Center for Integrated Nanotechnologies

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James Henry Werner

James Werner

Email
Phone (505) 667-8842

Capabilities

  • Materials
  • Microfabrication
  • Optics and fiber optics
  • Biological assemblies
  • Center for Integrated Nanotechnologies (CINT)
  • CINT
  • Structure Measurements
  • Property Measurements
  • Function/Response Measurements

Expertise

Biophysics

Optics

Nanotechnology

Instrument Development

Education

B.S., Applied Physics, California Institute of Technology, 1992

M.S., Applied Physics, Cornell University, 1994

Ph.D., Applied Physics, Cornell University, 1998

 

Professional Appointments

Technical Staff Member, 2002 - present

Postdoctoral Research Associate, 1998 - 2002

 

Professional Societies

Biophysical Society

American Chemical Society

American Physical Society

 

Awards

Fellow, American Physical Society, 2016

Los Alamos Distinguished Patent Award, 2011

R&D 100 Award “NanoCluster Beacons” , 2011

Los Alamos Postdoctoral Distinguished Mentor Award, 2011

R&D 100 Award “3D Tracking Microscope” (2008)

Hertz Foundation Fellowship (1992-1997)

 

Patents

 

"Apparatus and method for tracking a molecule or particle in three dimensions," Werner, JH, Goodwin PM, and Lessard GA, US Patent 7,498,551 (2009).

3 Dimensional Imaging at Nanometer Resolutions," Werner, JH, Goodwin, PM and Shreve, AP, US Patent 7,675,045, (2010).

"Probe and Method for DNA Detection," Yeh, HC, Sharma, JK, Martinez, JS and Werner, JH, US Patent Application No. 20110212540, (2011).

 

Publications

 

PUBLICATIONS

http://scholar.google.com/citations?user=x87I1j4AAAAJ&hl=en

[61] "Light-sheet microscopy by confocal line scanning of dual-Bessel beams," Zhang, P., Phipps, ME, Goodwin, P, and Werner, J., Journal of Biomedical Optics 21(10), 100502 (2016).

[60] "Note: Time-gated 3D single quantum dot tracking with simultaneous spinning disk imaging," DeVore, M, Stich, D, Keller, A, Cleyrat, C, Phipps, M, Hollingsworth, J, Lidke, D, Wilson, B, Goodwin, P and Werner, J, Review of Scientific Instruments 86, 126102, (2015).

[59]  "Three dimensional time-gated tracking of non-blinking quantum dots in live cells," DeVore, MS, Stich, DG, Keller, AM, Ghosh, Y, Goodwin, PM, Phippsa, ME, Stewart, MH, Cleyrat, C, Wilson, BS, Lidke, DS, Hollingsworth, JA and Werner, JH, Proc. of the SPIE 9338, 1-12, (2015).

[58]  "Interferometric three-dimensional single molecule localization microscopy using a single high-numerical-aperture objective," Zhang, P, Goodwin, P and Werner, J, Applied Optics 53, 7415-7421, (2014).

[57] "3Dimensional Tracking of Nonblinking ‘Giant’Quantum Dots in Live Cells," Keller, AM, Ghosh, Y, DeVore, MS, Phipps, ME, Stewart, MH, Wilson, BS, Lidke, DS, Hollingsworth, JA and Werner, JH, Advanced Functional Materials 24, 4796-4803, (2014).(Work Featured in Frontispiece)

[56] "Confocal line scanning of a Bessel beam for fast 3D Imaging," Zhang, P, Phipps, M, Goodwin, P and Werner, J, Optics Letters 39, 3682-3685, (2014).

[55] "Fast, super resolution imaging via Bessel-beam stimulated emission depletion microscopy," Zhang, P, Goodwin, P and Werner, J, Optics Express 22, 12398-12409, (2014). (Work among top 10 most downloaded articles for Optics Express in May 2014).

[54] "Fast, 3D imaging via confocal line scanning of a Bessel beam using a single galvo mirror " Zhang, P, Goodwin, P and Werner, J, Proc. of the SPIE 8947, 1-8, (2014).

[53] "Enhanced 3D localization of individual RNA transcripts via astigmatic imaging," Perillo, EP, De Haro, L, Phipps, ME, Martinez, JS, Yeh, HC, Dunn, AK, Shepherd, DP and Werner, JH, Proc. of the SPIE 8950, 1-11, (2014).

[52] "Actin restructuring during Salmonella typhimurium infection investigated by confocal and super-resolution microscopy," Han, JJ, Kunde, YA, Hong-Geller, E and Werner, JH, Journal of Biomedical Optics 19, 016011-016011, (2014).

