Faculty Candidate Seminar

Faculty Candidate Seminar: Antonio Del Rio Flores, Feb. 21

Anonymous — Sun, 01 Jan 2023 23:34:19 +0000

Faculty Candidate Seminar: Antonio Del Rio Flores, Feb. 21 Anonymous (not verified) Sun, 01/01/2023 - 16:34

Biosynthesis and Mechanistic Investigation of Unusual Synthons in Natural Products

Speaker: Antonio Del Rio Flores, University of California, Berkeley

Host: Jerome Fox

Tuesday, February 21, 2023 – 2:45pm – JSCBB A108

Seminar Abstract
Natural products, often referred to as specialized metabolites, are small molecules known for their potent bioactivities relevant to treating human health conditions. Unique functional groups like the isonitrile and N-hydroxytriazene often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. By exploiting biosynthetic machinery associated with unique synthons, it is possible to enhance, vary or diminish the biological activities of parent compounds and apply the biosynthetic machinery to new systems for functional group installation. Here, we focus on our recent efforts in functional characterization and mechanistic interrogation of enzymes responsible for generating isonitrile and N-hydroxytriazene pharmacophores.

Biosketch
Antonio Del Rio Flores was born in a small town in Mexico named Sahuayo that is famous for their artisan crafts and regional cuisine. He subsequently moved to the United States at a young age and grew up in the Bay Area. He attended the University of California, Davis and received a double major in Chemical and Biochemical Engineering. His research spanned in the fields of bioprocess engineering, process control simulations, plant biology and metabolomics. After his undergraduate studies, Antonio attended the University of California, Berkeley and is currently a fifth-year PhD candidate in Chemical and Biomolecular Engineering. His research deals with studying the biosynthesis and enzymology associated with natural products from environmental bacteria and human pathogens. His efforts led to advances in understanding the biogenesis of functional groups that are widely utilized for bioorthogonal transformations in chemical biology. Antonio is also the lead graduate student instructor for the biochemical engineering laboratory class, a course that Antonio developed during his doctoral studies to prepare undergraduate/master’s students for careers as bioprocess engineers.

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Faculty Candidate Seminar: Carolyn Mills, March 7

Anonymous — Sun, 01 Jan 2023 18:41:29 +0000

Faculty Candidate Seminar: Carolyn Mills, March 7 Anonymous (not verified) Sun, 01/01/2023 - 11:41

Engineering Spatial Organization in Biology via Protein-Driven Phase Separation and Assembly

Speaker: Carolyn Mills, postdoctoral fellow, Northwestern University

Host: Tim Whitehead

Tuesday March 7, 2023 - 2:45 p.m., JSCBB A108

Seminar Abstract
Engineering biology efforts have yielded remarkable progress towards addressing emerging societal challenges in areas from sustainability to human health. However, many of these efforts largely overlook the potential of spatial control that is central to the efficiency of processes like pathogen invasion and carbon fixation. Protein-driven spatial organization is a promising strategy for realizing this control, as proteins can drive many types of macromolecular assembly, from liquid-liquid phase separation to well-defined nanocontainer formation. Our ability to program this spatial organization, however, is limited by our understanding of the physical principles underlying protein assembly. In this talk, I will discuss two examples in which examining fundamental protein phase behavior and assembly directly furthered engineering applications. In the first example, I will describe our discovery that proteins called elastin-like polypeptides (ELPs) exhibit cononsolvency, where solvents like ethanol help drive ELP phase separation. I will then explain how our understanding of this phase transition facilitated development of a high-throughput, centrifugation-based desalting method for protein materials. In the second example, I will discuss our investigation into the assembly mechanism of naturally-occurring multi-protein assemblies called bacterial microcompartments (MCPs), and how we leveraged our newfound understanding of this assembly to reprogram MCPs for bioproduction applications. Overall, these case studies illustrate how a fundamental understanding of protein-driven assembly and phase transitions can address diverse problems in engineering biology.

