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Soft Matter

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Discover seminars, jobs, and research tagged with soft matter across World Wide.
33 curated items33 Seminars
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33 items · soft matter
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SeminarPhysics of LifeRecording

Crystallinity characterization of white matter in the human brain

Erin Teich
University of Pennsylvania
May 8, 2022

White matter microstructure underpins cognition and function in the human brain through the facilitation of neuronal communication, and the non-invasive characterization of this structure remains an elusive goal in the neuroscience community. Efforts to assess white matter microstructure are hampered by the sheer amount of information needed for characterization. Current techniques address this problem by representing white matter features with single scalars that are often not easy to interpret. Here, we address these issues by introducing tools from soft matter for the characterization of white matter microstructure. We investigate structure on a mesoscopic scale by analyzing its homogeneity and determining which regions of the brain are structurally homogeneous, or ``crystalline" in the context of materials science. We find that crystallinity is a reliable metric that varies across the brain along interpretable lines of anatomical difference. We also parcellate white matter into ``crystal grains," or contiguous sets of voxels of high structural similarity, and find overlap with other white matter parcellations. Our results provide new means of assessing white matter microstructure on multiple length scales, and open new avenues of future inquiry.

SeminarPhysics of LifeRecording

Better energies for low-dimensional elastic systems under combined bending and stretching

Eduardo Vitral
University of Nevada, Reno
Apr 10, 2022

We present new kinematic bending measures and quadratic energies for isotropic elastic plates and shells, with certain desirable features not present in commonly employed models in mechanics and soft matter. These are justified both by simple physical arguments related to the through-thickness variation in strain, and through a detailed reduction from a three-dimensional energy quadratic in stretch. The measure of plate bending is a dilation-invariant surface tensor that couples stretch and curvature in a natural extension of primitive generalized bending strains for straight rods. The extension to naturally-curved rods and shells, for which the pure stretching of a curved rest configuration is not a dilation, contrasts with previous ad hoc postulated forms. Our results provide a clean basis for simple models of low-dimensional elastic systems, and should enable more accurate probing of the structure of singularities in soft sheets and membranes.

SeminarPhysics of LifeRecording

Flow singularities in soft materials: from thermal motion to active molecular stresses

Mehdi Molaei
Pritzker School of Molecular Engineering, University of Chicago
Aug 15, 2021

The motion of passive or active agents in soft materials generates long ranged deformation fields with signatures informed by hydrodynamics and the properties of the soft matter host. These signatures are even more complex when the soft matter host itself is an active material. Measurement of these fields reveals mechanics of the soft materials and hydrodynamics central to understanding self-organization. In this talk, I first introduce a new method based on correlated displacement velocimetry, and use the method to measure flow fields around particles trapped at the interface between immiscible fluids. These flow fields, decomposed into interfacial hydrodynamic multipoles, including force monopole and dipole flows, provide key insights essential to understanding the interface’s mechanical response. I then extend this method to various actomyosin systems to measure local strain fields around myosin molecular motors. I show how active stresses propagate in 2d liquid crystalline structures and in disordered networks that are formed by the actin filaments. In particular, the response functions of contractile and stable gels are characterized. Through similar analysis, I also measure the retrograde flow fields of stress fibers in single cells to understand subcellular mechanochemical systems.

SeminarPhysics of LifeRecording

Trapping active particles up to the limiting case: bacteria enclosed in a biofilm

