Biophysics Seminars Archive

María de la Paz Fernández: Sex Differences in the Drosophila Circadian System
Mon, May 13, 2024, 12:30 pm1:30 pm

Circadian clocks regulate the timing of various behavioral and physiological activities in most organisms on a 24-hr scale such that they are phased appropriately to external, cyclic changes in the environment. The clock neuronal network in Drosophila melanogaster is comprised of  ~150 neurons distributed bilaterally in the brain,…

Michael Hinczewski: The price of evolution: how thermodynamics shapes gene regulation
Mon, May 6, 2024, 12:30 pm1:30 pm

Many of the physical processes in a cell consume energy, but we are only beginning to understand how these costs have influenced the course of evolution. Biology is strewn with counter-intuitively complex mechanisms whose evolutionary predecessors must have consumed significant energy resources without any clear fitness benefit.  So…

Amy Shyer & Alan Rodrigues: Supracellular organization of morphogenesis: epigenetics beyond the cell
Mon, Apr 29, 2024, 12:30 pm1:30 pm

In recent decades, much progress has been made in understanding how genes within cells contribute to organ-specific fates or disease phenotypes. However, it is becoming more widely acknowledged that increasing understanding at the molecular scale has not been sufficient to fully grasp how tissues comprised of thousands of cells generate their…

Canceled. To be re-scheduled: Patrick Secor: Filamentous bacteriophages: Master manipulators of bacterial virulence potential
Mon, Apr 22, 2024, 12:00 pm1:30 pm

Pseudomonas aeruginosa is an opportunistic bacterial pathogen. Most P. aeruginosa isolates are infected by a filamentous virus (phage) called Pf. At sites of infection, filamentous Pf virions accumulate where they increase mucus viscosity, promote bacterial colonization, and directly stimulate innate anti-viral immune…

Canceled. To be re-scheduled: Jasmine Nirody: TBA
Mon, Apr 15, 2024, 12:30 pm1:30 pm
Allyson Sgro: Understanding the emergence of microbial collective behaviors
Mon, Apr 8, 2024, 12:00 pm1:30 pm

Groups of cells of all kinds work together as part of multicellular behaviors ranging from collective migration to development. These behaviors are coordinated at the level of single cells, where information about other cells and the environment are encoded in intracellular signaling dynamics that then drive cellular-level behaviors. We face…

Jonas Cremer: Causes and consequences of bacterial growth - from protein synthesis to the human gut microbiota
Mon, Apr 1, 2024, 12:30 pm1:30 pm

Growth is central to life, shaping physiology, ecology, and evolution. In this talk, I discuss our efforts to elucidate the causes and consequences of bacterial growth across scales. Starting from resource allocation models and the molecular and energetic demands of protein synthesis, I first introduce how bacterial cells adjust their…

Mathieu Louis: Neural computations directing olfactory navigation in the Drosophila larva
Mon, Mar 25, 2024, 12:30 pm1:30 pm

Behavioral strategies employed for chemotaxis have been studied across phyla, but the neural computations underlying navigational decisions remain elusive. By combining electrophysiology, quantitative behavioral analysis and computational modeling, we explore how olfactory signals experienced during free motion are processed by the olfactory…

Quan Wen: Organizing Motor Behaviors Across Timescales
Tue, Mar 19, 2024, 12:30 pm1:30 pm

Animal behaviors are complex and hierarchical spatiotemporal patterns. In the popular model organism Caenorhabditis elegans, behavioral sequences on a slower timescale emerge from ordered and flexible transitions between different motor states, such as forward movement, reversal, and turn. On a faster timescale, intricate head…

Douglas Shepherd: Exploring the 'rules of life' through optical microscopy
Mon, Feb 19, 2024, 12:30 pm1:30 pm

One governing principle of the microscopic world is "predictable randomness," where snapshots of a fluctuating process may appear random, but the average outcome of the process is predictable. An exciting frontier in biological physics is evaluating if predictable randomness extends to more complex, multi-component biophysical systems, such as…

Ben Eysenbach: Contrastive Successor Representations
Mon, Feb 12, 2024, 12:30 pm1:30 pm