Biosketch
Carolyn Mills, PhD, (she/they) is a postdoctoral fellow at Northwestern University in the lab of Professor Danielle Tullman-Ercek. Carolyn completed her BS in chemical engineering in 2013 at the University of California, Santa Barbara, where she carried out research using atomistic simulations to study peptide self-assembly with Professor M. Scott Shell. Carolyn received her PhD in chemical engineering in 2019 at the Massachusetts Institute of Technology, working in Professor Bradley Olsen’s lab on self-assembly and high-throughput processing of fusion protein materials. During her PhD, Carolyn was supported by an NSF Graduate Research Fellowship and recognized as a finalist in the Excellence in Graduate Polymer Research session at the AIChE national meeting in 2018. At Northwestern, Carolyn is researching self-assembling protein nanoreactors with a focus on how they can benefit metabolic engineering applications and has been recognized as a rising star in chemical engineering and a speaker in the Synthetic Biology Young Speaker Series. During her time at Northwestern, she organized the inaugural Context, Community, and Connections Symposium (C3S) to highlight the research accomplishments of those holding underrepresented identities in Northwestern’s chemical engineering, chemistry and materials science research communities. Carolyn’s work on the C3S was recognized by the Chemical and Biological Engineering Department’s Distinguished Postdoctoral Service Award.

Carolyn Mills, PhD, is a postdoctoral fellow at Northwestern University in the lab of Professor Danielle Tullman-Ercek.

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Faculty Candidate Seminar: Vivian Feig, Feb. 28

Anonymous — Sat, 03 Dec 2022 00:29:58 +0000

Faculty Candidate Seminar: Vivian Feig, Feb. 28 Anonymous (not verified) Fri, 12/02/2022 - 17:29

Dynamic Bio-Interfacing Functional Materials

Speaker: Vivian Feig, post-doctoral research fellow, Schmidt Science Fellow, Massachusetts Institute of Technology, Brigham and Women’s Hospital,

Host: Stephanie Bryant

Tuesday, Feb. 28, 2023 - 2:45 p.m., JSCBB A108

Seminar Abstract
Functional materials with dynamic mechanical properties are needed to enable next-generation medical technologies to be less invasive and more convenient for patients. However, imparting dynamic properties like stretchability and injectability often comes at the expense of functional performance. In this talk, Feig will show how soft matter can enable bio-interfacing materials to circumvent the tradeoff between dynamism and functionality for two particularly difficult use cases: bio-electronics and load-bearing materials.

First, bio-electronic devices traditionally are limited by their extreme mismatch in mechanical properties compared to soft tissues. We addressed this mismatch by harnessing the toolkit of polymer science and engineering to design novel conductors that are as soft as biological tissue, stretchable enough to conform to moving organ surfaces, and capable of being injected without sacrificing conductivity.

Next, high-strength metal-based devices like orthopedic implants typically require invasive insertion and retrieval methods, while passively-degradable metals continuously weaken over time. To eliminate the need for device retrieval without compromising on mechanical properties, we used a biocompatible liquid metal to develop a strategy to trigger the on-demand breakdown of high-strength biomedical metals.

These examples highlight the significant potential for soft matter to transform next-generation biomaterials and medical devices. I will conclude the talk by sharing my vision of a generalizable design strategy for realizing dynamic bio-interfacing functional materials.

Biosketch
Vivian Feig, PhD, is a Schmidt Science Fellow and postdoctoral researcher in the labs of Assistant Professor Giovanni Traverso and Professor Robert Langer at MIT and the Brigham and Women’s Hospital. Trained as a materials engineer, Feig designs novel bio-interfacing systems with unprecedented functionalities to enhance human health. In 2020, she received her PhD from Stanford University with Professor Zhenan Bao. As a National Defense Science and Engineering Graduate (NDSEG) fellow at Stanford, Feig designed new conducting polymer-based materials to address the challenge of intimately coupling electronics with biological systems, which is critical for emerging therapies in areas like neuromodulation and regenerative medicine. Her research culminated in numerous honors, including the 2022 American Chemical Society (ACS) Global Outstanding Graduate Student Award in Polymer Science and Engineering, as well as selection to the graduate award symposia of the Materials Research Society (MRS) and the American Institute of Chemical Engineers (AIChE). Besides research, she is also passionate about mentorship and scientific outreach, and was honored to receive the 2020 MRS Arthur Nowick Graduate Student Award for her efforts in these areas.

Vivian Feig, PhD, is a Schmidt Science Fellow and postdoctoral researcher in the labs of Assistant Professor Giovanni Traverso and Professor Robert Langer at MIT and the Brigham and Women’s Hospital. In this talk, Feig will show how soft matter can enable bio-interfacing materials to circumvent the tradeoff between dynamism and functionality for two particularly difficult use cases: bio-electronics and load-bearing materials.

