2017

P. Subramanian, S. Pirbadian, M.Y. El-Naggar, G.J Jensen, The ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryo-tomography, bioRxiv, 2017
doi: 10.1101/103242

L.A. Zacharoff, M.Y. El-Naggar. Redox Conduction in Biofilms: From Respiration to Living Electronics, Current Opinion in Electrochemistry, 2017
doi: 10.1016/j.coelec.2017.09.003

H.S. Byun, M.Y. El-Naggar, R.K. Kalia, A. Nakano, P. Vashishta, A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics, Computer Physics Communications, 219, 246-254, 2017
doi: 10.1016/j.cpc.2017.05.028

A.R. Rowe, P. Rajeev, A. Jain, S. Pirbadian, A. Okamoto, J.A. Gralnick, M.Y. El-Naggar, K.H. Nealson, Tracking electron uptake from a cathode into Shewanella cells: implications for generating maintenance energy from solid substrates, bioRxiv, 2017
doi: 10.1101/116475

N.P. Shroff, S. Xu, J. Acevedo, J. Lima, M.Y. El-Naggar, S.E. Finkel, A novel microenvironment for Shewanella oneidensis MR-1 exists within graphite felt electrodes, Journal of The Electrochemical Society, 164, 2017
doi: 10.1149/2.0161703jes

2016

M. D. Yates, S.M. Strycharz-Glaven, J. P. Golden, J. Roy, S. Tsoi, J. S. Erickson, M.Y. El-Naggar, S. Calabrese Barton, L. M. Tender. Measuring conductivity of living Geobacter sulfurreducens biofilms, Nature Nanotechnology, 11, 2016
doi: 10.1038/nnano.2016.186

S. E. Barchinger, S. Pirbadian, C. Sambles, C.S. Baker, K.M. Leung, N.J. Burroughs, M.Y. El-Naggar and J.H. Golbeck. Regulation of Gene Expression During Electron Acceptor Limitation and Bacterial Nanowire Formation in Shewanella oneidensis MR-1, Applied and Envrionmental Microbiology, 82, 5428-5443, 2016
doi: 10.1128/AEM.01615-16

T. Kunoh, N. Nagaoka, I.R. McFarlane, K. Tamura, M.Y. El-Naggar, H. Kunoh, and J. Takada. Dissociation and Re-Aggregation of Multicell-Ensheathed Fragments Responsible for Rapid Production of Massive Clumps of Leptothrix Sheaths, Biology, 5(3), 32, 2016
doi: 10.3390/biology5030032

T. Kunoh, H. Hashimoto, I.R. McFarlane, N. Hayashi, T. Suzuki, E. Taketa, K. Tamura, M. Takano, M.Y. El-Naggar, H. Kunoh, and J. Takada. Abiotic Deposition of Fe Complexes onto Leptothrix Sheaths, Biology, 5(2), 26, 2016.
doi: 10.3390/biology5020026

Y. Jangir, S. French, L.M. Momper, D.P. Moser, J.P. Amend, and M.Y. El-Naggar. Isolation and Characterization of Electrochemically Active Subsurface Delftia and Azonexus Species, Frontiers in Microbiology, 7, 756, 2016. 
doi: 10.3389/fmicb.2016.00756

S. Xu, Y. Jangir, and M.Y. El-Naggar. Disentangling the roles of free and cytochrome-bound flavins in extracellular electron transport from Shewanella oneidensis MR-1, Electrochimica Acta, 198, 49-55, 2016. 
doi: 10.1016/j.electacta.2016.03.074

C. Masato Nakano, E. Moen, H.S. Byun, H. Ma, B. Newman, A. McDowell, T. Wei and M.Y. El-Naggar, iBET: Immersive visualization of biological electron-transfer dynamics, Journal of Molecular Graphics and Modelling, 65, 94-99, 2016.
doi: 10.1016/j.jmgm.2016.02.009

N. Michelusi, J. Boedicker, M.Y. El-Naggar, and U. Mitra, Queuing models for abstracting interactions in bacterial communities, IEEE Journal on Selected Areas in Communications, 34, 584-599, 2016.
doi: 10.1109/JSAC.2016.2525558

2015

M.D. Yates, J. Golden, J. Roy, S.M. Strycharz-Glaven, S. Tsoi, J. Erickson, M.Y. El-Naggar, S. Calabrese Barton, L. Tender, Thermally activated long range electron transport in living biofilms, Physical Chemistry Chemical Physics, 17, 32564-32570, 2015.
doi: 10.1039/C5CP05152E

B.J. Gross, M.Y. El-Naggar. A combined electrochemical and optical trapping platform for measuring single cell respiration rates at electrode interfaces, Review of Scientific Instruments, 86, 064301, 2015.
doi: 10.1063/1.4922853