Goal-reaching problems are ubiquitous in both the natural and engineered world. While learning to achieve goals is often considered an aspect of intelligence in biological systems, it is challenging to design practical algorithms for learning such behavior in high-dimensional environments. In this talk, I'll discuss recent work on contrastive…

Wolfgang Losert: Sensing Physical Signals with Cytoskeletal Dynamics
Mon, Feb 5, 2024, 12:30 pm1:30 pm

The dynamic assembly and disassembly of the cytoskeleton can create waves and oscillations that are critical to cell migration and other important cell behaviors.  Chemical signals have been found to trigger and steer these waves, facilitating the guidance e.g. of immune cells to their target.   Here we consider the role of these…

Daniel Goldman: Life at Low Coasting Number
Mon, Dec 11, 2023, 12:30 pm1:30 pm

In 1974 Purcell authored a paper “Life at Low Reynolds Number” to describe the counterintuitive world of microscopic organisms in which viscous dissipation so dominates inertia that “coasting” is impossible, and that the geometry of a path in an internal movement space dominates self-propulsion. It is typically assumed that a key difference…

Tatiana Engel: The dynamics and geometry of choice in premotor cortex
Mon, Nov 27, 2023, 12:30 pm1:30 pm

Neural responses in association brain areas during cognitive tasks are heterogeneous, and the widespread assumption is that this heterogeneity reflects complex dynamics involved in cognition. However, the complexity may arise from a fundamentally different coding principle: the collective dynamics of a neural population encode simple…

Nikhil Malvankar: How Do Electric Bacteria Breathe Without Oxygen or Soluble Electron Acceptors? Protein Nanowires: Structures, Functions, and Ultrafast Electron Transfer Mechanisms
Mon, Nov 13, 2023, 12:30 pm1:30 pm

Deep in the ocean or underground, where there is no oxygen, Geobacter “breathe” by projecting tiny hair-like protein filaments called "nanowires" into the soil, to dispose of excess electrons resulting from the conversion of nutrients to energy, cleaning up radioactive sites. Although it is long known that Geobacter use…

To be re-scheduled: Alon Rubin: The internal structure of neuronal codes for space
Mon, Nov 6, 2023, 12:30 pm1:30 pm

Recent advances in electrophysiology and optical imaging technologies enable recordings in behaving animals from hundreds or even thousands of neurons simultaneously. Since neural coding, computation, and communication rely on coordinated activity patterns across large cell populations, such data facilitate the study of the global structure of…

Jerelle Joseph: Accurate computer models for understanding and engineering biomolecular condensates
Mon, Oct 30, 2023, 12:30 pm1:30 pm

The interior of cells contains numerous components that need to be carefully organized in space to fulfill a wide range of biological functions. The most widespread form of intracellular compartments completely lack membranes. In the place of membranes, these compartments—so called biomolecular condensates—are sustained and segregated in space…

David Smith: Upper Atmosphere Microbiology and Insights for Solar System Exploration
Mon, Oct 23, 2023, 12:30 pm1:30 pm

Earth’s atmosphere provides a thin barrier to the severe conditions of space. Globally, terrestrial microorganisms from our planet’s surface move through and interact with the blanketing atmosphere, analogous to how marine microbes drift through vast oceans. Whereas a century of exploration has allowed oceanographers to characterize…

Susan Rosenberg: The DNA Damageome, Cancer and Drugging Evolution
Mon, Oct 9, 2023, 12:30 pm1:30 pm

TBA

Walter Reisner: Nanofluidic Devices for Single-Molecule Analysis, Manipulation and Control
Mon, Sep 25, 2023, 12:30 pm1:30 pm

Nanofluidic devices, e.g. based on nanochannels or nanopores, are networks of fluid-filled structures on a chip with dimensions ~1-100 nm.  These dimensions are on order of molecular length scales, giving rise to the ability to directly analyze, manipulate and confine single biomolecules.  In this talk I will focus on two different…

Arup Chakraborty: The Evolution of Antibody Responses upon Vaccination
Mon, Sep 18, 2023, 12:30 pm1:30 pm

Infectious disease-causing pathogens have plagued humanity since antiquity, and the COVID-19 pandemic has been a vivid reminder of this perpetual existential threat. Vaccination has saved more lives than any other medical procedure, and effective vaccines have helped control the COVID-19 pandemic. However, we do not have effective vaccines…

Bill Bialek & Josh Shaevitz: State of the Center
Mon, Sep 11, 2023, 12:30 pm1:30 pm
Biophysics Seminar - Arseny Finkelstein
Mon, May 1, 2023, 12:30 pm1:30 pm

In the first part of my talk, I will focus on mechanisms that regulate interactions between brain regions and describe how state-dependent frontal cortex dynamics can gate information flow from the sensory cortex during decision-making in mice.

