Scientific Publications
Displaying 1 - 76 of 76
2024
Influence of Fluorescence Lifetime Selections and Conformational Flexibility on Brightness of FusionRed Variants
Mukherjee S., N. Douglas, and R. Jimenez, The Journal Of Physical Chemistry Letters 15, 1644-1651 (2024).
Excited State Vibrational Dynamics Reveals a Photocycle That Enhances the Photostability of the TagRFP-T Fluorescent Protein
Yabushita A., C.-Y. Cheng, Y.K. Ko, T. Kobayashi, I. Iwakura, and R. Jimenez, The Journal Of Physical Chemistry B (2024).
2023
Backbone 1H, 15N and 13C resonance assignments of the 27kDa fluorescent protein mCherry
Sette M., L.A. Johnson, R. Jimenez, and F.A.A. Mulder, Biomolecular Nmr Assignments 17, 243-247 (2023).
2022
Conformational dynamics of mCherry variants: a link between sidechain motions and fluorescence brightness
Mukherjee S., P. Manna, N. Douglas, P.P. Chapagain, and R. Jimenez, The Journal Of Physical Chemistry B 127, 52–61 (2022).
Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections
Mukherjee S., The Journal Of Physical Chemistry B 126, 4659-4668 (2022).
Characterizing dark state kinetics and single molecule fluorescence of FusionRed and FusionRed-MQ at low irradiances
Mukherjee S., C. Thomas, R. Wilson, E. Simmerman, S.-T. Hung, and R. Jimenez, Physical Chemistry Chemical Physics 24, 14310-14323 (2022).
Temperature-Dependent Fluorescence of mPlum Fluorescent Protein from 295 to 20 K
Lyu T., S. Sohn, R. Jimenez, and T. Joo, The Journal Of Physical Chemistry B (2022).
Hot-Band Absorption Can Mimic Entangled Two-Photon Absorption
Mikhaylov A., R.N. Wilson, K.M. Parzuchowski, M.D. Mazurek, C.H. Camp, M.J. Stevens, and R. Jimenez, The Journal Of Physical Chemistry Letters 13, 1489-1493 (2022).
Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies
Mukherjee S., and R. Jimenez, The Journal Of Physical Chemistry B (2022).
Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances
Mukherjee S., C. Thomas, R. Wilson, E. Simmerman, S.T. Hung, and R. Jimenez, Chem Archive (2022).
2021
Photo-Switching of Protein Dynamical Collectivity
Xu M., D. George, R. Jimenez, and A. Markelz, Photonics 8, 302 (2021).
Witnessing the survival of time-energy entanglement through biological tissue and scattering media
Lum D.J., M.D. Mazurek, A. Mikhaylov, K.M. Parzuchowski, R.N. Wilson, R. Jimenez, T. Gerrits, M.J. Stevens, M. Cicerone, and C.H. Camp Jr., Optics Express 12, 3658 (2021).
Setting Bounds on Entangled Two-Photon Absorption Cross Sections in Common Fluorophores
Parzuchowski K.M., A. Mikhaylov, M.D. Mazurek, R.N. Wilson, D.J. Lum, T. Gerrits, C.H. Camp, M.J. Stevens, and R. Jimenez, Physical Review Applied 15, 044012 (2021).
2020
Engineering of a brighter variant of the FusionRed fluorescent protein using lifetime flow-cytometry and structure-guided mutations
Mukherjee S., S.-T. Hung, N. Douglas, P. Manna, C. Thomas, A. Ekrem, A. Palmer, and R. Jimenez, Biochemistry 59, 3669–3682 (2020).
Ultrafast spectroscopy of biliverdin dimethyl ester in solution: pathways of excited-state depopulation
Liu Y., Z. Chen, X. Wang, S. Cao, J. Xu, R. Jimenez, and J. Chen, Physical Chemistry Chemical Physics 22, 19903-19912 (2020).
Setting limits on two-photon absorption cross sections in common fluorescent molecules with entangled photon pairs excitation
Mikhaylov A., K.M. Parzuchowski, M.D. Mazurek, R.N. Wilson, T. Gerrits, D.J. Lum, C.H. Camp, M.J. Stevens, and R. Jimenez, Conference On Lasers And Electro-Optics JTh3N.4 (2020).
