Examining biology through the lens of physics has led to a more fundamental and quantitative understanding of many biological systems. The El-Naggar Lab and the Boedicker Lab are at the forefront of this effort, implementing cutting edge experimental tools to dissect the biology of charge transfer, regulation, biosynthesis, and complex behavior.
The El-Naggar Lab focuses on the fundamentals, implications, and technological applications of biological charge transfer, using environmental microbes as model systems. This is a highly interdisciplinary area, drawing from the toolboxes of nanoscience, condensed matter physics, electrochemistry, and environmental microbiology. In contrast to solid state systems (e.g. metals and semiconductors), where the mechanisms of charge transfer are well understood, with immense technological consequences ranging from computers to solar cells, comparatively little is known about the physics of biological charge transfer, especially over long distances. This is an immense knowledge gap, as charge transfer lies at the heart of cellular respiration. The research in this group examines the physics of the problem over large length scales and in the full biological context of microbial physiology and biotic-abiotic interactions.
Group Website: NanoBio Group
The Boedicker Lab is interested in understanding the rules that make complex networks of microbes work. Microbial communities play an important role in our everyday lives, and we aim to increase their benefit to society by developing experimental and theoretical tools to control, predict, and design the functional outputs of both synthetic and natural microbial ecosystems. Towards this goal, they have been developing predictive and quantitative models of biological decision making, using the tools of synthetic biology to test and expand the understanding of gene regulation, and investigating the role of microscale spatial structure on signal exchange and interspecies gene regulation.
Group Website: Boedicker Lab
Current research topics include:
Theoretical Biological Physics
The Theoretical Biological Physics group seeks a mechanistic understanding of biological phenomena in terms of physical models. Current research mainly concerns the physical basis for the organization, dynamics, shape, and signaling properties of cell membranes. Pertinent theoretical concepts are sharpened and put to the test in the context of specific biological phenomena exhibited by cell membranes, such as the formation and regulation of membrane domains of synaptic receptor molecules, chemotactic signaling across cell membranes, and elastic interactions between mechanosensitive membrane proteins and the surrounding lipid bilayer. The overall aim of the Theoretical Biological Physics group is to uncover novel physical mechanisms underlying living systems and, on this basis, to suggest new experimental approaches for the quantitative control of living systems.
This group includes Professor Christoph Haselwandter. Current research topics include
The high performance computing and simulation group has considerable experience in multiscale simulations combining density functional, molecular dynamics, and finite element schemes on a Grid of distributed parallel supercomputers and immersive and interactive visualization platforms. Their group is investigating molecular mechanisms of small interfering RNA (siRNA) interaction with phospholipid membranes, cholesterol flip-flop dynamics in lipid bilayers, and pore formation in lipid membranes due to shock–induced collapse of nanobubbles. Their group is also involved in hybrid quantum mechanical-atomistic-mesoscale simulations of ion transport and translocation of biopolymers such as DNA and RNA through nanometer scale pores and channels in solid-state fluidic devices that underlie “lab-on-a-chip” technology, single nanotube nanofluidic transistors, and solid-state nanopore “microscopy” for molecular structure and high-speed sequencing. They are also investigating thermomechanical properties of three-dimensional crystalline structures of nanometer size particles functionalized with DNA and self-assembled with molecular-scale spatial precision using programmable interactions.
This group includes Professors Rajiv Kalia, Aiichiro Nakano, Priya Vashishta. Current research topics include:
The group is also involved in hybrid quantum mechanical-atomistic-mesoscale simulations of:
Group Website: Collaboratory for Advanced Computing and Simulations
Computational Condensed Matter Physics
We are collaborating with a team of USC neuroscientists in an NIH sponsored Biomedical Research Project on modeling and simulating glutamate receptors. During this project, we have developed exciting numerical tools that allow us to discover and study the relevant mechanisms and conditions at the synaptic level which participate in the conversion of incoming neurotransmitter spikes into action potentials. Together with our collaborators, Bouteiller, Baudry and Berger, this has already resulted in an efficient system level simulation tool that allows a better understanding of the mechanisms regulating synaptic transmission and plasticity.. The contribution of the computational condensed matter group to this has been the development and application of a multi-parameter optimization algorithm, which matches these simulations with multiple experimental measurements, thus identifying realistic and relevant parameter sets. Ultimately, this technique will enable us to approach questions addressing learning and neural plasticity in a much more quantitative manner, and harness this new and powerful method to predict experiments and to control and strategically manipulate neural networks.
This group includes Professor Stephan Haas. Current research topics include:
Group Website: Computational Condensed Matter Theory