Martin Gruebele

Description

Address

  • 3424 Beckman Institute
  • 405 North Mathews Avenue
  • Urbana, Illinois 61801

Biography

Martin Gruebele received his Ph.D. from the University of California, Berkeley in 1988. He is a Professor in the U of I Departments of Chemistry, Physics and Center for Biophysics and a full-time faculty member in the Beckman Institute Nanoelectronics and Nanomaterials group. His fields of professional interest are the dynamics of complex chemical and biological systems, as studied by experimental laser and computational techniques.

Honors

Coblentz Award, Coblentz Society (1999); Dreyfus New Faculty Award; NSF National Young Investigator Award; Packard Fellowship; Cottrell Scholarship; Fellow, Center for Advanced Study, UIUC; A. P. Sloan Fellow; Camille and Henry Dreyfus Fellow; University Scholar.

Research

Martin Gruebele's research group uses lasers to study the dynamics of complex molecular systems and electronic and molecular nanostructures.

Chemical reactions are controlled in a two-step procedure: A high-resolution or femtosecond laser excites a well-defined quantum state of a reactive molecule. A shaped femtosecond pulse then pumps it to a reactive energy surface, where reactivity depends on the nature of the intermediate state and the shape of the second laser pulse. Such experiments allow one to dissect chemical pathways and look at them individually to study reaction mechanisms.

An important issue related to this is the loss of vibrational coherence in large molecules or in the condensed phase: Excitation energy leaks into undesirable molecular motions before it can lead to a reaction. Gruebele's group is investigating this problem computationally and experimentally. Theoretical and computational advances result in a complete model of energy flow, which predicts that chemical selectivity is possible even in the presence of vibrational relaxation.

Laser techniques can also be used to study the motions of very large molecules, such as proteins. Presently, Gruebele's group is studying how proteins fold into their native structure on a nanosecond to millisecond time scale. Collaborations with other Beckman faculty include Klaus Schulten and Jeff Moore. The formation of protein molten globule states from an unfolded protein, a process occurring on a time scale of a few microseconds, can now be observed.

Gruebele's newest research area, in collaboration with Beckman faculty members Brady, Lyding, and Makri, involves the control of electronic energy flow in macromolecular assemblies anchored to Si surfaces. An optical STM technique is used to study molecular switches.

Gruebele's research support includes several private foundations, as well as grants from the NSF, American Chemical Society, and NIH.

Publications

  • 2016
    • Dave, K.; Davtyan, A.; Papoian, G. A.; Gruebele, M.; Platkov, M., Environmental Fluctuations and Stochastic Resonance in Protein Folding. Chemphyschem 2016, 17, (9), 1341-1348, DOI:10.1002/cphc.201501041.
    • Dave, K.; Jager, M.; Nguyen, H.; Kelly, J. W.; Gruebele, M., High-Resolution Mapping of the Folding Transition State of a Ww Domain. Journal of Molecular Biology 2016, 428, (8), 1617-1636, DOI:10.1016/j.jmb.2016.02.008.
    • Dave, K.; Gelman, H.; Thu, C. T. H.; Guin, D.; Gruebele, M., The Effect of Fluorescent Protein Tags on Phosphoglycerate Kinase Stability is Nonadditive. Journal of Physical Chemistry B 2016, 120, (11), 2878-2885, DOI:10.1021/ACS.jpcb.5b11915
    • Davis, C. M.; Guzman, I.; Gruebele, M., Towards Three-Color Live-Cell Imaging of Spliceosome Assembly. Biophysical Journal 2016, 110, (3), 387a-387a.
    • Davtyan, A.; Platkov, M.; Gruebele, M.; Papoian, G. A., Stochastic Resonance in Protein Folding Dynamics. Chemphyschem 2016, 17, (9), 1305-1313, DOI:10.1002/cphc.201501125.
    • Gelman, H.; Wirth, A. J.; Gruebele, M., Reash as a Quantitative Probe of in-Cell Protein Dynamics. Biochemistry 2016, 55, (13), 1968-1976, DOI:10.1021/ACS.biochem.5b01336.
    • Guin, D.; Sye, K.; Dave, K.; Gruebele, M., Dodine as a Transparent Protein Denaturant for Circular Dichroism and Infrared Studies. Protein Science 2016, 25, (5), 1061-1068, DOI:10.1002/pro.2914.
    • Sukenik, S.; Pogorelov, T. V.; Gruebele, M., Can Local Probes Go Global? A Joint Experiment-Simulation Analysis of Lambda(6-85) Folding. Journal of Physical Chemistry Letters 2016, 7, (11), 1960-1965, DOI:10.1021/ACS.jpclett.6b00582.
    • Tai, J.; Dave, K.; Hahn, V.; Guzman, I.; Gruebele, M., Subcellular Modulation of Protein VLSE Stability and Folding Kinetics. Febs Letters 2016, 590, (10), 1409-1416, DOI:10.1002/1873-3468.12193.
    • Zhang, Y.; Schulten, K.; Gruebele, M.; Bansal, P. S.; Wilson, D.; Daly, N. L., Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophysical Journal 2016, 110, (8), 1744-1752, DOI:10.1016/j.bpj.2016.03.027.
    • Zhang, Y.; Bansal, P.; Wilson, D.; Schulten, K.; Daly, N.; Gruebele, M., Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophysical Journal 2016, 110, (3), 210a-210a.
  • 2015
    • Guzman, I.; Ghaemi, Z.; Baranger, A.; Luthey-Schulten, Z.; Gruebele, M., Native Conformational Dynamics of the Spliceosomal U1a Protein. Journal of Physical Chemistry B 2015, 119, (9), 3651-3661, DOI: 10.1021/Jp511760m.

