Biophysics Seminars Archive

The metabolic function of microbial communities emerges through a complex hierarchy of genome-encoded processes, from gene expression to interactions between diverse taxa. Therefore, a central challenge for microbial ecology is deciphering how genomic structure determines metabolic function in communities.

When experimenting with a large pool of species, a common problem is to determine a priori whether a certain subset of species can coexist when co-cultured. We propose a simple statistical model in which a number of species assemblages are observed, and the coexistence of novel assemblages is predicted out-of-fit.

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The study of small experimental communities has been key to the development of ecology as a discipline. Yet, for most ecological communities, the number of experiments required to build, model, or analyze the system vastly exceeds what is feasible, rendering these communities experimentally intractable.

Cells across the tree of life respond to a sudden, nonlethal rise in temperature--heat shock--in similar ways. Following heat shock, proteins and mRNAs form clumps, certain genes turn on, and protein synthesis and cell growth sharply decline.

Spinning disk confocal modules are “core facility friendly”; they insert conveniently between a commercial microscope base and camera, improve image quality and add no significant drawbacks. In contrast, high numerical aperture (NA) light sheet microscopy often requires radical sample modification, substantial user re-training and fully...

The immune responses that defend us against pathogens are driven by stochastic processes amongst populations of cells. Enormous progress in immunology over the last few decades has identified most of the components of this complex system, including the cell types and the molecules used for communication.

Two of the most fundamental questions of sensory neuroscience are: 1) how is stimulus information represented by neuronal activity? and 2) what features of this activity are read out to guide behavior? The first question has been the subject of a large body of work across different sensory modalities.

Organisms are an evolutionary masterpiece of feedback control, featuring a mind-boggling capacity to self-correct. In this talk, we discuss our attempts to both understand feedback control in cells and to forward engineer it with de novo designed proteins.

Nucleosomes help structure chromosomes by compacting DNA into fibers.  Chromatin organization plays an important role for regulating gene expression; however, due to the highly crowded nuclear environment and the nanometer length scales of chromatin fibers, it has been very difficult to visualize chromatin in vivo.

I will describe a new approach that we are currently developing to describe developmental dynamics. We are using simple machine learning techniques to project the dynamics of the Drosophila gap genes onto a low dimensional space, allowing us to build "geometric" models.

The immune repertoire responds to a wide variety of pathogenic threats. Immune repertoire sequencing experiments give us insight into the composition of these repertoires. Since the functioning of the repertoire relies on statistical properties, statistical analysis is needed to identify responding clones.

The physical limits to chemical sensing have been established and tested for single cells. However, recent experiments have demonstrated that cells can surpass these limits when they communicate. The theoretical limits to the precision of collective sensing are still poorly understood.

In physics and engineering dimensionless numbers frequently help to characterize the state of a system. I will present a series of vignettes about unusually large dimensionless numbers that arise in brain science. These can indicate issues that are poorly understood, and in some cases clearly misunderstood.

Optical reporters of neural activity have improved dramatically over the past decade. Recent developments in optical imaging approaches have unlocked the power of these indicators and can now provide real-time read-outs from large populations of brain cells in a wide range of living organisms.

In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (minimal chromatin model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data will be presented.

Complex life above a certain size would not be possible without a circulatory system. Both plants and animals have developed vascular systems of striking complexity to solve the problem of nutrient delivery, waste removal, and information exchange. Vascular networks are intimately linked to the fitness of organisms.

As an animal moves in space and receives external sensory inputs, it must dynamically maintain the representations of its position and environment at all times. How the hippocampus, a brain area crucial for spatial representations, achieves this task, and manages possible conflicts between different inputs remains unclear.

Individuals animals vary in their behaviors even when their genetics and environment are held constant. The mechanisms underlying this variation is still largely uncharacterized, though we have made some progress in understanding genetic and circuit variants that lead a population of animals to exhibit high or low variability in behavior.

The ability to move is a trait of all animals. Yet how do animals, including ourselves, get around in this complex and uncertain world with an ease and agility we find hard to recreate in engineered systems? Using an organismal physics approach my group explores the physical and physiological mechanisms that enable agile movement in living...

The electrosensory lobe (ELL) in mormyrid electric fish is a cerebellar-like structure that cancels the sensory effects of self-generated electric fields, allowing prey to be detected. Like the cerebellum, the ELL involves two stages of processing, analogous to the Purkinje cells and output cells of the deep cerebellar nuclei.

Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution.