Previous Talks: 2024
Jan 2024
10
Wed 12:15
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Jack Szostak,
Host: Arvind Murugan
Organizer: Daniel Seara
RNA dynamics: from picoseconds to days
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In trying to understand how RNA might catalyze its own replication, we must confront RNA motions on time scales ranging from picoseconds to days. For example, MD simulations reveal rapid shifts between preferred conformations. Metal ion binding can slow these fluctuations by stabilizing a particular conformation. This stabilized conformation can direct copying chemistry on a scale of minutes. The primer-template complexes required for copying chemistry can form and dissociate in seconds to days depending on the number of interacting species. I will describe our efforts to study these diverse phenomena as we attempt to build up an integrated picture of nonenzymatic RNA copying and replication during the origin of life.
Jan 2024
17
Wed 12:15
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Neil Shubin,
Host: Arvind Murugan
Organizer: Martin Falk
Fossils, Embryos and Genes: The Origin of Novelty in Evolution
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New fossil discoveries, coupled with the analyses of genome structure and function during appendage development, reveal the ways in which novelties arise in evolution. Here we will investigate how tetrapod locomotion originally arose within a fish body plan. A regionalized axial skeleton, enhanced pelvic appendages, and appendages with the three major segments of tetrapod limbs are first seen in the lobe finned fish that are most closely related to tetrapods. Genomic analyses on extant fish reveal the deep conservation of regulatory architecture and gene functions involved with the patterning of both fins and limbs. Because these genomic and functional similarities underlie the development of both paired and unpaired appendages they also provide insights into the origin of appendages in vertebrates.
Jan 2024
24
Wed 12:15
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Mark W. Westneat,
Host: Stephanie Palmer
Organizer: Carlos Floyd
Phylogenetics and Biomechanics of Coral Reef Fishes
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Coral reef fishes have developed a wide range of intriguing structural and functional novelties during a hundred million years of evolution. We will explore genetic and computational approaches to resolving the fish tree of life, and visualize the branching network of relationships among species in several diverse fish families. In addition we will explore the engineering linkage design of highly kinetic jaw mechanisms, the evolution of propulsor shape and material properties in fish swimming mechanisms, and the unusual sediment burrowing behaviors of diverse reef fish groups.
Jan 2024
31
Wed 12:15
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Robert Rosner,
Host: William Irvine
Organizer: Martin Falk
A Physicist’s Look at Removing CO2 from the Atmosphere
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The APS Panel on Public Affairs (POPA) decided last year to look into the issues faced by the potential need to remove CO2 from our atmosphere, as suggested by the latest IPCC report on climate change. I have been part of the collaboration working on this project, and our report is currently under review. My talk will focus on the main issues we’ve identified and - unlike the report, which studiously avoids policy opinions and recommendations - I will comment on the policy issues that flow from this investigation.
Feb 2024
7
Wed 12:15
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Nachi Stern,
Host: Arvind Murugan
Organizer: Carlos Floyd
Learning in physical machines
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From electrically responsive neuronal networks to the adaptive immune response, biological systems can learn to perform complex tasks. In this seminar, we explore physical learning, a framework inspired by computational learning theory and biological systems, where networks physically adapt to applied forces to adopt desired functions. Unlike traditional engineering approaches, physical learning is facilitated by physically realizable learning rules, requiring only local responses and no explicit information about the desired functionality. Our research shows that such local learning rules can be derived for broad classes of physical networks, and that physical learning is indeed physically realizable through laboratory experiments. By leveraging the advances of statistical learning theory in physical machines, we propose autonomous physical learning as a promising bridge between computational machine learning and biology, with the potential to enable the development of new classes of smart metamaterials that adapt in-situ to users’ needs.
Feb 2024
14
Wed 12:15
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Miles Stoudenmire,
Host: Peter Littlewood
Organizer: Martin Falk
Harnessing Quantum Functions for Classical Computing
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Quantum algorithms are prized for their potential to outpace classical computing, but since quantum algorithms first started to be developed 25 years ago, classical algorithms closely mimicking quantum computers have been developed based on tensor networks. The analogy is so precise that tasks originally conceived for quantum computers, such as performing Fourier transforms of low-dimensional functions, can be carried out entirely on classical computers in many cases. Remarkably, these algorithms can be better than any previous classical algorithm for certain tasks. I will give an overview of algorithms based on quantum-inspired encodings of functions and argue that they are already useful for tackling diverse problems while using a single unified framework.
Feb 2024
21
Wed 12:15
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Steve Granick,
Host: William Irvine
Organizer: Carlos Floyd
Fun, Profit and the Meaning of Life as an Experimentalist
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One of the pleasures of an experimentalist is the chance to try to understand how molecules think, giving nature the opportunity to open new questions though we may begin by trying to answer older ones. My lab’s experience is that experiments don’t always confirm theoretical expectations. I will give examples.