    • Girdhar, K.; Feng, R.; Shukla, S.; Benitez, M. J.; Gruebele, M.; Chemla, Y., The Behavioral Space and Neural Model of Locomotion Repertoire of Zebrafish. Integrative and Comparative Biology 2015, 55, E263-E263.

    • Feng, R.; Chemla, Y. R.; Gruebele, M., 3D Behavior Analysis of Zebrafish Larvae Swimming. Integrative and Comparative Biology 2015, 55, E254-E254.

    • Dave, K.; Gruebele, M., Fast-Folding Proteins under Stress. Cellular and Molecular Life Sciences 2015, 72, (22), 4273-4285, DOI:10.1007/s00018-015-2002-3.
    • Ghaemi, Z.; Guzman, I.; Gruebele, M.; Luthey-Schulten, Z., Electrostatic Interaction Effects on the Binding of Spliceosomal U1a Protein-Sl2 RNA Hairpin. Biophysical Journal 2015, 108, (2), 15a-15a.
    • Girdhar, K.; Gruebele, M.; Chemla, Y. R., The Behavioral Space of Zebrafish Locomotion and Its Neural Network Analog. Plos One 2015, 10, (7), DOI:ARTN e0128668 10.1371/jouRNAl.pone.0128668.
    • Nguyen, D.; Nienhaus, L.; Haasch, R. T.; Lyding, J.; Gruebele, M., Sub-Nanometer Glass Surface Dynamics Induced by Illumination. Journal of Chemical Physics 2015, 142, (23), DOI:Artn 234505 10.1063/1.4922695.
    • Nienhaus, L.; Goings, J. J.; Nguyen, D.; Wieghold, S.; Lyding, J. W.; Li, X. S.; Gruebele, M., Imaging Excited Orbitals of Quantum Dots: Experiment and Electronic Structure Theory. Journal of the American Chemical Society 2015, 137, (46), 14743-14750, DOI:10.1021/jACS.5b09272.
    • Nienhaus, L.; Wieghold, S.; Nguyen, D.; Lyding, J. W.; Scott, G. E.; Gruebele, M., Optoelectronic Switching of a Carbon Nanotube Chiral Junction Imaged with Nanometer Spatial Resolution. ACS Nano 2015, 9, (11), 10563-10570, DOI:10.1021/ACSnano.5b04872.
    • Pogorelov, T. V.; Prigozhin, M. B.; Chao, S. H.; Gruebele, M., Mapping the Mechanism of Fast Protein Folding with Multiple Probes. Biophysical Journal 2015, 108, (2), 347a-348a.
    • Prigozhin, M. B.; Chao, S. H.; Sukenik, S.; Pogorelov, T. V.; Gruebele, M., Mapping Fast Protein Folding with Multiple-Site Fluorescent Probes. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, (26), 7966-7971, DOI:10.1073/pnas.1422683112.
    • Wirth, A. J.; Liu, Y. X.; Prigozhin, M. B.; Schulten, K.; Gruebele, M., Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations. Journal of the American Chemical Society 2015, 137, (22), 7152-7159, DOI:10.1021/jACS.5b02474.
  • 2014
    • Chao, S. H.; Matthews, S. S.; Paxman, R.; Aksimentiev, A.; Gruebele, M.; Price, J. L., Two Structural Scenarios for Protein Stabilization by PEG. Journal of Physical Chemistry B 2014, Published Online.

