Seminars Spring 2010
Our seminars have moved!
Seminars are on Tuesdays at 4 pm in Smith Hall Annex, B-Level, Physics Library preceded by tea at 3:45, unless otherwise noted.
- The language of cells: forceful and dynamicHost: N. ArkusLiving cells sense and respond to physical forces that are mediated through their microenvironment. In vivo, these physical forces arise through the agencies of substrate adhesion, substrate stretch, and substrate rigidity, as well as through cell-cell contacts. To reproduce these physical forces within in-vitro cultures, my laboratory has developed novel nanotechnologies. Using these technologies, we have uncovered altogether novel phenomenon to describe how living cells contract, deform and communicate. In the etiology of excessive airway narrowing during asthma or endothelial cell barrier disruption during vascular disease these phenomena are ever-present, inescapable and dominant.
Jan 19: Daniel Needleman, Harvard UniversityCell Biology and Active Liquid Crystals: Reevaluating the Tactoid Hypothesis of Spindle StructureHost: Tarun Kapoor
Jan 26: Aleksandra Walczak, Princeton UniversityInformation Processing in Small Gene Regulatory Networks and CascadesHost: M. MagnascoMany of the biological networks inside cells can be thought of as transmitting information from the inputs (e.g., the concentrations of transcription factors or other signaling molecules) to their outputs (e.g., the expression levels of various genes). On the molecular level, the relatively small concentrations of the relevant molecules and the intrinsic randomness of chemical reactions provide sources of noise that set physical limits on this information transmission. Given these limits, not all networks perform equally well, and maximizing information transmission provides a optimization principle from which we might hope to derive the properties of real regulatory networks. I will discuss the properties of specific small networks that can transmit the maximum information. Concretely, I will show how the form of molecular noise drives predictions not just of the qualitative network topology but also the quantitative parameters for the input/output relations at the nodes of the network. In an attempt to link these general theoretical considerations to real biological systems, I will illustrate the predictions on the example of transmission of positional information in the early development of the fly embryo. Lastly, I will discuss different approaches of how a stochastic molecular level description can be successfully expanded to larger regulatory systems.
Feb 2: Konstantin Mischaikow, Rutgers UniversityA Databases schema for the global dynamics of multiparameter nonlinear systemsHost: E. Siggia
Feb 8: Bernardo Pando, MIT (2PM, coffee prior)Contribution of gene duplications to the evolution of genetic networksHost: E. Siggia
- Probing mechanical principles of focal contacts in cell-matrix adhesion in a coupled stochastic-elastic modeling frameworkHost: N. ArkusCell-matrix adhesion depends on the collective behaviors of clusters of receptor-ligand bonds called focal contacts between cell and extracellular matrix. While the behavior of a single molecular bond is governed by statistical mechanics at the molecular scale, continuum mechanics should be valid at a larger scale. In this seminar, an overview will be given over a series of recent theoretical studies aimed at probing the basic mechanical principles of focal contacts in cell-matrix adhesion via stochastic-elastic models in which stochastic descriptions of molecular bonds and elastic descriptions of interfacial traction/separation are unified in a single modeling framework. The objective is to illustrate these principles using simple analytical and numerical models. The discussions are organized around the following questions: Why is there a micron-scale size limit on focal adhesions? Why do cells prefer stiffer substrates? How does the stability of focal adhesions depend on the stress fiber orientation? Why are cytoskeletal contractile forces necessary to stabilize focal adhesions? With these curiosities in mind, the effects of cluster size, cell/matrix elastic modulus, loading direction and cytoskeletal contractility on the lifetime of adhesion clusters have been systematically investigated, with results showing that intermediate adhesion size, stiff substrate, cytoskeleton stiffening, low-angle pulling and moderate cytoskeletal pretension are factors that contribute to stable focal adhesions. These results provide feasible explanations for a wide range of experimental observations and suggest possible mechanisms by which cells can actively control adhesion and de-adhesion via cytoskeletal contractile machinery in response to mechanical properties of their surroundings.