C.M. Nakano, H.S. Byun, H. Ma, T. Wei, M.Y. El-Naggar. A framework for stochastic simulations and visualization of biological electron-transfer dynamics, Computer Physics Communications, 193, 1-9, 2015.
doi: 10.1016/j.cpc.2015.03.009

I.R. McFarlane, J.R. Lazzari-Dean, M.Y. El-Naggar. Field effect transistors based on semiconductive microbially synthesized chalcogenide nanofibers, Acta Biomaterialia, 13, 364-373, 2015.
doi: 10.1016/j.actbio.2014.11.005 News Coverage: Materials Today - Bacteria turn nano fiber synthesis green

2014

N. Michelusi, S. Pirbadian, M.Y. El-Naggar, U. Mitra. A stochastic model for electron transfer in bacterial cables, IEEE Journal on Selected Areas in Communication, 32, 2402-2416, 2014.
doi: 10.1109/JSAC.2014.2367666

H.S. Byun, S. Pirbadian, A. Nakano, L. Shi, M.Y. El-Naggar. Kinetic Monte Carlo simulations and molecular conductance measurements of the bacterial decaheme cytochrome MtrF, ChemElectroChem, 1, 1932-1939, 2014.
doi: 10.1002/celc.201402211

P. Atanassov, M.Y. El-Naggar, S. Cosnier, U. Schröder. Biological Fuel Cells: Cardinal Advances and Critical Challenges, ChemElectroChem, 1, 1702-1704, 2014. 
doi: 10.1002/celc.201402361

S. Pirbadian, S. E. Barchinger, K.M. Leung, H.S. Byun, Y. Jangir, R.A. Bouhenni, S.B. Reed, M.F. Romine, D.A. Saffarini, L. Shi, Y.A. Gorby, J. H. Golbeck, and M.Y. El-Naggar. Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components, Proceedings of the National Academy of Sciences of the United States of America, 111, 12883-12888, 2014.
doi: 10.1073/pnas.1410551111 News Coverage: Nature Nanotechnology, Nature Chemical Biology, USC Press release, Discussion on Public Radio's Science Friday, Phys.Org, Popular Science.

N. Michelusi, S. Pirbadian, M.Y. El-Naggar, U. Mitra. A model for electron transfer and cell energetics in bacterial cables, IEEE CISS , 2014.
doi: 10.1109/CISS.2014.6814163

2013

K.M Leung, G Wanger, M.Y. El-Naggar, Y. Gorby, G. Southam, W.M. Lau and J. Yang. Shewanella oneidensis MR-1 Bacterial Nanowires Exhibit p-Type, Tunable Electronic Behavior, Nano Letters, 13, 2407-2411, 2013.
doi: 10.1021/nl400237p

M.Y. El-Naggar and S. E. Finkel. Live Wires: Electrical Signaling Between Bacteria, The Scientist, 27 (5), 38-43, 2013.
Feature Article

G. Wanger, Y. Gorby, M.Y. El-Naggar, T.D. Yuzvinsky, C. Schaudinn, A. Gorur, P.P. Sedghizadeh. Electrically conductive bacterial nanowires in bisphosphonate-related osteonecrosis of the jaw biofilms, Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology, 115, 71-78, 2013.
doi: 10.1016/j.oooo.2012.08.446

2012

S. Pirbadian and M.Y. El-Naggar. Multistep Hopping and Extracellular Charge Transfer in Microbial Redox Chains, Physical Chemistry Chemical Physics, 14, 13802-13808, 2012.
doi: 10.1039/C2CP41185G

C. Pfeffer, S. Larsen, J. Song, M. Dong, F. Besenbacher, R.L. Meyer, K. U. Kjeldsen, L. Schreiber, Y.A. Gorby, M. Y. El-Naggar, K. M. Leung, A. Schramm, N. Risgaard-Petersen and L. P. Nielsen. Filamentous bacteria transport electrons over centimeter distances, Nature, 491, 218-221, 2012. 
doi: 10.1038/nature11586

H.W. Harris, M.Y. El-Naggar, K. Nealson. Shewanella oneidensis MR-1 Chemotaxis Proteins and Electron Transport Chain Components Essential for Congregation Near Insoluble Electron Acceptors, Biochemical Society Transactions, 40(6), 1167-1177, 2012. 
doi: 10.1042/BST20120232

L.A. Fitzgerald, E.R. Petersen, B.J. Gross, C.M. Soto, B.R. Ringeisen, M.Y. El-Naggar, J.C. Biffinger. Aggrandizing power output from Shewanella oneidensis MR-1 microbial fuel cells using calcium chloride, Biosensors and Bioelectronics, 31(1), 492-498, 2012.
doi: 10.1016/j.bios.2011.11.024

2010

M.Y. El-Naggar, G. Wanger, K.M. Leung, T.D. Yuzvinsky, G. Southam, J. Yang, W.M. Lau, K.H. Nealson, and Y.A. Gorby. Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1, Proceedings of the National Academy of Sciences of the United States of America, 107(42), 18127-18131, 2010. 
doi: 10.1073/pnas.1004880107 News coverage: USC News, The Scientist, Science News, MSNBC, This Week in PNAS.

