Ralph Jimenez

The Jimenez group is composed of chemists, biochemists, and physicists working at the interface of physical chemistry and biology. There are three on-going projects that build on optical and microfluidic technologies developed in our lab.

Ultrafast spectroscopy and molecular dynamics

We have developed a new generation of femtosecond multidimensional spectrometers that enables molecular dynamics to be simultaneously resolved on multiple electronic states. These 2-D and 3-D nonlinear optical methods are analogous to multidimensional NMR experiments, but with the significant difference that the femtosecond optical pulses are shorter than the molecular dynamics timescales, so we can directly observe molecular motions. These techniques are particularly useful for studying protein dynamics, because the optical spectra are often congested with multiple transitions, each of which is coupled to motions occurring over many orders of magnitude in time (femtoseconds to seconds). We are applying this new technology to the study of active-site dynamical asymmetry in heme proteins, protein-ligand interactions, and flexibility and conformational diversity in protein folding.

Microfluidic-based selection strategies for investigating the photophysics of fluorescent proteins

The development of fluorescent proteins (FPs) as molecular probes has revolutionized our ability to study cellular processes with high spatial and temporal resolution. Yet, there are a number of limitations to FPs, including decreased brightness relative to traditional fluorophores, poor photostability, and tendency to convert to dark states that limit the signal output, particularly for single molecule measurements. Most efforts to engineer and optimize these properties have resulted in improvement of one property (e.g. brightness) at the expense of another (e.g. photostability). Consequently, existing FPs are far from achieving optimal signal output.

Our goal is to generate FPs that dramatically improve ensemble imaging and enable single molecule imaging in cells. This goal will be achieved by directly targeting properties such as brightness, photobleaching, and dark state formation that diminish the number of photons emitted before photobleaching. Our approach is to generate targeted libraries of these proteins, express the libraries in mammalian cells, and screen for decreased dark state conversion, increased photostability, and increased brightness using a microfluidic cellular spectroscopy and optical force-switching instrument recently developed in our lab. Our unique selection technology permits high throughput screening and sorting of mammalian cells based on the measurement of multiple photophysical parameters. We are applying closely-related microfluidics technology to the development of genetically-encoded FRET-based sensors for metal ion detection.

Biofuels from algae

The development of renewable energy sources with minimal environmental impact is a compelling global priority. Microalgae are attractive candidates for achieving this goal, but they still require transforming development before they can serve as competent biofuel producers. We have designed a lab-on-a-chip microfluidic system to accelerate the process of screening genetic libraries of algae and rapidly assessing and optimizing growth conditions. The prototype device is being developed to measure photosynthetic light use and lipid accumulation on a cell-by-cell basis. The new technique measures the distribution of photosynthetic activity and its correlation with lipid production. This method of measuring the distribution of cellular behavior provides a faster, more precise assessment of productivity than low-throughput techniques.

E.A. Gibson and R. Jimenez “Three-pulse photon echo spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding” Proceedings of the XVI International Conference on Ultrafast Phenomena (2008).

J.D. Satterlee, C. Suquet, A.K. Bidwai, J.E. Erman, L. Schwall, R. Jimenez (2008) “Mass instability in isolated recombinant FixL heme domains of Bradyrhizobium Japonicum (BjFixLH)” Biochemistry 47, 1540-1553.

W. Amir, D. N. Schafer, C. G. Durfee, J. A. Squier, E. A. Gibson, L. Kost, R. Jimenez (2008) “Linear spatio-temporal characterization of a UV microscope objective for nonlinear imaging and spectroscopy by using two-dimensional Spectral Interferometry,” Journal of Microscopy, 230 part 1, 4.

D. Schafer, E.A. Gibson, W. Amir, R. Erickson, J. Lawrence, T. Vestad, J. Squier, R. Jimenez, D.W.M. Marr (2007) “Three-dimensional chemical concentration maps in a microfluidic device using two-photon absorption fluorescence imaging” Optics Letters 32, 2568.

B. Cho, C.F. Carlsson, and R. Jimenez (2006) Photon echo spectroscopy of heme proteins and porphyrins: effects of quasi-degenerate electronic structure on the peak shift decay, J. Chem. Phys., 124, 144905.

E.A. Gibson, D.M. Gaudiosi, H.C. Kapteyn, R. Jimenez, S. Kane, R. Huff, C. Durfee, and J. Squier (2006) Efficient reflection grisms for pulse compression and dispersion compensation of femtosecond pulses, Optics Letters, 31, 3363-5.

T. Stiles, R. Fallon, T. Vestad, J. Oakey, D.W.M. Marr, J. Squier and R. Jimenez (2005) Hydrodynamic Focusing for vacuum-pumped microfluidics, Nanofluidics and Microfluidics, 1, 280-283