Chantal Valeriani
Complutense Madrid
May 25, 2021

Active matter systems are composed of constituents, each one in nonequilibrium, that consume energy in order to move [1]. A characteristic feature of active matter is collective motion leading to nonequilibrium phase transitions or large scale directed motion [2]. A number of recent works have featured active particles interacting with obstacles, either moving or fixed [3,4,5]. When an active particle encounters an asymmetric obstacle, different behaviours are detected depending on the nature of its active motion. On the one side, rectification effects arise in a suspension of run-and-tumble particles interacting with a wall of funnelled-shaped openings, caused by particles persistence length [6]. The same trapping mechanism could be responsible for the intake of microorganisms in the underground leaves [7] of Carnivorous plants [8]. On the other side, for aligning particles [9] interacting with a wall of funnelled-shaped openings, trapping happens on the (opposite) wider opening side of the funnels [10,11]. Interestingly, when funnels are located on a circular array, trapping is more localised and depends on the nature of the Vicsek model. Active particles can be synthetic (such as synthetic active colloids) or alive (such as living bacteria). A prototypical model to study living microswimmers is P. fluorescens, a rod shaped and biofilm forming bacterium. Biofilms are microbial communities self-assembled onto external interfaces. Biofilms can be described within the Soft Matter physics framework [12] as a viscoelastic material consisting of colloids (bacterial cells) embedded in a cross-linked polymer gel (polysaccharides cross-linked via proteins/multivalent cations), whose water content vary depending on the environmental conditions. Bacteria embedded in the polymeric matrix control biofilm structure and mechanical properties by regulating its matrix composition. We have recently monitored structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress [13,14]. We have demonstrated that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions. REFERENCES [1] C. Bechinger et al. Rev. Mod. Phys. 88, 045006 (2016); [2] T. Vicsek, A. Zafeiris Phys. Rep. 517, 71 (2012); [3] C. Bechinger, R. Di Leonardo, H. Lowen, C. Reichhardt, G. Volpe, and G. Volpe, Reviews of Modern Physics 88, 045006 (2016); [4] R Martinez, F Alarcon, DR Rodriguez, JL Aragones, C Valeriani The European Physical Journal E 41, 1 (2018); [5] DR Rodriguez, F Alarcon, R Martinez, J Ramírez, C Valeriani, Soft matter 16 (5), 1162 (2020); [6] C. O. Reichhardt and C. Reichhardt, Annual Review of Condensed Matter
Physics 8, 51 (2017); [7] W Barthlott, S Porembski, E Fischer, B Gemmel Nature 392, 447 (1998); [8] C B. Giuliano, R Zhang, R.Martinez Fernandez, C.Valeriani and L.Wilson (in preparation, 2021); [9] R Martinez, F Alarcon, JL Aragones, C Valeriani Soft matter 16 (20), 4739 (2020); [10] P. Galajada, J. Keymer, P. Chaikin and R.Austin, Journal of bacteriology, 189, 8704 (2007); [11] M. Wan, C.O. Reichhardt, Z. Nussinov, and C. Reichhardt, Physical Review Letters 101, 018102 (2008); [12] J N. Wilking , T E. Angelini , A Seminara , M P. Brenner , and D A. Weitz MRS Bulletin 36, 385 (2011); [13]J Jara, F Alarcón, A K Monnappa, J Ignacio Santos, V Bianco, P Nie, M Pica Ciamarra, A Canales, L Dinis, I López-Montero, C Valeriani, B Orgaz, Frontiers in microbiology 11, 3460 (2021); [14] P Nie, F Alarcon, I López-Montero, B Orgaz, C Valeriani, M Pica Ciamarra

SeminarPhysics of Life

Flocks and crowds: a Gulliver travel

Denis Bartolo
ENS de Lyon
May 4, 2021

In the first part of my talk, combining experimental, numerical and theoretical results, I will explain how self-propelled colloidal particles self-organize in one of the most robust ordered state found in nature: flocks. I will explain how to describe macroscopic flocking motion as the spontaneous flows of an active fluid, and use this framework to elucidate the phase ordering dynamics of polar active matter. In the second part of my talk, I will show that the same tools and concepts can be effectively used to infer a hydrodynamic description of active fluids composed of particles 6 order of magnitude larger in size: pedestrian crowds.

SeminarPhysics of Life

How can we learn from nature to build better polymer composites?

Megan Valentine
UCSB
Apr 27, 2021

Nature is replete with extraordinary materials that can grow, move, respond, and adapt. In this talk I will describe our ongoing efforts to develop advanced polymeric materials, inspired by nature. First, I will describe my group’s efforts to develop ultrastiff, ultratough materials inspired by the byssal materials of marine mussels. These adhesive contacts allow mussels to secure themselves to rocks, wood, metals and other surfaces in the harsh conditions of the intertidal zone. By developing a foundational understanding of the structure-mechanics relationships and processing of the natural system, we can design high-performance materials that are extremely strong without compromising extensibility, as well as macroporous materials with tunable toughness and strength. In the second half of the talk, I will describe new efforts to exploit light as a means of remote control and power. By leveraging the phototransduction pathways of highly-absorbing, negatively photochromic molecules, we can drive the motion of amorphous polymeric materials as well as liquid flows. These innovations enable applications in packaging, connective tissue repair, soft robotics, and optofluidics.