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Faculty Candidate Seminar: Andrew Rosen, Feb. 16

Anonymous — Fri, 02 Dec 2022 17:26:00 +0000

Faculty Candidate Seminar: Andrew Rosen, Feb. 16 Anonymous (not verified) Fri, 12/02/2022 - 10:26

Discovering Tunable Materials with Unprecedented Properties via High-Throughput Quantum Chemistry

Speaker: Andrew S. Rosen, Miller Research Fellow
University of California, Berkeley

Host: Michael Shirts

Thursday, Feb. 16, 2023 - 2:45 p.m., JSCBB A108

Seminar Abstract
The solutions to many of society’s most pressing problems rely on the discovery of materials with unprecedented physical and chemical properties that are tailored to an application of interest. Typically, it is not a matter of incremental improvements over existing technologies; rather, there is often an urgent need to identify new kinds of materials altogether. The conventional trial-and-error approach of experimental materials discovery, however, can be extremely time-consuming and may not identify truly top-performing candidates, particularly when they exist beyond the limits of our current chemical intuition.

In this talk, I will discuss how quantum chemistry, high-throughput computing and machine learning can help guide experiments and accelerate the discovery of novel materials to address a variety of global challenges relevant to the field of chemical engineering. To demonstrate the impact and versatility of this approach, I will highlight how a novel computational screening platform that I developed can drastically accelerate the discovery of porous framework solids for heterogeneous catalysis, industrial gas separations and next-generation (opto)electronic devices as it relates to the more sustainable production of valuable chemical products. With advances in data science in mind, I will also discuss my recent work building upon the Materials Project — a publicly accessible database of computed physicochemical properties for over 100,000 solid-state materials — and how such a resource can aid both theorists and experimentalists in the design of materials with targeted electronic properties. Overall, this work demonstrates how high-throughput virtual screening methods rooted in the fundamental principles of quantum mechanics have set the stage for autonomous materials discovery platforms of the future.

Biosketch
Andrew Rosen is a Miller Research Fellow at the University of California, Berkeley where his research has focused on uncovering unique electronic structure properties in solid-state materials as part of the Materials Project team led by Professor Kristin Persson. Andrew earned his PhD in chemical engineering at Northwestern University where he studied redox processes in metal – organic frameworks in the groups of Professor Randall Snurr and Professor Justin Notestein. Beyond his current role as a Miller Fellow, Andrew has been named a CAS Future Leader by the American Chemical Society, a National Defense Science and Engineering Graduate Fellow, a Ryan Fellow of the International Institute for Nanotechnology and a Presidential Fellow of Northwestern University. Andrew is also particularly passionate about accessible and equitable education in engineering; he has received several teaching and mentorship awards in this area, and his STEM education website “Rosen Review” has been viewed over a million times with visitors from 190 countries around the world.

In this talk, Andrew Rosen, Miller Research Fellow, will discuss how quantum chemistry, high-throughput computing and machine learning can help guide experiments and accelerate the discovery of novel materials to address a variety of global challenges relevant to the field of chemical engineering.

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Faculty Candidate Seminar: Juan Manuel Restrepo-Flórez

Anonymous — Mon, 07 Feb 2022 22:42:46 +0000

Faculty Candidate Seminar: Juan Manuel Restrepo-Flórez Anonymous (not verified) Mon, 02/07/2022 - 15:42

A Road Toward Sustainability – from Materials to Processes

Speaker: Juan Manuel Restrepo-Flórez, Postdoctoral Associate
University of Wisconsin-Madison

Host: Will Medlin

Tuesday, March 8, 2022 - 2:45 p.m., JSCBB A108

Seminar Abstract

Industrial processes and transportation account for more than 70% of the United States energy consumption. Finding strategies to either reduce energy consumption or to enable the use of renewables in these sectors may prove instrumental in the context of sustainability. To achieve this vision innovations from the material to the process scale are needed.

At the industrial level, the need for energy-efficient separations is one of the main innovation drivers, provided that (1) they account for more than 50% of the energy consumption in the sector and (2) they are dominated by thermally driven processes. In this context, membranes appear as attractive alternatives. Understanding the different physical processes underlying these separation operations is important to develop new applications. In the first part of this talk, I will discuss how mass diffusion metamaterials theory can be used to engineer new membranes capable of performing separations by controlling independently the flux direction of different components. This is in contrast, to typical membranes that operate by controlling the flux magnitude.

