Competition between phase separation and crystallization in attractive colloids. Motility-induced phase separation in suspensions of active Brownian particles. The dispersion of swimming algae: consequences for photobioreactors. Imaging the microstructure of colloidal suspensions to understand their non-Newtonian flow behavior. Motility control in suspensions of swimming cells. Equality and Diversity: What you need to know and why you need to know it. Toni Collis. Nutrient-dependent switching in microbial ecosystems.
Timothy Bush. Evolution of combinatorial communication. What happens at freezing. A perspective from suspension of hard sphere-like particles. How many different cancers are in a solid tumour? The self-assembly of the tooth enamel protein, amelogenin. The propulsion mechanism of catalytic Janus swimmers. Super-resolution imaging of rapid biological processes in real-time.
Terri Amos. Julian Schmehr. X-rays mark the spot: grain mapping in polycrystals. William Whitley. Fluid entrainment by individual microswimmers. Magnetic and transport measurements at very high pressures and low temperatures. Structural Studies of Europium at High Pressure. Rachel Husband. Paul Clegg. Listening to Magnetism: Using ultrasound at high pressures as a probe to study uranium intermetallics.
Michal Kepa. A possible key role of hydrodynamic interactions in colloidal gelation. Competition for space in growing bacterial populations: what determines the winners and losers? Diarmuid Lloyd. High pressure gas hydrates of the H2O-CO2 system. Daniel Amos. Identifying the molecular processes leading to the formation of fibrillar protein aggregates.
Aqueous phase structuring and rheology in food and personal care products. Elucidating the locking mechanism of peptides onto growing amyloid fibrils. Walking the back alleys: a modelling study of symplastic transport. The bacterial colonisation of microplastic debris in coastal marine sediments. Jesse Harrison. Superparamagnetic colloidal flats: A route to studying the non-linear mechanics of actin networks. Emergence of motifs in model gene regulatory networks. Antimicrobial peptide action on E.
Novel molecular design and dielectrophoretic manipulation for enhancing biosensors. Mira Nishimura. An Alternative Protein Aggregation Pathway. Jay Gillam. Biophysics of protein aggregation. Spontaneous emulsification by ionic surfactants and responsive nanoparticles, and theoretical models of inhomogeneous, correlated Coulomb fluids. Molecular dynamics simulations of radiation damage in metals. Graham Galloway. Surface functionalized particles for Pickering stabilization.
Elena Blanco. Colloids in active fluids: simulations of microrheology experiments. Giulia Foffano. Entropy-driven self-assembly of novel phases. From wrinkly elastomers to Janus Particles. Pattern formation in active matter systems. Fred Farrell. Simulating biochemical pathways. Steven Court. The early stages of insulin fibrillogenesis explored with mass spectrometry and molecular modelling. Evolution of antibiotic resistance in the presence of antibiotic gradients.
Granular rheology near jamming and engineering models. Non-equilibrium fluctuations of intracellular filaments generated by motor activity. Ross Howie. Emma McBride. A Physicists view on measuring poverty. Simulation and modeling of materials with atomic detail at IBM: From biophysics to high-tech application. The Transformations and Nature of Amorphous Ices.
John Loveday. Michiel Hermes. Using dielectrophoretic manipulation with nucleic acid sensors. The rheology of nanoparticle layers and the relation to foam stability. Squeezing particle-stabilized emulsions into biliquid foams. Job Thijssen. Yielding and flow of colloidal glasses and gels. Noise-induced dynamical transition in systems with symmetric absorbing states. Dominic Russell. Phase Stability of Titanium Alloys.
Bengt Tegner. Thomas Scheler. Colloidal Particles at a Cholesteric Liquid Crystal interface. The role of particle size and shape in highly size-asymmetric mixtures. Robert Concannon. Con Healy. Metastable intermediate phases on molecular crystallisation pathways. Rotator phases and twist solitons in polyethylene and n-alkanes. Craig Wilson. Polydispersity in Colloid-Polymer Mixtures.
Siobhan Liddle. Modeling of mild fractionation of suspensions. A dynamical phase transition in a model for evolution with migration. Modelling swimmers in a bag using hydrodynamics. Elsen Tjhung. The blistering of viscoelastic filaments. Niek Hijnen. Joe Tavacoli. Exploring early stage processes involved in amyloid fibril formation.
Simulating particle stabilised thin films using surface evolver. Molecular dynamics MD simulations of osmosis. Analysis of slurred transients in brass instrument playing. Shona Logie. A Most Unnatural Act! Adam Apostoli. Juho Lintuvuori. Analytical Study of a Genetic Toggle Switch. Active transport on random filament networks. Philip Greulich. What it takes to grow at pressure. Lucas Black. Spatiotemporal regulation of chemical reactions by active cytoskeletal remodeling.
