Happening @ Michigan https://events.umich.edu/list/rss RSS Feed for Happening @ Michigan Events at the University of Michigan. Data Science, Time Complexity, and Spacekime Analytics (September 11, 2020 12:00pm) https://events.umich.edu/event/76500 76500-19719162@events.umich.edu Event Begins: Friday, September 11, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

Digital information flows impact all human experiences. The proliferation of large, heterogeneous, and spatio-temporal data requires novel approaches for managing, modeling, analyzing, interpreting, and visualizing complex information. The scientific community is developing, validating, productizing, and supporting novel mathematical techniques, advanced statistical computing algorithms, transdisciplinary tools, and effective artificial intelligence apps.

Spacekime analytics is a new technique for modeling high-dimensional longitudinal data. This approach relies on extending the notions of time, events, particles, and wavefunctions to complex-time (kime), complex-events (kevents), data, and inference-functions. We will illustrate how the kime-magnitude (longitudinal time order) and kime-direction (phase) affect the subsequent predictive analytics and the induced scientific inference. The mathematical foundation of spacekime calculus reveals interesting statistical implications including inferential uncertainty and a Bayesian formulation of spacekime analytics. Complexifying time allows the lifting of all commonly observed processes (e.g., time-series) from the classical 4D Minkowski spacetime to a 5D spacekime manifold (e.g., kime-surfaces), where a number of mathematical problems remain to be solved.

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Livestream / Virtual Tue, 01 Sep 2020 14:53:10 -0400 2020-09-11T12:00:00-04:00 2020-09-11T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Ivo D. Dinov
Biophysics Virtual Seminar Series (September 18, 2020 12:00pm) https://events.umich.edu/event/76959 76959-19780559@events.umich.edu Event Begins: Friday, September 18, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

*Please see below for the link to join the Zoom livestream*

The Biophysics Virtual Seminar Series Presents:

Zhenyu Tan - Biophysics Ph.D. Candidate (Cianfrocco Group)

The mitochondrial cargo adaptor TRAK1 has overlapping binding sites for kinesin-1 and dynein

Abstract: Positioning of axonal mitochondria into target locations is critical for the physiology of neurons as they supply energy and calcium buffering capacity. The outer mitochondrial membrane protein Miro cooperates with TRAK1 and TRAK2 to scaffold kinesin and dynein, driving anterograde and retrograde mitochondrial transport. To understand how TRAK1 regulates both kinesin and dynein, we utilized biochemical reconstitution to define the minimal region of TRAK1 sufficient for promoting motor activation. We characterized that TRAK1 has overlapping binding sites for kinesin-1 and dynein that is capable of activating both motors *in vitro*.

Thomas Paul - Postdoctoral Researcher (Brooks Group)

pH Dependent Dissociation of Folate from Folic Acid Receptors

Abstract: The pH dependent binding and release of folate from folic acid receptors (FRs) is not well understood. Therefore, we have studied pKa shifts for two isoforms of FRs (FOLR1 and FOLR2) in their apo and holo forms using explicit solvent constant pH molecular dynamics (CPHMD^MSλD). Our key findings highlight amino acid residues that have upward pKa shifts that contribute significantly to destabilizing the FRs:folate complex at pH values consistent with an endosomal environment which allows us to propose a potential mechanism of release.

Zoom passcode: 677763

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Livestream / Virtual Wed, 16 Sep 2020 10:45:33 -0400 2020-09-18T12:00:00-04:00 2020-09-18T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Zhenyu Tan, PhD Candidate and Thomas Paul, Researcher
Biophysics Virtual Seminar Series (October 2, 2020 12:00pm) https://events.umich.edu/event/77871 77871-19939555@events.umich.edu Event Begins: Friday, October 2, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

*Please see below for link to join the Zoom event. Passcode: Biophysics*

The Biophysics Virtual Seminar Series Presents:

Nirupama Sumangala - Biophysics Ph.D. Candidate (Ramamoorthy Group)

"Lipid Membrane Plays an Important Role for Facilitating Electron Transfer in Cytochrome P450"

Abstract: Cytochrome P450s (CYP450s) are a ubiquitous superfamily of enzymes that play a vital role in the metabolism of many exogenous and endogenous substrates including over 70% of the drugs on the market. For the catalytic reaction, CYP450 requires two electrons to be subsequently delivered, with the first one coming from cytochrome P450 reductase (CPR) and the second one from either CPR or cytochrome b5 (cytb5). We are interested in understanding the role of membrane in mediating the electron transfer from redox partners to CYP450. Our findings reveal that the lipid membrane is crucial to mediate a productive CYP450-CPR complex for electron transfer. Our data emphasizes the importance of studying the structure, dynamics and kinetics of CYP450 metabolon in a biologically relevant membrane mimetic system.