Verifying the Survival of Time-Energy Entanglement Through Tissue
Lum D.J., M.D. Mazurek, A. Mikhaylov, K. Parzuchowski, R.N. Wilson, M.T. Cicerone, R. Jimenez, T. Gerrits, M.J. Stevens, and C.H. Camp, Conference On Lasers And Electro-Optics (2020).
A comprehensive experimental system for measuring molecular two-photon absorption using an ultrafast entangled photon pair excitation source
Mikhaylov A., K. Parzuchowski, M. Mazurek, D.J. Lum, T. Gerrits, C.H. Champ, M. Stevens, and R. Jimenez, Advanced Optical Techniques For Quantum Information, Sensing, And Metrology Proceedings of SPIE, 112950Q (2020).
Enrichment of rare events using a multi-parameter high throughput microfluidic droplet sorter
Hung S.-T., S. Mukherjee, and R. Jimenez, Lab On A Chip 20, 834 (2020).
2019
Erratum: Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter
Manna P., S.-T. Hung, S. Mukherjee, P. Friis, D.M. Simpson, M. Lo, A. Palmer, and R. Jimenez, Integrative Biology 11, 372-372 (2019).
Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range
Slocum J., A. Palmer, and R. Jimenez, The Journal Of Physical Chemistry B 123, 3079–3085 (2019).
Ultrafast internal conversion dynamics of bilirubin bound to UnaG and its N57A mutant
Cao X., C. Zhang, Z. Gao, Y. Liu, Y. Zhao, Y. Yang, J. Chen, R. Jimenez, and J. Xu, Phys. Chem. Chem. Phys. 21, 2365-2371 (2019).
2018
Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter
Manna P., S.-T. Hung, S. Mukherjee, P. Friis, D.M. Simpson, M.N. Lo, A. Palmer, and R. Jimenez, Integrative Biology 10, 516-526 (2018).
A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells
Braselmann E., A.J. Wierzba, J.T. Polaski, M. Chromiński, Z.E. Holmes, S.-T. Hung, D. Batan, J.R. Wheeler, R. Parker, R. Jimenez, and D. Gryko, Nature Chemical Biology 14, 964-971 (2018).
2017
Critical Comparison of FRET-Sensor Functionality in the Cytosol and Endoplasmic Reticulum and Implications for Quantification of Ions
Carter K.P., M.C. Carpenter, B.L. Fiedler, R. Jimenez, and A. Palmer, Analytical Chemistry 89, 9601-9608 (2017).
Nondestructive determination of protein structural stability
Xu M., D.K. George, R. Jimenez, and A.G. Markelz, in Unknown (IEEE, Cancun, Mexico, 2017).
Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution
Mo G.C.H., B. Ross, F. Hertel, P. Manna, X. Yang, E. Greenwald, C. Booth, A.M. Plummer, B. Tenner, Z. Chen, and Y. Wang, Nature Methods 14582, 427-434 (2017).
Ultrafast Time-Resolved X-ray Absorption Spectroscopy of Ferrioxalate Photolysis with a Laser Plasma X-ray Source and Microcalorimeter Array
O'Neil G., L. Miaja-Avila, Y.I. Joe, B.K. Alpert, M. Balasubramanian, D.M. Sagar, W.B. Doriese, J.W. Fowler, W.K. Fullagar, N. Chen, and G.C. Hilton, The Journal Of Physical Chemistry Letters 8, 1099-1104 (2017).
2016
Droplet Microfluidic Flow Cytometer for Sorting on Transient Cellular Responses of Genetically-Encoded Sensors
Fiedler B.L., S. van Buskirk, K.P. Carter, Y. Qin, M.C. Carpenter, A. Palmer, and R. Jimenez, Analytical Chemistry (2016).
Microfluidic System for In-Flow Reversible Photoswitching of Near-Infrared Fluorescent Proteins
Lychagov V.V., A.A. Shemetov, R. Jimenez, and V.V. Verkhusha, Analytical Chemistry 88, 11821-11829 (2016).
Ultrafast Time-Resolved Hard X-Ray Emission Spectroscopy on a Tabletop
Miaja-Avila L., G.C. \ textquoterightNeil, Y.I. Joe, B.K. Alpert, N.H. Damrauer, W.B. Doriese, S.M. Fatur, J.W. Fowler, G.C. Hilton, R. Jimenez, and C.D. Reintsema, Physical Review X 6, (2016).
Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675
Konold P.E., E. Yoon, J. Lee, S.L. Allen, P.P. Chapagain, B.S. Gerstman, C.K. Regmi, K.D. Piatkevich, V.V. Verkhusha, T. Joo, and R. Jimenez, The Journal Of Physical Chemistry Letters 7, 3046-3051 (2016).
Far-Red Emission of mPlum Fluorescent Protein Results from Excited-State Interconversion between Chromophore Hydrogen-Bonding States
Yoon E., P.E. Konold, J. Lee, T. Joo, and R. Jimenez, The Journal Of Physical Chemistry Letters 7, 2170-2174 (2016).
Using Pyridinium Styryl Dyes as the Standards of Time-Resolved Instrument Response
Li L., M. Chang, H. Yi, M. Jia, X. Cao, Z. Zhou, S. Zhang, H. Pan, C.-W. Shih, R. Jimenez, and J. Xu, Applied Spectroscopy 70, 1195-1201 (2016).
Dark State Dynamics of Red Fluorescent Proteins in the Cell Environment Measured in Microfluidic Flow
Manna P., F. Vietmeyer, and R. Jimenez, Biophysical Journal 110, 492a - 493a (2016).
Multi-Parametric Microfluidic Screening and Sorting for Simultaneous Evolution of Photophysical Parameters of Fluorescent Proteins
Vietmeyer F., P. Manna, P. Friis, A. Palmer, and R. Jimenez, Biophysical Journal 110, 166a (2016).
2015
Femtosecond Measurements Of Size-Dependent Spin Crossover In FeII(pyz)Pt(CN)4 Nanocrystals
Sagar D.M., F.G. Baddour, P.E. Konold, J.N. Ullom, D.A. Ruddy, J.C. Johnson, and R. Jimenez, The Journal Of Physical Chemistry Letters 7, 148-153 (2015).
Observation of iron spin-states using tabletop x-ray emission spectroscopy and microcalorimeter sensors
Joe Y.I., G. O'Neil, L. Miaja-Avila, J.W. Fowler, R. Jimenez, K.L. Silverman, D.S. Swetz, and J.N. Ullom, Journal Of Physics B: Atomic, Molecular And Optical Physics 49, 024003 (2015).
High-Speed Multiparameter Photophysical Analyses of Fluorophore Libraries
Dean K.M., L.M. Davis, J.L. Lubbeck, P. Manna, P. Friis, A. Palmer, and R. Jimenez, Analytical Chemistry 150429131032000 (2015).
Laser plasma x-ray source for ultrafast time-resolved x-ray absorption spectroscopy
Miaja-Avila L., G. O'Neil, J. Uhlig, C.L. Cromer, M.L. Dowell, R. Jimenez, A.S. Hoover, K.L. Silverman, and J.N. Ullom, Structural Dynamics 2, 024301 (2015).
Time and Frequency-domain Measurement of Ground State Recovery Times in Red Fluorescent Proteins
Manna P., and R. Jimenez, The Journal Of Physical Chemistry B 150317145315006 (2015).
Excited State Electronic Landscape of mPlum Revealed by Two-Dimensional Double Quantum Coherence Spectroscopy
Konold P.E., and R. Jimenez, The Journal Of Physical Chemistry B 119, 3414-3422 (2015).
2014
Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching
Dean K.M., J.L. Lubbeck, L.M. Davis, C.K. Regmi, P.P. Chapagain, B.S. Gerstman, R. Jimenez, and A. Palmer, Integative Biology (2014).
Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants
Konold P.E., C.K. Regmi, P.P. Chapagain, B.S. Gerstman, and R. Jimenez, The Journal Of Physical Chemistry B 118, 2940-2948 (2014).
2013
Microfluidic cell sorter for use in developing red fluorescent proteins with improved photostability
Davis L.M., J.L. Lubbeck, K.M. Dean, A. Palmer, and R. Jimenez, Lab On A Chip 13, 2320 (2013).
Microfluidic cytometer for high-throughput measurement of photosynthetic characteristics and lipid accumulation in individual algal cells
Erickson R.A., and R. Jimenez, Lab On A Chip 13, 2893 (2013).