Thur. Feb 11: Alexander Grosberg, NYULarge scale organization of DNA in chromosomesHost: P. Kumar
Feb 16: Alex Hoffmann, UCSDA Temporal Code in Inflammatory SignalingHost: E. Siggia
Feb 17 (NOTE SPECIAL TIME: 1PM, coffee prior): Jingshan Zhang, Harvard UniversityOptimality and evolution: from proteome size to affinity maturationHost: E. Siggia
Feb 19 (NOTE SPECIAL TIME: 2PM, coffee prior):Adel Dayarian, Rutgers UniversityStatistical mechanics and next-generation sequence assemblyHost: E. SiggiaDe novo assembly of genomes from short reads generated from high throughput sequencing platforms remains a significant challenge. Given the small size of the contigs built from these reads, it is essential to use some additional information to stitch these contigs together into large scaffolds. One way is to utilize the mate pair technology, which provides pairs of short reads separated by an approximately known distance and orientation along the genome. The problem is that a part of the mate-pair information could be false or misleading. To deal with this problem, we have developed SOPRA, a scaffold building tool which manages to select a consistent and reliable subset of mate pair constraints. Scaffold assembly is presented as a series of optimization problems for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs connected by mate pairs. These optimization problems are related to finding ground states of well-known hamiltonians in statistical physics. We show that, for the typical structure of these graphs generated by real sequence data, these optimization problems can be solved quite satisfactorily by our method. Applying SOPRA to real data from bacterial genomes, we were able to assemble contigs into scaffolds of significant length (N50 up to 200 Kb) with very few errors introduced in the process.
Feb 23: Pankaj Mehta, Princeton UniversityFrom biological networks to complex behaviorsHost: E. SiggiaIt is now clear that Phil Andersonâs famous maxim âMore is Differentâ holds true even in biology. For example, microbiologists now agree that bacteria commonly engage in complicated collective behaviors that require individual cells to receive, interpret, and respond to information from one another and their environment. Underlying these behaviors are complex biological signaling networks. Understanding these signaling networks poses interesting new physics problems. In this talk, I will discuss two examples from my own research: 1) how the identification of transcription factor binding sites naturally leads to fascinating questions about the âinverseâ statistical mechanics of hard rods in a disordered potential and 2) how we can use methods from information theory and statistical physics for quantifying the information processing capabilities of the Vibrio harveyi quorum sensing network.
Thur. Feb 25: Margaret Gardel, University of ChicagoMechanics of Contractile Actomyosin NetworksHost: N. ArkusThe biophysical properties of contractile actomyosin networks play a predominate role in the ability of adherent cells to regulate how mechanical forces are sensed and generated at points of adhesion to the extracellular matrix. Although much is known about the mechanochemistry of individual myosin II motors and actin filaments, little is known how these properties drive the self assembly and biophysical properties of larger length scale networks and bundles that span the entire cell. Furthermore, the requirements of passive actin filament cross-linking in generating contractile structures is unknown. To address how myosin-II ATPase activity drives the dynamic organization of the F-actin cytoskeleton into structures capable of efficient force transmission, we have studied the dynamics and biophysical properties of actomyosin networks both in live cells and reconstituted networks of purified proteins. These studies isolate the minimal set of proteins and biophysical parameters required for regulating contractile matter.
Fri. Feb 26 (2PM): S. Jamal Rahi, MITScattering theory approach to electrodynamic Casimir interactionsHost: Eric SiggiaWe have derived methods for calculating the Casimir force to arbitrary accuracy, for any number of objects, arbitrary shapes, susceptibility functions, and separations. The technique is applicable to objects immersed in media other than vacuum, nonzero temperatures, and spatial arrangements in which one object is enclosed in another. The method combines each object's classical electromagnetic scattering amplitude with universal translation matrices, which convert between the bases used to calculate scattering for each object, but are otherwise independent of the details of the individual objects. We have explored various novel geometries using these techniques, including objects interacting with cavities and objects with sharp edges. The method is further used to examine whether fluctuation-induced forces can lead to stable levitation. Neglecting permeabilities, we find that any equilibrium position of items subject to such forces is also unstable if the permittivities of all objects are higher or lower than that of the enveloping medium; the former being the generic case for ordinary materials in vacuum. Thus, the Casimir force cannot produce stable equilibria in vacuum for ordinary materials.
