Fall 2020

Departmental Seminars

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August 10, 2020
10:30 AM
Via Zoom
Dr. Julia Phillips
National Academy of Engineering

I have been most fortunate to have had, and to continue to have, a fascinating, rewarding, and varied career and life.  While my career has always centered on science, it has not taken many of the paths that students probably first consider as they plot their own careers. I will give a very brief overview of my career, factors affecting the choices I made, and circumstances that made certain opportunities open to me.  This will lead me to pose questions that every individual has to answer for themselves about their personal priorities which may guide them in their career decisions.  I will then discuss general advice about things that make a student or postdoc a desirable candidate (especially in a non-academic position) and that continue to open doors for them throughout their career.  I will illustrate some of these thoughts with examples from my career or from the development of young researchers I have mentored.

August 17, 2020
10:30 AM
Via Zoom
Dr. Nathan Gianneschi
Northwestern University

We describe the organization of functional peptides as sidechains on polymer scaffolds as a class of poly(peptide). For these protein-like polymers (PLPs), the key structural feature is that every sidechain is a peptide, forming an array of displayed peptides with maximum density. Peptides organized in this manner imbue polymers with a range of functional qualities inherent to their specific sequences. Synergistically, the polymer enforces changes in peptide activity and function by virtue of packing and constraining the peptide. Properly designed, the polymer can serve to protect the peptide from proteolysis, change the pharmacokinetic profile of a systemically administered peptide, increase the cellular uptake of an otherwise cell impermeable therapeutic peptide, or change peptide substrate activity entirely. Herein, we describe the development of synthetic strategies for accessing this class of biomolecule polymer conjugate, and discuss utility in a range of settings, including as a new class of peptide therapeutics of importance in ophthalmology, liver/kidney disease, neurological disorders and cancer.

August 24, 2020
10:30 AM
Via Zoom
Dr. Debashish Kuila
North Carolina A&T State University

One of the main objectives of our NSF-CREST Bioenergy Center is to develop stable catalysts for Fischer-Tropsch (F-T) synthesis using syngas (CO:H2) enriched with CO2 from biomass gasification. Previous F-T studies in Si-microchannel microreactor were carried out to examine the effect of silica, alumina and titania 1 sol-gel support on the activities of Co, Fe, and Ru catalysts.  The F-T studies and kinetics of the reactions using different bimetallic catalysts and mesoporous silica have been investigated in 3-D printed SS microreactor to understand the effect of metals and the structure of the support.2  In order to investigate synergistic effects of bimetallic oxide (BMO) supports on F-T synthesis, mesoporous  silica-alumina, silica-titania and titania-alumina were synthesized. The best catalytic activity in terms of CO conversion, stability and product selectivity to C1-C3 alkanes was observed for the 10Fe5Ru catalyst.

To address the Green Chemistry challenges, we are also developing catalysts for steam reforming of bio-derived alcohols using a tubular reactor.  Methanol steam reforming (SRM) studies with different metals and mesoporous silica and TiO2 show very significant interactions between metal and the support that govern methanol conversion and H2 selectivity.3a These studies have been extended to steam reforming of glycerol (SRG), a byproduct of biodiesel. Both Ni/Co-MCM-41 and Ni/Co-SBA-15 catalysts yielded better H2 selectivity (85% vs 78%) and glycerol conversion (99% vs 88%) at 650 °C with higher glycerol to water feed ratio (1:12).3

References:  1. R. Y. Abrokwah et al, Molecular Catalysis, 2019, 478, 110566. 2. N. Mohammad et al, (a) Catalysts 2019, 9, 872;  4;  (b) Catalysis Today 2020; in press. 3. (a) R. Abrokwah et al..Taylor & Francis, Fuel Processing and Technology, 2019, Ch-6, 93-108; (b). S. Al-Salihi- et al, Int. J. Hydrogen Energy, 2020, 45,14183-14198.