SeminarPhysics of Life

Optical and acoustic forces for biomedical applications

Monika Ritsch-Marte
Medical University of Innsbruck
Apr 20, 2021

Exerting controlled forces in a non-contact way is important in biomedical investigations which require holding, moving, or mechanically probing biomedical samples. Optical and acoustic manipulation of microscopic samples both play a prominent role among suitable technologies. The differences in the physical laws and in the typical length scales governing acoustic and optical forces make them complementary: Acoustic forces can levitate large and heavy particles, which optical tweezers could not handle without adverse high-power effects, while optical forces cover subcellular scales. The talk will contrast the two modalities, and identify situations where one or the other is favorable, or when a combination of both is the best choice.

SeminarPhysics of LifeRecording

Frustrated Self-Assembly of Non-Euclidean Crystals of Nanoparticles

Xioaming Mao
University of Michigan
Apr 13, 2021

Self-organized complex structures in nature, e.g., viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional (3D) complex structures using simple building blocks, and reach similar or higher level of sophistication in engineered materials? Here we present an analytic theory for the self-assembly of polyhedral nanoparticles (NPs) based on their crystal structures in non-Euclidean space. We show that the unavoidable geometrical frustration of these particle shapes, combined with competing attractive and repulsive interparticle interactions, lead to controllable self-assembly of structures of complex order. Applying this theory to tetrahedral NPs, we find high-yield and enantiopure self-assembly of helicoidal ribbons, exhibiting qualitative agreement with experimental observations. We expect that this theory will offer a general framework for the self-assembly of simple polyhedral building blocks into rich complex morphologies with new material capabilities such as tunable optical activity, essential for multiple emerging technologies.

SeminarPhysics of LifeRecording

Self-organization of chemically active colloids with non-reciprocal interactions

Ramin Golestanian
Max Planck Institute
Apr 6, 2021

Cells and microorganisms produce and consume all sorts of chemicals, from nutrients to signalling molecules. The same happens at the nanoscale inside cells themselves, where enzymes catalyse the production and consumption of the chemicals needed for life. In this work, we have found a generic mechanism by which such chemically-active particles, be it cells or enzymes or engineered synthetic colloids, can "sense" each other and ultimately self- organize in a multitude of ways. A peculiarity of these chemical-mediated interactions is that they break action-reaction symmetry : for example, one particle may be repelled from a second particle, which is in turn attracted to the first one, so that it ends up "chasing" it. Such chasing interactions allow for the formation of large clusters of particles that "swim" autonomously. Regarding enzymes, we find that they can spontaneously aggregate into clusters with precisely the right composition, so that the product of one enzyme is passed on, without lack or excess, to the next enzyme in the metabolic cascade.

SeminarPhysics of LifeRecording

Tissue fluidization at the onset of zebrafish gastrulation

Carl-Philipp Heisenberg
IST Austria
Mar 30, 2021

Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables at criticality. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context.

SeminarPhysics of LifeRecording

Inertial active soft matter

Hartmut Löwen
universität düsseldorf
Mar 23, 2021

Active particles which are self-propelled by converting energy into mechanical motion represent an expanding research realm in physics and chemistry. For micron-sized particles moving in a liquid (``microswimmers''), most of the basic features have been described by using the model of overdamped active Brownian motion [1]. However, for macroscopic particles or microparticles moving in a gas, inertial effects become relevant such that the dynamics is underdamped. Therefore, recently, active particles with inertia have been described by extending the active Brownian motion model to active Langevin dynamics which include inertia [2]. In this talk, recent developments of active particles with inertia (``microflyers'', ``hoppers'' or ``runners'') are summarized including: inertial delay effects between particle velocity and self-propulsion direction [3], tuning of the long-time self-diffusion by the moment of inertia [3], the influence of inertia on motility-induced phase separation and the cluster growth exponent [4], and the formation of active micelles (“rotelles”) by using inertial active surfactants. References [1] C. Bechinger, R. di Leonardo, H. Löwen, C. Reichhardt, G. Volpe, G. Volpe, Reviews of Modern Physics 88, 045006 (2016). [2] H. Löwen, Journal of Chemical Physics 152, 040901 (2020). [3] C. Scholz, S. Jahanshahi, A. Ldov, H. Löwen, Nature Communications 9, 5156 (2018). [4] S. Mandal, B. Liebchen, H. Löwen, Physical Review Letters 123, 228001 (2019). [5] C. Scholz, A. Ldov, T. Pöschel, M. Engel, H. Löwen, Surfactants and rotelles in active chiral fluids, will be published