Mar 2: David Kleinfeld, UCSDOne vessel, one stroke? Redundancy versus fragility in cortical vascularizationHost: M. Magnasco & E. Katifori
Mar 8 (2PM): Gonzalo Otazu, Ludwig-Maximilians Universitat MunchenA recursive cortical circuit model for invariant sound source identification in mixturesHost: M. Magnasco/M. Geffen
Mar 9: Pablo A. Iglesias, John Hopkins UniversityAn information-theoretic view of signaling pathwaysHost: E. Siggia
- Cellular organization and function of a bacterial biochemical pathwayHost: M. MagnascoCells need to perform and regulate in a confined space a myriad of biochemical reactions. The variability due to fluctuations in enzyme levels is in part smoothened by the architecture of biochemical networks . However, no detailed molecular explanation for this effect is known. While trying to determine how the spatio-temporal distribution of enzymes from a metabolic cascade optimizes their function inside a cell, the central questions are: What is the intracellular organization of enzymes allowing efficient and non-interfering chemical reactions? What are the molecular interactions permitting these reactions? The study of cell wall synthesis during sporulation in the bacterium Bacillus subtilis is a good system to start answering these questions.
Mar 23: Peng Yin, Harvard UniversityProgramming Nucleic Acid Self-AssemblyHost: N. ArkusThis talk will describe our research on engineering information directed self-assembly of nucleic acid (DNA/RNA) structures and devices, and will discuss how such systems can be exploited to do useful molecular work. Specifically, I will first present a rudimentary programming language that enables user-friendly design of the dynamic behavior of synthetic nucleic acid systems. The language is based on the graphical abstraction of a DNA hairpin motif, which physically implements a programmable kinetic trap. A high level molecular program specifies the connection of such kinetic traps on a free energy landscape, and defines the system's reaction pathway and dynamic behavior. A variety of molecular programs were experimentally executed: the catalytic formation of DNA branch junctions, a cross catalytic circuit, the triggered growth of a binary molecular "tree", and the autonomous unidirectional motion of a DNA "walker". In a related work, the abstraction of a 42 base single-stranded DNA motif is used to direct the self-assembly of molecular tubes with monodisperse, programmable circumferences. We will discuss how such nucleic acid systems can be interfaced with the larger molecular world for technological applications.
- Modeling the large-scale dynamics of bacterial baths as an active suspension.Host: N. ArkusSwimming microorganisms affect each other's paths through their mutual hydrodynamic interactions, and experimental observation of highly concentrated bacterial baths show large-scale spatially and temporally complex flows that presumably result from such interactions. While the biological importance of such dynamics is unclear, such internally driven systems are fascinating in their own right, and may even be of technological utility. Using particle-based simulations of many simple hydrodynamically interacting swimmers, as well as a recently developed kinetic theory for active suspensions, I will investigate how hydrodynamically mediated interactions lead to large-scale system instability, coherent flow structures, and fluid mixing. I will also show how the macroscopic dynamics is directly determined by the micromechanics of swimming.
- Bioresponsive Matrices: from drug delivery to circuitsHost: N. ArkusAltering the distribution of drugs within the body can increase therapeutic efficacy and diminish systemic toxicity, dramatically altering therapeutic outcomes and the quality of life of patients. Conventional drug delivery typically controls (1) the release of molecules based on the polymer's chemical structure and (2) the distribution of therapeutics by covalently anchoring a targeting moiety homogenously to a nanoparticle surface. Our drug delivery strategy relies on the design of materials that can respond to physiologically relevant environmental changes. In order to change the biodistribution of molecules, we have focused on (1) triggered delivery based on minute changes in the bloodstream pH (<0.2 pH units) and (2) targeted delivery that aims to address the dynamic cellular membrane. Profoundly, material properties of the vehicle, and not the encapsulated drug, can affect cell behavior. In addition, we have synthesized multifunctional materials that integrate a physiological stimulus with conductivity for use in tissue engineering and sensing applications.