    • Gelman, H.; Gruebele, M., Fast Protein Folding Kinetics. Quarterly Reviews of Biophysics 2014, 47, (2), 95-142, DOI: 10.1017/s003358351400002x.

    • Guzman, I.; Gelman, H.; Tai, J.; Gruebele, M., The Extracellular Protein Vise Is Destabilized inside Cells. Journal of Molecular Biology 2014, 426, (1), 11-20, DOI: 10.1016/j.jmb.2013.08.024.

    • Liu, Y. X.; Prigozhin, M. B.; Schulten, K.; Gruebele, M., Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment. Journal of the American Chemical Society 2014, 136, (11), 4265-4272, DOI: 10.1021/ja412639u.

    • Nienhaus, L.; Scott, G. E.; Haasch, R. T.; Wieghold, S.; Lyding, J. W.; Gruebele, M., Transparent Metal Films for Detection of Single-Molecule Optical Absorption by Scanning Tunneling Microscopy. Journal of Physical Chemistry C 2014, 118, (24), 13196-13202.

    • Shyshlov, D.; Berrios, E.; Gruebele, M.; Babikov, D., On Readout of Vibrational Qubits Using Quantum Beats. Journal of Chemical Physics 2014, 141, (22), DOI:Artn 224306 Doi 10.1063/1.4903055.

    • Platkov, M.; Gruebele, M., Periodic and Stochastic Thermal Modulation of Protein Folding Kinetics. Journal of Chemical Physics 2014, 141, (3), DOI:Artn 035103 DOI 10.1063/1.4887360.

    • Nienhaus, L.; Gross, D. E.; Xue, Z.; Moore, J. S.; Gruebele, M., Intramolecular Energy Transfer in a Synthetic Dendron-Based Light Harvesting System. Journal of Photochemistry and Photobiology a-Chemistry 2014, 295, 26-33, DOI:10.1016/j.jphotochem.2014.08.014.

    • Nguyen, D.; Mallek, J.; Cloud, A. N.; Abelson, J. R.; Girolami, G. S.; Lyding, J.; Gruebele, M., The Energy Landscape of Glassy Dynamics on the Amorphous Hafnium Diboride Surface. Journal of Chemical Physics 2014, 141, (20), DOI:Artn 204501 Doi 10.1063/1.4901132.

    • Guzman, I.; Gruebele, M., Protein Folding Dynamics in the Cell. Journal of Physical Chemistry B 2014, 118, (29), 8459-8470, DOI: 10.1021/Jp501866v.

    • Guzman, I.; Gruebele, M., Protein Folding Dynamics in the Cell. Journal of Physical Chemistry B 2014, 118, (29), 8459-8470, DOI: 10.1021/Jp501866v.

    • Guo, M. H.; Gelman, H.; Gruebele, M., Coupled Protein Diffusion and Folding in the Cell. Plos One 2014, 9, (12), DOI:ARTN e113040 DOI 10.1371/journal.pone.0113040.

    • Gruebele, M., Carpe Diem. Biophysical Journal 2014, 107, (1), 3-4, DOI: 10.1016/j.bpj.2014.04.059.

    • Chao, S. H.; Matthews, S. S.; Paxman, R.; Aksimentiev, A.; Gruebele, M.; Price, J. L., Two Structural Scenarios for Protein Stabilization by PEG. Journal of Physical Chemistry B 2014, 118, (28), 8388-8395, DOI: 10.1021/Jp502234s.

  • 2013
    • Berrios, E.; Pratt, S.; Tripathi, P.; Gruebele, M., More Protected Vibrational States at the Dissociation Limit of SCCI2. Journal of Physical Chemistry A 2013, 117, (46), 12082-12090, DOI: 10.1021/jp404834y.

    • Berrios, E.; Sundaradevan, P.; Gruebele, M., Franck-Condon Fingerprinting of Vibration-Tunneling Spectra. Journal of Physical Chemistry A 2013, 117, (32), 7535-7541, DOI: 10.1021/jp401848p.

    • Boulos, S. P.; Prigozhin, M. B.; Liu, Y.; Wirth, A. J.; Boppart, S. A.; Gruebele, M.; Murphy, C. J., The Gold Nanorod-Biology Interface: From Proteins to Cells to Tissue. Current Physical Chemistry 2013, 3, 128-135.

    • Gelman, H.; Perlova, T.; Gruebele, M., Dodine as a Protein Denaturant: The Best of Two Worlds? Journal of Physical Chemistry B 2013, 117, (42), 13090-13097, DOI: 10.1021/jp4028113.

    • Gruebele, M.; Thirumalai, D., Perspective: Reaches of Chemical Physics in Biology. Journal of Chemical Physics 2013, 139, (12), DOI: 10.1063/1.4820139.