SeminarPhysics of LifeRecording

Acoustically Levitated Granular Matter

Heinrich M. Jaeger
University of Chicago
Mar 9, 2021

Granular matter can serve as a prototype for exploring the rich physics of many-body systems driven far from equilibrium. This talk will outline a new direction for granular physics with macroscopic particles, where acoustic levitation compensates the forces due to gravity and eliminates frictional interactions with supporting surfaces in order to focus on particle interactions. Levitating small particles by intense ultrasound fields in air makes it possible to manipulate and control their positions and assemble them into larger aggregates. The small air viscosity implies that the regime of underdamped dynamics can be explored, where inertial effects are important, in contrast to typical colloids in a liquid, where inertia can be neglected. Sound scattered off individual, levitated solid particles gives rise to controllable attractive forces with neighboring particles. I will discuss some of the key concepts underlying acoustic levitation, describe how detuning an acoustic cavity can introduce active fluctuations that control the assembly statistics of small levitated particles clusters, and give examples of how interactions between neighboring levitated objects can be controlled by their shape.

SeminarPhysics of LifeRecording

Bend, slip, or break?

Karen Daniels
NC State University
Mar 2, 2021

Rigidity is the ability of a system to resist imposed stresses before ultimately undergoing failure. However, disordered materials often contain both rigid and floppy subregions that complicate the utility of taking system-wide averages. I will talk about 3 frameworks capable of connecting the internal structure of disordered materials to their rigidity and/or failure under loading, and describe how my collaborators and I have applied these frameworks to laboratory data on laser-cut lattices and idealized granular materials. These are, in order of increasing physics content: (1) centrality within an adjacency matrix describing its connectivity, (2) Maxwell constraint counting on the full network of frictional contact forces, and (3) the vibrational modes of a synthetic dynamical matrix (Hessian). The first two rely primarily on topology, and the second two contrast the utility of considering interparticle forces (Coulomb failure) vs. the energy landscape. All three methods, while successfully elucidating the origins of rigidity and brittle vs. ductile failure, also provide interesting counterpoints regarding how much information is enough to make predictions.

SeminarPhysics of LifeRecording

Driving Soft Materials with Magnetic Fields

Monica Olvera de la Cruz
Northwestern University
Feb 23, 2021

Magnetic fields exert controllable forces that generate microscopic actuation and locomotion in soft materials with superparamagnetic or ferromagnetic components. I will describe the shape changes and materials parameters required to drive and direct matter including filaments, membranes and hydrogels with magnetic components using precessing magnetic fields

SeminarPhysics of LifeRecording

Mixed active-passive suspensions: from particle entrainment to spontaneous demixing

Marco Polin
University Warwick
Feb 16, 2021

Understanding the properties of active matter is a challenge which is currently driving a rapid growth in soft- and bio-physics. Some of the most important examples of active matter are at the microscale, and include active colloids and suspensions of microorganisms, both as a simple active fluid (single species) and as mixed suspensions of active and passive elements. In this last class of systems, recent experimental and theoretical work has started to provide a window into new phenomena including activity-induced depletion interactions, phase separation, and the possibility to extract net work from active suspensions. Here I will present our work on a paradigmatic example of mixed active-passive system, where the activity is provided by swimming microalgae. Macro- and micro-scopic experiments reveal that microorganism-colloid interactions are dominated by rare close encounters leading to large displacements through direct entrainment. Simulations and theoretical modelling show that the ensuing particle dynamics can be understood in terms of a simple jump-diffusion process, combining standard diffusion with Poisson-distributed jumps. Entrainment length can be understood within the framework of Taylor dispersion as a competition between advection by the no-slip surface of the cell body and microparticle diffusion. Building on these results, we then ask how external control of the dynamics of the active component (e.g. induced microswimmer anisotropy/inhomogeneity) can be used to alter the transport of passive cargo. As a first step in this direction, we study the behaviour of mixed active-passive systems in confinement. The resulting spatial inhomogeneity in swimmers’ distribution and orientation has a dramatic effect on the spatial distribution of passive particles, with the colloids accumulating either towards the boundaries or towards the bulk of the sample depending on the size of the container. We show that this can be used to induce the system to de-mix spontaneously.