[51]  "Counting Small RNA in Pathogenic Bacteria," Shepherd, DP, Li, N, Micheva-Viteva, S, Munsky, B, Hong-Geller, E and Werner, JH, Analytical Chemistry 85, 4938-4943, (2013). (Work Featured on Cover).

[50] "DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters," Obliosca, JM, Liu, C, Batson, RA, Babin, MC, Werner, JH and Yeh, H-C, Biosensors 3, 185-200, (2013).

[49] "A Fluorescence Light-Up Ag Nanocluster Probe That Discriminates Single-Nucleotide Variants by Emission Color," Yeh, HC, Sharma, J, Shih, IM, Vu, DM, Martinez, JS and Werner, JH, Journal of the American Chemical Society 134, 11550-11558, (2012). (Work featured in C&E News Highlight).

[48] "Time-Resolved, Confocal Single Molecule Tracking of Individual Organic Dyes and Fluorescent Proteins in Three Dimensions," Han, JJ, Kiss, C, Bradbury, A and Werner, JH, ACS Nano 6, 8922–8932, (2012).

[47] "Disorder Limited Exciton Transport in Colloidal Single-Wall Carbon Nanotubes," Crochet, JJ, Duque, JG, Werner, JH, Lounis, B, Cognet, L and Doorn, SK, Nano Letters 12, 5091-5096, (2012).

 

[46] "Photoluminescence imaging of electronic-impurity-induced exciton quenching in single-walled carbon nanotubes," Crochet, JJ, Duque, JG, Werner, JH and Doorn, SK, Nature Nanotechnology 7, 126-132, (2012).

[45] "Bright two-photon emission and ultra-fast relaxation dynamics in a DNA-templated nanocluster investigated by ultra-fast spectroscopy," Yau, SH, Abeyasinghe, N, Orr, M, Upton, L, Varnavski, O, Werner, JH, Yeh, HC, Sharma, J, Shreve, AP, Martinez, JS and Goodson, T, Nanoscale 4, 4247-4254, (2012).

[44] "A DNA-templated fluorescent silver nanocluster with enhanced stability," Sharma, J, Rocha, RC, Phipps, ML, Yeh, HC, Balatsky, KA, Vu, DM, Shreve, AP, Werner, JH and Martinez, JS, Nanoscale 4, 4107-4110, (2012).

[43] "New tools for discovering the role sRNA plays in cellular regulation," Shepherd, DP, Li, N, Hong-Geller, E, Munsky, B and Werner, JH, Proc. of the SPIE 8228, 822801-822810, (2012).

[42] "Sizing the oligomers of Azami Green fluorescent protein with FCS and Antibunching," Temirov, J, Werner, JH, Goodwin, PM and Bradbury, ARM, Proc. of the SPIE 8228, 8228-1 to 8228-10, (2012).

 [41] "Visualizing Core-shell Structure in Substituted PPV Oligomer Aggregates using Fluorescence Lifetime Imaging Microscopy (FLIM)," Peteanu, LA, Sherwood, GA, Werner, JH, Shreve, AP, Smith, TM and Wildeman, J, Journal of Physical Chemistry C 115, 15607-15616, (2011).

[40] "NanoCluster Beacon- A new Molecular Probe for Homogeneous Detection of Nucleic Acid Targets," Yeh, HC, Sharma, J, Martinez, JS and Werner, JH, IEEE Nanotechnology Magazine 5, 28-33, (2011).

[39] "Silver nanocluster aptamers: In situ generation of intrinsically fluorescent recognition ligands for protein detection," Sharma, J, Yeh, HC, Yoo, H, Werner, JH and Martinez, JS, Chemical Communications 47, 2294-2296, (2011).

[38] "Time-resolved three-dimensional molecular tracking in live cells," Wells, NP, Lessard, GA, Goodwin, PM, Phipps, ME, Cutler, PJ, Lidke, DS, Wilson, BS and Werner, JH, Nano Letters 10, 4732-4737, (2010).

[37] "A DNA- Silver Nanocluster Probe That Fluoresces upon Hybridization," Yeh, HC, Sharma, J, Han, JJ, Martinez, JS and Werner, JH, Nano Letters 10, 13308-13313, (2010).

[36] "Effect of shell thickness and composition on blinking suppression and the blinking mechanism in "giant" CdSe/CdS nanocrystal quantum dots," Vela, J, Htoon, H, Chen, Y, Park, YS, Ghosh, Y, Goodwin, PM, Werner, JH, Wells, NP, Casson, JL and Hollingsworth, JA, Journal of Biophotonics 3, 706-717, (2010).