    • Kocherginsky, N.; Gruebele, M., A Thermodynamic Derivation of the Reciprocal Relations. Journal of Chemical Physics 2013, 138, (12).

    • Matsumura, Y.; Shinjo, M.; Kim, S. J.; Okishio, N.; Gruebele, M.; Kihara, H., Transient Helical Structure During PI3K and Fyn SH3 Domain Folding. Journal of Physical Chemistry B 2013, 117, (17), 4836-4843, DOI: 10.1021/jp400167s.

    • Meister, K.; Ebbinghaus, S.; Xu, Y.; Duman, J. G.; DeVries, A.; Gruebele, M.; Leitner, D. M.; Havenith, M., Long-Range Protein-Water Dynamics in Hyperactive Insect Antifreeze Proteins. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (5), 1617-1622.

    • Prigozhin, M. B.; Gruebele, M., Microsecond Folding Experiments and Simulations: A Match Is Made. Physical Chemistry Chemical Physics 2013, 15, (10), 3372-3388, DOI: 10.1039/c3cp43992e.

    • Prigozhin, M. B.; Liu, Y. X.; Wirth, A. J.; Kapoor, S.; Winter, R.; Schulten, K.; Gruebele, M., Misplaced Helix Slows Down Ultrafast Pressure-Jump Protein Folding. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (20), 8087-8092, DOI: 10.1073/pnas.1219163110.

    • Wirth, A. J.; Gruebele, M., Quinary Protein Structure and the Consequences of Crowding in Living Cells: Leaving the Test-Tube Behind. Bioessays 2013, 35, (11), 984-993, DOI: 10.1002/bies.201300080.

    • Wirth, A. J.; Platkov, M.; Gruebele, M., Temporal Variation of a Protein Folding Energy Landscape in the Cell. Journal of the American Chemical Society 2013, 135, (51), 19215-19221, DOI: 10.1021/ja4087165.

  • 2012
    • Gelman, H.; Platkov, M.; Gruebele, M., Rapid Perturbation of Free-Energy Landscapes: From in Vitro to in Vivo. Chemistry-a European Journal 2012, 18, (21), 6420-6427.

    • Liu, Y. X.; Strumpfer, J.; Freddolino, P. L.; Gruebele, M.; Schulten, K., Structural Characterization of Lambda-Repressor Folding from All-Atom Molecular Dynamics Simulations. Journal of Physical Chemistry Letters 2012, 3, (9), 1117-1123.

    • Anunciado, D.; Guzman, I.; Dhar, A.; Gruebele, M.; Baranger, A. M., Multistep Kinetics of the U1A-SL2 RNA Complex Dissociation (vol 408, pg 896, 2011). Journal of Molecular Biology 2012, 422, (1), 159-160.

    • Ashtekar, S.; Nguyen, D.; Zhao, K.; Lyding, J.; Wang, W. H.; Gruebele, M., Communication: An Obligatory Glass Surface. Journal of Chemical Physics 2012, 137, (14).

    • Berrios, E.; Gruebele, M.; Shyshlov, D.; Wang, L.; Babikov, D., High Fidelity Quantum Gates with Vibrational Qubits. Journal of Physical Chemistry A 2012, 116, (46), 11347-11354.

    • Ebbinghaus, S.; Meister, K.; Prigozhin, M. B.; DeVries, A. L.; Havenith, M.; Dzubiella, J.; Gruebele, M., Functional Importance of Short-Range Binding and Long-Range Solvent Interactions in Helical Antifreeze Peptides. Biophysical Journal 2012, 103, (2), L20-L22.

    • Guo, M. H.; Xu, Y. F.; Gruebele, M., Temperature Dependence of Protein Folding Kinetics in Living Cells. Proceedings of the National Academy of Sciences of the United States of America 2012, 109, (44), 17863-17867

  • 2011
    • Price, J. L.; Culyba, E. K.; Hanson, S. R.; Dhar, A.; Wong, C. H.; Gruebele, M.; Powers, E. T.; Kelly, J. W., Protein Native State Stabilization by Strategic Placement of Aromatic Side Chains in N-Glycosylated Reverse Turns. Biopolymers 2011, 96, (4), 433-433.

    • Prigozhin, M. B.; Gruebele, M., The Fast and the Slow: Folding and Trapping of λ6-85. Journal of the American Chemical Society 2011, 133, (48), 19338-19341.

    • Girdhar, K.; Scott, G.; Chemla, Y. R.; Gruebele, M., Better Biomolecule Thermodynamics from Kinetics. Journal of Chemical Physics 2011, 135, DOI: 10.1063/1.3607605.

