Biophysics Seminars Archive

Stefano Allesina: Predicting coexistence in experimental ecological communities

Mon, Oct 19, 2020, 12:15 pm

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.

Gurol Suel: The role of inorganic ions in bacterial resilience

Mon, Sep 28, 2020, 12:15 pm

We have been working to measure and understand how ion fluxes and ionic interactions regulate fundamental biological processes, and in particular promote stress tolerance in bacteria. I will present our recent work that builds on our discovery of action potentials generated within bacterial biofilms.

Bill Bialek & Josh Shaevitz: State of the Center

Andrew Leifer - Princeton Open Ventilation Monitor: Project Update

Mon, May 18, 2020, 12:00 pm

Zoom meeting ID: 935 3760 0219

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Vir Bulchandani: Digital herd immunity and COVID-19

Mon, May 11, 2020, 12:00 pm

Video recording is available at 

Zoom meeting ID: 967 8799 8386

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Xiaoliang Sunney Xie - In Search of the COVID-19 Cure: Neutralizing Antibodies via Single Cell Genomics

Mon, May 4, 2020, 10:00 am

Zoom meeting ID: 988 1991 5715

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Cristiano Galbiati: The Milano Mechanical Ventilator

Mon, Apr 20, 2020, 12:00 pm

Please join us here

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Bryan Grenfell and Jessica Metcalf: Dynamics of acute epidemic disease: from measles and influenza to Coronavirus

Mon, Apr 13, 2020, 12:00 pm

Please join us here

We review the dynamics of acute immunizing infections. We then use this as a backdrop to discuss the dynamics and control of the ongoing Coronavirus pandemic.

Canceled - Stefano Allesina: Predicting coexistence in ecological communities

Mon, Mar 30, 2020, 12:00 pm

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.

Canceled - Na Ji: Imaging the brain at high spatiotemporal resolution

Mon, Mar 23, 2020, 12:00 pm

To understand computation in the brain, one needs to understand the input-output relationships for neural circuits and the anatomical and functional relationships of individual neurons therein. Optical microscopy has emerged as an ideal tool in this quest, as it is capable of recording the activity of neurons distributed over millimeter...

Canceled - Allan Drummond: Rethinking the cellular response to heat shock, from biophysics to physiology

Mon, Mar 16, 2020, 12:00 pm

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.

Andreas Gahlmann: Visualizing Bacterial Physiology at High Resolution using Single-Molecule Tracking and Lattice-Light Sheet Microscopy

Mon, Mar 9, 2020, 12:00 pm

Our lab develops new imaging approaches for visualizing bacterial physiology in relevant contexts: We use live-cell single-molecule localization microscopy and lattice-light sheet microscopy to access 3D spatial and temporal information with high resolution.

Andrew York: A bolt-on single-objective light-sheet design with uncompromised numerical aperture

Mon, Feb 24, 2020, 12:00 pm

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...

Cancelled. To Be Rescheduled. Stephanie Palmer: How behavioral and evolutionary constraints sculpt early visual processing

Mon, Feb 17, 2020, 12:00 pm

While efficient coding has been a successful organizational principle in visual neuroscience, to make a more general theory behavioral, mechanistic, and even evolutionary constraints need to be added to this framework. In our work, we use a mix of known computational goals and detailed behavioral measurements to add constraints to the notion of...

Elizabeth Jerison: Dynamics of adaptive immunity in zebrafish

Mon, Feb 10, 2020, 12:00 pm

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.

Sven van Teeffelen: Control of cell volume in rod-shaped bacteria

Mon, Feb 3, 2020, 12:00 pm

Bacteria exhibit a high degree of intracellular macromolecular crowding. To control the level of crowding cells must increase their volumes in response to the accumulation of biomass during growth. This coordination is fundamentally not understood in any cell type.

Dmitry Rinberg: Cracking the olfactory code using behavior

Mon, Jan 27, 2020, 12:00 pm

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.

Navish Wadhwa: Environmentally regulated self-assembly of the bacterial flagellar motor

Mon, Dec 16, 2019, 12:00 pm

Macromolecular protein complexes perform essential biological functions across life forms. The assembly of such complexes is known to be regulated at the level of gene transcription, but little is known about the factors that control their assembly once the mature protein subunits enter their target space (cytoplasm, membrane, or cell wall).