Small particles in liquid crystal phases. Entangled liquid crystal colloids: knots and links. Protein structure prediction and folding dynamics. Katrin Wolff. How do fluorescent surfactants affect particle-stabilized emulsions? Swimming bacteria: from individual swimmers to dense suspensions.
The puzzle of delayed gel collapse. Ordering by random copying on complex networks. Simulation studies of phase behaviour in highly size asymmetrical mixtures. High-Pressure Incommensurate Structures in Nanomaterials. Coarse-grained simulations of DNA nanostructures, the self-assembly of virus-like objects, and the evolution of protein complexes. Andre Costa. Scattering techniques applied to reveal internal structure and orientational behaviour of colloidal particles. Christine Wong. Shear localization in colloidal glasses. Rut Besseling. Crystallization of hard aspherical particles.
Computer models for DNA organisation: bacteriophages and the human nucleus. Charge models of disordered alloys for electron spectroscopy. Tom Underwood. Deformation of elastic nanotubes via self-assembly of surface-adhesive nanoparticles. Harriet Cole. Jenny Jeppsson. Microscopic swimmers at surfaces. DNA-directed self-assembly of micro- and nano-particles: towards self-replicating materials. Statics and dynamics of a zero-range process with saturated condensation. Capillary filling and drop dynamics on structured surfaces. Secondary Structure Determination of gp41 Craig Gregor.
Oliver Henrich. Tiffany Wood.
Investigating the assembly of actin networks. A soft-core spherocylinder model for coarse-grained simulations of self-assembling system. Andrew Jones. Hard Spheres: Crystallization and Glass Formation.
Towards Autonomous Soft Matter Systems : Experiments on Membranes and Active Emulsions
Peter Pusey. Growth and dynamics in a size-structured spatial population. Tom Adams. Nanoparticle self-assembly at liquid-liquid interfaces SALI : what's the point? Localization of maximal entropy random walk. Phase diagrams of low valence patchy particles. Metastable Dynamics of Colloidal Hard Spheres. Vincent Martinez. Quantitative snapshots of bacterial motility.
Laurence Wilson. Scaling of the current-current time correlation function of a suspension of hard sphere-like particles; Exposing when the motion of particles is Brownian. Investigations of the coalescence of emulsion droplets with microfluidics. Interfacial water structure, peptide adsorption and ion-specificity. Particle Stabilised Emulsions with Hydrophobic Additives. Strong Mobility in Weakly Disordered Systems. Statistical physics of switching bacteria. Nucleation of crystals: Experimental studies of protein crystallisation and computer simulations of simple models.
Understanding the lag phase variability of insulin fibrillation. Caroline Miles. Emulsion Engineering: A convenient route to structured oils using polymer mediated, reversible emulsion droplet assembly. Time-resolved fluorescence microspectroscopy of visible fluorescent proteins in isolated form and in their natural cellular environment. Two-dimensional colloidal systems in optical and magnetic fields: micromechanics and band-formation.
The long-term fate of the attractive colloidal glass. Wilson Poon. An Introduction to Photoelectrochemical Solar Cells. Aggregation and solvent electrostriction in a simple dipeptide: a molecular dynamics investigation. Paul Tulip. Porous media, Surfactants, and Petrodollars. Kevin Stratford. Statistical Mechanics of Convergent Evolution. Bhavin Khatri. Andrew Schofield.
What's a physicist got to do with 'ecological genetics'? Diffusion in population genetics and ecology. Condensed phases of paramagnetic colloids. Water Interactions with Calcium Carbonate Nanoparticles and 2. Catching up on Bijels. Relaxation towards a nonequilibrium steady state: an unexpected spectral property of the asymmetric exclusion process.
Arno Proeme. Cellular networks of colloids via the demixing and remixing of binary liquids. Colloidal Liquids, Crystals, and Glasses. Advanced optical microscopy techniques. Orbital ordering, reduced dimensionality and spin gap in correlated oxides. The Statistical Mechanics of Word Learning.
Purely-elastic flow instabilities. Hopping particles on a growing lattice. Martin Li. Bacterial motility in polymer solutions. Andrew Harrison. Microfluidic devices: surface modification and analysis. Sickle hemoglobin fibers - self assembly, interactions, growth and depolymerisation. Direct simulation of rare events following Darwin. Julien Tailleur. Time dependent quantum transport and nuclear motion.
