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Biophysics & Neuroscience

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Large-scale imaging reveals neural Ca2+ dynamics across cortex in active mice (Schnitzer group)

Biophysics in the Department of Applied Physics explores the physical laws governing life

Billions of years of evolution has led to a rich diversity of biological processes that exploit the laws of physics in fascinating ways to grow, move, learn and compute, in a manner that far eludes the capabilities of our best artificially engineered machines. The Department of Applied Physics is dedicated to understanding all aspects of life across multiple scales of spatiotemporal organization, including how complex molecular machines function at the nanoscale, how systems of interacting chemicals give rise to life at the cellular scale, how higher level perceptions, thoughts and actions emerge from networks of neurons, how networks of species interact to give rise to complex ecologies, and how the nature of evolutionary dynamics can give rise to the diversity of life itself.

Biophysics research within the Department of Applied physics is characterized by a tight interplay between theory, experiment, and technology development, all driven by an intense desire to elucidate the physical laws governing life. Such research has lead to novel measurement technologies, like optical tweezers, microfluidic assays, and miniature microscopes, that enable us to probe the immense richness of biological dynamics in fundamentally new ways. Moreover, the resultant datasets are analyzed using state of the art methods from machine learning and high dimensional statistics, and such analyses lead to new theoretical models of biological phenomena, grounded in nonlinear dynamics, statistical mechanics, control theory, and theories of information processing and computation. And in turn, these theories themselves drive the design of new experiments and measurement technologies.

As a result of this highly interdisciplinary interaction between technology, experiments, analysis and theory, the biophysics effort within Applied Physics is tightly connected to many other departments on campus, including physics, biology, biochemistry, genetics, neurobiology, electrical engineering, and computer science. Also, our faculty are tightly embedded in many institutes across campus, including Bio-X, the Wu-Tsai Neurosciences Institute, the Center for Brain, Mind, Computation and Technology, the Institute for Human-Centered Artificial Intelligence, the Stanford Institute for Theoretical Physics, and the Stanford Linear Accelerator Biosciences Programs.

We explore:

Molecular and Cellular Biophysics


Evolution and Ecology


Example traces of neural Ca2+ activity traces acquired by epi-fluorescence imaging (Schnitzer Group)

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Map of the 1,166 cells identified computationally in epi-fluorescence Ca2+ videos (Schnitzer Group)

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An estimated 25,000–50,000 GCaMP6f-expressing pyramidal cells are optically accessible through the crystal skull by one-photon Ca2+ imaging (Schnitzer Group)