Feb 2024
28
Wed 12:15
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Herbert Levine,
Host: Stephanie Palmer
Organizer: Martin Falk
Physics can help make sense of immune system dynamics
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Understanding the dynamics of the immune system has been gaining increasing importance, as a consequence of progress in immunotherapy applied to cancer and due to the importance of vaccines re the COVID-19 pandemic. This talk will survey examples which show physics can help address some of the important conceptual and also practical issues that arise in this research area, specifically focusing on issues related to cancer. Specific topics to be discussed includes the detection of neoantigens as a way to target tumor cells, the spatiotemporal dynamics of immune cell infiltration into tumors, the ecology of the immune microenvironment and the role of evasion by cancer cells.
Mar 2024
13
Wed 12:15
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Damien Vandembroucq,
Host: Tom Witten
Organizer: Daniel Seara
Plasticity and memory effects in amorphous solids
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Due to their out-of-equilibrium nature, materials such as amorphous solids, glasses or dense suspensions exhibit a history-dependent mechanical behavior. Thermal and mechanical annealing drastically affect the modes of deformation and failure. In recent years experiments and numerical simulations of disordered materials under cyclic loading have unveiled puzzling properties such as the convergence to reversible plastic cycles or the possibility to record and read a past state of deformation. We discuss recent results about such memory effects obtained in atomistic simulations and in lattice-based elastoplastic models of amorphous solids.
Mar 2024
20
Wed 12:15
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Gavin E. Crooks,
Host: Arvind Murugan
Organizer: Carlos Floyd
Thermodynamic Linear Algebra
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Linear algebraic primitives are at the core of many modern algorithms in engineering, science, and machine learning. Hence, accelerating these primitives with novel computing hardware would have tremendous economic impact. I'll discuss how a variety of linear algebra problems can be solved by sampling from the thermodynamic equilibrium distribution of a collection of coupled harmonic oscillators.
Mar 2024
27
Wed 12:15
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Manu Prakash,
Host: Arvind Murugan
Organizer: Daniel Seara
TBA
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Apr 2024
3
Wed 12:15
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Peter Chung,
Host: Arvind Murugan
Organizer: Martin Falk
An engineered platform for high-throughput characterization of peptide binding to membranes
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A common motif amongst peripheral membrane-binding proteins is a disordered polypeptide domain that can be induced into an amphipathic helix (whereby polar and hydrophobic residues segregate to opposing helix surfaces) with a cognate membrane, thereby controlling protein subcellular localization. However, these peptides are often difficult to characterize in isolate, as they are prone to aggregation and methods to measure binding are low throughput. Herein, we present an engineered platform to enable high-throughput characterization of peptide binding to membranes via fluorescence anisotropy that has been cross-validated with corresponding tryptophan fluorescence measurements. These results represent the first steps in a highly scalable program to not only understand the ability of peptides to detect membrane composition but synthesize novel motifs for subcellular localization of therapeutics.
Apr 2024
10
Wed 12:15
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OPEN
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Apr 2024
17
Wed 12:15
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Peter Bolhuis,
Host: Aaron Dinner
Organizer: Martin Falk
Activating self-assembled patchy particle architectures
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Patchy particles have become a standard model in soft matter physics to investigate complex molecular behavior, from proteins to large colloidal systems. Synthetic colloidal particles with specific directional interactions can act as a playground to deeper understand their molecular counterparts (such as proteins and smaller molecules), but also open up avenues in the design of novel materials, and even mimic active, living matter. A particularly sensitive way of experimentally controlling the attraction between the patches is by critical Casimir interactions, which allows colloids to assemble into various superstructures, such as chains and networks. To understand and explore the behavior of these Casimir systems, we developed a quantitatively accurate potential model. Using these optimized potentials in large-scale simulations we can predict the phase behavior of mixtures of patchy particles, understand the relaxation behavior of colloidal molecules, and explain the experimentally observed anomalous excess of monomers. Next, we take the system out of equilibrium by including self-propelled active particles, causing rings and chains in the network to undergo breakage and rearrangement. Experiments and simulation show that even a low activity already induces dramatic changes into the dynamical behaviour of these colloidal networks. Such activated viscoelastic architectures can possibly act as model for understanding the behavior of living matter.