    • Anunciado, D.; Dhar, A.; Gruebele, M.; Baranger, A. M., Multistep Kinetics of the U1A-SL2 RNA Complex Dissociation. Journal of Molecular Biology 2011, 408, (5), 896-908.

    • Culyba, E. K.; Price, J. L.; Hanson, S. R.; Dhar, A.; Wong, C. H.; Gruebele, M.; Powers, E. T.; Kelly, J. W., Protein Native-State Stabilization by Placing Aromatic Side Chains in N-Glycosylated Reverse Turns. Science 2011, 331, (6017), 571-575. 

    • Gruebele, M., A triple threat to single molecules. Nature Methods 2011, 8, (3), 213-215.

    • Gruebele, M., Two- and Higher Point Correlation Functions in Proteins. Journal of Biomolecular Structure & Dynamics 2011, 28, (4), 615-616.

    • Prigozhin, M. B.; Sarkar, K.; Law, D.; Swope, W. C.; Gruebele, M.; Pitera, J., Reducing Lambda Repressor to the Core. Journal of Physical Chemistry B 2011, 115, (9), 2090-2096. 

    • Walters, P. L.; Prigozhin, M. B.; Takeshita, T. Y.; Xu, L.; Olivarez, F. M.; Gruebele, M., Conformational energy gaps and scaling of conformer density in chain molecules. Chemical Physics Letters 2011, 507, (1-3), 15-18. 

    • Ashtekar, S.; Scott, G.; Lyding, J.; Gruebele, M., Direct observation of two-state surface dynamics on amorphous silicon. Physical Review Letters 2011, 106.

    • Piana, S.; Sarkar, K.; Lindorff-Larsen, K.; Guo, M. H.; Gruebele, M.; Shaw, D. E., Computational Design and Experimental Testing of the Fastest-Folding beta-Sheet Protein. Journal of Molecular Biology 2011, 405, (1), 43-48. 

    • Dhar, A.; Girdhar, K.; Singh, D.; Gelman, H.; Ebbinghaus, S.; Gruebele, M., Protein Stability and Folding Kinetics in the Nucleus and Endoplasmic Reticulum of Eucaryotic Cells. Biophysical Journal 2011, 101, (2), 421-430.

    • Dhar, A.; Gruebele, M., Fast Relaxation Imaging in Living Cells. Current Protocols in Protein Science 2011, 28, DOI: 10.1002/0471140864.ps2801s65.

    • Dhar, A.; Prigozhin, M.; Gelman, H.; Gruebele, M., Studying IDP Stability and Dynamics by Fast Relaxation Imaging in Living Cells, In Intrinsically Disordered Proteins: Volume I. Experimental Techniques; Uversky, V., Dunker, A. K., Eds.; Springer, Berlin, 2011.

  • 2010
    • Price, J. L.; Shental-Bechor, D.; Dhar, A.; Turner, M. J.; Powers, E. T.; Gruebele, M.; Levy, Y.; Kelly, J. W., Context-Dependent Effects of Asparagine Glycosylation on Pin WW Folding Kinetics and Thermodynamics. Journal of the American Chemical Society 2010, 132, (43), 15359-15367. 

    • Benalcazar, W. A.; Chowdary, P. D.; Jiang, Z.; Marks, D. L.; Chaney, E. J.; Gruebele, M.; Boppart, S. A., High-Speed Nonlinear Interferometric Vibrational Imaging of Biological Tissue With Comparison to Raman Microscopy. IEEE Journal of Selected Topics in Quantum Electronics 2010, 16, (4), 824-832.

    • Chowdary, P. D.; Jiang, Z.; Chaney, E. J.; Benalcazar, W. A.; Marks, D. L.; Gruebele, M.; Boppart, S. A., Molecular Histopathology by Spectrally Reconstructed Nonlinear Interferometric Vibrational Imaging. Cancer Research 2010, 70, (23), 9562-9569.

    • Sarkar, K.; Nguyen, D. A.; Gruebele, M., Loop and stem dynamics during RNA hairpin folding and unfolding. RNA-A Publication of the RNA Society 2010, 16, (12), 2427-2434. 

    • Scott, G.; Ashtekar, S.; Lyding, J.; Gruebele, M., Direct Imaging of Room Temperature Optical Absorption with Subnanometer Spatial Resolution. Nano Letters 2010, 10, (12), 4897-4900. 

    • Scott, G.; Gruebele, M., Solving the Low Dimensional Smoluchowski Equation with a Singular Value Basis Set. Journal of Computational Chemistry 2010, 31, (13), 2428-2433. 