[35] "Photophysical characterization of fluorescent metal nanoclusters synthesized using oligonucleotides, proteins and small reagent molecules," Yeh, HC, Sharma, J, Martinez, JS and Werner, JH, Proceedings of the SPIE 7576, 7576-1 to 7576-10, (2010).

[34] "Formation and Stabilization of Fluorescent Gold Nanoclusters Using Small Molecules," Bao, Y, Yeh, H-C, Zhong, C, Ivanov, SA, Sharma, JK, Neidig, ML, Vu, DM, Shreve, AP, Dyer, RB, Werner, JH and Martinez, JS, The Journal of Physical Chemistry C (2010).

[33] "A complementary palette of fluorescent silver nanoclusters," Sharma, J, Yeh, HC, Hyojong, Y, Werner, JH and Martinez, JS, Chemical Communications 46, 1-3, (2010).

[32] "Aggregation Effects on the Emission Spectra and Dynamics of Model Oligomers of MEH-PPV," Sherwood, GA, Cheng, R, Smith, TM, Werner, JH, Shreve, AP, Peteanu, LA and Wildeman, J, The Journal of Physical Chemistry C 113, 18851-18862, (2009).

[31] "Formation and Dynamics of Supported Phospholipid Membranes on a Periodic Nanotextured Substrate," Werner, JH, Montano, GA, Garcia, AL, Zurek, NA, Akhadov, EA, Lopez, GP and Shreve, AP, Langmuir 25, 2986-2993, (2009).

[30] "Going Beyond 2D: Following membrane diffusion and topography in the IgE–Fc[Epsilon]RI system using 3-dimensional tracking microscopy," Wells, NP, Lessard, GA, Phipps, ME, Goodwin, PM, Lidke, DS, Wilson, BS and Werner, JH, Proceedings of the SPIE 7185, 7185-1 to 7185-13, (2009).

[29] "Confocal, 3-Dimensional Tracking of Individual Quantum-Dots in High Background Environments," Wells, NP, Lessard, GA and Werner, JH, Analytical Chemistry 80, 9830-9834, (2008).

[28] "Measuring an Antibody Affinity Distribution Molecule by Molecule," Temirov, JP, Bradbury, A and Werner, JH, Analytical Chemistry 80, 8642-8648, (2008).

[27] "Probing dimerization and Intraprotein fluorescence resonance energy transfer in a far red fluorescent protein from the sea anemone Heteractis crispa," Lessard, GA, Habuchi, S, Werner, JH, Goodwin, PM, De Schryver, FC, Hofkens, J and Cotlet, M, Journal of Biomedical Optics 13, 031212-1 to 031212-7, (2008).

[26] "Using T7 phage display to select GFP-based binders," Dai, M, Temirov, J, Pesavento, E, Kiss, C, Velappan, N, Pavlik, P, Werner, JH and Bradbury, ARM, Protein Engineering Design and Selection 21, 413-424, (2008).

[25] "Three dimensional tracking of individual quantum dots," Lessard, GA, Goodwin, PM and Werner, JH, Applied Physics Letters 91, 2224106 /1-3, (2007).

[24] "Increasing the resolution of single pair fluorescence resonance energy transfer measurements in solution via molecular cytometry," Werner, JH, McCarney, ER, Keller, RA, Plaxco, KW and Goodwin, PM, Analytical Chemistry 79, 3509-3513, (2007).

[23] "The creation of a novel fluorescent protein by guided consensus engineering," Dai, M, Fisher, H, Temirov, JP, Kiss, C, Phipps, ME, Pavlik, P, Werner, JH and Bradbury, A, Protein Engineering Design and Selection 20, 69-79, (2007).

[22] "A two dimensional view of the folding energy landscape of cytochrome c," Werner, JH, Joggerst, R, Dyer, RB and Goodwin, PM, Proceedings of the National Academy of Sciences 103, 11130-11135, (2006).

[21] "Surface-immobilized antibody-antigen binding affinity studies by single molecule fluorescence imaging," Temirov, JP, Bradbury, A and Werner, JH, Proceedings of the SPIE 6092, 60920O1 to 60920O10, (2006).

[20] "Three dimensional tracking of single fluorescent particles," Lessard, GA, Goodwin, PM and Werner, JH, Proceedings of the SPIE 6092, 609205-1 to 609205-8, (2006).

[19] "Single Molecule Spectroscopic Characterization of a Far-Red Fluorescent protein (HcRed) from the Anthozoa Coral Heteractis Crispa," Cotlet, M, Habuchi, S, Whitier, JE, Werner, JH, De Schryver, FC, Hofkens, J and Goodwin, PM, Proc. of the SPIE 6098, 609804-1 to 690804-11, (2006).

[18] "Time-resolved Detection of the One- and Two-Photon Excited Fluorescence of Single Molecules of a Folding Enhanced Green Fluorescent Protein," Cotlet, M, Goodwin, PM, Waldo, GS and Werner, JH, Proc. of the SPIE 6092, 609204-1 to 609204-10, (2006).

[17] "A comparison of the fluorescence dynamics of single molecules of a green fluorescent protein: one- vs two-photon excitation," Cotlet, M, Goodwin, PM, Waldo, GS and Werner, JH, ChemPhysChem 7, 250-260, (2006).

[16] "Exonuclease I hydrolyzes DNA with a distribution of rates," Werner, JH, Cai, H, Keller, RA and Goodwin, PM, Biophysical Journal 1403-1412, (2005).

[15] "Site-specific dimensions across a highly denatured protein; a single molecule study," McCarney, ER, Werner, JH, Bernstein, SL, Ruczinski, I, Makarov, DE, Goodwin, PM and Plaxco, KW, Journal of Molecular Biology 352, 672-682, (2005).

[14] "Progress towards single-molecule DNA sequencing: A one color demonstration," Werner, JH, Cai, H, Jett, JH, Reha-Krantz, L, Keller, RA and Goodwin, PM, Journal of Biotechnology 102, 1-14, (2003).

[13] "Aspects of chemical recognition and biosolvation within room temperature ionic liquids," Baker, GA, Baker, SN, McCleskey, TM and Werner, JH, ACS Symposium Series: Ionic Liquids as Green Solvents 856, 212-224, (2003).

[12] "Fluorescence correlation spectroscopic studies of diffusion within the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate," Werner, JH, Baker, SN and Baker, GA, Analyst 128, 786-789, (2003).

[11] "Dynamics of the primary processes of protein folding: Helix nucleation," Werner, JH, Dyer, RB, Fesinmeyer, RM and Andersen, NH, Journal of Physical Chemistry B 106, 487-494, (2002).

[10] "Single molecule nucleic acid analysis by fluorescence flow cytometry," Goodwin, PM, Ambrose, WP, Cai, H, Grace, WK, Larson, EJ, Marrone, BL, Jett, JH, Werner, JH and Keller, RA, NATO Advanced Research Workshop on Biological, Biophysical and Theoretical Aspects of Polymer Structure and Transport 87, 351-370, (2002).

[9] "Effects of fluorescence excitation geometry on the accuracy of DNA fragment sizing by flow cytometry," Werner, JH, Larson, EJ, Goodwin, PM, Ambrose, WP and Keller, RA, Applied Optics 39, 2831-9, (2000).

[8] "Kinetics of the combustion of trichloroethylene for low Cl/H ratios," Werner, JH and Cool, TA, Combustion and Flame 120, 125-142, (2000).

[7] "Single molecule fluorescence spectroscopy at ambient temperature," Ambrose, WP, Goodwin, PM, Jett, JH, Van Orden, A, Werner, JH and Keller, RA, Chemical Reviews 99, 2929-2956, (1999).

[6] "Kinetic model for the decomposition of DMMP in a hydrogen/oxygen flame," Werner, JH and Cool, TA, Combustion and Flame 117, 78-98, (1999).

[5] "Current status of DNA sequencing by single molecule detection," Werner, JH, Cai, H, Goodwin, PM and Keller, RA, Proceedings of the SPIE 3602, 355-366, (1999).

[4] "The combustion of trichloroethylene studied with vacuum ultraviolet photoionization mass spectrometry," Werner, JH and Cool, TA, 27th International Symposium on Combustion 413-423, (1998).

[3] "Flame sampling photoionization mass spectrometry of dichloro-ethenol.," Werner, JH and Cool, TA, Chemical Physics Letters 290, 81-7, (1998).

[2] "Flame sampling photoionization mass spectrometry of CH3PO2 and CH3OPO2," Werner, JH and Cool, TA, Chemical Physics Letters 275, 278-82, (1997).

[1] "An extended flame zone in the combustion of CH3Cl," Satyapal, S, Werner, JH and Cool, TA, Combustion Science and Technology 106, 229-238, (1995).

 

INVITED BOOK CHAPTERS

[2] "Super-Resolution Optical Microscopy," Han, JJ, Shreve, AP and Werner, JH, Characterization of Materials 1026-1040, (2012). EL Kaufmann, editor.

[1] "DNA Fragment Sizing by Flow Cytometry," Ambrose, WP, Cai, H, Goodwin, PM, Grace, KG, Habbersett, RC, Jett, JH, Larson, EJ, Werner, JH and Keller, RA, Topics in Fluorescence VI:  DNA Technology (2003). JR Lakowicz, editor.