Keanu Guardiola Flores - Biophysics Ph.D. Candidate (Wood Group)

"Drug Effects on *Enterococcus Faecalis* Biofilms: Growth, Topology, and Population Dynamics"

Abstract: The emergence of antibiotic resistance poses a growing threat to public health and increasingly limits our ability to treat and control infections. Recently, researchers have shifted their focus to length scales where ecological and evolutionary dynamics of bacterial communities highlight new approaches for slowing resistance with currently available drugs. By combining confocal microscopy with simple mathematical models I will show how antibiotics shape the composition of biofilms as well as their spatial architecture at the single-cell level. Our results suggest that in spatially structured populations, which may more accurately reflect natural bacterial communities, the selection of resistance is not a simple result of homogenous selections but depends critically on the spatial arrangement of cells.

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Livestream / Virtual Tue, 29 Sep 2020 08:47:28 -0400 2020-10-02T12:00:00-04:00 2020-10-02T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual
Biophysics Virtual Seminar Series (October 9, 2020 12:00pm) https://events.umich.edu/event/76961 76961-19782523@events.umich.edu Event Begins: Friday, October 9, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

*Please see below for the link to join the Zoom livestream*

The Biophysics Virtual Seminar Series Presents:

Hong Qian - Olga Jung Wan Endowed Professor of Applied Mathematics, Department of Applied Mathematics, University of Washington

“A Mathematical Principle of Stochastic Chemical Kinetics and
Emergent Chemical Thermodynamics that Applies to Living Cells”

Abstract: In contrast to featureless point masses in Mechanics, a macromolecule in biochemistry has a large number of internal degrees of freedom in terms of atoms. The behavior of even a single protein in an aqueous environment, is often so complex that the mathematical representation of biochemical kinetics has to be statistical. In this talk, I present a stochastic formulation of general chemical reaction systems, with *N* species and *M* stochastic elementary reactions in solution and show how J. W. Gibbs’ macroscopic equilibrium chemical thermodynamics can be derived as a mathematical result, with an entropic force as its center piece. Our theory is actually applicable to mesoscopic open chemical systems with a chemostat, such as a single living cell. I then discuss the application of this theory to understand the notion of non-genetic phenotype switching, in terms of a landscape, in cell differentiation and cancer heterogeneity.

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Livestream / Virtual Fri, 09 Oct 2020 10:27:08 -0400 2020-10-09T12:00:00-04:00 2020-10-09T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Zoom Passcode: Biophysics
Biophysics Seminar Series (October 16, 2020 12:00pm) https://events.umich.edu/event/77916 77916-19941582@events.umich.edu Event Begins: Friday, October 16, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

*Please see below for the link to join the Zoom event.*

The Biophysics Virtual Seminar Series presents:

Dr. Jamie Cate - Professor of Molecular & Cell Biology, and Chemistry,
University of California - Berkeley

“Selective modulation of human translation: potential for new therapeutics”

ABSTRACT: Small molecules that target the ribosome such as antibiotics generally impact a substantial fraction of the proteome. We recently identified a class of small molecules that bind the human ribosome and selectively stall the translation of a small subset of proteins. I will present biochemical and cell-based experiments, along with structures of human ribosome nascent chain complexes (RNCs) stalled by these compounds, determined by cryo-electron microscopy (cryo-EM). These small molecules bind in the ribosome exit tunnel in a eukaryotic-specific pocket formed by the 28S ribosomal RNA (rRNA) and arrest the translating ribosome through their interactions with the growing polypeptide chain. Intriguingly, a given compound can either inhibit or enhance translation, depending on the sequence of the protein nascent chain. These results begin to reveal how small molecules can be made to control human translation and suggest a new strategy for developing small molecules that selectively inhibit or enhance the production of proteins previously considered “undruggable.”