2012
High-Throughput Examination of Fluorescence Resonance Energy Transfer-Detected Metal-Ion Response in Mammalian Cells
Ma H., E. Gibson, P. Dittmer, R. Jimenez, and A. Palmer, Journal Of The American Chemical Society 134, 2488-2491 (2012).
Pressure Induced Changes in the Fluorescence Behavior of Red Fluorescent Proteins
Pozzi E.A., L.R. Schwall, R. Jimenez, and J.M. Weber, The Journal Of Physical Chemistry B 116, 10311-10316 (2012).
Microfluidic Flow Cytometer for Quantifying Photobleaching of Fluorescent Proteins in Cells
Lubbeck J.L., K.M. Dean, H. Ma, A. Palmer, and R. Jimenez, Analytical Chemistry 84, 3929-3937 (2012).
Heterogeneity and Kinetics of FRET-Based Ca2+ and Zn2+ Sensors in HeLa~Cells
Ma H., E. Gibson, P. Dittmer, K.M. Dean, A. Palmer, and R. Jimenez, Biophysical Journal 102, 209a (2012).
Microfluidic Cytometer For Simultaneous High-Throughput Screening of Fluorescent Proteins on the Basis of Fluorescence Lifetime, Photostability, and Brightness
Lubbeck J.L., K.M. Dean, L.M. Davis, A. Palmer, and R. Jimenez, Biophysical Journal 102, 208a - 209a (2012).
Real-time analysis of multi-laser-beam fluorescence for timed control of laser tweezers in a microfluidic cell-sorting device
Davis L.M., J.L. Lubbeck, K.M. Dean, A. Palmer, and R. Jimenez, in Unknown (SPIE, Montreal, Canada, 2012).
2011
Analysis of Red-Fluorescent Proteins Provides Insight into Dark-State Conversion and Photodegradation
Dean K.M., J.L. Lubbeck, J.K. Binder, L.R. Schwall, R. Jimenez, and A. Palmer, Biophysical Journal 101, 961-969 (2011).
High-Throughput Cell Elastic Modulus Cytometry using Single Diode Laser Bar Optical Stretchers
Sraj I., J. Chichester, E. Hoover, R. Jimenez, J. Squier, C.D. Eggleton, and D.W.M. Marr, Biophysical Journal 100, 191a (2011).
High-Throughput Screening of Response Kinetics of Genetically-Encoded Metal Sensors with Microfluidics Technology
Ma H., P. Dittmer, A. Palmer, and R. Jimenez, Biophysical Journal 100, 316a (2011).
A Microfluidic Cell Sorter for Directed Evolution of Fluorescent Proteins Based on Dark-State Conversion and Photobleaching
Lubbeck J.L., K.M. Dean, L.M. Davis, A. Palmer, and R. Jimenez, Biophysical Journal 100, 175a (2011).
3D optical trapping calibration and optical micromanipulation using 808-nm diode-laser bar
Potcoava M., L. Krzewina, E. Hoover, M.K. Kim, J. Squier, D.W.M. Marr, and R. Jimenez, in Unknown (SPIE, San Francisco, California, 2011).
Dynamics of optically trapped red blood cells by phase contrast microscopy
Potcoava M., E. Hoover, K.C. Roth, G. Riccota, J. Squier, R. Jimenez, and D.W.M. Marr, in Unknown (SPIE, San Francisco, California, 2011).
2010
Cell deformation cytometry using diode-bar optical stretchers
Sraj I., C.D. Eggleton, R. Jimenez, E. Hoover, J. Squier, J. Chichester, and D.W.M. Marr, Journal Of Biomedical Optics 15, 047010 (2010).
Distinguishing between Two and Three-State Equilibrium Folding with Three-Pulse Photon Echo Peak Shift (3PEPS) Spectroscopy
Shen Z., E. Gibson, and R. Jimenez, in Unknown (OSA, Snowmass Village, Cowashington, D.c., 2010).
2009
Three-pulse photon echo spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding
Gibson E., and R. Jimenez, in Unknown (Springer Series in Chem. Phys. Vol. 92, 562-564, 2009).
Three-pulse photon echo spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding
Gibson E., Z. Shen, and R. Jimenez, Chem. Phys. Lett. 473, 330-335 (2009).