Hana El-Samad: Biological Feedback Control

Mon, Dec 9, 2019, 12:00 pm

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.

Damon Clark: Mechanisms underlying visual illusions in flies

Mon, Dec 2, 2019, 12:00 pm

Visual systems detect many features of natural scenes, including motion. Motion detection guides critical behaviors like hunting, evading predators, and finding mates. It can be framed as an inference problem, in which light intensity measurements are combined to estimate a latent variable of image velocity.

Melike Lakadamyali: Super-resolution imaging of chromatin structure and dynamics

Mon, Nov 25, 2019, 12:00 pm

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.

Marija Zanic: Dynamic Architecture of the Microtubule Cytoskeleton

Mon, Nov 18, 2019, 12:00 pm

Microtubules are active biological polymers known to stochastically switch between phases of growth and shrinkage, a behavior termed ‘dynamic instability’. Microtubule treadmilling, in which the microtubule plus end grows while the minus end shrinks, is also observed in cells.

Paul Francois: Geometric model in latent space for fly development

Mon, Nov 11, 2019, 12:00 pm

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.

Ashley Carter: "DNA Folding in Sperm"

Mon, Nov 4, 2019, 12:00 pm

In sperm, DNA is tightly compacted to create a small, hydrodynamic sperm head. This dramatic reorganization of the nucleus is carried out by protamine proteins that fold the DNA into loops and toroids.

Aleksandra Walczak: Response in immune repertories

Mon, Oct 21, 2019, 12:00 pm

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.

John Marko: Mechanics, geometry and topology of cell nuclei and metaphase chromosomes

Mon, Oct 14, 2019, 12:00 pm

 I will discuss studies of the mechanics and structure of metaphase chromosomes and nuclei extracted from mammalian cells using glass micropipettes.

Andrew Mugler: Physics of collective cell sensing

Mon, Sep 30, 2019, 12:00 pm

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.

Zaida Luthey-Schulten: Modeling the minimal cell: Integration of experiments, theory, and simulations

Mon, Sep 23, 2019, 12:00 pm

JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the principles of life (Breuer et al. eLife 2019). Using the vast amount of experimental information available on its precursor, Mycoplasma mycoides capri, we assembled a near-complete essential metabolic network with 98% of enzymatic...

Bill Bialek & Josh Shaevitz: state of the Center

Jaume Casademunt: Hydrodynamics of epithelia: waves, wetting, and fingering

Fri, Jun 14, 2019, 12:30 pm

Collective migration of cohesive groups of cells is a hallmark of the tissue remodeling events that underlie embryonic morphogenesis, wound repair and cancer invasion. In this collective migration, supra-cellular properties such as collective polarization or force generation emerge and eventually control large- scale tissue organization.

Markus Meister: Large Ratios in Brain Science

Mon, Apr 15, 2019, 12:00 pm

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.


Massimo Vergassola: Waves and flows in the early embryogenesis of Drosophila melanogaster

Mon, Apr 8, 2019, 12:00 pm

Early embryogenesis of most metazoans is characterized by rapid and synchronous cleavage divisions. After fertilization, Drosophila embryos undergo 13 swift rounds of DNA replication and mitosis without cytokinesis, resulting in a multinucleated syncytium containing about 6,000 nuclei.

Elizabeth Hillman: High-speed imaging of real-time brain activity

Mon, Apr 1, 2019, 12:00 pm

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.

Benny Chain: The T cell receptor repertoire in health and disease

Mon, Mar 25, 2019, 12:00 pm

The human adaptive immune system makes robust decisions which regulate quantitative and qualitative parameters of a complex physiological system, to prevent invasion and destruction of tissues by the enormous array of microorganisms which share our environment. Remarkably, these decisions are made by a distributed system made up of moving parts...

Jose Onuchic - The three-dimensional architecture of the human genome: understanding the physical mechanisms controlling gene expression

Mon, Mar 11, 2019, 12:00 pm

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.

Valentina Emiliani: Toward circuits optogenetics

Mon, Feb 18, 2019, 12:00 pm

Since the discovery of Channelrhodopsin and the first demonstration of photo-evoked action potentials in mammalian cells, optogenetics is progressively revolutionizing neuroscience research, opening perspectives both in fundamental and in medical research still unimaginable until few years ago.

Eleni Katifori: Pattern formation and self-organization in biological flows

Mon, Feb 11, 2019, 12:00 pm

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.

