Past Colloquia: 2015-2016

Spring 2016

"Genome in 3D: some physical considerations"

January 19, 2016

Leonid Mirny, MIT
Host: Zvonimir Dogic

Abstract: DNA of the human genome is 2m long and is folded into a structure that fits in a cell nucleus. One of the central physical questions here is the question of cross-scale communication: How can molecules a few nanometers in size control chromosome geometry and topology at micron length scales? Recently developed Chromosome Conformation Capture technique (Hi-C) provides comprehensive information about frequencies of spatial interactions between genomic loci. Inferring principles of 3D organization of chromosomes from these data is a challenging biophysical problem. We develop a top-down approach to biophysical modeling of chromosomes. Starting with a minimal set of biologically motivated interactions we build polymer models of chromosome organization that can reproduce major features observed in Hi-C experiments. I will present our work on modeling organization of human metaphase and interphase chromosomes. Our works suggests that active processes of loop extrusion can be a universal mechanism responsible for formation of domains in interphase and chromosome compaction in metaphase.

"Can Soft Signals Be Oncogenic"

January 26, 2016

Ravi Radhakrishnan, University of Pennsylvania
Joint Quantitative Biology/Martin Weiner Lecture Series
Physics Department Colloquium
Host: Michael Hagan

Abstract: There are emerging links between the stiffness of the tissue microenvironment and the tumorogenicity in several tumors of soft tissues, thereby bringing to light the importance of how cells transduce mechanical signals to alter signals and cell fate. This talk will focus on molecular and subcellular mechanisms of curvature induction and sensing in cell membranes by a novel class of membrane remodeling proteins. I will discuss how thermally induced membrane undulations can couple to the induced curvature field by such proteins thereby providing a mechanism for curvature focusing. The curvature-undulation coupling also leads to a mechanism for long-range curvature sensing whereby such proteins can migrate toward preferred curvature locations at distances much larger than their size. Consistent with in vitro biophysical as well as cellular experiments, the curvature sensing/generating proteins can also be shown to be exquisite sensors of membrane tension thereby representing an important class of transducers of mechanical signals. I will describe a theory guided set of experiments, which demonstrate how such proteins can initiate and sustain survival signaling pathways that are initiated solely by physical stimulus and without any biochemical cues. We hypothesize that such survival mechanisms can be significant in enhanced survival of cells under conditions of altered mechanics (such as stiffness) of the tumor microenvironment.

"Spontaneous flow in active fluids"

February 2, 2016

Zvonimir Dogic, Brandeis

Abstract: The laws of equilibrium statistical mechanics impose severe constraints on the properties of conventional materials assembled from inanimate building blocks. Consequently, such materials cannot exhibit spontaneous motion or perform macroscopic work. Inspired by biological phenomena such Drosophila cytoplasmic streaming, our goal is to develop a new category of soft active materials assembled from the bottom-up using animate, energy-consuming building blocks such as kinesin molecular motors and microtubule filaments. Released from the constraints of the equilibrium, these internally driven gels, liquid crystals and emulsions are able to change-shape, crawl, flow, swim, and exert forces on their boundaries to produce macroscopic work. In particular we describe properties of an active fluid that upon confinement transitions from a quiescent to a spontaneously flowing state. We characterize the properties of the emergent flows as well as how the transition to a flowing state depends on the properties of the confining geometry. Our results illustrate how active matter can serve as a platform for testing theoretical models of non-equilibrium statistical mechanics, developing new microfluidic applications and potentially even shedding light on self-organization processes occurring in living cells.

"From Higgs Discovery to the Halls of Congress: How Scientists Can Engage In Public Policy"

February 9, 2016

Dan Pomeroy, MIT
Host: Craig Blocker

Abstract: National policy decisions increasingly involve complex issues with strong technological and scientific components. Scientists can play an important role in informing public policy both from within academia and by pursuing a career in public policy. This talk will provide examples of how a scientist may engage in public policy as well as a detailed discussion of the role of a science policy advisor to a United States Senator.