Apr 12 (2PM): Madan Rao, Raman Research Institute/National Centre for Biological Sciences BangaloreActive organization of cell surface molecules induced by cortical actin: implications to sorting, signaling and endocytosisHost: A. LibchaberI will discuss our recent work on the nanoscale organization of lipid-anchored proteins on the surface of living cells. This organization is dynamic and regulated by the activity of cortical actin, leading to a novel form of clustering. I will discuss a theoretical proposal based on an active coupling of the membrane with cortical actin which explains many of the unusual features of this clustering. In addition, it makes predictions on the nature of fluctuations of lipid-anchored proteins, which we verify in our fluorescence-based experiments. This active organization may have implications for the spatiotemporal regulation of chemical reactions on the cell surface and consequently on sorting, signaling and endocytosis of lipid-anchored proteins.
- The Dynamics of Conformity & DissentHost: N. ArkusNature is ripe with dynamical aggregation phenomena, in which an initially homogeneous collection of interacting particles fragment, disperse, and coalesce. Condensation & droplet formation is, of course, a well-known example in physics, galaxy formation and clustering another. The formation of swarms, schools, herds, or even the flocking of birds provide compelling biological illustrations. Rich stochastic behavior, as well as phase transition phenomena, are evident in different evolutionary minority (e.g., El Farol Bar), public goods, and other societal selection games, such as the Seceder Model, which introduces a novel dynamical frustration via the competing tendencies to be distinct, yet part of the group. The Seceder Model reveals that an iterative microscopic mechanism favoring dissent, yet permitting conformity, leads not only to the genesis of distinct groups, but also yields an abundant diversity of cluster-forming dynamics. In this talk, we will discuss population fragmentation, ideological symmetry-breaking and nonlinear group dynamics characteristic of this intriguing model.
Apr 20: Christian Degen, MITNanoscale magnetic resonance imagingHost: S. KuehnDetermination of the atomic structure of large and complex macromolecules, indispensable for the complete understanding of the mechanisms of biological processes, is one of the most difficult problems in molecular biology. Examples of such structures include subcellular entities, giant protein and nucleic acid assemblies, molecular machines, fibrils, as well as enveloped viruses and small bacteria. The two standard tools for delivering structures at atomic resolution, X-ray crystallography and NMR spectroscopy, are overwhelmed by the complexity of such large assemblies, while cryo-electron tomography, the highest resolution 3D microscopy used by structural biologists, is hindered by heterogeneity and disorder and moreover suffers from radiation damage and low contrast. In this talk I will discuss our lab’s efforts in developing high-resolution magnetic resonance imaging (MRI) as an alternative microscopy tool for the direct imaging of molecular complexes. I will introduce the basics of Magnetic Resonance Force Microscopy (MRFM), a combination of MRI with scanning probe microscopy that permits detection of NMR signals typically 108 times smaller than in conventional MRI instruments. I will then talk about recent efforts at imaging nanoscale objects in 3D, including individual virus particles and molecular adsorption layers at spatial resolutions of better than 10 nm. Finally I will review the recent proposal of optical diamond magnetometry as an alternative path to nanometer-scale MRI under ambient conditions.
Apr 27: Eric Dufresne, Yale UniversityNascent Adhesions are Noisy, Floppy and ResponsiveHost: N. ArkusCells crawl to close wounds, fight infections and wire-up the nervous system. To crawl, they typically reach forward, grab onto a substrate, and pull. Cells reach and pull using their actincytoskeleton. Cells grab onto substrates with adhesion complexes – which connect the force-generating machinery of the cytoskeleton to the outside world. While the mechanics of the actin cytoskeleton have been a major focus of biophysics for well over a decade, the mechanics of adhesions are essentially unknown. To quantify the mechanics of adhesions, we combine optical tweezers with confocal microscopy, enabling direct comparison of cytoskeletal dynamics with traction forces. We find that nascent adhesions couple and decouple to the substrate stochastically. When coupled, they are anchored on well-defined locations along the flowing actin cytoskeleton at one end and Ig CAMs at the other. We show that nascent adhesions are highly elastic, strain hardening and adjust their stiffness to match that of the substrate. Our experimental force-extension curves are well described by the entropic elasticity of unstructured polymers binding stochastically to the substrate according to the Bell model.