In the second part, I will focus on information flow within the frontal cortex…

José Alvarado : Connecting active “hardware” to biological “software”
Mon, Apr 24, 2023, 12:30 pm1:30 pm

The actomyosin cytoskeleton is a naturally occurring active gel found in virtually all mammalian cells. Its ability to contract allows cells to move, change shape, exert force, sense stiffness, and maintain constant tension. In order for the “hardware” of actomyosin gels to support such a diverse set of mechanical tasks, it is tightly coupled…

Jasmine Nirody: TBA
Sat, Apr 15, 2023, 12:30 pm1:30 pm
Biophysics Seminar Series - Dr. Harald Hess
Mon, Mar 27, 2023, 12:30 pm1:30 pm

 

Volume or 3D electron microscopy EM continues to expand its potential for imaging ever larger biological entities. Images from diamond knife cut sections launched the field of volume EM. An alternative of imaging the sequentially cut block face offered easier use and registration. FIB-SEM or Focused Ion Beam Scanning Electron…

Biophysics Seminar Series - Alison Patteson
Mon, Mar 20, 2023, 12:30 pm1:30 pm

 

Cell migration is a critical process underlying proper tissue maintenance. While a soft nucleus allows a cell to squeeze through small pores, the resulting physical stress can lead to nuclear damage and genomic variability. We have shown that the cytoskeletal intermediate filament protein vimentin protects against DNA damage…

Heather Lynch: Emergent pattern formation in penguin colonies: Life at the crossroads of ecology, geology, computational geometry, and computer vision
Mon, Feb 20, 2023, 12:30 pm1:30 pm

Aggregations are common in biological systems at a range of scales and may be driven by exogenous constraints such as environmental heterogeneity and resource availability or by “self-organizing” interactions among individuals. One mechanism leading to self-organized animal aggregations is captured by Hamilton’s “selfish herd” hypothesis, which…

Joerg Bewersdorf: All-optical Super-resolution Imaging of Molecules in Their Nanoscale Cellular Context
Mon, Feb 13, 2023, 12:30 pm1:30 pm

Super-resolution optical microscopy has become a powerful tool to study the nanoscale spatial distribution of molecules of interest in biological cells, tissues and other structures over the last years. Imaging these distributions in the context of other molecules or the general structural context is, however, still challenging. I will present…

Thibaud Taillefumier: Replica-mean field limits of metastable dynamics
Mon, Feb 6, 2023, 12:30 pm1:30 pm

In this talk, we propose to decipher the activity of neural networks via a “multiply and conquer” approach. This approach considers limit networks made of infinitely many replicas with the same basic neural structure. The key point is that these so-called replica-mean-field networks are in fact simplified, tractable versions of neural networks…

Na Ji: Imaging the brain at high spatiotemporal resolution
Mon, Dec 12, 2022, 12:30 pm1:30 pm

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

Fellow candidate symposium II
Tue, Dec 6, 2022, 9:00 amWed, Dec 7, 2022, 5:00 pm
Bradley H. Dickerson: Functionally stratified encoding in a biological gyroscope
Mon, Dec 5, 2022, 12:30 pm1:30 pm

Flies are among nature’s most agile flying creatures. This exquisite maneuverability is due in part to their possession of specialized mechanosensory organs known as the halteres. The halteres are evolved from the hindwings and provide flies with dynamic mechanosensory feedback on a wingstroke-to-wingstroke basis. Additionally, halteres are…

Mustafa Mir : Molecular Kinetics of nuclear organization and transcription regulation during embryonic development
Mon, Nov 28, 2022, 12:30 pm1:30 pm