"What should we do with a small quantum computer?"

February 23, 2016

Aram Harrow, MIT
Host: Matthew Headrick

Abstract: A large-scale quantum computer would be able to solve problems that existing classical computers would take much longer than the age of the universe to solve. This would have dramatic implications for cryptography, chemistry, material science, nuclear physics and probably other areas that are still unknown. But what about quantum computers that will be available in the next few years? Experimentalists working with ion traps and superconducting qubits have plans to build quantum computers with 50-100 qubits capable of performing some thousands of quantum gates. The company D-Wave is already selling devices with over 1000 qubits, although they can only run a single algorithm (the adiabatic algorithm) and they suffer high rates of noise.In this talk, I will analyze two algorithms that can be run on current and near-term quantum computers. First I will look at the adiabatic algorithm, which has shown promise in its ability to use quantum tunneling to solve optimization problems more efficiently than classical local search. Here I will show that a different classical algorithm can simulate the adiabatic algorithm in these cases, suggesting that this is not a promising approach to quantum speedup. Second, I will look at a recently proposed Quantum Approximate Optimization Algorithm (QAOA), which is a method of performing combinatorial optimization using very few gates. I will show that conjectures from complexity theory imply that this algorithm cannot in general be simulated by classical computers.

"The Dark Energy Survey and Gravitational Waves"

March 1, 2016

Marcelle Soares-Santos, Fermilab
Host: Gabriella Sciolla

Abstract: DES is an ongoing imaging sky survey, the largest such survey to date. Its main science goal is to shed light onto dark energy by making precision measurements of the expansion history and growth of structure in the universe. In this talk I present our latest results and introduce a new DES initiative: searches for optical counterpart of gravitational wave events.

"Quantum Quenches"

March 8, 2016

Aditi Mitra, NYU
Host: Albion Lawrence

Abstract: The non-equilibrium dynamics of isolated quantum systems following a "quench" of some parameter of the Hamiltonian raises many fundamental questions, that can now even be probed in experiments. I will first give an overview of the topic and the status of experiments. I will then show how quantum quenches in the vicinity of a critical point can lead to universal out of equilibrium dynamics with new critical exponents that are not related to thermodynamic critical exponents. I will also highlight what quantum information measures such as entanglement entropy and entanglement spectrum reveal about a system which is out of equilibrium following a quantum quench, applying them both to systems near critical points, as well as to systems with topological order.

"What's going on inside of a proton? The story of lattice QCD"

March 22, 2016

Paul Mackenzie, Fermilab
Host: Albion Lawrence

Abstract: The forces between quarks inside a proton are much stronger than the other forces known in fundamental physics, so strong that the perturbative approximation methods that work well for the other forces don’t work for the strong interactions. They can be solved to high accuracy using large-scale computer simulations. The history of lattice QCD has been closely intertwined with the history of modern supercomputing, and I’ll also tell part of this story. Lattice calculations play a critical role in teasing out the fundamental properties of the quarks from the observed properties of the particles containing them. They are also critical in understanding the observed properties of nucleii in terms of fundamental physics.

"What does the Golden Ratio have to do with friction? An answer atom by atom"

March 29, 2016

Vladan Vuletic, MIT
Host: Matthew Headrick

Abstract: Friction is the basic, ubiquitous mechanical interaction between two surfaces that results in resistance to motion and energy dissipation. In spite of its technological and economic significance, our ability to control friction remains modest, and our understanding of the microscopic processes incomplete. To test long-standing atomistic models of friction processes at the nanoscale, we implemented a synthetic nanofriction interface using laser cooled ions subject to the periodic potential of an optical standing wave. We show that stick-slip friction can be tuned from maximal to nearly frictionless via arrangement of the atoms relative to the periodic potential, and that friction at the nanoscale can substantially differ from the simple phenomenological laws observed at the macroscale.