- Self-assembly of DNA into nanoscale three-dimensional shapesHost: N. ArkusI will present a general method for solving a key challenge for nanotechnology: programmable self-assembly of complex, three-dimensional nanostructures. Previously, scaffolded DNA origami had been used to build arbitrary flat shapes 100 nm in diameter and almost twice the mass of a ribosome. We have succeeded in building custom three-dimensional structures that can be conceived as stacks of nearly flat layers of DNA. Successful extension from two-dimensions to three-dimensions in this way depended critically on calibration of folding conditions. We also have explored how targeted insertions and deletions of base pairs can cause our DNA bundles to develop twist of either handedness or to curve. The degree of curvature could be quantitatively controlled, and a radius of curvature as tight as 6 nanometers was achieved. This general capability for building complex, three-dimensional nanostructures will pave the way for the manufacture of sophisticated devices bearing features on the nanometer scale.
- Toward Artificial Genomes: Sustaining the Growth of Living Cells with Molecular Parts Designed De NovoHost: N. ArkusThe entire collection of genes and proteins in all the living systems on earth comprises a minuscule fraction of sequence space. From the enormous diversity of possible gene and protein sequences, billions of years of evolution have selected a very small collection of “molecular parts” to sustain living organisms (only ~4,000 genes in E. coli bacteria and ~20,000 in humans.) These considerations might lead one to assume that DNA sequences and protein structures capable of sustaining life must be very special. Is this true? Or can we produce biological activity in the laboratory from sequences designed “from scratch”? To address these questions, we designed and constructed a collection containing millions of artificial proteins (a model “proteome”) encoded by a library of synthetic genes (an artificial “genome”). Next, we showed that several of these artificial genes and proteins provide essential biochemical functions supporting the growth of cells. Thus, artificial sequences, which never before existed on earth, possess activities that can sustain life. This initial foray into artificial genomics suggests that (i) the toolkit for biology need not be limited to genes and proteins that already exist in nature; and (ii) the construction of entirely artificial genomes may soon be within reach.
May 18: David Mooney, Harvard UniversityMaterials to program cells in situHost: N. ArkusThere are hundreds of clinical trials of cell therapy currently underway, but simple cell infusions lead to large-scale cell death, little control over cell fate, and a typically poor clinical outcome. We propose a new approach, in which material systems are first used either as cell carriers or attractors of host cell populations, and in either case the material then programs the cells in vivo and ultimately disperses the cells. Key features of these material systems include the ability to create gradients of chemotactic molecules to recruit and/or disperse cells, and immobilization of signals that regulate cell activation/differentiation of cells in contact with the material. The potential utility of this approach will be demonstrated with examples from regenerative medicine and cancer immunotherapy.
May 21 (2PM): Marcus Roper, University of California, BerkeleyThe fluid dynamics of fungal growth and dispersalHost: E. KatiforiTo grow and disperse effectively, fungi must solve hard physical problems. I'll show how math modeling and table top experiments have illuminated two of these problems: #1. The forcibly launched spores of ascomycete fungi must eject through a boundary layer of nearly still air in order to reach dispersive air flows. Because of their microscopic size, singly ejected spores are almost immediately brought to rest by fluid drag. However, by coordinating the ejection of thousands or hundreds of thousands of spores, some fungi are able to sculpt a flow of air that carries spores across the boundary layer and around any intervening obstacles. #2. Growing filamentous fungi are commonly multi-genomic. There is evidence that internal genetic diversity, arising from mutation, fusion between different individuals and parasexuality, makes pathogenic fungi more virulent, and allows fungi in general to better exploit heterogeneous substrates. I'll describe our experiments to map out how new genomes spread through a colony, and how stable populations are of multiple different genomes are maintained.