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Livestream / Virtual Thu, 08 Oct 2020 12:47:14 -0400 2020-10-16T12:00:00-04:00 2020-10-16T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Jamie Cate
Biophysics Seminar Series (October 23, 2020 12:00pm) https://events.umich.edu/event/77918 77918-19941583@events.umich.edu Event Begins: Friday, October 23, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

*Please see below for the link to join the Zoom event.*

The Biophysics Virtual Seminar Series presents:

Dr. Sandra Schmid - Chief Scientific Officer, Chan Zuckerberg Biohub

“Dynamin: A catalyst for fission, collaboration and controversy”

ABSTRACT: Kazuo Ikeda’s beautiful electron micrographs of neuromuscular junctions of Drosophila *shibire* mutants revealed the presence of collar-like structures around the necks of trapped endocytic intermediates. They inspired my 30 year-long obsession with dynamin, the mammalian homologue of *shibire.* Our subsequent studies of dynamin, which began in the early 90s provide benefitted from the development of new technologies and from interdisciplinary collaboration. I’ll describe the twists and turns of our efforts to understand the mechanisms underlying dynamin-catalyzed fission, the value of interdisciplinary collaborations, and the importance of taking all data into account when formulating models. I’ll detail our current understanding of dynamin-catalyzed fission, now supported by independent studies of others, and briefly describe the many remaining unanswered questions, keeping in mind (in the words of George Box) that, *“All models are wrong, but some are useful."*

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Livestream / Virtual Mon, 19 Oct 2020 15:12:59 -0400 2020-10-23T12:00:00-04:00 2020-10-23T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Sandra Schmid
Biophysics Seminar Series (October 30, 2020 12:00pm) https://events.umich.edu/event/77919 77919-19941584@events.umich.edu Event Begins: Friday, October 30, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

Join us on Zoom: https://umich.zoom.us/j/91037518250

The Biophysics Virtual Seminar Series presents:

Dr. Ido Golding - Professor of Physics, School of Molecular & Cellular Biology, University of Illinois Urbana-Champaign

"Illuminating bacterial individuality"

ABSTRACT: Single-cell measurements of mRNA copy numbers inform our understanding of stochastic gene expression, but these measurements coarse-grain over the individual copies of the gene, where transcription and its regulation take place stochastically. We recently combined single-molecule quantification of mRNA and gene loci to measure the transcriptional activity of an endogenous gene in
individual Escherichia coli bacteria. When interpreted using a theoretical model for mRNA dynamics, the single-cell data allowed us to obtain the probabilistic rates of promoter switching, transcription initiation and elongation, mRNA release and degradation. Unexpectedly, we found that gene activity can be strongly coupled to the transcriptional state of another copy of the same gene present in the cell, and to the event of gene replication during the bacterial cell cycle. These gene-copy and cell-cycle correlations demonstrate the limits of mapping whole-cell mRNA numbers to the underlying stochastic gene activity and highlight the contribution of previously hidden variables to the observed population heterogeneity.

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Livestream / Virtual Mon, 26 Oct 2020 09:26:15 -0400 2020-10-30T12:00:00-04:00 2020-10-30T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Ido Golding
Biophysics Seminar Series (November 6, 2020 12:00pm) https://events.umich.edu/event/77920 77920-19941585@events.umich.edu Event Begins: Friday, November 6, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Virtual Seminar Series presents:

Dr. Nozomi Ando - Assistant Professor of Chemistry & Chemical Biology, Cornell University

*"Protein Allostery: Evolution and Correlated Motions"*

Join us on Zoom: https://umich.zoom.us/j/99976448506

ABSTRACT: Understanding the relationship between protein sequence, structure, dynamics, and function is the ultimate goal of structural biology. For this reason, my lab studies protein allostery - a special property of macromolecules that connects molecular motion and action. In this talk, I'll present two stories. First, I'll talk about how the evolution of allosteric mechanisms and the tools of structural biology can teach us about the relationship between protein sequence and function. In the second story, I'll talk about how one can learn about correlated motions that give rise to allostery.

