The Department of Physics and Astronomy Colloquium is held on Monday afternoons at 4:15 pm in room SLH 102 unless otherwise noted. Refreshments are served at 4:00 pm.

Spring 2013

January 14

Levitation by Casimir forces in and out of equilibrium

Mehran Kardar
Dept. of Physics

View Abstract

A generalization of Earnshaw's theorem constrains the possibility of levitation by Casimir forces in equilibrium. The
scattering formalism, which forms the basis of this proof, can be used
to study fluctuation-induced forces for different materials, diverse
geometries, both in and out of equilibrium. In the off-equilibrium
context, I shall discuss non-classical heat transfer, and some
manifestations of the dynamical Casimir effect.

January 21
University holiday: No colloquium

January 28

Fluctuation Theorems for Quantum Processes

Tameem Albash
Physics and Astronomy

View Abstract

We will present fluctuation theorems and moment generating function equalities for generalized thermodynamic observables and quantum dynamics described by completely positive trace preserving (CPTP) maps. Our results include the quantum Jarzynski equality and Crooks fluctuation theorem, and clarify the special role played by the thermodynamic work and thermal equilibrium states in previous studies. We show that for projective measurements unitality replaces micro-reversibility as the condition for the physicality of the reverse process in our fluctuation theorems. We present an experimental application of our theory to the problem of extracting the system-bath coupling magnitude, which we do for a system of pairs of coupled superconducting flux qubits undergoing quantum annealing.

February 4

Counting molecules one at a time by Pointillism optical nanoscopy

Sang-Hyuk Lee
Department of Physics and QB3 Institute
University of California, Berkeley

View Abstract

Super-resolution fluorescence localization microscopy, represented by PALM and STORM, has rapidly emerged as a revolutionary tool for revealing intercellular processes with unprecedented resolution in vivo. Although the methods are based on single-molecule detection of Photoactivatable Fluorescence Proteins (PA-FPs), the fluorescence markers specialized for PALM, the intrinsic fluorescence blinking of PA-FPs has been a big practical obstacle to the application of PALM for molecular counting. To solve this problem, I first have fully characterized, through in vitro single-molecule study, the blinking properties of two popular PA-FPs, mEos2 and Dendra2. Secondly, based on the measured single-molecule properties, I have developed a set of experimental and analytical methods to minimize the error in counting multiple of the PA-FPs. Finally, I have applied the super-resolution microscopy and the newly developed molecular counting method to the study of organization and function of SpoIIIE, the DNA-pumping motor protein during sporulation of B. subtilis bacterial cells.

February 11

"Predicting and Controlling Microbial Activity through Quantitative Theory and Experiments"

James Q. Boedicker
Department of Applied Physics
California Institute of Technology

View Abstract

Controlling the functional outputs of microbial communities will be an essential tool for addressing many of today’s scientific and
technological challenges, ranging from meeting our energy needs to improving human health. Developing a predictive understanding of how these networks of cells work together and coordinate their activities is a grand challenge in biophysics given the spatial, chemical, and biological complexity of these systems. The goal of my research is to develop experimental and theoretical tools to predict and control the behavior of multispecies microbial communities. Towards this goal I
will discuss the application of predictive theoretical models based on statistical mechanics to develop a quantitative understanding of how transcription factors and DNA mechanical properties influence gene regulation. I will also demonstrate how microfluidic technologies can be used to control the microscale spatial structure of microbial systems in order to gain new insights as to how the spatial arrangement of cells controls gene regulation and signal exchange.

February 18
University holiday: No colloquium

February 22

Single-molecule studies of replicative DNA helicases

Special Seminar

Hasan Yardimici
Harvard Medical School

View Abstract

Faithful duplication of the genome is crucial for proper cell division and thus the genetic integrity of all organisms. Errors in DNA replication can lead to genomic instability, a characteristic feature of most cancer cells. A key component of the replication machinery (replisome) is the DNA helicase, which separates the double helix into its component strands so they can be copied.