SeminarPhysics of LifeRecording

Non-equilibrium molecular assembly in reshaping and cutting cells

Anđela Šarić
University College London
Feb 9, 2021

A key challenge in modern soft matter is to identify the principles that govern the organisation and functionality in non-equilibrium systems. Current research efforts largely focus on non-equilibrium processes that occur either at the single-molecule scale (e.g. protein and DNA conformations under driving forces), or at the scale of whole tissues, organisms, and active colloidal and microscopic objects. However, the range of the scales in-between — from molecules to large-scaled molecular assemblies that consume energy and perform work — remains under-explored. This is, nevertheless, the scale that is crucial for the function of a living cell, where molecular self-assembly driven far from equilibrium produces mechanical work needed for cell reshaping, transport, motility, division, and healing. Today I will discuss physical modelling of active elastic filaments, called ESCRT-III filaments, that dynamically assemble and disassemble on cell membranes. This dynamic assembly changes the filaments’ shape and mechanical properties and leads to the remodelling and cutting of cells. I will present a range of experimental comparisons of our simulation results: from ESCRT-III-driven trafficking in eukaryotes to division of evolutionary simple archaeal cells.

SeminarPhysics of LifeRecording

Light-bacteria interactions

Roberto Di Leonardo
Sapienza University of Rome
Feb 2, 2021

In 1676, using candle light and a small glass sphere as the lens, van Leeuwenhoek discovered the microscopic world of living microorganisms. Today, using lasers, spatial light modulators, digital cameras and computers, we study the statistical and fluid mechanics of microswimmers in ways that were unimaginable only 50 years ago. With light we can image swimming bacteria in 3D, apply controllable force fields or sculpt their 3D environment. In addition to shaping the physical world outside cells we can use light to control the internal state of genetically modified bacteria. I will review our recent work with light-bacteria interactions, going from some fundamental problems in the fluid and statistical mechanics of microswimmers to the use of bacteria as propellers for micro-machines or as a "living" paint controlled by light.

SeminarPhysics of LifeRecording

The physics of cement cohesion

Emanuela Del Gado
Georgetown University
Jan 26, 2021

Cement is the main binding agent in concrete, literally gluing together rocks and sand into the most-used synthetic material on Earth. However, cement production is responsible for significant amounts of man- made greenhouse gases—in fact if the cement industry were a country, it would be the third largest emitter in the world. Alternatives to the current, environmentally harmful cement production process are not available essentially because the gaps in fundamental understanding hamper the development of smarter and more sustainable solutions. The ultimate challenge is to link the chemical composition of cement grains to the nanoscale physics of the cohesive forces that emerge when mixing cement with water. Cement nanoscale cohesion originates from the electrostatics of ions accumulated in a water-based solution between like-charged surfaces but it is not captured by existing theories because of the nature of the ions involved and the high surface charges. Surprisingly enough, this is also the case for unexplained cohesion in a range of colloidal and biological matter. About one century after the early studies of cement hydration, we have quantitatively solved this notoriously hard problem and discovered how cement cohesion develops during hydration. I will discuss how 3D numerical simulations that feature a simple but molecular description of ions and water, together with an analytical theory that goes beyond the traditional continuum approximations, helped us demonstrate that the optimized interlocking of ion-water structures determine the net cohesive forces and their evolution. These findings open the path to scientifically grounded strategies of material design for cements and have implications for a much wider range of materials and systems where ionic water-based solutions feature both strong Coulombic and confinement effects, ranging from biological membranes to soils. Construction materials are central to our society and to our life as humans on this planet, but usually far removed from fundamental science. We can now start to understand how cement physical-chemistry determines performance, durability and sustainability.

