type I Proteins	Andrzej Wierzbicki et al Biophysical Journal, 93(2007)1442

Spring 2007

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
3/28/07		Organizational meeting
4/4/07	Natalya Pertaya	Fluorescence Microscopy Studies of Ice Surface Antifreeze Protein Interactions	Biophysical Journal, May 2007, Scientific American Physics update March 2007
4/11/07	Acharya Dandapani	LT-STM for imaging, manipulation, molecular recognition and spectroscopy
4/18/07	Maya Bar	Antifreeze Protein Scaffold for the Design of Novel Surface Binding Biomolecules	Weizman Institute, Israel
4/25/07	No meeting	NanoSumit
5/2/07	Yeliz Celik	Microfluidic devices for ice crystal growth experiments
5/9/07	Tatyana Engel	Firing Statistics in Neurons as Non-Markovian First Passage Time Problem	Humboldt University, Berlin
5/16/07	Andrey Shilnikov	Routes to bursting in neuronal models	Georgia State Univ, Atlanta
5/30/07	Ido Braslavsky	Optical tweezers & fluorescence microscopy: a lab setup for a Biophysics course

Winter 2007

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
01/03/07		Organizational meeting
1/10/07	Natalie Goldberger	Using Proteomics and Immunofluorescence to Investigate Potential Mechanisms Responsible for SARM Tissue-Selectivity	Best presentation award in OSU biophysics seminar, Fall 2006
1/17/07	David Tees	Catch-Bond Model Derived from Allostery Explains Force-Activated Bacterial Adhesion, Thomas et al . Biophysical Journal 90(2006) 753–764
01/24/07	Arun Sridhar	"BEWARE OF DOGMA" - The tale of "I_Kur-like" current in the cardiac ventricle	Best presentation award in OSU biophysics seminar, Fall 2006
01/31/07	Sulaiman Kareem	`Mechanics of actomyosin bonds in different nucleotide states are tuned to muscle contraction. PNAS. 103(26):9844-9849. June 27, 2006. By`B. Guo and W. H. Guilford.
02/07/07	David Russell	Murata Y, Iwasaki H, Sasaki M, Inaba K, Okamura Y. Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor. Nature. 2005 vol.435(7046):1239-1243.
02/21/07	Peter Jung	Can the Ca2+ hypothesis and the Ca2+-voltage hypothesis for neurotransmitter release be reconciled?, Proc Natl Acad Sci U S A. 2002 Dec 24;99(26)
02/28/07	Jong-Hoon Nam	Virtual Hair Cell: Computational Study on the Structure, Dynamics and Mechanoelectric Transduction of Vestibular Hair cell

Fall 2006

Date

Speaker

Subject

Supporting materials

09/06/2006

Organizational meeting

Sept 13

Web lecture

No Coli is an Island
	31 January 2004
	Robert Austin (Princeton University)

Web lectures: Opportunities in Biology for Physicists

Sept 20

David Tees

Sub-angstrom conformational changes of a single molecule captured by AFM variance analysis. Kirstin A. Walther, Jasna Brujic, Hongbin Li, and Julio M. Fernández. Biophysical Journal, 90(2006)3806

Sept 27

Andrew Nevai

A mathematical model of plant competition for sunlight

QBI Talk at Morton 320

Oct 4

Prithu Sundd

Neutrophil-Bead Collision Assay: Pharmacologically Induced Changes in MembraneMechanics Regulate the PSGL-1/P-Selectin Adhesion Lifetime
K. E. Edmondson W. S. Denney and S. L. Diamond
Biophysical Journal 89:3603-3614 (2005)

Nov 1

Ru Zhang

In-Chul Yeh and Gerhard Hummer, Nucleic acid transport through carbon nanotube membranes, PNAS, 101(33):12177-12182, August 17, 2004

Nov 1

Yeliz Celik

Yannick Rondelez et al., Microfabricated arrays of femtoliter chambers allow single molecule enzymology, Nature Biotechnology, 23(3):361-365, 2005

Nov 8

Silki Arora

The Stability of a Stochastic CaMKII Switch: Dependence on the Number of Enzyme Molecules and Protein Turnover. Public Library of Science - Biology. 3(4):e107, April 2005

Paul Miller, Anatol M. Zhabotinsky, John E. Lisman, Xiao-Jing Wang.

Nov 8

YoungEun Choi

Pressure-driven transport of confined DNA polymers in fluidic channels. PNAS. 103(43):15853-15858, October 24, 2006, Derek Stein, Frank H. J. van der Heyden, Wiepke J. A. Koopmans, and Cees Dekker.