Crystal nucleation in ionic and covalent systems. Lost in the thicket: how agar can suppress bacterial chemotaxis. Probing nanoscale structure and dynamics of soft matter by synchrotron X-ray scattering. Computer simulations of microrheology in dense colloidal systems. Simulating ''Swimmers'': Point-like self-propelled particles in lattice Boltzmann. Rupert Nash. Out of equilibrium processes in oppositely charged colloidal suspensions. Eduardo Sanz. Kathryn White. Slip of glassy hard-sphere colloidal suspensions.
Laser manipulation and transfer of angular momentum in liquid crystal systems. A structural route for dynamical arrest: locally favoured structures in colloidal gels and glasses. Cytoplasmic streaming: Helical shear flows in giant algal cells and their implications for molecular transport. Nonlinear Rheology of Colloidal Suspensions.
Power injected in a granular gas. Clustering, wetting and demixing in colloid-microemulsion composites. Steady-State Chemotactic Response in E. Non-linear instabilities in parallel shear flows of visco-elastic fluids. Electrostatic interactions across a charged lipid bilayer. Modelling dissipation in statistical mechanics. The hydrodynamics of active fluids. Ionic Assemblies: Patterns and Symmetries. Nanoparticles in binary mixture of liquid crystal and dodecanol. Colloidal Particle Structures at Liquid Interfaces. Coupling electrostatic and polymeric surface interactions in soft matter and biology.
The simulations of complex colloidal fluids by Lattice Boltzmann. Reporting the noise: physics looks at finance. Nucleation in the 2D Ising model under shear. Rosalind Allen. Structure and Deformation of Soft Colloidal Co-crystals. Piconewton forces in dense colloids, applied and measured by optical tweezers. On the expansion of bacteria through soft agar. Experimental work on interconnected super-emulsions. Phase separating proteins and cellular switches. Complex dynamics of shear banded flows. Point forces in lattice Boltzmann: Approaching unsettled questions in sedimentation and learning to swim.
Understanding cell-cell interactions for biological aggregation: Working at the interface between engineering and biology. Micro-channel flow of high volume fraction colloidal glasses: velocity profiles, fluctuations and Antoni Gaudi. Nonequilibrium Kinetics of the Triangular Antiferromagnetic Ising model.
Drops on Chemically Patterned and Superhydrophobic Surfaces. Atomistic simulations of martensitic transformations in 2D Lennard-Jones solids. Faraday instability in complex fluids. Chain reactions, hexosomes and unexpected shades of the colour blue. Self-assembly of polypeptides as inspiration for new materials. Cait MacPhee. Imaging and rheology of colloidal glasses under steady shear. Malcolm McMahon. Connecting simulation and experiment: classical molecular dynamics of simple peptides in water. Proline - of ants, tubes and quantum corrections.
Modelling soft active materials. Non linear rheology and dynamic yielding of a simple glass: A molecular dynamics study. Evolutionary genetics and thermodynamics. Bacterial gene networks and the cell cycle. Statistical Physics and Fungal Growth. Directional Interactions Amongst Encapsulated Clusters. Topological mixing in viscous fluids. Getting to the bottom of rugged energy landscapes. Pattern formation in thin film suspensions. Techniques for trapping and studying colloids on liquid-liquid interfaces. Controlling drop impact by additives. A simple model for the excess entropy of mixing of methanol-water mixtures.
Mode-coupling glasses and liquid structure. Spatial and temporal inhomogeneities in the flow of dense colloidal suspensions into geometrical constrictions. Phase separation in lipid bilayers. X-ray Photon Correlation Spectroscopy as a new tool to investigate the dynamics of soft condensed matter. Iris Coe. Mutation of albedo and growth response produces oscillations in a spatial Daisyworld. Investigating Extreme Condition Microbiology.
Realtime 3D microscopy of colloidal glasses under shear. Noise in Biochemical Reaction Networks. Patrick Warren. Condensed matter neutron science down-under: From magnetic cobaltates to polymer substrates for biosensing applications. Phase Transitions in Stochastic Models of Flow. Opening up into two dimensions: insights into liquid structure. Correlation spectroscopy with photons and electrons - insight into medium-range order in amorphous materials.
Self Assembled Monolayers and Soft Lithography. Nhan Pham. From interparticle potentials to free energies - or the challenge of doing atomistic simulations with the right thermodynamics. Colloids in external fields: theory and simulation. Colloidal Analog of the Ionic Fluid: computer simulation study. The Physics of Filamentous Fungi. Armadillos, a dead dinosaur and the glass transition.
The Mechanics and Statistics of Active Matter. Simulating the flipping of genetic switches and other rare events.