Efforts to decipher the molecular mechanisms of two helicases: the MCM2-7 complex that acts as the replicative helicase in eukaryotes, and large T antigen (T-ag), the replicative helicase of Simian Virus 40 that serves as a paradigm for eukaryotic replication. Despite decades of study, the basic mechanisms by which these helicases unwind DNA at the replication fork have been controversial. Both enzymes were proposed to function as a physically coupled pair of hexamers that pumps double-stranded DNA through the helicase central channel, splitting the duplex apart when it emerges from the protein complex. Others challenged this view and proposed that they function as single hexamers that encircle and translocate along a single strand and unwind DNA by excluding the other strand from the central channel (“steric exclusion”). Determining which model is correct has profound implications for the spatial organization and inner workings of the replisome. However, due to limitations inherent to conventional biochemical approaches, it has been difficult to answer which model applies to MCM2-7 and T-ag. I developed novel methodologies that combine single-molecule imaging and DNA nanomanipulation in extract-based systems. These tools, together with conventional bulk assays, not only differentiated between different models of unwinding by MCM2-7 and T-ag, but also led to a new model regarding how T-ag deals with replication barriers. In the future, I will study eukaryotic DNA replication at the single-molecule level that will lend important new insights into the mechanism and dynamics of the complex molecular machines that carry out genome duplication.

Hasan received his bachelor’s degree in physics from the Bogazici University (Istanbul, Turkey) in 1999. He obtained PhD in the field of soft condensed matter physics from Johns Hopkins University in 2006. He then joined Paul Selvin's laboratory at University of Illinois at Urbana-Champaign for post-doctoral training where he studied microtubule motor proteins using single-molecule imaging techniques. In 2008, he moved to Harvard Medical School where as a post-doc in the laboratories of Antoine van Oijen and Johannes Walter investigated eukaryotic DNA replication at the single-molecule level.

February 25

"Why are chemotaxis receptors clustered but other receptors aren’t"

Ned S. Wingreen
Dept. of Molecular Biology
Princeton University

View Abstract

"Why are chemotaxis receptors clustered but other receptors aren’t"

The chemotaxis network of bacteria such as E. coli is remarkable for
its sensitivity to minute relative changes in chemical concentrations
in the environment. Indeed, E. coli cells can detect concentration
changes corresponding to only ~3 molecules in the volume of a cell.
Much of this acute sensitivity can be traced to the collective
behavior of teams of chemoreceptors on the cell surface. Instead of
receptors switching individually between active and inactive
configurations, teams of 6-20 receptors switch on and off, and bind or
unbind ligand, collectively. Similar to the binding and unbinding of
oxygen molecules by tetramers of hemoglobin, the result is a sigmoidal
binding curve. Coupled with a system for adaptation that tunes the
operating point to the steep region of this sigmoidal curve, the
advantage for chemotaxis is gain – i.e., small relative changes in
chemical concentrations are transduced into large relative changes in
signaling activity (specifically, the rate of phosphorylation of the
response regulator CheY). However, something is troubling about this
simple explanation: in addition to providing gain, the coupling of
receptors into teams also increases noise, and the net result is a
decrease in the signal-to-noise ratio of the network. Why then are
chemoreceptors observed to form cooperative teams? We present a novel
hypothesis that the run-and-tumble chemotactic strategy of bacteria
leads to a “noise threshold”, below which noise does not significantly
decrease chemotactic velocity, but above which noise dramatically
decreases this velocity.

March 4

"Probing the mechanical properties of cells and their nuclei"

Amy Rowat
Department of Integrative Biology and Physiology

View Abstract

Probing the mechanical properties of cells and their nuclei

A major goal of our work is to unravel the physical and molecular origins of cell nucleus shape stability, and their consequences for physiology and disease. The cell nucleus represents a major step in evolution that enables eukaryotic cells to compartmentalize, preserve, and spatially organize genetic material, which is critical for biochemical processes such as gene expression. This organelle also plays a central role in the transduction of physical forces through living tissue; the nucleus is typically about ten-fold stiffer than the surrounding cytoplasm, therefore its physical and mechanical properties are critical. Studies focusing on specific proteins provide insight: for example, we previously determined how the density of a particular biopolymer, lamin A, regulates the deformability of cells. However, the mechanical properties of cellular biopolymer networks typically depend upon the interactions among multiple proteins. To develop a more complete understanding of the molecular origins of nuclear physical properties requires measurements over a larger number of conditions, including both environmental and genetic perturbations. To this end, we are using insights from physics to develop instrumentation that will enable us to efficiently determine the mechanical properties of multiple cell variants in parallel. For example, by exploiting knowledge of flow through porous media, we developed a filtration assay that can distinguish between cell types with altered nuclear mechanical properties while simultaneously probing hundreds of individual samples. Given the wide spectrum of diseases where altered cell and nucleus mechanical properties are implicated, such technology may have broader applications, for example, to screen cells against a library of drugs.