- TBAHost: T. Reichenbach
May 27 (4PM): Pradeep Kumar, Rockefeller UniversityWater in BiologyHost: A. LibchaberI will discuss the thermodynamic bounds imposed by water being the solvent on two class of biomolecules 1) Proteins, in which case stability and kinetics are intricately related 2) RNA/DNA, which are extremely stable at high pressures and temperatures and can also perform certain kinetics by binding with purene A-based based molecules such as AMP-aa, ATP etc. I will show that solvation/hydrophobicity plays an important role and one can draw thermodynamic bounds in the pressure-temperature plane on both classes of kinetics. Finally, I will discuss the consequences of these in experimental studies of the growth of bacterial cells at non-ambient conditions.
Wed Aug 4 (12:30pm): Pierre-Olivier Polack, University of Pennsylvania School of MedicineVoltage sensitive dye imaging of the evoked network activity in the mouse primary and high order visual corticesHost: Maria Geffen
- Molecular evolution in fitness landscapes and seascapesHost: Stanislas Leibler
Organisms need to perform, encode, and evolve multiple complex functions. In this talk, I discuss fitness landscapes for specific molecular functions, which demonstrate the link between their evolution and their underlying biophysics. Examples include fitness landscapes for transcriptional regulation and for processing of micro-RNA molecules. Based on these examples, we address some fundamental questions on fitness landscapes: How does natural selection correlate the evolution of parts contributing the same function? Conversely, what determines modularity in the evolution of an organism, that is, the independence of different functions? When can we think of molecular evolution as dynamics in a static fitness landscape, and when is selection itself a dynamic fitness seascape?Bacterial strategies of chemotaxisVisiting Scientist at the Center for Studies in Physics and BiologyBacteria respond to chemical cues by performing a biased random walk that enables them to migrate towards attractants and away from repellents. Bias is achieved by regulating the duration of the bacterial runs as a function of the environment, inferred from the history of chemoattractant detections experienced by the bacterium. This time-signal is processed using a time convolution function that can be assayed measuring the response of the bacterium to short pulses of chemoattractant. The convolution constitutes an elementary form of memory, which is encoded at the molecular level by the processes of (de-)methylation and (de-)phosphorylation of the underlying biochemical network. While the latter is being characterized in detail, the functional reasons shaping the bacterial chemotactic response are largely unknown. We show that the chemotactic response observed experimentally is the strategy that ensures the highest minimum (MaxiMin) uptake of chemoattractant, in any field thereof. The consequence is that adaptation of the chemotactic bacterial system appears to be evolutionary driven by the need to cope with space-time environmental fluctuations rather than the extension of the dynamic range of response.
Wed Sep 22: S. Fred Singer, chairman of the Science and Environmental Policy Project; professor emeritus at the University of Virginia; founding director of the U.S. Weather Satellite ServiceThe Super-Rotation of the Earth's Core: How the Moon maintains life on EarthHost: J. BreslowThe hypothesis put forward identifies lunar tidal forcing as the cause of the observed super-rotation and thereby as the agent maintaining the geomagnetic field. In turn, the existence of a magnetosphere has protected the earth's atmosphere and oceans from erosion by the solar wind. While this chain of events may appear speculative, it does not violate any physical laws and also helps to explain many puzzling features of the terrestrial planets; for example, planetary magnetic fields; the origin of the Martian moons Phobos and Deimos; the origin of the Moon.Towards the Next Generation of Advanced BioMaterials and Stem Cell Based TherapeuticsHost: N. ArkusThis talk will explore platform technologies that are currently being developed in the KarpLab to tackle some of the most challenging medical problems. Namely, sealing tissues/closing wounds, enhancing engraftment of exogenously delivered stem cells, achieving long term local drug delivery for treatment of diseases such as rheumatoid arthritis and glioblastoma, development of surfaces to separate cells for disposable point of care diagnostics and for cell therapy, and needles that sense different levels of tissue for the delivery of cells and drugs.Optogenetic monitoring and control of electrical spikes in E. coliHost: N. ArkusTo probe neural function, one would like to monitor the simultaneous electrical activity in a large number of neurons, with high resolution in space and time. Genetically encoded optical indicators of membrane potential are a promising approach to this challenge. But thus far these molecules have lacked adequate sensitivity and speed. We developed a voltage indicator based on a mutant of green proteorhodopsin. In the wild, bacteria use this light-driven proton pump to convert sunlight into electrochemical energy. We engineered the protein to run backward: to convert changes in membrane potential into a measureable optical signal. Bacteria expressing this protein show periodic flashes of fluorescence, indicating spontaneous electrical spiking. I will discuss possible mechanisms and biological significance for this spiking behavior.