Towards Autonomous Soft Matter Systems : Shashi Thutupalli :
MC measurement of the isotropic nematic interfacial tension in suspensions of soft rods. Microimmiscible aqueous alcohols: dynamics and thermodynamics. Simon Bates. With these statistical mechanics I language change and population genetics wed. Dilatancy, Jamming, and the Physics of Granulation.
Attraction and Repulsion in Glasses. Interaction between Colloids and Cells. How industrial problems expose gaps in fundamental colloid science. Pattern formation in particle laden viscous fluid thin film flow. An exactly solvable phase transition in an Ising system with a grain boundary. Conducting Polymer Micropatterns.
An Einstein relation for nonequilibrium steady states. Clusters in methanol-water mixtures. Statics and dynamics of poly ethylene glycol -stabilized colloids. Gels, clusters and phase separation in sticky particle systems. Bridging in Colloidal Sediments. Unbinding Books and Demixing Mixtures.
Jamming in 2-Dimensional Granular Flow. Untangling hair conditioners: The swelling of surfactant bilayer phases. The hydrodynamic interaction in confined suspensions. Remoteness: studying the structure of concentrated particulate systems. Domain Formation in Binary Lipid Vesicles. Layer-by-layer removal of insulating few-layer mica flakes for asymmetric ultra-thin nanopore fabrication J.
Towards autonomous soft matter systems: Experiments on membranes and active emulsions Shashi Thutupalli. References Publications referenced by this paper. The Machinery of Life David S. Related Papers. Close Figure 4: Number of small beads measured to cross the membrane after three minutes, as a function of membrane thickness, for the two flow directions cf.
The loaded side of the membrane initially had a mixture of small beads and large beads. In addition to stable synchronized states, the network can have stable N-1,1 states, in which all but one of the oscillators are in sync, as well as families of neutrally stable fixed states or closed orbits, in which none of the oscillators are in sync. And in special cases, the dynamics are equivalent to the 2D electric field given by a collection of point charges on the boundary of the disc. We will conclude with some suggestions for extending these techniques to more general oscillator networks.
Thursday, May 2, Kirill Korolev , Boston University MRSEC Seminar: Universality classes in the evolutionary dynamics of expanding populations Abstract: Reaction-diffusion waves describe diverse natural phenomena from crystal growth in physics to range expansions in biology. Two classes of waves are known: pulled, driven by the leading edge, and pushed, driven by the bulk of the wave.
Recently, we examined how demographic fluctuations change as the density-dependence of growth or dispersal dynamics is tuned to transition from pulled to pushed waves. We found three regimes with the variance of the fluctuations decreasing inversely with the population size, as a power law, or logarithmically. These scalings reflect distinct genealogical structures of the expanding population, which change from the Kingman coalescent in pushed waves to the Bolthausen-Sznitman coalescent in pulled waves.
The genealogies and the scaling exponents are model-independent and are fully determined by the ratio of the wave velocity to the geometric mean of dispersal and growth rates at the leading edge. Our theory predicts that positive density-dependence in growth or dispersal could dramatically alter evolution in expanding populations even when its contribution to the expansion velocity is small. On a technical side, our work highlights potential pitfalls in the commonly-used method to approximate stochastic dynamics and shows how to avoid them.
Thursday, April 11, Thomas Fai , Brandeis Applied Mathematics MRSEC Seminar: Fluid dynamics of vesicle transport in dendritic spines Abstract: We model the fluid dynamics of vesicle transport into dendritic spines, micron-sized structures located at the postsynapses of neurons. Dendritic spines are characterized by their thin necks and bulbous heads, and recent high-resolution 3D images show a fascinating variety of spine morphologies.
Our model reduces the fluid dynamics of vesicle motion to two essential parameters representing the system geometry and elasticity and allows us to thoroughly explore phase space. Upon including competing molecular motor species that push and pull on vesicles, we observe multiple stable solutions reminiscent of the observed behavior.
We discuss whether it would be feasible that neurons could exploit such a switch to control the strength of synapses. The quantity cited in support of this conclusion, however, does not pertain to ordered assembly. Moreover, these single-molecule tracking experiments aim to infer what takes place at DNA binding loci by following transcription factors, and this inference requires a more in-depth biophysical analysis than had been carried out.
We performed such an analysis and found that the data were inconclusive with respect to the hypothesis of ordered assembly, but we also found something novel: that the expression of Sox2 in these cells increased genomic binding by Oct4, while the expression of Oct4 decreased genomic binding by Sox2.