    • Larios, E.; Gruebele, M., Protein stability at negative pressure. Methods 2010, 52, (1), 51-56.

    • Denos, S.; Gotkowski, E.; Gruebele, M., A Learning Algorithm to Discover Soluble Vesicle-Binding Helical Peptides. Journal of Physical Chemistry B 2010, 114, (14), 4909-4914.

    • Dhar, A.; Ebbinghaus, S.; Shen, Z.; Mishra, T.; Gruebele, M., The Diffusion Coefficient for PGK Folding in Eukaryotic Cells. Biophysical Journal 2010, 99, (9), L69-L71. 

    • Dhar, A.; Samiotakis, A.; Ebbinghaus, S.; Nienhaus, L.; Homouz, D.; Gruebele, M.; Cheung, M. S., Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding. Proceedings of the National Academy of Sciences of the United States of America 2010, 107, (41), 17586-17591. 

    • Ebbinghaus, S.; Meister, K.; Born, B.; DeVries, A. L.; Gruebele, M.; Havenith, M., Antifreeze Glycoprotein Activity Correlates with Long-Range Protein-Water Dynamics. Journal of the American Chemical Society 2010, 132, (35), 12210-12211. 

    • Gruebele, M., ANALYTICAL BIOCHEMISTRY Weighing up protein folding. Nature 2010, 468, (7324), 640-641. 

    • Gruebele, M., Protein folding Introduction. Methods 2010, 52, (1), 1-2. 

    • Ashtekar, S.; Scott, G.; Lyding, J.; Gruebele, M., Direct Visualization of Two-State Dynamics on Metallic Glass Surfaces Well Below T-g. Journal of Physical Chemistry Letters 2010, 1, (13), 1941-1945. 

    • Benalcazar, W. A.; Chowdary, P. D.; Jiang, Z.; Marks, D. L.; Chaney, E. J.; Gruebele, M.; Boppart, S. A., High-Speed Nonlinear Interferometric Vibrational Imaging of Biological Tissue With Comparison to Raman Microscopy. IEEE Journal of Selected Topics in Quantum Electronics 2010, 16, (4), 824-832. 

    • Berrios, E.; Hui, H. Y.; Gruebele, M., Vibrationally resolved emission of thiophosgene dimer. Chemical Physics Letters 2010, 497, (4-6), 163-167. 

    • Chen, K.; Eargle, J.; Sarkar, K.; Gruebele, M.; Luthey-Schulten, Z., Functional Role of Ribosomal Signatures. Biophysical Journal 2010, 99, (12), 3930-3940. 

    • Chowdary, P. D.; Jiang, Z.; Chaney, E. J.; Benalcazar, W. A.; Marks, D. L.; Gruebele, M.; Boppart, S. A., Molecular Histopathology by Spectrally Reconstructed Nonlinear Interferometric Vibrational Imaging. Cancer Research 2010, 70, (23), 9562-9569. 

    • Ebbinghaus, S.; Dhar, A.; McDonald, D.; Gruebele, M., Protein folding stability and dynamics imaged in a living cell. Nature Methods 2010, 7, (4), 319-323.

    • Liu, F.; Gao, Y. G.; Gruebele, M., A Survey of lambda Repressor Fragments from Two-State to Downhill Folding. Journal of Molecular Biology 2010, 397, (3), 789-798.

    • Liu, F.; Gruebele, M., Mapping an Aggregation Nucleus One Protein at a Time. Journal of Physical Chemistry Letters 2010, 1, (1), 16-19.

    • Liu, F.; Maynard, C.; Scott, G.; Melnykov, A.; Hall, K. B.; Gruebele, M., A natural missing link between activated and downhill protein folding scenarios. Physical Chemistry Chemical Physics 2010, 12, (14), 3542-3549.

    • Liu, F.; Nakaema, M.; Gruebele, M., The transition state transit time of WW domain folding is controlled by energy landscape roughness. Journal of Chemical Physics 2009, 131, (19), doi:10.1063/1.3262489.

    • Chowdary, P. D.; Benalcazar, W. A.; Jiang, Z.; Marks, D. M.; Boppart, S. A.; Gruebele, M., High Speed Nonlinear Interferometric Vibrational Analysis of Lipids by Spectral Decomposition. Analytical Chemistry 2010, 82, (9), 3812-3818.

  • 2009
    • Chowdary, P. D.; Gruebele, M., Molecules: What Kind of a Bag of Atoms? Journal of Physical Chemistry A 2009, 113, (47), 13139-13143.