SeminarPhysics of LifeRecording

Soft matter physics and the COVID-19 pandemic

William Poon
The University of Edinburgh
Dec 8, 2020

Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids complexed to proteins surrounded by a protein-studded lipid bilayer shell. A dominant route for transmission is via air-borne aerosols and droplets. Viral interaction with polymeric body fluids, particularly mucus, and cell membranes controls their infectivity, while their interaction with skin and artificial surfaces underpins cleaning and disinfection and the efficacy of masks and other personal protective equipment. The global response to COVID-19 has highlighted gaps in the soft matter knowledge base. I will survey these gaps, especially as pertaining to the transmission of the disease, and suggest questions that can (and need to) be tackled, both in response to COVID-19 and to better prepare for future viral pandemics.

SeminarPhysics of LifeRecording

Multistable structures - from deployable structures to robots

Katia Bertoldi
Harvard University
Dec 1, 2020

Multistable structures can reversibly change between multiple stable configurations when a sufficient energetic input is provided. While originally the field focused on understanding what governs the snapping, more recently it has been shown that these systems also provide a powerful platform to design a wide range of smart structures. In this talk, I will first show that pressure-deployable origami structures characterized by two stable configurations provide opportunities for a new generation of large-scale inflatable structures that lock in place after deployment and provide a robust enclosure through their rigid faces. Then, I will demonstrate that the propagation of transition waves in a bistable one-dimensional linkage can be exploited as a robust mechanism to realize structures that can be quickly deployed. Finally, while in the first two examples multistability is harnessed to realize deployable architectures, I will demonstrate that bistable building blocks can also be exploited to design crawling and jumping robots. Unlike previously proposed robots that require complex input control of multiple actuators, a simple, slow input signal suffices to make our system move, as all features required for locomotion are embedded into the architecture of the building blocks.

SeminarPhysics of LifeRecording

Surprises in self-deforming self-propelling systems

Daniel Goldman
Georgia Institute of Technology
Nov 17, 2020

From slithering snakes, to entangling robots, self-deforming (shape changing) active systems display surprising dynamics. This is particularly true when such systems interact with environments or other agents to generate self-propulsion (movement). In this talk, I will discuss a few projects from my group illustrating unexpected effects in individual and collectives of self-deformers. For example, snakes and snake-like robots mechanically “diffract” from fixed environmental heterogeneities, collections of smart-active robots (smarticles) can locomote (and phototax) as a collective despite individual immobility, and geometrically actively entangling ensembles of blackworms and robots can self-propel as a unit to thermo or phototax without centralized control.

SeminarPhysics of LifeRecording

Endless forms most beautiful: how to program materials using geometry, topology and singularities

Christian Santangelo
Syracuse University
Nov 10, 2020

The dream of programmable matter is to create materials whose physical properties (shape, moduli, response to perturbations, etc.) can be changed on the fly. For many years, my group has been thinking about how to program flat sheets that fold up into three dimensional shapes, most recently by exploiting the principles of origami design. Unfortunately, a combinatorial explosion of folding pathways makes robust folding particularly challenging. In this talk, I will discuss how this pluripotency arises from the topology of the configuration space. This suggests a broader understanding of a larger class of materials spanning from folding forms to spring networks to mechanical structures that perform computational logic.

SeminarPhysics of LifeRecording

Holographic control of neuronal circuits

Valentina Emiliani
Vision Institut, France
Nov 3, 2020

Genetic targeting of neuronal cells with activity reporters (calcium or voltage indicators) has initiated the paradigmatic transition whereby photons have replaced electrons for reading large-scale brain activities at cellular resolution. This has alleviated the limitations of single cell or extracellular electrophysiological probing, which only give access to the activity of at best a few neurons simultaneously and to population activity of unresolved cellular origin, respectively. In parallel, optogenetics has demonstrated that targeting neuronal cells with photosensitive microbial opsins, enables the transduction of photons into electrical currents of opposite polarities thus writing, through activation or inhibition, neuronal signals in a non-invasive way. These progresses have in turn stimulated the development of sophisticated optical methods to increase spatial and temporal resolution, light penetration depth and imaging volume. Today, nonlinear microscopy, combined with spatio-temporal wave front shaping, endoscopic probes engineering or multi scan heads design, enable in vivo in depth, simultaneous recording of thousands of cells in mm 3 volumes at single-spike precision and single-cell resolution. Joint progress in opsin engineering, wave front shaping and laser development have provided the methodology, that we named circuits optogenetics, to control single or multiple target activity independently in space and time with single- neuron and single-spike precision, at large depths. Here, we will review the most significant breakthroughs of the past years, which enable reading and writing neuronal activity at the relevant spatiotemporal scale for brain circuits manipulation, with particular emphasis on the most recent advances in circuit optogenetics.