"Gravitational Wave Detection with Advanced LIGO"

April 5, 2016

Matthew Evans, MIT
Host: Matthew Headrick

Abstract: The Laser Interferometer Gravitational-wave Observatory (LIGO) recently made the first direct detection of gravitational waves; minute distortions in space-time caused by cataclysmic events far away in the universe. I will talk about the source of the signal we detected, the physics behind the detectors, and prospects for the future of this emerging field.

"Emergent Fine-tuning to Environmental Drives in a Random Chemical Mixture"

April 12, 2016

Jeremy England, MIT
Host: Michael Hagan 

Abstract: The steady-state behavior of an undriven mixture of reaction chemical species is the equilibrium point where the concentrations obey a simple exponential relationship to free energy. Once external environmental drives are introduced, however, steady-state concentrations may deviate from these equilibrium values via processes that require sustained absorption and dissipation of work. From a physical standpoint, the living cell is a particularly intriguing example of such a nonequilibrium system because the environmental work sources that power it are relatively difficult to access – only the proper orchestration of many distinct catalytic actors leads to a collective behavior that is competent to harvest and exploit available metabolites. Here, we study the dynamics of an in silico chemical network with random connectivity in a driving environment that only makes strong chemical forcing available to rare combinations of concentrations of different molecular species. We find that the long-time dynamics of such systems are typified by the spontaneous extremization of forcing, so that the molecular composition converges on states that exhibit exquisite fine-tuning to available work sources.

"Fiber-forming filaments figure out frustration: how impossible packing shapes the assembly of chiral filaments"

April 19, 2016

Gregory Grason, UMass Amherst
Host: Zvonimir Dogic

Abstract: Filament assemblies are basic structural motifs of diverse materials, from macroscopic materials (textiles, cables) to the nanostructure assemblies that compose living matter (filamentous proteins). Yet, the highly non-trivial rules that govern packing and higher-order assembly of one-dimensional elements are largely unknown, arguably lagging decades, if not centuries, behind our knowledge of sphere-packing models of matter. In this talk, I will discuss the “metric” constraints imposed on dense bundles by the complex geometries (i.e. twist, bend) realized in self-organized assemblies. I will describe a surprising geometric connection between filament packing and the packing problem on non-Euclidean surfaces (e.g. the Thompson problem) that has critical implications for the structure and thermodynamics of “self-spinning” rope-like assemblies chiral filaments, a basic model of filamentous protein assembly, from extracellular bundles to amyloid fibers.

Fall 2015

"The Rise of Jet Substructure: Boosting the Search for New Physics at the LHC"

September 8, 2015

Jesse Thaler, MIT
Host: Albion Lawrence

"Airway Surface Brush Sweeps Lungs Clean: Polymer Physics Helps Us Breathe Easier"

September 22, 2015

Michael Rubinstein, UNC
Host: Zvonimir Dogic

Abstract: The classical view of the airway surface liquid (ASL) is that it consists of two layers – mucus and periciliary layer (PCL). Mucus layer is propelled by cilia and rides on the top of PCL, which is assumed to be a low viscosity dilute liquid. This model of ASL does not explain what stabilizes the mucus layer and prevents it from penetrating the PCL. I propose a different model of ASL in which PCL consists of a dense brush of mucins attached to cilia. This brush stabilizes mucus layer and prevents it penetration into PCL, while providing lubrication and elastic coupling between beating cilia. Both physical and biological implications of the new model will be discussed.

"Measuring Entanglement Entropy in Synthetic Quantum Matter"

October 6, 2015

Markus Greiner, Harvard University
Host: Matthew Headrick

Abstract: With quantum gas microscopy we are now able to take the control of ultra cold quantum gases in an optical lattice to the next and ultimate level of high fidelity: addressing, manipulation and readout of single particles. In my talk I will first give an introduction to this field of research and present an overview of recent experiments. I will then focus on presenting experiments in which we are for the first time able to directly measure entanglement entropy in a quantum many-body system.