Either the cell must expend energy so as to maintain the system away from thermodynamic equilibrium, or Sox2 and Oct4 must bind at diverse genomic loci in such a way that at some of these loci they assist each other in binding, while at others they hinder each other. The analytical techniques used to derive these results are of general interest, and increasingly so as single-molecule tracking techniques continue to develop. Thursday, March 28, Alexander Petroff, Clark University MRSEC Seminar: Fast-moving bacteria self-organize into active two-dimensional crystals of rotating cells Abstract: We investigate a new form of collective dynamics displayed by Thiovulum majus, one of the fastest-swimming bacteria known.
Cells spontaneously organize on a surface into a visually striking two-dimensional hexagonal lattice of rotating cells. As each constituent cell rotates its flagella, it creates a tornado like flow that pulls neighboring cells towards and around it. In the first part of the talk, we describe the earliest stage of crystallization, the attraction of two bacteria into a hydrodynamically-bound dimer. In the second part of the talk, we present the dynamics of bacterial crystals, which are composed of 5— hydrodynamically bound cells. As cells rotate against their neighbors, they exert forces on one another, causing the crystal to rotate and cells to reorganize.
We show how these dynamics arise from hydrodynamic and steric interactions between cells.
We derive the equations of motion for a crystal, show that this model explains several aspects of the observed dynamics, and discuss the stability of these active crystals. However, the powerful predictive tools that have been designed for passive matter do not translate to active systems. Despite many recent contributions and advances, the connection between the microscopic properties of the components and the behavior of the ensemble is still difficult to predict.
We observe that both the structural and dynamic properties of the clusters are strongly dependent on the direction of self-propulsion, enabling a switch between effective Markovian behavior and periodic behavior with long characteristic time scales. Certain topologies enable loops in state space that have characteristic time scales and connect to the emergence of periodic behavior. We conclude that if a Boltzmann-type distribution could be formulated for active matter, it would need to incorporate not only the interaction potential, but also the character of the microscopic motion. Furthermore, we demonstrate that relatively simple active systems can harness a complex dynamic behavior with a hierarchy of characteristic time scales.
Thursday, March 14, Shuang Zhou , UMass Amherst MRSEC Seminar: Living liquid crystals Abstract: Active matter formed by self-propelled particles exhibits fascinating patterns and dynamics, shaped by the interactions of the active particles among themselves and with the environment. Many studies deal with self-propelled particles in an isotropic Newtonian fluid, where the interactions are mainly hydrodynamic or steric.
Spontaneous orientational order only emerges at high particle density. The situation is different when the fluid itself is a nematic liquid crystal. In this talk, I will introduce an active matter system called living liquid crystal, which combines lyotropic chromonic liquid crystals with living bacteria Bacillus Subtilis. I will show a wealth of interesting phenomena in this system, including 1 controlling bacteria trajectories through liquid crystal director field, 2 optical visualization of the motion of nanometer-thick bacteria flagella, 3 local melting of the liquid crystal by bacteria flow, 3 cargo particle transportation, 4 bend instability, 5 low Reynolds number turbulence with topological defects, and 6 modified tumbling behavior of bacteria, among others.
I will explain them by the long range interactions, both elastic and hydrodynamic, mediated by the nematic media, and make connections to the very remarkable viscoelastic properties of the chromonic liquid crystals themselves. Friday, March 1, Melissa Rinaldin, Leiden University Kraft and Giomi groups Special Seminar: Demixing on curved surfaces Abstract: Like oil in water in vinaigrette or lava lamps, artificial lipid membranes undergo liquid-liquid phase separation.
Unraveling the physical mechanisms behind the organization of these liquid phases in membranes is a central goal in biophysics, while the ability to reproduce them in synthetic structures holds great potential for applications in self-assembly, bio-sensing, and drug delivery. Previous studies on vesicles and supported lipid bilayers have unveiled a fundamental interplay between the membrane geometry and position of different lipid domains.
However, the detailed mechanisms behind this coupling remain incompletely understood, because of the impossibility of independently controlling the membrane geometry and composition. In this talk, I will show how we overcome this limitation by fabricating multicomponent lipid bilayers supported by colloidal scaffolds of prescribed shape. Thanks to a combination of experiments and theoretical modeling, we demonstrate that the substrate local curvature and the global chemical composition of the bilayer determine both the spatial arrangement and the amount of mixing of the lipid domains. Thursday, February 28, Timothy Atherton , Tufts University MRSEC Seminar: Shape Sculpting and Shapeshifting with Soft Matter Abstract: Soft materials are ideal candidates for advanced engineering applications including soft, biomimetic robots, self-building machines, shape-shifters, artificial muscles, and chemical delivery packages.
