BIOLOGICAL PHYSICS


The importance of biological systems, together with their complexity, has made biological physics one of the fastest growing subfields of physics. Biological physics is not a narrow discipline, however. It comprises a very broad range of research areas at the interface of physics, biology, chemistry, and medicine: it includes molecular biophysics, biomedical imaging and detection, neurobiological physics, nanoscale biophysical studies, as well as genomics. Research in these areas has advanced tremendously through the work of physicists who apply techniques from soft condensed matter, computational science, imaging and optics, magnetic resonance spectroscopy, microfabrication, and nonlinear dynamics, as well as other fields. Biological physics is thus highly interdisciplinary, and researchers in the University of Florida Physics Department benefit from close interactions with the UF College of Medicine, the Evelyn and William McKnight Brain Institute, the National High Magnetic Field Laboratory, the Institute for Food and Agricultural Sciences, and other departments and centers located either on or near campus.

Biological physics research at UF spans the range from basic studies at the molecular and cellular scale to whole-organism studies and biomedical imaging. Active research presently includes:

Molecular Biophysics: Prof. Hagen is studying the physics of the critically important biological process of protein folding, through which protein molecules can spontaneously acquire stable three-dimensional structure. Even for the simplest molecules, this process can occur on time scales as long as seconds, or as short as microseconds or even nanoseconds. Prof. Hagen uses a variety of laser-based spectroscopic techniques to study these fast dynamics in natural and synthetic proteins. His research interests also include the dynamics of gene expression, including stochastic gene expression and bacterial communication. In these activities he maintains active collaborations with faculty in the UF College of Medicine and the UF Cancer & Genetics Institute.

Image: (Top) A two-dimensional solid state NMR spectrum of Alzheimer's beta amyloid fibrils. (Bottom) Molecular structure model of "agitated" beta amyloid fibrils, based on solid state NMR data (Petkova).

Magnetic Resonance Imaging and Spectroscopy: Prof. Mareci uses nuclear magnetic resonance techniques to explore questions of tissue structure and biochemical processes in the nervous system. Magnetic resonance imaging and spectroscopy techniques allow spatially localized studies of the biochemical processes and physical structures in living tissue, which provides insight into - for example - the response of tissue to injury or disease. One current focus is the study of brain fibrous tissue structure using measurements of water translational diffusion to map the white matter structure of the intact brain. To support this work, specialized magnetic resonance antennas are constructed for specific measurements. In addition, excitation and detection techniques are developed for unique measurements, which are supported by the development of data processing routines.

Biomagnetism and related work: Prof. Meisel, along with collaborators in the Department of Horticultural Sciences, is studying the effect of strong magnetic fields, up to 30 Tesla, on in vivo gene regulation in Arabidopsis thaliana. Extensions to in vitro transcription experiments are made using T7 RNA Polymerase. Ancillary activities lead to new directions, and one example is the modeling of the electromagnetic fields arising from stimulating needles.

Computation and Simulation: Prof. Roitberg uses computational methods, including molecular dynamics simulation and quantum mechanical calculation, to study biomolecules. The catalytic properties and mechanisms of enzymes, and the structure and folding dynamics of proteins and peptides, are current areas of research. The Roitberg group is also developing methods for enhancing and optimizing sampling in computer simulations of biomolecules.

Image: Microarray data showing the effect of high magnetic fields on gene expression in Arabidopsis (Meisel)

Molecular Biophysics and Solid State NMR: Prof. Petkova is studying the fundamental biophysical process of protein folding that leads to the formation of insoluble protein and peptide aggregates. Misfolded peptides and proteins with cross-beta structure, also known as amyloid fibrils, are toxic to cells, and are involved in conformational diseases such as Alzheimer’s disease, amyotrophic lateral sclerosis and prion diseases. Prof. Petkova uses solid state nuclear magnetic resonance and other biophysical techniques (in collaboration with faculty from the Evelyn and William McKnight Brain Institute) to investigate the structure-toxicity relationship of amyloid fibrils, prefibrillar aggregates, and the membrane-associated assemblies that are formed by the amyloid peptides and proteins in model membranes.

Image at top-right of page: Photon-counting microscopy image showing bioluminescence of individual bacterial