Howard Stone: Seeking Intersections of Mechanics and (Molecular) Biology

Mon, Feb 4, 2019, 12:00 pm

I will survey some of the research of my group in areas that sit at the intersection of mechanics and biology. First, I will offer some perspective of how classical physics, and in particular both fluid mechanics and elasticity, as they are considered in modern engineering curricula, are well suited to materials-centric  studies of biology in...

Remi Monasson: Inference of effective networks form neural data to better understand spatial navigation

Mon, Dec 17, 2018, 12:00 pm

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.

Daniel Cohen: Applying Swarm Engineering to Control Collective Cell Dynamics

Mon, Dec 10, 2018, 12:00 pm

Multicellular life is driven by collective cell migration spanning morphogenesis, growth, wound healing, and even cancer invasion.  Our group seeks to better understand such collective behaviors in living tissues in order that we can learn to control them, much as a shepherd and sheepdog herd sheep.

Benjamin Lovegren de Bivort: The neural circuit basis of behavioral individuality

Mon, Dec 3, 2018, 12:00 pm

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.

CPBF November Symposium

Mon, Nov 19, 2018, 9:00 am to 4:30 pm

Lisa Manning: What do guitar strings and balloons have in common with biological networks and tissues?

Mon, Nov 12, 2018, 12:00 pm
Both guitar strings and balloons are floppy unless rigidified by geometrically induced self-stresses

Alvaro Sanchez: Metabolic rules of microbial community assembly

Mon, Oct 22, 2018, 12:00 pm

Microbes form complex multi-species communities that play important roles across the biosphere.

Simon Sponberg: Emergent Simplicity and Multiscale Mechanisms of Agile Animal Movement

Mon, Oct 15, 2018, 12:00 pm

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...

Chuck Stevens: Shared properties of the fly olfactory system and the monkey human face patch neurons

Mon, Oct 8, 2018, 12:00 pm

Perhaps unexpectedly, two quite different types of brain systems – the fruit fly olfactory system and the monkey inferotemporal face patches responding to human faces – share a number of properties. In both cases, the systems represent stimuli (odors and faces) by points and a high-dimensional space, one that is 50- dimensional for the fly and...

Larry Abbott: Operating Principles of a Learning Network in Electric Fish

Mon, Oct 1, 2018, 12:00 pm

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.

Thomas T. Perkins: Watching individual proteins unfold and refold by 1-µs resolution force spectroscopy

Mon, Sep 24, 2018, 12:00 pm
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.

Watching individual proteins unfold and refold by 1-µs resolution force spectroscopy

Mon, Sep 24, 2018, 12:00 pm

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.

Bill Bialek & Josh Shaevitz: “state of the Center”

Biophysics Seminar: Mala Murthy

Mon, Apr 2, 2018, 12:00 pm

Biophysics Seminar: Miriam Goodman, Stanford "Deciphering Touch Sensation and Neuronal Mechanoprotection"

Biophysics Seminar: William Bialek "Statistical mechanics for networks of real neurons"

Biophysics Seminar: Ned Wingreen

Mon, Feb 26, 2018, 12:00 pm

Biophysics Seminar: Robert Austin

Mon, Feb 19, 2018, 12:00 pm

Biophysics Seminar: Benjamin H Good, Berkeley

Mon, Feb 5, 2018, 12:15 pm to 1:15 pm

Please join us at 12 noon for lunch, seminar from 12:15-1:15.

Biophysics Seminar: Joshua Shaevitz

Mon, Dec 4, 2017, 12:00 pm

Biophysics Seminar: Thomas Gregor

Mon, Nov 27, 2017, 12:00 pm

Biophysics Seminar: Ilya Nemenman

Mon, Nov 6, 2017, 12:00 pm

Biophysics Seminar: Vijay Balasubramanian

Mon, Oct 23, 2017, 12:00 pm

Biophysics Seminar: Eric Wieschaus

Mon, Oct 9, 2017, 12:00 pm

Biophysics Seminar: Meredith Betterton

Mon, Oct 2, 2017, 12:00 pm

Biophysics Seminar: Mark J. Schnitzer

Mon, Sep 25, 2017, 12:00 pm

Biophysics Seminar: Cliff Brangwynne

Mon, Sep 18, 2017, 12:00 pm