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Livestream / Virtual Mon, 02 Nov 2020 09:56:44 -0500 2020-11-06T12:00:00-05:00 2020-11-06T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Nozomi Ando
Biophysics Seminar Series (November 13, 2020 12:00pm) https://events.umich.edu/event/77921 77921-19941586@events.umich.edu Event Begins: Friday, November 13, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Virtual Seminar Series presents:

Dr. Nancy Forde - Department of Physics, Simon Fraser University

*“Collagen: a fascinating responsive material building block from Nature”*

Join us on Zoom: https://umich.zoom.us/j/96009492561

Abstract: Multicellular life is scaffolded by structures that maintain cells in the desired locations and organizations. Conventionally these extracellular scaffolds have been viewed as rigid, unchanging supports laid down during development and unaltered except by injury or disease. Recent scientific advances are revealing instead that these matrices are highly dynamic and respond to changes in their local microenvironment, in turn affecting cells. The collagen family of proteins has been selected via evolution as the preferred building block of these extracellular structures.

In this talk, I will introduce some of the fascinating physical properties of the unique triple-helix structure of collagen, and will highlight the results of our investigations into its mechanical properties. Our single-molecule approaches include centrifuge force microscopy, optical tweezers and atomic force microscopy, and many parallels can be drawn with the mechanics of DNA. Our work is revealing clues as to how stability is encoded within collagen’s sequence, and how collagen’s triple helix balances structural stability with responsiveness to applied force and chemical environment.

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Livestream / Virtual Wed, 04 Nov 2020 11:44:26 -0500 2020-11-13T12:00:00-05:00 2020-11-13T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Nancy Forde
Biophysics Seminar Series (November 20, 2020 12:00pm) https://events.umich.edu/event/77922 77922-20319908@events.umich.edu Event Begins: Friday, November 20, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Virtual Seminar Series presents:

Dr. Gabriele Varani - Department of Chemistry, University of Washington

*"Small drug-like molecules targeting RNA with nanomolar affinity and cellular activityon"*

Join us on Zoom: https://umich.zoom.us/j/99793210061

ABSTRACT: The ever expanding appreciation of the role of RNA in healthy and disease cellular states has created ever increasing opportunities to redress human disease by targeting RNA with small molecules. However, the chemistry of small molecules targeting RNA remains a challenge. The academic literature has been littered since the mid-1990s with reports of small molecules binding to RNA that, in most cases, did not have the pharmaceutical properties of successful drug candidates and did not bind to RNA potently nor specifically. Screening protein-directed chemical libraries allows the discovery of drug-like molecules that bind to RNA, but success rates are low, typically 1/10,000, and affinity typically in the low to mid-uM range. We have discovered RNA-binding small molecules that obey Lipinski and RO5 rules and bind to RNA potently (low to mid nM) and specifically (discriminate single nucleotide changes). These molecules target RNAs considered 'undruggable' with low nM affinity. Their size (<400 Da), absence of charge, and in vitro pharmacological properties (ADME and in vitro pharmacology) are those of favorable drug candidates. We will illustrate two examples of the application of this chemistry by reporting 10 nM ligands for HIV TAR and 100 nM ligands for pre-miR-21 with specific biochemical and cellular activity against this potent oncogene.

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Livestream / Virtual Mon, 16 Nov 2020 13:13:38 -0500 2020-11-20T12:00:00-05:00 2020-11-20T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Gabriele Varani
Biophysics Seminar Series (December 4, 2020 12:00pm) https://events.umich.edu/event/77923 77923-19941588@events.umich.edu Event Begins: Friday, December 4, 2020 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Virtual Seminar Series presents:

Dr. Oleg Igoshin - Professor of Bioengineering & BioSciences, Associate Chair of Bioengineering, Rice University

*“Understanding Trade-offs in Biological Error Correction”*

Join us on Zoom: https://umich.zoom.us/j/96475935279

Abstract: High accuracy of major biological processes relies on the ability of the participating enzymatic molecules to preferentially select the correct substrate from a pool of chemically similar substrates by activating the so-called proofreading mechanisms. While the importance of such mechanisms is widely accepted, it is still unclear how evolution has optimized the biological systems with respect to their characteristic properties. We developed a comprehensive first-passage theoretical framework that allowed us to quantitatively investigate the trade-offs between four properties of enzymatic systems namely, error, speed, noise and energy dissipation. Within this framework, we simultaneously analyzed speed and accuracy of several fundamental biological processes, including DNA replication, tRNA charging, and tRNA selection during the translation. The results indicate that contrary to typical assumptions speed-accuracy trade-off is not always observed. However, when the trade-off is present, the biological systems tend to optimize the speed rather than the accuracy of the processes, as long as the error level is tolerable. When systems function in the regime where no speed-accuracy trade-off is observed, constraints due to energy dissipation in the proofreading play a key role. Our theory demonstrates a universal Pareto front in error-dissipation trade-off and shows how naturally selected kinetic parameters position their system close to this boundary. Our findings, therefore, provide a new system-level picture of how complex biological processes are able to function so fast with a high accuracy and low dissipation.