During early development gene expression patterns progressively emerge as cell fates are determined and the embryo takes form. The regulation of patterning occurs across a broad range of spatial and temporal scales. These scales range from the molecular scale dynamics of regulatory proteins binding to genomic loci to activate or repress…

Tian-Ming Fu: Probing Biological Dynamics in Multicellular Organisms: from long-term electrophysiology to high-resolution imaging
Mon, Nov 21, 2022, 12:30 pm1:30 pm

The urgency to probe biological dynamics is impeded by a major challenge: the large dynamic range of biological processes—interactions of molecules within milliseconds can lead to changes across the whole-organism over days to years. It calls for measurements with both high spatiotemporal resolution and large-scale long-term coverage. However,…

Anders Hansen: Dynamics of 3D Genome Structure and Function
Mon, Nov 14, 2022, 12:30 pm1:30 pm

Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop extruding cohesins. These loops and domains are thought to play critical roles in regulating gene expression by regulating long-range enhancer-promoter interactions. But whether CTCF/cohesin loops are stable or dynamic structures was…

Kandice Tanner: Microenvironment regulation of metastasis
Mon, Nov 7, 2022, 12:30 pm1:30 pm

In the event of metastatic disease, emergence of a lesion can occur at varying intervals from diagnosis and in some cases following successful treatment of the primary tumor.  Genetic factors that drive metastatic progression have been identified, such as those involved in cell adhesion, signaling, extravasation and metabolism. However,…

Fellow candidate symposium I
Tue, Nov 1, 2022, 9:00 amWed, Nov 2, 2022, 5:00 pm

Nov 1, 2022, 9:00 am – Nov 2, 2022, 5:00 pm

Location

Joseph Henry Room - Jadwin Hall

 

Sponsor

CPBF and NSF

CANCELLED: Roseanna Zia: How Colloidal Physics Instantiate Life in Biological Cells
Mon, Oct 31, 2022, 12:30 pm1:30 pm

We are interested in how physics at the colloidal scale instantiate life in biological cells. While principles from physics have driven recent paradigm shifts in how collective biomolecular behaviors orchestrate life, many mechanistic aspects of e.g. transcription, translation, and condensation remain mysterious because…

Marc Gershow: Maggots! Making Memories and Reading Minds
Mon, Oct 10, 2022, 12:30 pm1:30 pm

My lab studies the brains of larval fruit flies as models of neural computation. We are interested in the rules by which the larval brain transforms sensory input into motor output to navigate an uncertain environment, how the larva’s brain changes these rules as it learns new information, and how these rules and changes are encoded in the…

CPBF Retreat
Wed, Sep 28, 2022, 9:00 am5:00 pm
Stephen Floor: On measurement in RNA biology
Mon, Sep 26, 2022, 12:30 pm1:30 pm

Measurement of natural systems typically involves perturbation and interpretation. In this talk, I will discuss the implications of measurement in the context of RNA in gene expression in human cells. I will focus on measurements of RNA biology using high-throughput sequencing, which are powerful for their scale but also involve perturbations…

Shenshen Wang: Limit and potential of immune learning against changing targets
Mon, Sep 19, 2022, 12:30 pm1:30 pm

The adaptive immune system is able to learn from changing experiences to better fit an unforeseen future, thanks to a large and diverse collective of cells expressing unique antigen receptors and capable of rapid Darwinian evolution. However, naturally occurring immune responses exhibit limits in efficacy, speed and capacity to adapt to novel…

Canceled and will be re-scheduled: Marc Gershow: Maggots! Making Memories and Reading Minds
Mon, May 2, 2022, 12:30 pm12:30 pm

My lab studies the brains of larval fruit flies as models of neural computation. We are interested in the rules by which the larval brain transforms sensory input into motor output to navigate an uncertain environment, how the larva’s brain changes these rules as it learns new information, and how these rules and changes are encoded in the…

Andrea Liu: How Materials Can Learn
Mon, Apr 25, 2022, 12:30 pm12:30 pm

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. An alternative is to encode local rules into those…

David Wolpert: Stochastic Thermodynamics of Distributed Systems
Mon, Apr 18, 2022, 12:30 pm12:30 pm