Spring 2006 Schedule

Date	Speaker	Subject	Supporting materials
April 5		NanoSummit
April 12	Ghanim Ulla	Calcium signaling differentiation during oocyte maturation, Wassim et al. Developmental Biology 288 (2005) 514 – 525
April 19	David Tees	Nanopore Unzipping of Individual DNA Hairpin Molecules Mathe et al., Biophysical Journal, 87 ( 2004) 3205	Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel Mathe et al. PNAS 102(2005)12377
April 26	Anand Pai	Regulated Degradation Is a Mechanism for Suppressing Stochastic Fluctuations in Gene Regulatory Networks, El-Samad and Khammash, Biophysical Journal 90:3749-3761 (2006)
May 3	Alexander Neiman	How strongly electric fish generate electric discharges
May 10	Peter Jung	Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. English et al, Nature Chemical Biology, Vol.2, 87 (2006)
May 17	Sulaiman Kareem	Enforced Detachment of Red Blood Cells Adhering to Surfaces: Statics and Dynamics, Pierrat et al. Biophysical Journal 87 (2004) 2855
May 24	Timur

Winter 2006 Schedule

Date	Speaker	Subject	Supporting materials
01/04/06		Organizational meeting
01/11/06	Sasuke Miyazima	3D modeling for sagittal suture. Y Ootaa, K Onob, S Miyazimac,Physica A 359 (2006) 538–546	An exact threshold value of a four-dimensional hyper-cube
01/18/06	Ido Braslavsky	Materials for and from Biology: Inspiration from Biological Optics for Advanced Photonic Systems, Lee and Szema, Science 310(2005)1148	Direct Fabrication of Large Micropatterned Single Crystals, Aizenberg et al, Science299( 2003) 1205
01/25/06	Celik Yeliz	Diffusion and Tissue Microstructure, Sen, Journal of Physics:Condensed Matter 16(2004)S5213
02/01/06	Yohann Misquitta(OSU)	Crystallization of membrane proteins in lipidic bilayers	Best presentation award in OSU biophysics seminar, Fall 2005
02/08/06	Wei Zang	Magnetic nanoparticles: Applications in biomedicine, L. R. Moore, J. Magnetism and Magnetic Materials 225(2001)277	R. E. Rosensweig,Heating magnetic fluid with alternating magnetic field J. M. M. M. 252, 370 (2002)
02/15/06	Rong Yang	Nanowire Nanosensors for Highly Sensitive and Selective Detection of Biological and Chemical Species, Yi Cui, Qingqiao Wei, Hongkun Park,Charles M. Lieber, SCIENCE 293(2001)1289	Label-free detection of small-molecule–protein interactions by using nanowire nanosensors,Wayne U. Wang, Chuo Chen, Keng-hui Lin, Ying Fang, and Charles M. Lieber, PNAS 102( 2005)3211
02/22/06	Violeta Lancu	Single molecule switch made of chlorophyll-a from spinach
03/01/06	Rinku Jain(OSU)	"Mass Spectrometry as a tool for Structural Biology"	Best presentation award in OSU biophysics seminar, Fall 2005
03/08/06	Natalya Pertaya	"Fluorescence Microscopy Studies of Antifreeze Proteins"