In many of these, the material must make a dramatic change in shape with an accompanying re-ordering of the material; in others changes in the ordering can be used to drive or even interrupt shape change. To optimize the materials and structures, it is necessary to have a detailed understanding of how the microstructure and macroscopic shape co-evolve. To develop the description, we draw upon differential geometry, topology, optimization theory and computer simulations, and connect our results to other work on jamming and crystallography on curved surfaces.
Not only does chromatin structure vary with position, as there is significant heterogeneity in the degree of local compaction within the global DNA complex, but it also changes with time, showing dependence on, e.
The condensation state of DNA is intimately coupled to gene accessibility and expression: changes to DNA organization can modulate transcription and, in turn, transcribed RNA can re-organize chromatin structure. In this talk, I will discuss our research with condensed phases of self-assembled NSs, highlighting key structural properties of the system's two phases i. I will start by discussing the mechanisms that control the mammalian brain development. The required fidelity is achieved not only by high selectivity during nucleotide incorporation polymerization but also through proofreading by excision exonucleolysis during misincorporation.
To elucidate the mechanism by which these two complementary functions are regulated we use optical tweezers to probe the three-subunit subassembly of the E. Because polymerization or exonucleolysis alters the length of the substrate DNA, mechanical manipulation of the template tension allows us to probe the catalytic trajectory of a single pol III core molecule. By analyzing the template tension and protein concentration dependence of polymerization and exonucleolysis, we demonstrate that the process of switching between polymerase and exonuclease substrates is governed solely by primer stability, which changes with temperature, force, and the presence of mismatches.
Thursday, November 29, Philip Pearce , MIT MRSEC Seminar: Physical determinants of bacterial biofilm architectures Abstract: In many situations bacteria aggregate to form biofilms: dense, surface-associated, three-dimensional structures populated by cells embedded in matrix. Biofilm architectures are sculpted by mechanical processes including cell growth, cell-cell interactions and external forces.
Using single-cell live imaging in combination with simulations we characterize the cell-cell interactions that generate Vibrio cholerae biofilm morphologies. Fluid shear is shown to affect biofilm shape through the growth rate and orientation of cells, despite spatial differences in shear stress being balanced by cell-cell adhesion. Our results demonstrate the importance of cell dynamics mediated by adhesion proteins and matrix generation in determining the global architecture of biofilm structures.
Recently, we have started to investigate a chief challenge in contemporary Systems Chemistry research, that is, to synthetically construct "bottom-up" peptide-based networks that display bistable behaviour and oscillations. Towards this aim, we utilize replicating coiled coil peptides, which have already served to study emergent phenomena in complex mixtures. In the first part of this talk, we describe the kinetic behaviour of small networks of coupled oscillators, producing various functions such as logic gates, integrators, counters, triggers and detectors.
These networks are also utilized to simulate the connectivity and network topology observed for the Kai-proteins circadian clocks, producing rhythms whose constant frequency is independent of the input intake rate and robust towards concentration fluctuations. Then, in the second part, we disclose our experimental results, showing for that the peptide replication process can also lead to bistability in product equilibrium distribution.
We believe that these recent studies may help further reveal the underlying principles of complex enzymatic processes in cells and may provide clues into the emergence of biological clocks. Thursday, November 8, Arthur Michaut , Harvard Medical School MRSEC Seminar: Biomechanics of anteroposterior axis elongation in the chicken embryo Abstract: In vertebrates, the elongation of the anteroposterior axis is a crucial step during embryonic development as it results in the establishment of the basic body plan.
It was proposed that a gradient of random cell motility, downstream of a morphogen gradient, results in a biased posterior movement of PSM cells and drives axis extension. To date, the potential interaction between well-established molecular signaling and physical mechanisms involved in axis elongation remains largely unexplored. In particular, several mechanical questions need to be addressed. First, can the cell motility gradient lead to PSM extension? Second, is the force generated by PSM extension capable of promoting axis elongation?
Third, how is PSM extension mechanically coupled with the elongation of other embryonic tissues? In order to tackle these questions, a better description of the mechanical properties of embryonic tissues is required. Therefore, we report an experimental investigation of the chicken embryo mechanics. In particular, we measure how the viscoelastic properties of both the PSM and the neural tube vary along the anteroposterior axis.
We also demonstrate that isolated PSM explants are capable of autonomous elongation and we measure their contribution to the total force production in the embryo. Thursday, October 25, Katja Taute , Rowland Institute at Harvard MRSEC Seminar: " Physics and ecology of bacterial motility strategies" Abstract: Most motile bacteria move by rotating helical flagella, but species differ widely in the number, shape and arrangement of these flagella. The natural habitats of motile bacteria are similarly diverse, ranging from aqueous solutions such as oceans and lakes to complex environments such as mucus or soil.
