Biological Physics

Our current biological physics projects include investigations of DNA self-assembly as a promising method for nano-electronics. Another project investigates genetic regulatory networks, where the sequencing of full genomes and monitoring of the concentrations of thousands of molecular species within cells have given us new windows into the physical nature of life. Investigations of tissue mechanics in developmental biology are determining the role of molecular-scale and cellular-scale dynamics and larger scale emergent properties in pattern formation. Another project uses radioisotopes to track changes in plant physiology as a consequence of environmental changes.

Our Current Projects

Bio-enabled nano-electronics

Conventional microelectronic processing techniques cease working on the scales of about 10 nm. Biochemical methods of self-assembly attract researchers’ attention as an alternative cheap and versatile method to fabricate nanostructures. Duke electronic nanostructures laboratory works on three directions of controlled self-assembly based on the methods of organic chemistry/biochemistry: – use self-assembling DNA templates to target precise positioning of metallic nanoparticles; – metallize DNA to create nanowire interconnects; – modify surface chemistry to create interface DNA nanostructures with silicon substrates. These three subjects are unified by the goal of reliably making nanoelectronic circuits based on inorganic nanoscale building blocks tethered on self-assembling DNA templates. The research is conducted in collaboration between the groups of Gleb Finkelstein in Physics and Thom LaBean in Chemistry and Computer Science.

Genetic regulatory networks

The sequencing of full genomes and monitoring of the concentrations of thousands of molecular species within cells have given us new windows into the physical nature of life. A host of scientific questions about the roles of genes and proteins in cellular functions, development, and evolution now seem within reach, and the answers will undoubtedly yield practical benefits ranging from medical therapies to microbe-based solutions to environmental problems. The challenge is to develop theories of the structure and dynamics of complex networks of interacting genes and proteins to complement our understanding of the physics and chemistry of biological molecules and materials. This is simultaneously a part of the advancing frontier of biology and a problem in the physics (or applied mathematics) of systems composed of many interacting elements. It requires the extension of statistical physics and nonlinear dynamics methods to systems with more complicated sets of interactions than those encountered in typical condensed matter systems. Joshua Socolar's research focuses on the dynamical properties of model regulatory networks and the dynamics of gene expression in real cells. This work involves several collaborations with Biology faculty in the Duke Center for Systems Biology.

Boolean network model of transcriptional oscillations in cyclin mutant yeast cells. [Orlando et al, Nature 453, 944 (2008).]

Emergent properties in tissue dynamics

Biological physics research in the Duke Physics Department includes an active program investigating the mechanisms governing tissue dynamics and their application to key problems in the biological and biomedical sciences. One project investigates the role of molecular-scale and cellular-scale dynamics and larger scale emergent properties in the pattern formation of developmental biology and wound healing. In particular, we are interested in understanding how these dynamical mechanisms connect to the genetic program of development in morphogenesis. In addition to the physicist Glenn Edwards, the multidisciplinary collaboration includes the biologist Dan Kiehart and the mathematician Stephanos Venakides.

A second collaboration has been developing human surgical applications of pulsed, infrared lasers. A detailed understanding of the nanosecond-scale thermodynamics and chemical kinetics resulting in laser-induced material failure of tissue has led to extremely precise cutting tools for surgical applications. This mechanistic understanding has provided a rationale for the development of compact and relatively inexpensive medical lasers. Glenn Edwards collaborates with the neuroscientist Robert Pearlstein and with optical scientists and neurosurgeons on this multidisciplinary project.

distorted cell shapes

A)    A series of microscopic images demonstrating the apoptotic force distorting cell shapes. The top row of images corresponds to the tissue surface and middle and lower rows are below the surface, as indicated in the figure. Time progresses from left to right, also as indicated in the figure.

B)    Color enhanced reproduction of the top row highlights that the neighboring (red) cells are pulled towards the apoptotic cells (white), rearrange their neighbor-neighbor configurations, and then span the gap. The distortion of a next-to-nearest neighbor cell in highlighted in blue.
Science 321, 1683-1686 (2008).

Radioisotope tracer investigation of environmental changes in plants

Primary plant productivity sustains life on Earth and is a principle component of the planet's system that regulates atmospheric carbon dioxide concentration. Better understanding of the mechanisms that balance carbon and nutrient resources in plants will provide insights critical to advancing modeling of processes and networks that determine plant productivity. The long-term goal of the collaboration between Calvin Howell (Physics) and Chantal Reid (Biology) is to increase understanding of the physiological response of plants to environmental changes across spatial and organizational scales from the whole plant to genes through gene expression in the production of enzymes that regulate cell activities important for plant growth and reproduction. Making the connection between physiological responses and gene expression may be done directly by studying genetic mutants or indirectly by identifying the biochemical reaction network involved in the response. Short-lived radioisotope tracer techniques enable plant studies that are sensitive to the organizational and temporal scale range that links the environment to the underlying cellular activities responsible for active mechanisms that drive physiological responses.

Theoretical Nonequilibrium Physics