P. Chellamuthu, K.L. Naughton, S. Pirbadian, K.P.T. Silva, M.S. Chavez, M.Y. El-Naggar, J.Q. Boedicker, Biogenic control of manganese doping in zinc sulfide nanomaterial using Shewanella oneidensis MR-1, Frontiers in Microbiology 10, 938, 2019

A.R. Rowe, S. Xu, E. Gardel, A. Bose, P. Girguis, J.P. Amend, M.Y. El-Naggar, Methane-linked mechanisms of electron uptake from cathodes by Methanosarcina barkeri, mBio, e02448-18, 2019

Y. Jangir, A.A. Karbelkar, N.M. Beedle, L.A. Zinke, G. Wanger, C.M. Anderson, B.K. Reese, J.P. Amend, M.Y. El-Naggar, In Situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA, bioRxiv (preprint), 2019

M. Kaplan, D. Ghosal, P. Subramanian, C.M. Oikonomou, A. Kjaer, S. Pirbadian, D.R. Ortega, A. Briegel, M.Y. El-Naggar, G.J. Jensen, The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type, eLife 8, e43487, 2019

P. Chellamuthu, F. Tran, K.P.T. Silva, M.S. Chavez, M.Y. El‐Naggar, J.Q. Boedicker, Engineering bacteria for biogenic synthesis of chalcogenide nanomaterials, Microbial Biotechnology 12, 161-172, 2019


S. Xu, A. Barrozo, L.M. Tender, A.I. Krylov, M.Y. El-Naggar, Multiheme cytochrome mediated redox conduction through Shewanella oneidensis MR-1 cells, Journal of the American Chemical Society, 140, 10085-10089, 2018

N.L. Ing, M.Y. El-Naggar, A.I. Hochbaum, Going the distance: long-range conductivity in protein and peptide bioelectronic materials, The Journal of Physical Chemistry, 122, 10403-10423. ACS Editors Choice.

G.W. Chong, A.A. Karbelkar, M.Y. El-Naggar, Nature’s conductors: what can microbial multi-heme cytochromes teach us about electron transport and biological energy conversion? Current Opinion in Chemical Biology, 47, 7-17, 2018.

M. Kaplan, P. Subramanian, D. Ghosal, C.M. Oikonomou, S. Pirbadian, R. Starwalt-Lee, J.A. Gralnick, M.Y. El-Naggar, G.J. Jensen, Stable sub-complexes observed in situ suggest a modular assembly pathway of the bacterial flagellar motor, bioRxiv (preprint), 2018

A. Barrozo, M.Y. El-Naggar, A.I. Krylov, Distinct Electron Conductance Regimes in Bacterial Decaheme Cytochromes, Angewandte Chemie, 57, 6805-6809, 2018

P. Subramanian, S. Pirbadian, M.Y. El-Naggar, G.J Jensen, The ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryo-tomography, Proceedings of the National Academy of Sciences of the United States of America, 115 (14) E3246-E3255, 2018

M. Yates, S. Strycharz-Glaven, J. Golden, J. Roy, S. Tsoi, J. Erickson, M.Y. El-Naggar, S. Barton Calabrese, L.M. Tender, Characterizing Electron Transport through Living Biofilms, Journal of Visualized Experiments, 136, 2018

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, mBio, 9, e02203-17, 2018

H.W. Harris, I. Sánchez-Andrea, J.S. McLean, E.C. Salas, W. Tran, M.Y. El-Naggar, K.H. Nealson, Redox Sensing Within the Genus Shewanella, Frontiers in Microbiology, 8, 2568 2018


L.A. Zacharoff, M.Y. El-Naggar. Redox Conduction in Biofilms: From Respiration to Living Electronics, Current Opinion in Electrochemistry, 4, 182-189, 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

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


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


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


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


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


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


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


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


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