What motility behaviors are enabled by different flagellar architectures? Which behaviors are advantageous in which environments? Our lab strives to learn how physics and ecology interplay in shaping the natural selection of bacterial motility strategies. I will show how a recently developed high-throughput 3D tracking method facilitates the rapid and label-free behavioral phenotyping of large bacterial populations at unprecedented efficiency and ease. By combining 3D tracking with microfluidically generated gradients, we can directly determine chemotactic drift velocities in different types of environments, such as hydrogels, while simultaneously resolving 3D motility patterns and their modification in response to the gradient.
I will discuss recent applications and insights into the motility behavior of bacterial pathogens in complex environments. Their large size enables the study of behaviors that cannot be visualized in lipid bilayers. Colloidal membranes are an experimental system composed of rod-like chiral particles. A tunable depletion interaction drives the self-assembly of these rods into one-rod-length thick monolayers. Membranes formed from a mixture of short right-handed rods and long left-handed rods exhibit a microphase separation regime, wherein one rod species forms finite-sized domains, or rafts, floating in a background membrane of the other rod species.
The short rods form right-handed rafts which have interactions mediated through the background membrane. We have a Ginzburg-Landau theory explaining the formation and interactions of these rafts. Recent experiments have studied how these rafts are affected upon tuning the background membrane chirality. This tuning can be achieved by having a mixture of two kinds of long rods that are of equal length but opposite handedness.
It is found that lowering the background chirality this way allows the short rods to form both right-handed and metastable left-handed rafts. We are working towards a theory of microphase separation which accounts for the existence of these metastable rafts. Georgios Katsikis, MIT Abstract: I will present three problems on biophysics, low-cost diagnostic devices, and microfluidics. Juxtaposing this model with biological experiments and robotic prototypes, I will show how these parasites break time-reversal symmetry and propagate at an optimal regime for efficient swimming.
Our centrifuge achieves speeds of , r. Finally, I will talk about a microfluidic platform that performs universal logic operations with droplets. I will start with a discussion of self-assembly in a very simple binary system of spherical particles, and gradually move towards a greater complexity of both the building blocks and the resulting structures. Eventually, from the problem of programmable self assembly we will shift to a pursue of the simplest system potentially capable of self-replication.
Detailed characterizations by NMR, Fourier transform infrared spectroscopy, high-resolution mass-spectrometry, X-ray, and cyclic voltammetry show that the topology of these molecules allows them to serve as both comonomers and crosslinkers in polymerization reactions. The BZ self-oscillations of such crosslinked hydrogels have been observed and quantified for both supported film and freestanding gel samples, demonstrating their potential as chemomechanically active modules for new functional materials.
I will present our approach of combining DNA nanotechnology with colloidal science to program precision self-assembly of micron-sized clusters with structural information stemming from a nanometric arrangement. We bridged the functional flexibility of DNA origami on the molecular scale, with the structural rigidity of colloidal particles on the micron scale, by tuning the mechanical properties of a DNA origami complex. We demonstrate the parallel self-assembly of three-dimensional micro-constructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.
We used the techniques developed to synthesize and study active systems: light driven fluid micro-particles, and sedimenting irregular clusters. June , Microfluidics Course, Summer Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibers.
Beyond the diversity of molecular mechanisms involved, we propose that fibers generically arise from the aggregation of irregular particles with short-range interactions. Using minimal models of frustrated aggregating particles, we demonstrate robust fiber formation for a variety of particle shapes and aggregation conditions. Geometrical frustration plays a crucial role in this process, and accounts for the range of parameters in which fibers form as well as for their metastable, yet long-lived character.
Thursday, May 24, MRSEC Seminar: Amoeba-like Living Crystallites in Active Colloids Paddy Royall, University of Bristol Abstract: Many kinds of swimmers and self-propelled particles constitute physical models to describe collective behaviour and motility of a wide variety of living systems, such as the cytoskeleton, bacteria colonies. Here study colloidal particles in an external DC electric field. Our experimental model system consists of quasi-two-dimensional arrays of electrically- driven particles and exhibits a rich phase behaviour.
At low field strength, the particles undergo Brownian motion, yet electrohydrodynamic flows lead to long-ranged non-reciprocal? With an increase in field strength, we observe self-propulsion of the particles due to the electrohydrodynamic phenomenon known as Quincke rotation, i. This activity leads to surface melting resulting in an ordered phase of active matter where crystallites move and constantly change shape and collide with one another in a manner reminiscent of ameobae. At higher field strengths, we reveal an activity-mediated gas-solid transition, with an intermediate phase possessing orientational order.
