Biophysics Seminars Archive

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