Fall 2005 Schedule

Date	Speaker	Subject	Supporting materials: additional articles, suggested readings
09/07/05		Organizational meeting
09/14/05	David Tees	Mechanism of actin-based motility: A dynamic state diagram. Anne Bernheim-Groswasser, Jacques Prost, and Cécile Sykes. Biophysical Journal. 89:1411-1419, August 2005
09/21/05	David Russell	"Survey of Electroreceptors"	Two Distinct Types of Noisy Oscillators in Electroreceptors of Paddlefish Alexander B. Neiman and David F. Russell J Neurophysiol 92: 492–509, 2004
9/28/05		Cenceled (Conference)
10/05/05	Peter Jung	Modeling Neurofilament Transport: The Stop-and-Go Hypothesis. Anthony Brown, Lei Wang, and Peter Jung, Molecular Biology of the Cell 16,(2005) 4243	Mini-Review: Axonal transport of membranous and nonmembranous cargoes: a unified perspective A. Brown ,JCB,160( 2003) 817
10/12/05	Anand Pai	Power-Law Rheology of Isolated Nuclei with Deformation Mapping of Nuclear Substructures, Kris Noel Dahl , Adam J. Engler , J. David Pajerowski and Dennis E. Discher, Biophysical Journal 89(2005 ) 2855
10/19/05	Wei Zhang	"Charge transport in DNA molecules"	Polarons with a twist, W. Zhang, A. O. Govorov, and S.E. Ulloa Phys. Rev. B 66, 060303 (2002) Extended states in disordered systems: Role of off-diagonal correlations ,Wei Zhang and Sergio E. Ulloa Phys. Rev. B 69, 153203 (2004)
10/26/05	Prithu Sundd	Leukocyte firm adhesion in capillary-sized, selectin coated micropipettes
11/02/05		Discussion on Biological Physics group poster for Physics Open House, Nov 4
11/09/05	Alexander Neiman	"Active mechanoelectrical transduction and amplification by hair cells"	1. Hudspeth,A.J. How the ear's works work : mechanoelectrical transduction and amplification by hair cells.C.R.Biol. 328: 155-162 (2005). 2. Martin,P.; Mehta,A.D.; Hudspeth,A.J. Negative hair-bundle stiffness betrays a mechanism for mechanical amplification by the hair cell. PNAS 97:12026 - 12031 (2000). 3. Eguiluz,V.M.; Ospeck,M.; Choe,Y.; Hudspeth,A.J.; Magnasco,M.O. Essential nonlinearities in hearing. Phys. Rev. Lett. 84: 5232-5235 (2000).

Spring 2005 Schedule

Date	Speaker	Subject	Supporting materials: additional articles, suggested readings
03/30/05		Organizational meeting
04/06/05	Liwei Chen	On the thermodynamics of force spectroscopy 1) Brownian Force Profile Reconstruction of Interfacial 1-Nonanol Solvent Structure, Ashby P.D, and Lieber ,J. AM. CHEM. SOC. 2004, 126, 16973-16980 3) How does a system respond when driven away from thermal equilibrium? Jarzynski C., PNAS 98(2001)3636–3638	2) Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski’s Equality, Liphardt J, Dumont S, Smith SB, I Tinoco Jr. I,Bustamante C, SCIENCE 96(2002)1832 4) Nonequilibrium Equality for Free Energy Differences Jarzynski C., Physical Review Letters 78(1997)2690
04/13/05	Ido Braslavsky	• A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion, Carl L. Hansen, Emmanuel Skordalakes, James M. Berger, and Stephen R. Quake, PNAS 99( 2002)16531	• Systematic investigation of protein phase behavior with a microfluidic formulator, Carl L. Hansen, Morten O. A. Sommer, and Stephen R. Quake, PNAS 101(2004) 14431
4/20/05	William Moravec	Differences Between Stereocilia Numbers on Type I and Type II Vestibular Hair Cells,W. J. Moravec and E. H. Peterson, J Neurophysiol 92(2004) 3153
04/27/05	Anand Pai	Cell Membrane Alignment along Adhesive Surfaces: Contribution of Active and Passive Cell Processes,A Pierres, P Eymeric, E Baloche, D Touchard, A Benoliel, and P Bongrand, Biophysical Journal 84(2003)2058
05/04/05		Not scheduled
05/11/05	Clapa, Vasil-Iulian	DNA in a material world Nadrian C. Seeman NATURE 421(2003) 427	DNA-Templated Self-Assembly Science,301(2003)1882 DNA computing on surfaces, NATURE 403(2000)175 DNA-templated assembly and electrode attachment of a conducting silver wire, Nature 391(1998)775
05/18/05	Jie Zhang	The thermal convection in a vertical soap film
05/25/05	Melanie Tomczak	Biomimetic Approaches to Materials Chemistry
06/01/05	Natalya Pertaya	b-Helix structure and ice-binding properties of a hyperactive antifreeze protein froman insect, S P. Graether, M J. Kuiper, S M. Gagne¬ß, V K. Walker, Z Jia, B D. Sykesß & L. Davies, Nature 406, (2000), 325-328.