Microfluidic cell counter with embedded optical fibers fabricated by femtosecond laser ablation and anodic bonding
Schafer D.N., E. Gibson, E.A. Salim, A. Palmer, R. Jimenez, and J. Squier, Opt. Express 17, (2009).
2008
Linear spatio-temporal characterization of a UV microscope objective for nonlinear imaging and spectroscopy by using two-dimensional spectra interferometry
Amir W., C.G. Durfee, D.N. Schafer, E. Gibson, K.E. Przekwas, R. Jimenez, and J. Squier, Journal Of Microscopy 230, (2008).
Mass Instability in Isolated Recombinant FixL Heme Domains of Bradyrhizobium japonicum
Satterlee J.D., C. Suquet, A.K. Bidwai, J.E. Erman, L.R. Schwall, and R. Jimenez, Biochemistry 47, 1540-1553 (2008).
2007
Three-dimensional chemical concentration maps in a microfluidic device using two-photon absorption fluorescence imaging
Schafer D.N., E. Gibson, R. Erikson, J. Lawrence, T. Vestad, J. Squier, R. Jimenez, and D.W.M. Marr, Optics Letters 32, 2568-2570 (2007).
Design and Fabrication of Efficient Reflection Grisms for Pulse Compression and Dispersion Compensation
Gibson E., H. Kapteyn, D.M. Gaudiosi, R. Jimenez, S. Kane, F. Tortajada, H. Dinger, B. Touzet, R. Huff, J. Squier, and C.G. Durfee, in (Springer Berlin Heidelberg, Berlin, Heidelberg, 2007), pp. 169-171.
Grism based stretcher/compressor system for amplified, femtosecond kilohertz lasers
Gaudiosi D.M., E. Gibson, S. Kane, R. Huff, M. Murnane, H. Kapteyn, C.G. Durfee, J. Squier, and R. Jimenez, in (Springer Berlin Heidelberg, Berlin, Heidelberg, 2007), pp. 95-97.
A Novel Fast-mixing Microfluidic Device for Studying Nonequilibrium Systems using Femtosecond Spectroscopies
Gibson E., D.N. Schafer, W. Amir, D.W.M. Marr, J. Squier, and R. Jimenez, in (Springer Berlin Heidelberg, Berlin, Heidelberg, 2007), pp. 172-174.
Reflection grisms compensate dispersion in ultrafast systems
Kane S., J. Squier, R. Jimenez, L. Kuznetsova, F. Wise, H. Kapteyn, and B. Touzet, Laser Focus World 43, 95-98 (2007).
2006
Efficient reflection grisms for pulse compression and dispersion compensation of femtosecond pulses
Gibson E., D.M. Gaudiosi, H. Kapteyn, R. Jimenez, S. Kane, R. Huff, C.G. Durfee, and J. Squier, Optics Letters 31, 3363 (2006).
Multi-kilohertz repetition rate Ti:sapphire amplifier based on down-chirped pulse amplification
Gaudiosi D.M., E. Gagnon, A.L. Lytle, J.L. Fiore, E. Gibson, S. Kane, J. Squier, M. Murnane, H. Kapteyn, R. Jimenez, and S. Backus, Optics Express 14, 9277-9283 (2006).
Grism based stretcher/compressor system for amplified femtosecond kilohertz lasers
Gibson E., S. Kane, R. Huff, D.M. Gaudiosi, H. Kapteyn, C.G. Durfee, J. Squier, and R. Jimenez, Conference On Lasers And Electro-Optics/Quantum Electronics And Laser Science Conference And Photonic Applications Systems Technologies (2006).
Photon echo spectroscopy of porphyrins and heme proteins: effects of quasidegenerate electronic structure on the peak shift decay
Cho B.M., C.F. Carlsson, and R. Jimenez, The Journal Of Chemical Physics 124, 144905 (2006).
2005
Hydrodynamic focusing for vacuum-pumped microfluidics
Stiles T., R. Fallon, T. Vestad, J. Oakey, D.W.M. Marr, J. Squier, and R. Jimenez, Microfluidics And Nanofluidics 1, 280-283 (2005).
2004
Protein dynamics and the immunological evolution of molecular recognition
Jimenez R., Proceedings Of The National Academy Of Sciences 101, 3803-3808 (2004).