SeminarPhysics of LifeRecording

Lab-on-a-chip and diagnostic tools for COVID-19

Connie B. Chang
Montana State University
Oct 27, 2020

The SARS-CoV-2 virus has rapidly evolved into a pandemic that is threatening public health, economics, and quality of life worldwide. The gold-standard for testing individuals for COVID-19 is using traditional RT-qPCR, which is expensive and can take up to several hours. Expanding surveillance across a global scale will call for new strategies and tests that are inexpensive, require minimal reagents, decrease assay time, and allow for simple point-of-care (POC) monitoring without need of trained personnel and with quick turnaround time. To expand the speed of COVID-19 surveillance, we are working on a point-of-care microfluidic chip to enable significantly faster and easier testing. This is based upon digital drop loop-mediated isothermal amplification that will allow for rapid testing of large populations at a reasonable cost. The device will employ a nucleic-acid based test called reverse transcriptase LAMP (RT- LAMP) that operates at a temperature of 60-65°C. RT-LAMP removes the bottleneck of thermal cycling and high temperatures required by traditional RT-qPCR thermocycling. The simplicity, speed, and sensitivity will enable early treatment and response to infection.

SeminarPhysics of LifeRecording

Soft Capricious Matter: The collective behavior of particles with “noisy” interactions

Bulbul Chakraborty
Brandeis University
Oct 20, 2020

Diversity in the natural world emerges from the collective behavior of large numbers of interacting objects. Statistical physics provides the framework relating microscopic to macroscopic properties. A fundamental assumption underlying this approach is that we have complete knowledge of the interactions between the microscopic entities. But what if that, even though possible in principle becomes impossible in practice ? Can we still construct a framework for describing their collective behavior ? Dense suspensions and granular materials are two often quoted examples where we face this challenge. These are systems where because of the complicated surface properties of particles there is extreme sensitivity of the interactions to particle positions. In this talk, I will present a perspective based on notions of constraint satisfaction that provides a way forward. I will focus on our recent work on the emergence of elasticity in the absence of any broken symmetry, and sketch out other problems that can be addressed using this perspective.

SeminarPhysics of LifeRecording

Shaping colloidal bananas to reveal biaxial, splay-bend nematic, and smectic phases

Roel Dullens
University of Oxford
Oct 13, 2020

Colloidal dispersions of rod-like particles are widely accepted as convenient model systems to study the phase behavior of liquid-crystal forming systems, commonly found in LCDs. This is due to the fact that colloidal rods exhibit analogous phase behavior to that of elongated molecules, while they can be directly observed by optical microscopy. Recently, there has been a surge of interest in the liquid crystalline behaviour of so-called bent-core, or banana-shaped, molecules. This is due to their ability to form exotic biaxial nematic phases such as the twist-bend and splay-bend nematic phase, which may be of particular interest inherent to their fast switching response in LCDs. Here, we develop model “banana-shaped” colloidal particles with tunable dimensions and curvature, whose structure and dynamics are accessible at the particle level. 
By heating initially straight rods made of SU-8 photoresist, we induce a controllable shape deformation that causes the rods to buckle into banana-shaped particles. We elucidate the phase behavior of differently curved colloidal bananas using confocal microscopy. Although highly curved bananas only form isotropic phases, less curved bananas exhibit very rich phase behavior, including biaxial nematic phases, polar and antipolar smectic-like phases, and even the long-predicted, elusive splay-bend nematic phase.

