Computations in Science Seminars

Previous Talks: 2024

Jan 2024
10
Wed 12:15
Jack Szostak, University of Chicago
Host: Arvind Murugan ()
Organizer: Daniel Seara ()
RNA dynamics: from picoseconds to days

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
Neil Shubin, University of Chicago
Host: Arvind Murugan ()
Organizer: Martin Falk ()
Fossils, Embryos and Genes: The Origin of Novelty in Evolution

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
Mark W. Westneat, University of Chicago
Host: Stephanie Palmer ()
Organizer: Carlos Floyd ()
Phylogenetics and Biomechanics of Coral Reef Fishes

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
Robert Rosner, University of Chicago
Host: William Irvine ()
Organizer: Martin Falk ()
A Physicist’s Look at Removing CO2 from the Atmosphere

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
Nachi Stern, University of Pennsylvania
Host: Arvind Murugan ()
Organizer: Carlos Floyd ()
Learning in physical machines

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
Miles Stoudenmire, Flatiron Institute
Host: Peter Littlewood ()
Organizer: Martin Falk ()
Harnessing Quantum Functions for Classical Computing

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
Steve Granick, University of Massachusetts Amherst
Host: William Irvine ()
Organizer: Carlos Floyd ()
Fun, Profit and the Meaning of Life as an Experimentalist

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
Herbert Levine, Northeastern University
Host: Stephanie Palmer ()
Organizer: Martin Falk ()
Physics can help make sense of immune system dynamics

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
Damien Vandembroucq, ESPCI ParisTech
Host: Tom Witten ()
Organizer: Daniel Seara ()
Plasticity and memory effects in amorphous solids

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
Gavin E. Crooks, Normal Computing
Host: Arvind Murugan ()
Organizer: Carlos Floyd ()
Thermodynamic Linear Algebra

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
Manu Prakash, Stanford University
Host: Arvind Murugan ()
Organizer: Daniel Seara ()
TBA
Apr 2024
3
Wed 12:15
Peter Chung, University of Southern California
Host: Arvind Murugan ()
Organizer: Martin Falk ()
An engineered platform for high-throughput characterization of peptide binding to membranes

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
OPEN