In the transportation sector, the need to find sustainable alternatives for middle distillates (diesel and jet fuel) is imperative, these fuels are consumed in sectors whose electrification is more challenging. In the second part of this talk, I will present a systematic approach to the design of advanced biofuels. The approach that I will describe integrates into a single framework the design of chemical processes and fuels with tailored properties. Thus, opening the door to the production of biofuels that are superior to their fossil counterparts. In particular, I will show how this approach can be applied to the upgrading of ethanol into diesel and jet fuel, and I will address three fundamental questions: (1) What are the energy requirements associated with the production of middle distillates? (2) What is the interplay among fuel properties, economics, and processes? and (3) What is the ability of the advanced fuels identified in this work to satisfy fuel demand and mitigate CO2 emissions?

Biosketch

Juan Manuel Restrepo-Flórez is a post-doctoral associate at the University of Wisconsin–Madison. Before accepting his position in Madison, he was a Ph.D. candidate at the Georgia Institute of Technology. He holds a bachelor’s degree in biological engineering from the National University of Colombia and a master’s degree in chemical and biochemical engineering from the University of Western Ontario.

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Faculty Candidate Seminar: Elizabeth Lee

Anonymous — Mon, 07 Feb 2022 22:32:20 +0000

Faculty Candidate Seminar: Elizabeth Lee Anonymous (not verified) Mon, 02/07/2022 - 15:32

Computational Engineering of Materials at the Nanoscale—where “Classical” meets “Quantum”

Speaker: Elizabeth Lee, Postdoctoral Researcher
University of Chicago

Host: Kayla Sprenger

Thursday, March 3, 2022 - 2:45 p.m., JSCBB A108

Seminar Abstract

Recent trends in materials have increasingly gone “nano”, transforming bulk material down to only a few hundred atoms. Owing to their unique optical, electronic, and chemical properties, materials at the nanoscale are actively studied for a wide variety of applications, from solving global energy crisis using solar cells and catalysis, to designing entirely new types of computing platforms in quantum information science. To leverage such materials for transformative applications, there is a need to not only design materials from their atomic building blocks, but also predict properties that lie at the boundary of classical and quantum phenomena.

I will present several classes of materials that require new computational modeling frameworks to investigate electron spins, exciton dynamics, and molecular reactions, as materials undergo chemical and physical changes at the nanoscale. I have developed quantum-classical models using theoretical and computational tools based on ab initio molecular dynamics, phenomenological modeling, and machine learning algorithms. The first part will focus on modeling the high-temperature formation of quantum defects in solids to realize scalable quantum systems. This study reveals that the underlying electronic structure and dynamics of spin defects are key to designing new quantum technologies. In the second part, I will show how nanoscale energy carriers, in the form of excitons, is transported in conjugated polymers, a fundamental microscopic process in flexible solar cells. The combination of theoretical and experimental studies demonstrates that energy transport and relaxation processes are sensitive to dynamical changes in conjugation lengths and conformational disorder of polymers. Finally, I will discuss the development of a neural network approach in simulating chemical reactions in condensed phase systems. These algorithms enable the simulation of long-timescale reactive processes, for instance, the molecular nitrogen dissociation on metal catalysts, which is the rate-determining step in ammonia synthesis.

Biosketch

Liza Lee is a postdoctoral researcher at the University of Chicago, where she works with Profs. Juan de Pablo and Giulia Galli to develop first-principles computational frameworks to investigate chemical bonding dynamics and equilibria in quantum materials and polymer precursors. She received her Ph.D. and master’s in chemical engineering from Massachusetts Institute of Technology (MIT), under the joint supervision of Profs. William Tisdale and Adam Willard, where she focused on modeling nanoscale energy transport phenomena in molecular semiconductors, such as colloidal quantum dots and conjugated polymers to design next-generation photovoltaics and LEDs. Prior to MIT, Liza earned her bachelor’s degrees in chemical engineering and chemistry from Johns Hopkins University. Her awards include NSF Graduate Research Fellowship, AIChE Electronics and Photonics Materials Award, and the University of Chicago Maria Lastra Excellence in Mentoring Award.