    • Weidinger, D.; Engel, M. F.; Gruebele, M., Freezing Vibrational Energy Flow: A Fitness Function for Interchangeable Computational and Experimental Control. Journal of Physical Chemistry A 2009, 113, (16), 4184-4191.

    • Born, B.; Kim, S. J.; Ebbinghaus, S.; Gruebele, M.; Havenith, M., The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin. Faraday Discussions 2009, 141, 161-173.

    • Carmichael, E. S.; Gruebele, M., Controlling the Smoothness of Optically Transparent Gold Films by Temperature Tuning. Journal of Physical Chemistry C 2009, 113, (11), 4495-4501.

    • Liu, F.; Dumont, C.; Zhu, Y. J.; DeGrado, W. F.; Gai, F.; Gruebele, M., A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha D-3. Journal of Chemical Physics 2009, 130, (6).

    • Chowdary, P. D.; Gruebele, M., An effective Hamiltonian survey of the anharmonic vibrational state space of SCCl2 up to the dissociation energy. Journal of Chemical Physics 2009, 130, (13).

    • Chowdary, P. D.; Gruebele, M., Regular vibrational state progressions at the dissociation limit of SCCl2. Journal of Chemical Physics 2009, 130, (2).

    • Gruebele, M., Protein Dynamics: From Molecules, to Interactions, to Biology. International Journal of Molecular Sciences 2009, 10, (3), 1360-1368.

    • Sarkar, K.; Meister, K.; Sethi, A.; Gruebele, M., Fast Folding of an RNA Tetraloop on a Rugged Energy Landscape Detected by a Stacking-Sensitive Probe. Biophysical Journal 2009, 97, (5), 1418-1427.

    • Fuller, A. A.; Du, D.; Liu, F.; Davoren, J. E.; Bhabha, G.; Kroon, G.; Case, D. A.; Dyson, H. J.; Powers, E. T.; Wipf, P.; Gruebele, M.; Kelly, J. W., Evaluating beta-turn mimics as beta-sheet folding nucleators. Proceedings of the National Academy of Sciences of the United States of America 2009, 106, (27), 11067-11072.

    • Gruebele, M., How to mark off paths on the protein energy landscape. Proceedings of the National Academy of Sciences of the United States of America 2009, 106, (45), 18879-18880.

    • Kim, S. J.; Matsumura, Y.; Dumont, C.; Kihara, H.; Gruebele, M., Slowing Down Downhill Folding: A Three-Probe Study. Biophysical Journal 2009, 97, (1), 295-302.

    • Dumont, C.; Emilsson, T.; Gruebele, M., Reaching the protein folding speed limit with large, sub-microsecond pressure jumps. Nature Methods 2009, 6, (7), 515-U70.

  • 2008
    • Jager, M.; Deechongkit, S.; Koepf, E. K.; Nguyen, H.; Gao, J. M.; Powers, E. T.; Gruebele, M.; Kelly, J. W., Understanding the Mechanism of beta-Sheet Folding From a Chemical and Biological Perspective. Biopolymers 2008, 90, (6), 751-758.

    • Kim, S. J.; Born, B.; Havenith, M.; Gruebele, M., Real-time detection of protein-water dynamics upon protein folding by terahertz absorption spectroscopy. Angewandte Chemie-International Edition 2008, 47, (34), 6486-6489.

    • Leitner, D. M.; Gruebele, M.; Havenith, M., Solvation dynamics of biomolecules: modeling and terahertz experiments. HFSP Journal 2008, 2, (6), 314-323.

    • Kim, S. J.; Dumont, C.; Gruebele, M., Simulation-based fitting of protein-protein interaction potentials to SAXS experiments. Biophysical Journal 2008, 94, (12), 4924-4931.

    • Leitner, D. M.; Gruebele, M., Quantum model of restricted vibrational energy flow on the way to the transition state in unimolecular reactions. Molecular Physics 2008, 106, (2-4), 433-442.

    • Liu, F.; Du, D. G.; Fuller, A. A.; Davoren, J. E.; Wipf, P.; Kelly, J. W.; Gruebele, M., An experimental survey of the transition between two-state and downhill protein folding scenarios. Proceedings of the National Academy of Sciences of the United States of America 2008, 105, (7), 2369-2374.

    • Liu, F.; Gruebele, M., Downhill dynamics and the molecular rate of protein folding. Chemical Physics Letters 2008, 461, (1-3), 1-8.

    • Chowdary, P. D.; Gruebele, M., Size and Energy Scaling of Nonstatistical Vibrational Quantum States. Physical Review Letters 2008, 101, (25).

    • Weidinger, D.; Gruebele, M., Simulations of quantum computation with a molecular ion. Chemical Physics 2008, 350, (1-3), 139-144.