The new field of stochastic thermodynamics allows us to analyze the thermodynamic behavior of dynamic systems arbitrarily far from thermal equilibrium, and has produced many powerful theorems concerning phenomena completely absent in traditional statistical physics. However, to date stochastic thermodynamics has (mostly) been applied to systems…

Gijsje Koenderink: Cytoskeletal crosstalk in cell shape and mechanics
Mon, Apr 11, 2022, 12:30 pm12:30 pm

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…

Sarah L. Keller: Phase-separating membranes of hungry yeast are tiny, living thermostats
Mon, Apr 4, 2022, 12:30 pm12:30 pm

Liquid-liquid phase separation of cell membranes exemplifies a biological system leveraging a physical concept to achieve a chemical end. Here, we show that yeast actively tune the transition temperature of their vacuole membranes to be close to the yeast's growth temperature, which implies that the membrane's proximity to the miscibility…

Arnold Mathijssen: Transport and delivery by active droplets and artificial microtubules
Mon, Mar 28, 2022, 12:30 pm12:30 pm

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…

Canceled and will be re-scheduled. Na Ji: Imaging the brain at high spatiotemporal resolution
Mon, Mar 21, 2022, 12:30 pm12:30 pm

To understand computation in the brain, one needs to understand the input-output relationships for neural circuits and the anatomical and functional properties 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 dimensions…

Madhav Mani: A Statistical (Physics) view of Organismal Development
Mon, Feb 28, 2022, 12:30 pm12:30 pm

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? In this talk I will attempt to pursue a statistical (physics) approach to discerning the design principles that…

Zvonimir Dogic: Sculpting liquid interfaces with active stresses
Mon, Feb 7, 2022, 12:30 pm12:30 pm

Controlling interfacial structure and dynamics of phase separating fluid mixtures is key to creating diverse functional materials. Traditionally, this is accomplished by controlling interface chemistry, through the presence of surface-modifying amphiphilic agents. Using a phase separating mixture of active and passive fluids, we study how…

Chris Wiggins, Just do the best you can: statistical physics approaches to reinforcement learning
Mon, Dec 13, 2021, 1:15 pm1:15 pm

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. The…

Andrew Gordus: Untangling the web of behaviors used in spider orb-weaving
Mon, Dec 6, 2021, 12:30 pm12:30 pm

Many innate behaviors are the result of multiple sensorimotor programs that are dynamically coordinated to produce higher-order behaviors such as courtship or architecture. Extended phenotypes such as architecture are especially useful for ethological study because the structure itself is a physical record of behavioral intent. A particularly…

Jeff Gore: Emergent phases of ecological diversity and dynamics mapped in microcosms
Mon, Nov 15, 2021, 12:30 pm12:30 pm

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. Using experimental bacterial microcosms, we have performed the first direct test of recent theory predicting that simple aggregate parameters…

Canceled. To be re-scheduled. Danielle Bassett: TBD
Mon, Nov 8, 2021, 12:30 pm12:30 pm
Alison Sweeney: The Physical Design of Optimum Solar Resource Utilization in Giant Clams
Mon, Nov 1, 2021, 12:30 pm12:30 pm

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. For example, even in agricultural systems bred for maximum resource efficiency such…

Jeanne Stachowiak: Disordered protein networks as synergistic drivers of membrane traffic
Mon, Oct 25, 2021, 12:30 pm12:30 pm

Membrane curvature is required for many cellular processes, from assembly of highly curved trafficking vesicles to extension of needle-like filopodia. Consequently, defects in membrane curvature play a role in most human diseases, including altered recycling of receptors in cancer and diabetes, targeting of filopodia by pathogens, and hijacking…

Louise Jawerth: Fiber growth, ultra-low surface tensions and glass-like aging: Protein condensates as novel materials
Mon, Sep 27, 2021, 12:30 pm12:30 pm

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. Increasingly, we find that the exact material nature of the liquid-like condensates (such as…

Andrej Kosmrlj: Pattern formation in biological systems via mechanical instabilities and phase separation
Mon, Sep 20, 2021, 12:15 pm12:15 pm

