Biophysics Seminars Archive

How does learning occur? Neural networks learn via optimization, where a loss function is minimized by a computer to achieve the desired result. But physical networks such as mechanical spring networks or flow networks have no central processor so they cannot minimize such a loss function.

Mechanical stability and shape changes of cells are determined by the dynamic interplay of four distinct cytoskeletal networks, made of actin filaments, microtubules, intermediate filaments and septins. These four filamentous systems contribute different structural and dynamical properties, enabling specific cellular...

Understanding the physics of living systems allows us to design new materials that are active and adaptive, akin to cells and tissues. Conversely, these active matter systems can reveal fundamental principles in physics and biology. In this talk, I will discuss three systems that feature this synergy, ranging from the molecular to the...

After a century of biochemical and genetic onslaught on the embryo we are left with an inexhaustive parts list with an increasingly baroque logic. How do we begin to assemble complex living systems from knowledge of the parts list?

The most celebrated corners of machine learning over the past decades are those successful at predicting - e.g., spam classification, medical diagnoses, or cat faces. But machine learning as actually used in practice is commonly prescriptive rather than predictive: decisions must be made in order to maximize a reward.

Natural ecological communities display striking features, such as high biodiversity and a wide range of dynamics, that have been difficult to explain in a unified framework.

Photosynthesis presents a paradox of solar energy: the maximum quantum efficiency of photosystem II likely surpasses that of any engineered system, but in environments with high solar flux, photosynthetic organisms are famously wasteful and resource inefficient.

We have recently discovered that there are biological proteins that phase separate out of solution to form protein-dense droplets. These so-called protein condensates have been identified in an extremely large range of important biological processes.

The rod-shaped bacterium Escherichia coli proliferates by a process of elongation, followed by constriction at its centre to create new cell poles. Despite intense study, some apparently simple questions about the dynamics of growth and division in E.

Living systems need to remember information about their environment in order to take decisions that ultimately ensure survival. But storing information about past experiences costs energy, while only a fraction of the vast amount of information available can be useful to the living system.

One of the characteristic features of many marine dinoflagellates is their bioluminescence, which lights up nighttime breaking waves or seawater sliced
by a ship’s prow. While the internal biochemistry of light production by these microorganisms is well established, the manner by which fluid shear or mechanical

Simple organisms manage to thrive in complex environments. Remembering information about the environment is key to take decisions. Physarum polycephalum excels as a giant unicellular eukaryote being even able to solve optimisation problems despite the lack of a nervous system.

An animal eye is only as efficient as the organism’s behavioral constraints demand it to be. Efficient coding has been a successful organizational principle in vision, and to make a more general theory, behavioral, mechanistic, and even evolutionary constraints need to be added to this framework.

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.