Apr 2024
24
Wed 12:15
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Luís A. N. Amaral,
Host: Arvind Murugan
Organizer: Carlos Floyd
Science and the Scientific Enterprise: The good, the bad and the ugly
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My lab pursues research directions that provide insight into the emergence, evolution, and stability of complex social and biological systems. In the past, we addressed questions concerning the structure of food webs, whether there are personality types, why some human genes are ignored by scientists, or how to help clinicians avoid errors of omission. Some of those research questions were prompted by their intrinsic value (the good), others because perhaps no one else would pursue them (the bad), and others because we felt the obligation to do so (the ugly). In this talk, I hope to cover three unpublished stories that illustrate those types of choices and the methods we use in our research. The first story asks whether electronic medical records contain information enabling the discovery of clinical states of critical care patients. The second story ask whether we have developed appropriate and reproducible methods for the analysis of CHIP-seq data that prevent cherry picking. The third story investigates the extraordinary increase in the amount of fraudulent publications and whether they pose a serious risk to the scientific enterprise.
May 2024
1
Wed 12:15
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Gautam Reddy,
Host: Arvind Murugan
Organizer: Daniel Seara
Towards a physics of animal learning and decision-making
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Living systems sense their physical environment and process this information to interact back with the environment. Physics plays a key role in this sensorimotor loop by imposing constraints on all of its basic elements, and long-standing efforts in biological physics have proved fruitful in highlighting these physical constraints across organismal scales. An enduring challenge is to explain the diversity of behaviors we observe in nature, which are generated by deceptively simple "learning rules": for e.g., natural selection and associative learning. I will present recent work on rodent navigation that shows how physics-inspired approaches can help explain emergent phenomena in biological learning.
May 2024
8
Wed 12:15
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S. Furkan Ozturk,
Host: Arvind Murugan
Organizer: Carlos Floyd
A New Spin on the Origin of Biological Homochirality
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Essential molecules of life—amino acids, nucleic acids, and sugars—are chiral; they exist in mirror-symmetrical pairs. However, biological systems exclusively use only one form of these pairs: right-handed sugars and nucleic acids, along with left-handed amino acids. This phenomenon characterizes life as homochiral. However, the origins of this asymmetry remain elusive, and it is this long-standing mystery that we address in our work. The chiral-induced spin selectivity (CISS) effect has established a strong coupling between electron spin and molecular chirality, and this coupling paves the way for breaking the chiral molecular symmetry by spin-selective processes. Achiral magnetic surfaces, when spin-polarized, can function as chiral agents due to the CISS effect, serving as templates for the asymmetric crystallization of chiral molecules. We studied the spin-selective crystallization of racemic ribo-aminooxazoline (RAO), a central precursor of RNA, on magnetite surfaces—achieving homochirality in two crystallization steps [1]. Moreover, we have shown the chirality-induced avalanche magnetization of magnetite by RAO molecules, which verifies the reciprocal nature of the effect and allows for a cooperative feedback between chiral molecules and magnetic surfaces [2]. Finally, based on empirical evidence, we propose a pathway through which the achieved homochirality in a single chiral compound, RAO, can efficiently propagate throughout the entire prebiotic network, starting from D-nucleic acids, to L-peptides, and then to homochiral metabolites [3]. Our results demonstrate a prebiotically plausible way of achieving systems-level homochirality from completely racemic starting materials.
References:
[1] S. F. Ozturk, Z. Liu, J. D. Sutherland, D. D. Sasselov, Science Advances 2023, 9, eadg8274.
[2] S. F. Ozturk, D. K. Bhowmick, Y. Kapon, Y. Sang, A. Kumar, Y. Paltiel, R. Naaman, D. D. Sasselov, Nature Communications 2023, 14, 6351.
[3] S. F. Ozturk, D. D. Sasselov, J. D. Sutherland, The Journal of Chemical Physics 2023, 159, 061102.
May 2024
15
Wed 12:15
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Stanislav Y. Shvartsman,
Host: Neil Shubin
Organizer: Martin Falk
Towards quantitative biology of developmental abnormalities
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Developmental disorders are severely understudied, in spite of their alarmingly high incidence, with 1 in 6 U.S. children having one or more disabilities or developmental delays. The main challenge is the design of statistically powered studies that can disentangle numerous genetic and environmental factors. We have been working towards addressing this challenge for the developmental abnormalities associated with the germline mutations within the ERK cascade. Focusing on mutations that affect MEK, a kinase that activates ERK, we demonstrated how studies of human mutations in Drosophila can answer the long-standing questions in the field. Specifically, we established how pathogenic mutations affect an isolated MEK protein, demonstrated how they disrupt the normal process of MEK activation in the cell, and quantified their effects on ERK signaling in embryos. More recently, our work shed light on the origins of phenotypic variability in the ERK-associated developmental disorders, demonstrating that they can be of purely stochastic origin. Given the generality of our approach, it should be applicable to other developmental abnormalities associated with genetically deregulated cell signaling.