Pattern formation is ubiquitous in biological systems. While pattern formations are often associated with Turing-like reaction-diffusion systems, biology also exploits many other mechanisms such as mechanical instabilities and phase separation. In this talk, I will discuss how mechanical instabilities cause the wrinkling of bacterial biofilms…

Welcome back lunch
Mon, Sep 13, 2021, 12:15 pm12:15 pm
Justin Kinney: Massively parallel assays, machine learning, and the biophysics of gene regulation
Mon, May 10, 2021, 12:15 pm12:15 pm

Gene expression in all organisms is controlled by short DNA and RNA sequences called cis-regulatory elements (CREs). Proteins in the cellular milieu bind to nucleic acid sequences present within CREs, interact with one another, and thus form macromolecular complexes that modulate the expression of nearby genes. My lab uses…

Rosalind Allen: Geometry of bacterial growth and division
Mon, May 3, 2021, 12:15 pm12:15 pm

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. coli continue to be debated - these include whether the cell length increases exponentially or…

Julia M. Yeomans: Active nematic physics in cell layers and tissues
Mon, Apr 26, 2021, 12:15 pm12:15 pm

Active materials such as bacteria, molecular motors and eukaryotic cells continuously transform chemical energy taken from their surroundings to mechanical work. Dense active matter shows mesoscale turbulence, the emergence of chaotic flow structures characterised by high vorticity and self-propelled topological defects. I shall describe the…

Susanne Still: Thermodynamics of information processing
Mon, Apr 19, 2021, 4:00 pm4:00 pm

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. An intelligent memory formation strategy should take…

Nikta Fakhri: Broken symmetries in living matter
Mon, Apr 12, 2021, 12:00 pm12:00 pm

Active processes in living systems create a novel class of non-equilibrium material composed of many interacting parts that individually consume energy and collectively generate motion or mechanical stress. In this talk, I will discuss experimental tools and conceptual frameworks we develop to uncover laws governing order, phase transitions and…

Gijsje Koenderink: TBD
Sun, Apr 11, 2021, 12:15 pm12:15 pm
Satu Palva: Multi-scale synchronization dynamics in human cognition
Mon, Mar 29, 2021, 12:15 pm12:15 pm

Perception, attention and working memory are fundamental cognitive functions, which are based on parallel processing in many brain areas. Neuronal oscillations at sub-second timescales and their phase correlations a.k.a. phase-synchronization are putative mechanisms for the coordination of neuronal processing and…

Raymond E. Goldstein: Fluid and Light: Dinoflagellate Bioluminescence at the Single Cell Level
Mon, Mar 22, 2021, 12:15 pm12:15 pm

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
forces trigger…

Kinneret Keren: Topological defects in the nematic order of actin fibers as organization centers of Hydra morphogenesis
Mon, Mar 1, 2021, 12:15 pm12:15 pm

Morphogenesis, the emergence of functional form in a developing organism, is one of the most remarkable examples of pattern formation in nature. Despite substantial progress, we still do not understand the organizational principles underlying the convergence of this process, across scales, to form viable organisms under variable conditions. We…

Karen Alim: Network morphology to store memories
Mon, Feb 22, 2021, 12:15 pm12:15 pm

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. Here, we follow experimentally the organism's response to a nutrient…

Biophysics Lunch
Mon, Feb 8, 2021, 12:15 pm12:15 pm
Stephanie Palmer: How behavioral and evolutionary constraints sculpt early visual processing
Mon, Feb 1, 2021, 12:15 pm12:15 pm

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. In our work, we use a mix of known computational…

Kranthi Mandadapu: On the role of motility and glassy dynamics in growth of bacterial monolayers into the third dimension
Mon, Nov 23, 2020, 12:15 pm12:15 pm

Many mature bacterial colonies and biofilms are complex three-dimensional (3D) structures. A key step in their developmental program is a transition from a two-dimensional (2D) monolayer into a 3D architecture. Despite the importance of controlling the growth of microbial colonies and biofilms in a variety of medical and industrial settings,…

Seppe Kuehn: A sparse mapping from structure to function in microbial communities
Mon, Nov 16, 2020, 12:15 pm12:15 pm

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. Here we show, for the process of…