March 11

"The physics of geological processes: examples from fracturing-assisted fluid flow through impermeable media"

Anders Malthe-Sorenssen
Department of Physics
University of Oslo

View Abstract

Developing a better understanding of the complex patterns and
processes in the Earth is a key to many of the challenges that face
humanity, such as reliable access to cleaner hydrocarbons and safe
storage of CO_2. However, geological processes are coupled across many
scales, and an improved understanding requires an effort that is
integrated across disciplines, methods and scales. In this talk I will
demonstrate through a set of examples how geology can provide us with
challenging physics problems that have both practical and fundamental
interest, and how physics-based modeling of cross-scale processes can
be used to provide a more quantitative foundation for our
understanding of geological processes – enriching both fields. For
example, the chemical transformation of rocks is often a
mechano-chemical transport process, driven by fluid infiltration
coupled to reaction and deformation of the host rock. If the rock
changes its volume during reaction with the fluid, the host rock will
deform and possible fracture, changing the fluid pathways into the
rock. This opens a rich field of coupled processes involving fluid
flow, rock deformation, fracturing and chemical reactions that can be
studied using tools from statistical physics. To address such
processes, we have developed models that couple discrete, statistical
models of fracturing with continuum models of chemical reactions and
transport, and we have demonstrated that this coupling significantly
accelerates rates of material transformation for both volume
decreasing and volume increasing reactions. These models form a basis
for improved understanding of chemical transformation processes such
as the reaction of CO_2 with Olivine during mineralogical CO_2 storage
or the coupling between flow, deformation, and fracture in tight rocks
such as shale.

March 18
Spring break: No colloquium

March 25

How electron cryotomography is opening a new window into microbial ultrastructure

Grant J. Jensen
Division of Biology and Howard Hughes Medical Institute

View Abstract

Electron cryotomography (ECT) is an emerging technology that allows small cells to be imaged in 3-D in an intact, near-native state to "macromolecular" (5-2 nm) resolution. The basic principles of ECT will be explained as well as its future promises and limitations. Example results that have helped us understand the structural biology/biophysics of microbial cell shape determination, motility, chemotaxis, division, and interspecies attack will be shown.

April 1

Cosmological and Astrophysical results from the 2013 Planck Data Release

Loris P. Colombo and Daisy Mak
Department of Physics & Astronomy

View Abstract

The European Space Agency Planck Satellite is the third generation space mission dedicated to measurements of the spatial anisotropies of the Cosmic Microwave Background (CMB) radiation in nine frequency bands from 30 to 857GHz, with unprecedented sensitivity and angular resolution. Launched in May 2009, Planck has been scanning the sky stably and continuously since 12 August 2009, providing a wealth of information of fundamental importance for Cosmology and Galactic Astrophysics. In March 2013, the first complete set of data, covering the the first 15 months of operations, was released to the public. In this talk we will give a summary of the main Cosmological and Astrophysical results of the present release.

In addition, we will also talk about one of the intermediate results from the analysis of Planck data: search of the "dark flow". The measurement of the dark flow has received much attention recently and its existence is, however, controversial. We show that investigations from the Planck data provide a robust measurement and resolution to this ongoing debate.

April 5

Engineering Peptides for Electronic Applications

Guest Speaker

Dr. Nurit Ashkenasy
Department of Materials Engineering
Ben Gurion University of the Negev, Beer-Sheva, Israel

View Abstract

In recent years there is a great interest in the integration of proteins within electronic devices. Since proteins did not evolve to carry out such tasks, the targeted design of proteins for these specific applications is of great importance. Our research focuses on the design and preparation of simple artificial protein systems for molecular electronics applications. This approach will be presented here using common protein motifs such as ?-helices and ?-sheets that are adopted to function in molecular junction configurations. In addition, I will show how inorganic peptide binders, which were selected by biological combinatorial libraries screening tests, can be used to control and modify the electronic properties of semiconductor surfaces. Our studies demonstrate the great potential of the use of specifically designed proteins as components of electronic devices. Moreover, I will show that these systems can be used as simple platforms for understanding the role of different charge transfer mechanisms in protein.

April 8

Speak, Memory! What can a material memorize?

Sidney Nagel
University of Chicago

View Abstract

Sidney R. Nagel is a Stein-Freiler Distinguished Service Professor in the Department of Physics at the University of Chicago. He was the Director of the Materials Research Center at the University of Chicago from 2006 to 2009. He won the Oliver E. Buckley Prize of the American Physical Society in 1999 and was elected to the National Academy of Sciences in 2003. Professor Nagel’s research focuses on complex everyday physics such as the anomalous flow of granular material, the long messy tendrils left by honey spooned from one dish to another, the pesky rings deposited by spilled coffee on a table after the liquid evaporates or the common splash of a drop of liquid onto a countertop. His work includes high-speed photography of splashing liquids and drop formation.