    • Ebbinghaus, S.; Kim, S. J.; Heyden, M.; Yu, X.; Gruebele, M.; Leitner, D. M.; Havenith, M., Protein sequence- and pH-dependent hydration probed by terahertz spectroscopy. Journal of the American Chemical Society 2008, 130, (8), 2374-2375.

    • Freddolino, P. L.; Liu, F.; Gruebele, M.; Schulten, K., Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal 2008, 94, (10), L75-L77.

    • Gruebele, M., Comment on probe-dependent and nonexponential relaxation kinetics: Unreliable signatures of downhill protein folding. Proteins-Structure Function and Bioinformatics 2008, 70, (3), 1099-1102.

  • 2007
    • Gruebele, M.; Wolynes, P. G., Quantizing Ulam's control conjecture. Physical Review Letters 2007, 99, (6).

    • Jaeger, M.; Nguyen, H.; Dendle, M.; Gruebele, M.; Kelly, J. W., Influence of hPin1 WWN-terminal domain boundaries on function, protein stability, and folding. Protein Science 2007, 16, (7), 1495-1501.

    • Ebbinghaus, S.; Kim, S. J.; Heyden, M.; Yu, X.; Heugen, U.; Gruebele, M.; Leitner, D. M.; Havenith, M., An extended dynamical hydration shell around proteins. Proceedings of the National Academy of Sciences of the United States of America 2007, 104, (52), 20749-20752.

    • Liu, F.; Gruebele, M., Pushing protein folding to the limit: a new downhill folder lambda repressor Q33H. Biophysical Journal 2007, 400A-400A.

    • Chowdary, P. D.; Strickler, B.; Lee, S.; Gruebele, M., The (X)over-tilde <-(A)over-tilde SEP spectra of jet-cooled thiophosgene. Chemical Physics Letters 2007, 434, (4-6), 182-187.

    • Carmichael, E. S.; Ballard, J. B.; Lyding, J. W.; Gruebele, M., Frequency-modulated, single-molecule absorption detected by scanning tunneling microscopy. Journal of Physical Chemistry C 2007, 111, (8), 3314-3321.

    • Chowdary, P. D.; Martinez, T. J.; Gruebele, M., The vibrationally adiabatic torsional potential energy surface of trans-stilbene. Chemical Physics Letters 2007, 440, (1-3), 7-11.

    • Denos, S. M.; Gruebele, M. H., Fast binding kinetics of, alpha helical peptides with small unilamellar vesicles. Biophysical Journal 2007, 585A-585A.

    • Dumont, C.; Gruebele, M., Refolding of lambda-repressor mutants using a novel pressure jump instrument. Biophysical Journal 2007, 400A-400A.

    • Engel, M.; Gruebele, M., Shifted-update rotation wavepacket propagation with a laser pulse. Chemical Physics Letters 2007, 433, (4-6), 368-372.

    • Liu, F.; Gruebele, M., Tuning lambda(6-85) towards downhill folding at its melting temperature. Journal of Molecular Biology 2007, 370, (3), 574-584.

    • Liu, F.; Gruebele, M., Pushing protein folding to the limit: a new downhill folder lambda repressor Q33H. Biophysical Journal 2007, 400A-400A.

    • Weidinger, D.; Gruebele, M., Quantum computation with vibrationally excited polyatomic molecules: effects of rotation, level structure, and field gradients. Molecular Physics 2007, 105, (13-14), 1999-2008.

  • 2006
    • Jager, M.; Zhang, Y.; Bieschke, J.; Nguyen, H.; Dendle, M.; Bowman, M. E.; Noel, J. P.; Gruebele, M.; Kelly, J. W., Structure-function-folding relationship in a WW domain. Proceedings of the National Academy of Sciences of the United States of America 2006, 103, (28), 10648-10653.

    • Lee, S.; Engel, M.; Gruebele, M., The state space model of vibrational energy flow: An experimental test using SEP spectra of jet-cooled thiophosgene. Chemical Physics Letters 2006, 420, (1-3), 151-156.

    • Leitner, D. M.; Havenith, M.; Gruebele, M., Biomolecule large-amplitude motion and solvation dynamics: modelling and probes from THz to X-rays. International Reviews in Physical Chemistry 2006, 25, (4), 553-582.

    • Dumont, C.; Matsumura, Y.; Kim, S. J.; Li, J. S.; Kondrashkina, E.; Kihara, H.; Gruebele, M., Solvent-tuning the collapse and helix formation time scales of lambda(*)(6-85). Protein Science 2006, 15, (11), 2596-2604.

Press

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