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Livestream / Virtual Tue, 01 Dec 2020 08:40:21 -0500 2020-12-04T12:00:00-05:00 2020-12-04T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Igoshin
Complex Systems Presents: A Nobel Symposium (December 10, 2020 1:10pm) https://events.umich.edu/event/79125 79125-20209862@events.umich.edu Event Begins: Thursday, December 10, 2020 1:10pm
Location: Off Campus Location
Organized By: The Center for the Study of Complex Systems

VIRTUAL SYMPOSIUM LINK: myumi.ch/v2ZYv

Registration not required. Free and open to the public. This virtual event features UM faculty experts in each of the six prize fields. Each will present for 25 minutes and take questions for 10 minutes

1:10 - 1:15 Welcome remarks Charlie Doering CSCS Director

1:15 - 1:50 CHEMISTRY | Nils Walter Chemistry, Biophysics and Biological Chemistry LSA and Medical School

1:50 - 2:25 MEDICINE OR PHYSIOLOGY | Katherine Spindler Microbiology and Immunology Medical School

2:25 - 3:00 PHYSICS | Lydia Bieri Mathematics and Doug Richstone  Astronomy LSA

3:00 - 3:35 ECONOMICS | Tilman Börgers Economics

3:35 - 4:10 LITERATURE | Linda Gregerson Literature LSA

4:10 - 4:45 PEACE | Susan Waltz Public Policy, Gerald R Ford School of Public Policy

Information about the 2020 prizes and our speakers:

*Chemistry:*
The Nobel Prize in Chemistry 2020 was awarded jointly to Emmanuelle Charpentier and Jennifer A. Doudna "for the development of a method for genome editing."

Speaker: *Nils Walter*, Francis S Collins Collegiate Professor of Chemistry, Biophysics and Biological Chemistry – College of Literature, Science, and the Arts and Medical School

*Physiology or Medicine:*
The 2020 Nobel Prize in Physiology or Medicine is awarded jointly to *Harvey J. Alter, Michael Houghton* and *Charles M. Rice* “for the discovery of Hepatitis C virus”. Thanks to their discovery, highly sensitive blood tests for the virus are now available and these have essentially eliminated post-transfusion hepatitis in many parts of the world, greatly improving global health.

Speaker: *Katherine Spindler,* Professor of Microbiology and Immunology – Michigan Medicine

*Physics:*
The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Physics 2020 with one half to *Roger Penrose* “for the discovery that black hole formation is a robust prediction of the general theory of relativity" and the other half jointly to *Reinhard Genzel* and *Andrea Ghez* "for the discovery of a supermassive compact object at the centre of our galaxy".

Speaker: *Lydia Bieri*, Associate Professor of Mathematics and Director, Michigan Center for Applied & Interdisciplinary Mathematics and *Doug Richstone*, Lawrence H Aller Collegiate Professor of Astronomy – College of Literature, Science, and the Arts

*Economics:*
This year’s Laureates, *Paul Milgrom* UM-LSA Mathematics Alum! and *Robert Wilson*, have studied how auctions work. They have also used their insights to design new auction formats for goods and services that are difficult to sell in a traditional way, such as radio frequencies. Their discoveries have benefitted sellers, buyers and taxpayers around the world.

Speaker:* Tilman Börgers*, Samuel Zell Professor of the Economics of Risk – College of Literature, Science, and the Arts

*Literature:*
The Nobel Prize in Literature for 2020 is awarded to the American poet Louise Glück “for her unmistakable poetic voice that with austere beauty makes individual existence universal”.

Speaker: *Linda Gregerson*, Caroline Walker Bynum Distinguished University Professor of English Language and Literature – College of Literature, Science, and the Arts

*Peace:*
'Combatting the threat of hunger' The Norwegian Nobel Committee has decided to award the Nobel Peace Prize for 2020 to the *World Food Programme (WFP)*. The World Food Programme is the world’s largest humanitarian organization addressing hunger and promoting food security. In 2019, the WFP provided assistance to close to 100 million people in 88 countries who are victims of acute food insecurity and hunger.