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Faculty Candidate Seminar: Kara Fong

Anonymous — Fri, 04 Feb 2022 20:18:13 +0000

Faculty Candidate Seminar: Kara Fong Anonymous (not verified) Fri, 02/04/2022 - 13:18

Bridging Length Scales in Electrolyte Transport Theory via the Onsager Framework

Speaker: Kara Fong, PhD Candidate, NSF Graduate Research Fellow
Department of Chemical & Biomolecular Engineering - University of California, Berkeley

Host: Ryan Hayward

Tuesday, Feb. 8, 2022 - 2:45 p.m. JSCBB A108

Seminar Abstract

Improved understanding of transport in concentrated electrolyte solutions has important implications for energy storage, water purification, biological applications, and more. This understanding should ideally persist across length scales: we desire both continuum-level insight into macroscopic concentration and electric potential profiles as well as a molecular-level understanding of the mechanisms governing ion motion. However, the most ubiquitous theory to describe continuum-level electrolyte transport, the Stefan-Maxwell equations, yields transport coefficients which lack clear molecular-level interpretation and cannot be easily computed from molecular simulations.

In this talk, I will present the development of an alternative theory, the Onsager transport framework, to analyze transport at both the continuum and molecular levels. I discuss the integration of continuum mechanics, nonequilibrium thermodynamics, and electromagnetism to derive internal entropy production in electrolytes, yielding the Onsager transport equations: linear laws relating the electrochemical potential gradients and fluxes of each species in solution. At the atomistic level, the transport coefficients emerging from this theory directly quantify correlations in ion motion. These transport coefficients may be computed directly from molecular simulations using Green-Kubo relations derived from Onsager’s regression hypothesis. At the continuum level, the Onsager transport framework provides governing equations for solving macroscopic boundary value problems in electrochemical systems. I present an application of the theory to nonaqueous polyelectrolyte solutions for Li-ion batteries, demonstrating how the Onsager framework allows us to quantify non-ideal contributions to transport which are very challenging to access experimentally but strongly impact transport in these systems. Overall, this work provides a paradigm for rigorously analyzing transport across length scales in complex electrolyte solutions.

Biosketch

Kara Fong is a PhD candidate and NSF Graduate Research Fellow in the Department of Chemical & Biomolecular Engineering at the University of California, Berkeley, where she is co-advised by Prof. Bryan McCloskey and Prof. Kristin Persson. She earned a B.S. in Chemical Engineering at Stanford University in 2016, then completed an M.Phil. in Materials Science at the University of Cambridge through the support of a Churchill Scholarship. Her current research focuses on understanding transport phenomena in electrolyte solutions for Li-ion batteries using molecular dynamics simulations and non-equilibrium thermodynamics.

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Faculty Candidate Virtual Seminar: Ivan A. Moreno-Hernandez

Anonymous — Wed, 26 Jan 2022 22:55:47 +0000

Faculty Candidate Virtual Seminar: Ivan A. Moreno-Hernandez Anonymous (not verified) Wed, 01/26/2022 - 15:55

Electrifying the Chemical Industry through Electrocatalyst Discovery and Nanoscale in situ Imaging

Speaker: Ivan A. Moreno-Hernandez, Postdoctoral Scholar, Department of Chemistry, University of California, Berkeley

Host: Joel Kaar

Tuesday, Feb. 1, 2022 - 2:45 p.m. via Zoom

Seminar Abstract

Electrochemical materials are required to store renewable energy and sustainably couple the chemical and energy industries. This talk will focus on advancements in both the discovery of new electrocatalysts with improved performance and the development of techniques to observe the nanoscale structural dynamics of electrochemical materials in liquid environments. We will first discuss the discovery of an earth-abundant class of electrocatalysts that are thermodynamically stable for the oxygen evolution and chlorine evolution reactions in acidic electrolytes. Our discussion will then focus on the development of a redox-mediated approach to control electrochemical reactions in liquid cell electron microscopy, a technique that allows reactions to be observed at near-atomic resolution over time.

Biosketch

Dr. Ivan A. Moreno-Hernandez is a postdoctoral scholar in the Department of Chemistry at the University of California, Berkeley, working with Prof. A. Paul Alivisatos on the study of nanomaterials with liquid cell electron microscopy. Ivan received his B.S. degree in Chemistry and Physics with University Honors from the University of Nebraska-Lincoln in 2014, and his Ph.D. degree as an NSF Graduate Research Fellow in Chemistry from the California Institute of Technology in 2019. His research at Caltech with Prof. Nathan S. Lewis focused on the study of earth-abundant materials for anodic reactions in acidic electrolytes. His current research interests focus on the application of electrochemistry to renewable energy, with an emphasis on understanding the structural dynamics of electrochemical materials with in situ liquid cell electron microscopy.

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