Winter 2005 Schedule

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
01/05/05		Organizational meeting
01/12/05	Prithu Sundd	Neutrophil Adhesive Contact Dependence on Impingement Force
01/19/05	Ghanim Ulla	"Statistical properties of elementary calcium release events (Puffs and blips); A theoretical approach" by Ghanim Ullah and Peter Jung.	Article 1 Article 2
01/26/05	David Tees	Simultaneous atomic force microscope and fluorescence measurements of protein unfolding using a calibrated evanescent wave, A Sarkar, R. B. Robertson, and J. M. Fernandez, PNAS 101(2004)12882
02/02/05	Larrry Wilen	Single metallic nanoparticle imaging for protein detection in cells, Cognet et al, PNAS 100(2003)11350
02/09/05	Doug Wylie	Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer, Yang et al. Science 302(2003)262.	The Motions of an Enzyme Soloist,Michel Orrit,Science, 302(2003) 239
02/16/05	Carlos Di Prinzio	A New Model for Simulating 3-D Crystal Growth and Its Application to the Study of Antifreeze Proteins Wathen et al J. AM. CHEM. SOC. 125(2003)730	Kinetic Pinning and Biological Antifreezes Leonard M. Sander and Alexei V. Tkachenko M , Physicsl Review Letters 93(2004) 128102-1:4
02/23/05	Natalya Pertaya	Fluorescence and confocal microscopy studies of the ice surface - antifreeze protein interactions
03/01/05	Jorge Brea	Stochastic phase resetting of stimulus-locked responses of two coupled oscillators: Transient response clustering, synchronization, and desynchronization, Peter A. Tassa, Chaos 13( 2003) 364
03/09/05	Sulaiman Kareem	Force History Dependence of Receptor-Ligand Dissociation, Marshall et al. Biophys. J. 2005 88: 1458-1466

Fall 2004

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
09/08/04		Organizational meeting
09/15/04	David Tees	Pseudopod Projection and Cell Spreading of Passive Leukocytes in Response to Fluid Shear Stress
09/22/04	Ido Braslavsky	Advanced Sequencing Technologies: Methods and Goals Nature Reviews, 5(2004)335
09/29/04	Clapa Vasile-Iulian	Mechanical switching and coupling between two dissociation pathways in a P-selectin adhesion bond, PNAS101(2004)11281
10/06/04	Ghanim Ullah	Inositol triphosphate receptors: the search for the structure and effects on mathematical modeling. TRENDS in Biochemical Sciences 29(2004)210
10/13/04	Shura Neiman	Oscillatory Activity in Electrosensory Neurons Increases with the Spatial Correlation of the Stochastic Input Stimulus, PRL 93(2004)048101-1	Related article: NATURE 421(2003)539
10/20/04		Not scheduled
10/27/04	Doug Wylie	Single-molecule high-resolution imaging with photobleaching, PNAS 101(2004)6462
11/03/04 A	Yue Pan	The hydrodynamics of DNA electrophoretic stretch and relaxation in a polymer solution, Biophysical Journal, 87(2004)468.
11/03/04 B	Allen Dahili	Single Particle Tracking: Brownian dynamics of viscoelastic materials, Biophysical Journal, 79(2000)137.
11/10/04 A	Sulaiman Kareem	Forces generated during actin-based propulsion: A direct measurement by micromanipulation, PNAS, 101: 5992-5997, 2004
11/10/04 B	Harsh Pratap	Neutrophil string formation: Hydrodynamic thresholding and cellular deformation during Cell Collisions, Biophys. J. 86: 4030-4039, 2004

Spring 2004

Date	Speaker	Subject	Supporting materials: abstract, suggested readings
03/31/04		Organizational meeting
04/07/04	Peter Jung	Neural-Glial Signaling: Modeling the Tripartite Synapse	Article1, Article2, Article3, Article4
04/14/04	Bob Rakowski	Determining the occupancy of ion channels: The Ussing flux ratio exponent	related article
04/21/04	Suhita Nadkarni	ATP Released by Astrocytes Mediates Glutamatergic Activity-Dependent Heterosynaptic Suppression	Review on the article Supplementary figures: fig1, fig2, fig3,fig4
28/04	David Tees	Dynamic Tension Spectroscopy and Strength of Biomembranes, Evans et al., Biophysical Journal, 85(2003)2342
05/05/04	Ghanim Ulla	Gating, regulation and physiological role of connexin 43 (Cx 43) hemichannels, PNAS 100(2003)11388.	Related article
05/12/04	Saw Hla	Self assembled molecular layers for Nanobio-electronics applications	OU-News: Spinach Power, STM study of self-organization of b-carotene
05/19/04	Baix Su	A nanodevice for rectification and pumping ions
05/26/04	Ido Braslavsky	The bacteriophage Phi 29 portal motor can package DNA against a large internal force, Smith et al, Nature 413(2001)752	Web lectures: Opportunities in Biology for Physicists "Grabbing the Cat by the Tail: Packaging of DNA by Single Particles of Baceriophage phi29" by Carlos Bustamante
06/02/04	Prithu Sundd	Cell adhesion in capillary-sized, ligand-coated micropipettes