The World Food Programme is the food-assistance branch of the United Nations and the world's largest humanitarian organization focused on hunger and food security. Founded in 1961, it is headquartered in Rome and has offices in 80 countries

Speaker: *Susan Waltz*, Professor of Public Policy, Gerald R Ford School of Public Policy

Read more about the details of each of the 2020 prizes here: https://www.nobelprize.org/prizes/

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Livestream / Virtual Mon, 07 Dec 2020 16:19:38 -0500 2020-12-10T13:10:00-05:00 2020-12-10T16:45:00-05:00 Off Campus Location The Center for the Study of Complex Systems Livestream / Virtual Nobel Symposium Poster
Biophysics Seminar Series (January 15, 2021 12:00pm) https://events.umich.edu/event/80417 80417-20719670@events.umich.edu Event Begins: Friday, January 15, 2021 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Virtual Seminar Series presents:

Dr. Michele Vendruscolo - Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge

*“Activity Relationship by Kinetics for Drug Discovery in Protein Misfolding Diseases”*

ABSTRACT: Protein oligomers are increasingly recognized as the most cytotoxic forms of protein aggregates. It has been very challenging, however, to target these oligomers with therapeutic compounds, because of their dynamic and transient nature. To overcome this problem, I will describe a 'structure kinetic-activity relationship' (SKAR) approach, which enables the discovery and systematic optimization of compounds that reduce the number of oligomers produced during an aggregation reaction. I will illustrate this strategy for the amyloid beta peptide, which is closely associated with Alzheimer's disease, by developing a rhodanine compound capable of dramatically reducing the production of amyloid beta oligomers. As this strategy is general, it can be applied to oligomers of any protein.

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Livestream / Virtual Wed, 06 Jan 2021 10:17:32 -0500 2021-01-15T12:00:00-05:00 2021-01-15T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Michele Vendruscolo
Biophysics Seminar Series (January 22, 2021 12:00pm) https://events.umich.edu/event/80727 80727-20777543@events.umich.edu Event Begins: Friday, January 22, 2021 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Virtual Seminar Series presents:

Dr. Katrin Heinze - Rudolf Virchow Center for Integrative and
Translational Bioimaging, Universität Würzburg

*“Boosting high-resolution fluorescence by tunable nano-coatings"*

ABSTRACT: The “Resolution Revolution" in fluorescence microscopy over the last decades has given rise to a variety of techniques that allow imaging beyond the diffraction limit with resolution up to the nanometer range. One particularly powerful technique is direct stochastic optical
reconstruction microscopy (dSTORM), a widely-used type of single molecule localization microscopy (SMLM), which is based on the temporal separation of the emission of individual fluorophores
and subsequent localization analysis. This eventually allows to reconstruct a super-resolved image revealing details down to typically 20 nm in a cellular setting. The key point here is the achievable localization precision, which mainly depends on the image contrast generated by the individual fluorophore’s emission. We found that reflective metal-dielectric nano-coatings represent a tunable nanomirror that can do both quenching and boosting fluorescence for high-contrast imaging on the nanoscale. Such mirror-enhanced fluorescence is very different from other surface effects based on total internal reflection microscopy or optoplasmonics. While surface-plasmon supported fluorescence methods provide much higher enhancement factors, mirror-enhanced approaches are more versatile and thus highly suitable for modern bio-imaging. The resolution improvement achieved with such mirror-enhanced STORM (meSTORM) is both spectrally and spatially tunable and thus allows for dual-color approaches on the one hand, and selectively highlighting region above the cover glass on the other hand. Even if the resulting resolution boost is based on a near-field effect and thus restricted to imaging near surfaces, a large variety of membrane fluorescence approaches even beyond SMLM benefit. Thus, live-cell
Fluorescence Correlation Spectroscopy and Fluorescence Resonance Energy Transfer are as well perfect candidates to be pushed to the next level.

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Livestream / Virtual Wed, 13 Jan 2021 15:37:36 -0500 2021-01-22T12:00:00-05:00 2021-01-22T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Katrin Heinze
Biophysics Seminar Series (January 29, 2021 12:00pm) https://events.umich.edu/event/81244 81244-20877916@events.umich.edu Event Begins: Friday, January 29, 2021 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

*“Ultrafast 2D IR Spectroscopy of Membrane Peptide Systems”*

Plasma membranes are the main liaisons between the intercellular and extracellular environment, playing a critical role in numerous biological processes. Recent research has challenged the long-standing “fluid mosaic model,” representing membranes as densely packed, heterogeneous environments. Within these complex membranes are transmembrane proteins which comprise up to 50% of the membrane mass, and are themselves diverse in sequence, structure, and function. Combining two-dimensional infrared spectroscopy (2D IR) and molecular dynamics simulations (MD), we have explored membrane complexity from two perspectives: first, we address the sequence heterogeneity in transmembrane peptides; and second, we explore the effect this crowded environment has on the lipids themselves and the implications this has on future membrane studies.

