Biological Physics

NanoBioPhysics

The NanoBio 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. Specifically, the group focuses on extracellular electron transfer by environmental microbes which have evolved a remarkable ability to transfer electrons to solid acceptors such as environmental minerals, essentially allowing them to “breathe rocks”. But how can a microbe interact with and transfer energy to a solid outside the cell itself? In addition to learning about the basic science, we are exploiting our understanding of the charge transfer for renewable energy recovery in biological fuel cells, and developing new nanomaterials for energy conversion.

This group includes Professor Moh El-Naggar. Current research topics include:

  • Microbial Nanowires
  • Experiments and Modeling of Extracellular Electron Transfer
  • Microbial Fuel Cells
  • Single-cell electrochemistry
  • Biogenic Synthesis of Nanomaterials

Group Website: NanoBio Group 

 

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

  • Stability, symmetry, and size of membrane polyhedra.
  • Structure of elastic bilayer deformations.
  • Cooperative interactions between membrane proteins.
  • Reaction-diffusion patterns in cell membranes.

Group Website: Theoretical Biological Physics Group

 

Computational Physics

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:

  • Molecular mechanisms of small interfering RNA interaction with phospholipid membranes
  • Cholesterol flip-flop dynamics in lipid bilayers
  • Pore formation in lipid membranes due to shock–induced collapse of nanobubbles

The group is also involved in hybrid quantum mechanical-atomistic-mesoscale simulations of:

  • DNA translocation through nanometer scale pores and channels in solid-state fluidic devices that underlie the solid-state nanopore “microscopy” technology for high-speed sequencing
  • Thermo-mechanical properties of three-dimensional crystalline structures of nanometer size particles functionalized with DNA and self-assembled with molecular-scale spatial precision using programmable interactions.

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:

  • building models of mechanisms that participate in the conversion occurring at the synaptic level from an electrical signal (action potential) to a biochemical signal, and its conversion back to electrical signal.
  • implementing forward propagation algorithms with adaptive time steps to simulate response to specific stimuli.
  • devising complementary semi-analytical technique, based on matrix diagonalization, which does not use time steps, but which breaks down when there are feedback mechanisms.
  • designing efficient way to encode fitness, i.e. match of simulated data with experimental observations in a computationally efficient way by using moments. The time series are analyzed like a probability distribution function, and only the leading lowest moments are considered.
  • implementing simulated annealing and genetic algorithm to identify multiple sets of optimized parameters.

Group Website: Computational Condensed Matter Theory

  • Department of Physics and Astronomy
  • University of Southern California
  • 825 Bloom Walk
  • ACB 439
  • Los Angeles, CA 90089-0484