H.W. Harris, M.Y. El-Naggar, O. Bretschger, M. Ward, M. Romine, A. Obraztsova, and K.H. Nealson. Electrokinesis is a microbial behavior that requires extracellular electron transport, Proceedings of the National Academy of Sciences of the United States of America, 107(1), 326-331, 2010. 
doi: 10.1073/pnas.0907468107

G.K. Surya Prakash, F.A. Viva, O. Bretschger, B. Yang, M. El-Naggar, and K.H. Nealson. Inoculation procedures and characterization of membrane electrode assemblies for microbial fuel cells, Journal of Power Sources 195 (1), 111-117, 2010.
doi: 10.1016/j.jpowsour.2009.06.081

2009

M.S. Waters, M.Y. El-Naggar, L. Hsu, C.A. Sturm, A. Luttge, F.E. Udwadia, D.G. Cvitkovitch, S.D. Goodman, and K.H. Nealson. Simultaneous interferometric measurement of corrosive/demineralizing bacteria and their mineral interface, Applied and Environmental Microbiology 75, 1445-1449, 2009.
doi: 10.1128/AEM.02039-08

2008

M.Y. El-Naggar, Y.A. Gorby, W. Xia, and K.H. Nealson. The molecular density of states in bacterial nanowires, Biophysical Journal 95 (1), L10-L12, 2008.
doi: 10.1529/biophysj.108.134411

Y.A. Gorby, J. McLean, A. Korenevsky, K. Rosso, M.Y. El-Naggar, and T.J. Beveridge. Redox-reactive membrane vesicles produced by Shewanella, Geobiology 6 (3), 232-241, 2008.
doi: 10.1111/j.1472-4669.2008.00158.x

M.S. Waters, C.A. Sturm, M.Y. El-Naggar, A. Luttge, F.E. Udwadia, D.G. Cvitkovitch, S.D. Goodman, and K.H. Nealson. In search of the microbe/mineral interface: quantitative analysis of bacteria on metal surfaces using vertical scanning interferometry, Geobiology 6 (3), 254-262, 2008.
doi: 10.1111/j.1472-4669.2008.00161.x

Previous Work (at Caltech) on Oxides and Ferroelectric Thin Films:

M.Y. El-Naggar, K. Dayal, D.G. Goodwin, and K. Bhattacharya. Graded ferroelectric capacitors with robust temperature characteristics, Journal of Applied Physics 100, 114115, 2006. doi: 10.1063/1.2369650

D.A. Boyd, L. Greengard, M. Brongersma, M.Y. El-Naggar, and D.G. Goodwin. Plasmon Assisted Chemical Vapor Deposition, Nano Letters 6 (11), 2592-2597, 2006. doi: 10.1021/nl062061m

D.A. Boyd, M.Y. El-Naggar, and D.G. Goodwin. In situ measurements of stress with temperature in thin film PbxBa1-xTiO3, Integrated Ferroelectrics 83, 155+, 2006. doi: 10.1080/10584580600950822

M.Y. El-Naggar, D.A. Boyd, and D.G. Goodwin. Characterization of highly-oriented ferroelectric PbxBa1-xTiO3 thin films grown by MOCVD, Journal of Materials Research 20 (11), 2969-2976, 2005. 
doi: 10.1557/JMR.2005.0374

D.A. Boyd, M.Y. El-Naggar, and D.G. Goodwin. In situ measurements of macroscopic film stress during growth, cooling, and thermal cycling of thin film PbTiO3, Integrated Ferroelectrics 71, 21+, 2005.
doi: 10.1080/10584580590965023

R.T. Brewer, D.A. Boyd, M.Y. El-Naggar, S. Boland, Y.-B. Park, S.M. Haile, D.G. Goodwin and H.A. Atwater. Growth of biaxially textured BaxPb1-xTiO3 ferroelectric thin films on amorphous Si3N4, Journal of Applied Physics 97 (3), 034103, 2005. doi: 10.1063/1.1806994

M.Y. El-Naggar, J.T. Klamo, M.-H. Tan, and H.G. Hornung. Experimental verification of the mach-number field in a supersonic ludwieg tube, AIAA Journal 42 (8), 1721-1724, 2004. doi: 10.2514/1.3416