Site-specific 2D IR has been used to directly study localized hydration effects in a lipid membrane upon insertion of pH (Low) Insertion Peptide (pHLIP), a model membrane peptide. Semi-quantitative results indicate enhanced water penetration in the membrane core concurrent with peptide insertion, suggesting the abundance of hydrophilic residues in the pHLIP sequence drives membrane hydration. Further, crowding experiments have probed ultrafast dynamics at the lipid-water interface of model membranes as a function of transmembrane peptide concentration, revealing a non-monotonic dependence on peptide concentration linked to interfacial water structure.

Zoom link: https://umich.zoom.us/j/99088330811

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Livestream / Virtual Tue, 26 Jan 2021 10:51:35 -0500 2021-01-29T12:00:00-05:00 2021-01-29T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Jennifer Flanagan
Biophysics Seminar Series (March 12, 2021 12:00pm) https://events.umich.edu/event/82542 82542-21116092@events.umich.edu Event Begins: Friday, March 12, 2021 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

The Biophysics Seminar Series Presents:

Dr. Pratyush Tiwary - Department of Chemistry & Biochemistry and Institute for Physical Science & Technology, University of Maryland

*“Can artificial intelligence help understand and predict biomolecular dynamics?”*

ABSTRACT: The ability to rapidly learn from high-dimensional data to make reliable predictions about the future of a given system is crucial in many contexts. This could be a fly avoiding predators, or the retina processing terabytes of data almost instantaneously to guide complex human actions. In this talk we draw parallels between such tasks, and the efficient sampling of complex molecules with hundreds of thousands of atoms. Such sampling is critical for predictive computer simulations in condensed matter physics and biophysics, including but not limited to problems such as crystal nucleation, protein loop movement and drug unbinding. For this we use the Predictive Information Bottleneck (PIB) and long short-term memory (LSTM) frameworks from artificial intelligence (AI), and re-formulate them for the sampling of biomolecular structure and dynamics, especially when plagued with rare events. We demonstrate the methods on different test-pieces, where we calculate the dissociation pathway and timescales much longer than milliseconds. These include ligand dissociation from the protein lysozyme, protein kinases and and from flexible RNA. We will also discuss some generic challenges and proposed solutions regarding reliability, interpretability and extrapolative powers of AI when used in molecular simulations, drawing mutually beneficial connections between the at first glance disconnected fields of theoretical chemistry and AI.

*Join us on zoom: https://umich.zoom.us/j/92734220731*

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Livestream / Virtual Thu, 25 Feb 2021 14:10:27 -0500 2021-03-12T12:00:00-05:00 2021-03-12T13:00:00-05:00 Off Campus Location LSA Biophysics Livestream / Virtual Dr. Pratyush Tiwary
“Ions and proteins: the essential partners that fold RNA and DNA” (April 9, 2021 12:00pm) https://events.umich.edu/event/81780 81780-20959267@events.umich.edu Event Begins: Friday, April 9, 2021 12:00pm
Location: Off Campus Location
Organized By: LSA Biophysics

Abstract: The nucleic acids, RNA and DNA, play versatile and critically important roles in biology. The information storage capacity of DNA has long been recognized, and awareness of RNA’s prominence in biology continues to grow. Because both RNA and DNA carry large negative charge, interaction with oppositely charged partners is required for folding and function. Despite the important roles of these partners, little is known about how they structure, or interact with nucleic acids. We design experiments to reveal the role of partners, ranging from ions through proteins, in systems ranging from single stranded DNA or RNA through large assemblies, like viruses. Simulation and computation are important components of our work, and often offer surprising insight into our results.

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Livestream / Virtual Fri, 02 Apr 2021 11:29:54 -0400 2021-04-09T12:00:00-04:00 2021-04-09T13:00:00-04:00 Off Campus Location LSA Biophysics Livestream / Virtual Lois Pollak