We combine our experiments with computer simulations, which reproduce the phase behaviour and moreover at higher field strengths than we reach in the experiments exhibit an activity-driven demixing to form a banded structure. However, we are only beginning to understand the mechanisms used by cells to reorganize actin network architecture.
In TIRF microscopy assays, these two proteins together induce dynamic crosslinking and sliding of filaments, resulting in filament coalescence and compaction into thick bundles as well as overall coarsening of the actin network. We further recapitulated this ATP-free, contractile system into oil-water interface and 3D emulsion system. The prospect of combining a contractile polymer system with an extensile system microtubule and kinesin raises exciting new possibilities for observing emergent properties. Thursday, March 29, MRSEC Seminar: Some studies on self-assembly of colloids and peptoids John Edison, Lawrence Berkeley National Laboratory Abstract: I will present three self-assembly problems I have recently worked on, beginning with theoretical and simulation studies on the phase behavior of colloids, suspended in a near-critical binary solvent.
The results show how interactions between the colloids mediated by the solvent, could potentially enable control of colloidal self-assembly in a reversible and in-situ manner. Next, I will discuss a simulation study on the phase behavior of a mixture of hard spheres colloids and freely-jointed hard chains polymers. The results show that the polymers can stabilize the hexagonally close packed HCP structure of colloids over the face-centered cubic FCC structure by exploiting the difference in distribution of void space between the two polymorphs.
Finally, I will present a novel secondary structure displayed by biomimetic sequence-specific peptoid polymers that is unseen in nature. This structure enables strands to densely pack into macroscopically large millimeter-sized bilayer nanosheets. There were workshops, training sessions, and discussion of research, as well as an opportunity to hike and explore the beautiful White Mountains with fellow MRSEC participants. Thursday, December 7, MRSEC Seminar: Quantifying the Energy Landscapes of Ribosome Function Paul Whitford, Northeastern University Abstract: The breadth of information available on ribosome structure and dynamics makes it the ideal system for systematically investigating the physical-chemical properties that enable large-scale biological processes.
In recent applications of these models, we have identified specific structural features that give rise to free-energy barriers during tRNA accommodation, hybrid-state formation and translocation. With this knowledge, it is now possible to interpret findings from these unique approaches within a consistent framework, which is allowing a unified description of the dynamics to emerge. These system transition from a passive gel to flowing states when supplied with ATP.
To capture this change in rheological properties we propose a minimal model of the stress organization in these system where the activity is captured by self-extending force dipoles that are part of a cross linked network.
This network can reorganize itself through buckling of extending filaments and cross linking events that alter the topology of the network. Mean field calculations and simulations of this network reveal that these force dipoles build up stress with time, coupled with an average dissociation time of these force dipoles this give a typical yield stress similar to a yielded plastic solid.
However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a re-transcriptional regulatory event that predictably modulates nascent mRNA output. In this talk, I will present a model system for exploring the physical mechanisms leading to self-assembly of colloidal particles bound to interfaces.
To start, we characterize the interactions between colloidal particles and a solid surface. Specifically, we graft single-stranded DNA onto colloidal particles and a glass coverslip, so that hybridization of complementary DNA molecules generates an attractive, specific force between them. Using a custom-made total internal reflection microscope, we measure particle-surface attractions with kT-scale precision and the associated binding kinetics with high temporal resolution.
We aim to explore how the strength, specificity, and dynamics of the interactions that emerge depend on the molecular attributes of the ligands and receptors. These experiments may help shed light on the self-assembly of small particles bound to membranes, and possibly the formation of complex membrane structures, such as the 'microribs' in Morpho butterfly wings, which give them their brilliant coloration and iridescence. The subject is challenging because there is no clear way to generalize the state variables and concepts, like entropy, that are so useful for understanding systems at equilibrium.
Relatively few nonequilibrium phenomena have been solved analytically. Giant acceleration of diffusion GAD is one of the few. GAD is a dynamical phenomenon exhibited by a Brownian particle in a tilted periodic potential. The hallmark of GAD is that the effective diffusivity of the particle peaks at a critical value of the tilt, where it can exceed the diffusivity in a uniform potential by orders of magnitude.
The entropic case is remarkable because entropy is not well defined out of equilibrium; entropic barriers can change or even vanish as the system is driven away from equilibrium. In this seminar, I will describe experiments and computer simulations which investigate giant acceleration of diffusion of DNA polymers in nanofluidic channels with nanotopographic features that create a periodic entropic array barriers. In presence of hydrodynamical flows, the Lagrangian advection of individual particles strongly influences their dispersion, segregation and clustering.
Range expansions of living cells resting on liquid substrates is of great importance in understanding the organization of microorganism populations.