SeminarPhysics of LifeRecording

On the nature of the entropic bond in colloidal crystals

Sharon Glotzer
University of Michigan
Oct 6, 2020
SeminarPhysics of LifeRecording

Spontaneous and driven active matter flows

Eric Clement
PMMH-ESPCI and Sorbonne University, Paris
Sep 22, 2020

Understanding individual and macroscopic transport properties of motile micro-organisms in complex environments is a timely question, relevant to many ecological, medical and technological situations. At the fundamental level, this question is also receiving a lot of attention as fluids loaded with swimming micro-organisms has become a rich domain of applications and a conceptual playground for the statistical physics of “active matter”. The existence of microscopic sources of energy borne by the motile character of these micro-swimmers is driving self-organization processes at the origin of original emergent phases and unconventional macroscopic properties leading to revisit many standard concepts in the physics of suspensions. In this presentation, I will report on a recent exploration on the question of spontaneous formation of large scale collective motion in relation with the rheological response of active suspensions. I will also present new experiments showing how the motility of bacteria can be controlled such as to extract work macroscopically.

SeminarPhysics of LifeRecording

Flow, fluctuate and freeze: Epithelial cell sheets as soft active matter

Silke Henkes
University of Bristol
Sep 15, 2020

Epithelial cell sheets form a fundamental role in the developing embryo, and also in adult tissues including the gut and the cornea of the eye. Soft and active matter provides a theoretical and computational framework to understand the mechanics and dynamics of these tissues.I will start by introducing the simplest useful class of models, active brownian particles (ABPs), which incorporate uncoordinated active crawling over a substrate and mechanical interactions. Using this model, I will show how the extended ’swirly’ velocity fluctuations seen in sheets on a substrate can be understood using a simple model that couples linear elasticity with disordered activity. We are able to quantitatively match experiments using in-vitro corneal epithelial cells.Adding a different source of activity, cell division and apoptosis, to such a model leads to a novel 'self-melting' dense fluid state. Finally, I will discuss a direct application of this simple particle-based model to the steady-state spiral flow pattern on the mouse cornea.

SeminarPhysics of LifeRecording

Design Principles of Living Matter

Margaret Gardel
University of Chicago
Sep 8, 2020

In this talk, I will describe my lab’s recent efforts to understand the design principles of the active, soft materials that drive cell morphogenesis. In particular, we are interested in how collections of myosin II motors and actin polymers generate, relax, sense and adapt to mechanical force. I will discuss how motor-filament interactions lead to either distributed extensile or contractile stresses as the mechanics of the system changes from fluid to solid. Using optical control of motors, we are now exploring how spatially structured stress can be used to drive local flows and motion. If time, I will also describe how feedbacks between local geometry and activity can be harnessed to drive morphogenetic changes in model systems.

SeminarPhysics of LifeRecording

(What) can soft matter physics teach us about biological function?

Workshop, Multiple Speakers
Emory University
Jul 30, 2020

The “soft, active, and living matter” community has grown tremendously in recent years, conducting exciting research at the interface between soft matter and biological systems. But are all living systems also soft matter systems? Do the ideas of function (or purpose) in biological systems require us to introduce deep new ideas into the framework of soft matter theories? Does the (often) qualitatively different character of data in biological experiments require us to change the types of experiments we conduct and the goals of our theoretical treatments? Eight speakers will anchor the workshop, exploring these questions across a range of biological system scales. Each speaker will deliver a 10-minute talk with another 10 minutes set aside for moderated questions/discussion. We expect the talks to be broad, bold, and provocative, discussing both the nature of the theoretical tools and experimental techniques we have at present and also those we think we will ultimately need to answer deep questions at the interface of soft matter and biology.

SeminarPhysics of LifeRecording

Can machine learning learn new physics, or do we need to put it in by hand?"\

Workshop, Multiple Speakers
Emory University
Jun 3, 2020

There has been a surge of publications on using machine learning (ML) on experimental data from physical systems: social, biological, statistical, and quantum. However, can these methods discover fundamentally new physics? It can be that their biggest impact is in better data preprocessing, while inferring new physics is unrealistic without specifically adapting the learning machine to find what we are looking for — that is, without the “intuition” — and hence without having a good a priori guess about what we will find. Is machine learning a useful tool for physics discovery? Which minimal knowledge should we endow the machines with to make them useful in such tasks? How do we do this? Eight speakers below will anchor the workshop, exploring these questions in contexts of diverse systems (from quantum to biological), and from general theoretical advances to specific applications. Each speaker will deliver a 10 min talk with another 10 minutes set aside for moderated questions/discussion. We expect the talks to be broad, bold, and provocative, discussing where the field is heading, and what is needed to get us there.