Out-of-equilibrium disordered systems may preserve a memory of external driving that can be read out at a later time. I will present one form of memory that does this in a remarkable fashion. The system remembers multiple values from a series of training inputs yet forgets nearly all of them at long times despite a continual repetition of the inputs. However, if noise is added to the system, all the memories can be preserved indefinitely. This provides a concrete example of “plasticity” in memory formation. Despite these surprising features, the cause of this memory formation is easily understood and appears to be generic.

April 15

"Nucleation in membrane pore formation, rupture, and particle translocation"

Zhen-Gang Wang
Division of Chemistry & Chemical Engineering
California Institute of Technology

View Abstract

The cell membrane defines the boundaries for cells and hence acts both as a first line of defense against pathogen invasion and as a significant barrier for the effective delivery of medical therapeutics. The fusion of membranes and the controlled transport of materials across cells involve the formation of transient membrane pores, while the resistance against cell lysis (rupture) is determined by the stability of the membrane against the formation of pores, e.g., during osmotic swelling. Because of the softness of the material, thermal fluctuations are important and many of the membrane processes of interest are thermally-nucleated (rare) events. In this talk, I will describe a method we developed for exploring a wide range of challenging and previously intractable membrane nucleation problems both in the absence and in the presence of particles. Our method combines the string method with a dynamic self-consistent field theory into an efficient "on-the-fly" algorithm for the determination of the minimum free energy path in the membrane pore formation, rupture, and nanoparticle translocation. For a uniform membrane in the tension regime where nucleation can occur on experimentally relevant time scales, the structure of the critical nucleus is between a solvophilic stalk and a locally thinned membrane. Classical nucleation theory fails to capture these molecular details and significantly overestimates the free energy barrier. The presence of a positively charged nanoparticle can lead to a significant reduction in the barrier to pore formation or rupture. Depending on the particle size, charge and hydrophobicity, we find that there can be at least three competing pathways: (1) particle-assisted membrane rupture, (2) particle translocation, and (3) particle insertion into a metastable pore followed by membrane rupture. The implications of these results on the endosomal escape mechanism in the context of polymer-based gene delivery systems will be discussed.

Zhen-Gang Wang is Professor of Chemical Engineering at California Institute of Technology. He received his Ph. D. in Chemistry from the University of Chicago. Prior to joining the faculty at Caltech, he was a Postdoctoral Fellow first at the Exxon Corporate Research Laboratory in New Jersey and then at UCLA. Prof. Wang’s research interests are in the area of statistical mechanics applied to soft materials and biophysical systems. Research topics include liquid-crystal polymers, gels and soft glasses; charged systems; nucleation; viral assembly; evolutionary protein design, and membrane biophysics.

April 22

"Pattern Formation in Development, Regeneration and Tissue Engineering"

Cheng-Ming Chuong
Dept.of Pathology

View Abstract

Patterns are orders embedded in randomness. Patterns may appear in spatial arrangements or temporal sequence. Patterns exist in the physical world as well as in the living system. Here we use feathers and hairs as experimental models to understand the self-organizing principles of patterning process in development and regeneration. They are good models because of the distinct pattern, approachability for experimentation, and that their stem cells regeneration cyclically in the adult under physiological condition. The knowledge on how to pattern a population of stem cells also has translational value in the context of tissue engineering.

April 29

Connecting the structural dynamics of cytoskeletal filaments with behavior

KC Huang
Department of Bioengineering
Stanford University

View Abstract

Determining how cells, tissues, and organisms determine their structure, and how this structure affects behavior, is a fundamental challenge for modern cell biology. In prokaryotes and eukaryotes alike, cytoskeletal proteins such as tubulin and actin form filaments that have been implicated in a vast array of cellular processes. The mechanisms by which cytoskeletal filaments generate force and affect cell morphology are often dynamic and require techniques that address both the submolecular and cellular scales. I will demonstrate that all-atom molecular dynamics (MD) simulations can be used to infer the properties of filaments, and to discover molecular mechanisms connecting mutations in these proteins to their phenotype. I will show that polymerization of the bacterial actin homolog MreB induces ATP hydrolysis and alters filament stiffness, with mutations near the ATP binding pocket resulting in altered cell size. I will then show that these properties are critical for the cellular morphogenetic program.
These studies illustrate that advanced computational methods with molecular resolution, in combination with emerging structural data, offer the potential to reveal the functional mechanisms of cytoskeletal proteins.