Oct 12: Matthew Rockman, NYUPopulation-genomic causes of heritable phenotypic variationHost: E. Siggia & N. ArkusMutation generates heritable variation while genetic drift and selection erode and transform it. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, while mutation and selection act trait-specifically to shape standing variation. We find that although trait-specific mutation and selection explain some of the pattern of heritable phenotypic variation among transcript abundance traits in the nematode C. elegans, most of the pattern is explained by trait-independent variation in the intensity of selection on linked sites. The effects of linked selection have long been recognized in molecular population genetics, but they are absent from models of phenotypic variation. We show that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of the effective population sizes of the genomic regions harboring their underlying loci.
Thur Oct 14: Erik van Nimwegen, University of BaselMacroscopic Laws in Prokaryotic Evolution and Regulatory Network StructureHost: E. SiggiaTheory of Motor Proteins that Promote Filament ShorteningVisiting Scientist at the Center for Studies in Physics and Biology
Oct 26: Herve Isambert, Institute CurieEvolutionary Constraints from Whole Genome DuplicationHost: E. SiggiaLinking Music and CognitionHost: E. SiggiaThe talk presents research showing that music and cognition have strong links at many levels. An example of a link at a deep level is the empirical support found for deeply-theorized properties of music such as a recent theory of musical tension. Confirmation of this theory demonstrates that the cognitive representation of musical structure includes hierarchical trees similar to those proposed for language. At a somewhat higher level, sensitivity to statistically frequent patterns in the sounded events enables listeners to abstract a tonal framework for encoding and remembering music. A machine-learning algorithm will be presented that uses statistical analyses to distill melodic structure. The application tests the importance of tone durations for identifying musically interpretable patterns. Finally, research on music recognition suggests a great deal of surface information is encoded in memory. Very short excerpts of popular music can be identified with artist, title, and release date. Even when an excerpt is not identified, emotion and style judgments are consistent. These results point to a long-term memory for music with large capacity and fine detail as well as schematic knowledge of style and emotional content.Optical techniques for light based electrophysiology and neural activity perturbation in the nematode C.elegansHost: N. Arkus
Nov 16: Jack Szostak, Harvard UniversityThe Origin of Cellular lifeHost: N. ArkusThe complexity of modern biological life has long made it difficult to understand how life could emerge spontaneously from the chemistry of the early earth. The key to resolving this mystery lies in the simplicity of the earliest living cells. Through our efforts to synthesize extremely simple artificial cells, we hope to discover plausible pathways for the transition from chemical evolution to Darwinian evolution. We view the two key components of a primitive cell as a self-replicating nucleic acid genome, and a self-replicating boundary structure. I will describe our recent finding of a simple and robust pathway for the coupled growth and division of a model primitive cell membrane. I will also discuss recent experimental progress towards the synthesis of self-replicating nucleic acids, and the implications of these experiments for our understanding of the origin of life.How the mammalian ear performs frequency tuning: theory and experimentHost: T. Reichenbach & J. Hudspeth
Fri Dec 3 Caspary Lecture: Stephen Quake, Stanford UniversitySequencing Single Cells and Single MoleculesHost: E. Siggia
Dec 14: Terry Hwa, U.C. San DiegoOn Growth Laws, Drug Resistance, and EvolutionHost: E. Siggia
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