"Understanding the Nature of Neutrinos: Recent Discoveries and Future Prospects"

October 13, 2015

Karsten Heeger, Yale
Host: Gabriella Sciolla

Abstract: The discovery of neutrino mass and oscillations have opened an intense field of study in the properties of neutrinos and their role in the Universe but many open questions remain. Recently the Daya Bay reactor experiment observed the oscillation of antineutrinos over kilometer-scale baselines and opened the window to the study of CP violation in the lepton sector. The search for neutrinoless double beta decay with CUORE will probe if neutrinos are their own antiparticles and probe the effective mass of neutrinos. New experiments are getting underway to study neutrino oscillation at short and long baselines and search for signs of new physics in the neutrino sector. I will review recent results and future prospects for neutrino studies with reactor neutrinos and in double beta decay.

Eisenbud Lectures in Mathematics and Physics

October 27, 2015

October 27 - October 29
Jeffrey Harvey, University of Chicago

October 27, 2015
"A physicist under the spell of Ramanujan and moonshine"

October 28, 2015
"Mock modular forms in mathematics and physics"

October 29, 2015
"Umbral Moonshine"

"Fingerprints of the Early Universe"

November 3, 2015

Cora Dvorkin, Harvard University
Host: Gabriella Sciolla

Abstract: Cosmological observations have provided us with answers to age-old questions, involving the age, geometry, and composition of the universe. However, there are profound questions that still remain unanswered. The origin of the small anisotropies that later grew into the stars and galaxies that we see today is still unknown. In this talk, I will explain how we can use measurements of the Cosmic Microwave Background, which was last scattered when the universe was 380,000 years old, to reconstruct the detailed physics of much earlier epochs, when the universe was only a tiny fraction of a second old. I will also discuss the potential of current and upcoming measurements of the large-scale structure of the universe to further constrain the physics underlying inflation.

"Geometry and symmetry in nanomaterial self-assembly"

November 10, 2015

Steve Whitelam, Lawrence Berkeley National Lab
Joint Quantitative Biology/Martin Weiner Lecture Series
Physics Department Colloquium
Host: Michael Hagan

"Hydrodynamics of Swimming Microorganisms in Complex Fluids"

November 17, 2015

Tom Powers, Brown University
Host: Zvonimir Dogic

Abstract: Since fluid mechanics at the scale of the cell is dominated by viscosity, swimming microorganisms use drag for propulsion. While there has been much work on the mechanics of swimming in water at micron scale, many microorganisms usually encounter complex fluids such as mucus, which are full of polymers. I will address the emerging area of swimming in complex fluids. We use theory and simple scale-model experiments to study how viscoelasticity affects the swimming speed of swimmers with simple illustrative stroke patterns, such as small-amplitude traveling waves and rigid-body rotation of helices. We also study swimming mechanics in anisotropic media such as liquid crystals. We find that the nature of anchoring conditions for the liquid-crystalline degrees of freedom plays a critical role in determining the swimming speed. Furthermore, we study the fluid transport induced by the swimmers motion by calculating the flux of fluid in the laboratory frame.

"Pattern formation in soft and biological matter"

December 1, 2015

Joern Dunkel, MIT
Host: Zvonimir Dogic

"Getting in Shape: how do microorganisms control their geometry?"

December 8, 2015

Ariel Amir, Harvard University
Host: Zvonimir Dogic

Abstract: Microorganisms such as bacteria and budding yeast are remarkably successful in accurately self-replicating themselves within several tens of minutes. How do cells decide when to divide? How do they control their morphology? I will show how ideas from statistical mechanics and materials science can help answer these questions. In particular, I will show how a stochastic model of cell size control, combined with single cell data, can be used to infer a particular strategy for cell size control in bacteria and budding yeast, and how the theory of elasticity can be utilized to understand the coupling of mechanical stresses and cell wall growth in bacteria.