August 31, 2020
10:30 AM
Via Zoom
Dr. Corey Wilson
Georgia Tech

The control of gene expression is an important tool for metabolic engineering, the design of synthetic gene networks, and protein manufacturing. The most successful approaches to date are based on modulating mRNA synthesis via an inducible coupling to transcriptional effectors. Traditionally engineered genetic circuits have almost exclusively used naturally occurring transcription factors. The Wilson Lab has recently introduced a biological programming edifice based on an engineered system of non-natural transcription factors and complementary genetic architectures. This technology represents an important advance in synthetic biology via expanding biological computing capacity, and lays the foundation for the development of a complete (non-natural) biological  programming language.

September 14, 2020
10:30 AM
Via Zoom
Dr. Diwakar Shukla
University of Illinois at Urbana-Champaign

Virtually all processes in living organisms, from nutrient transport to the regulation of growth, are mediated by proteins. Gaining a detailed view of the biological processes requires understanding of the structure and function of the proteins involved in these processes. Sequence information is widely available for proteins across organisms, but structural information is still lacking, especially for plant proteins. Structural biology has provided valuable insights and high-resolution views of the biophysical processes in plants, such as photosynthesis, hormone signaling and nutrient transport. However, structural biology only provides a few “snapshots” of protein structure, whereas in vivo, protein function involves complex dynamical processes such as ligand binding and conformational changes that structures alone are unable to capture in full detail. In this talk, we present methods that allow all-atom molecular dynamics (MD) simulations to be leveraged as a “computational microscope” providing detailed structural and dynamical information about the molecular machinery in plants and gain high-resolution insights into function of plant hormone receptors and transporters.

September 28, 2020
10:30 AM
Via Zoom
Dr. Stacey Deleria Finley
University of Southern California

Systems biology approaches, including computational models, provide a framework to test biological hypotheses and optimize effective therapeutic strategies to treat human diseases. In this talk, I present recent work in modeling signaling in cancer-targeting immune cells, with a focus on CAR T cells. Chimeric antigen receptors (CARs) are comprised of a variety of different activating domains and co-stimulatory domains that initiate signaling required for T cell activation. However, there is a lack of understanding of the mechanisms by which activation occurs. We aim to fill this knowledge gap by applying mathematical modeling to investigate how CAR structure influences downstream T cell signaling and develop new hypotheses for the optimal design of CAR-engineered T cell systems. Our work addresses questions regarding the role of signaling domains and kinase activity in the activation of engineered T cells and can be used to guide CAR T cell design.

Biography

Stacey D. Finley is the Gordon S. Marshall Early Career Chair and Associate Professor of Biomedical Engineering at the University of Southern California. Dr. Finley received her B.S. in Chemical Engineering from Florida A & M University and obtained her Ph.D. in Chemical Engineering from Northwestern University. She completed postdoctoral training at Johns Hopkins University in the Department of Biomedical Engineering. Dr. Finley joined the faculty at USC in 2013, and she leads the Computational Systems Biology Laboratory. Dr. Finley has joint appointments in the Departments of Chemical Engineering and Materials Science and Biological Science, and she is a member of the USC Norris Comprehensive Cancer Center. Dr. Finley is also the Director of the Center for Computational Modeling of Cancer at USC. Her research is supported by grants from NSF, NIH, and the American Cancer Society.

October 5, 2020
10:30 AM
Via Zoom
Dr. Petia Vlahovska
Northwestern University

Flocks of birds and schools of fish are familiar examples of emergent collective behavior, where interactions between self-propelled (active) individuals lead to coherent motion on a scale much larger than the isolated unit. Similar phenomena have been observed with active micro-particles such as bacteria and motile colloids.  Recently, the Quincke instability (spontaneous spinning of a dielectric particle in an applied uniform DC field) has attracted great interest as a means of propelling colloids, by simply letting the particles roll on a surface.   In this talk, I will present our experiments showing how Quincke rollers, previously studied mainly as active Brownian particles, can be designed to perform Run-and-Tumble-like locomotion mimicking bacteria such as E. coli. Populations of the Quincke random walkers self-organize and exhibit behaviors reminiscent of bacterial suspensions such as dynamic clusters and mesoscale turbulent-like flows. I will also discuss some novel collective dynamics of Quincke rotors levitating in a bulk fluid: unlike the rollers, the “hovers” form crystals, chains and other dynamical assemblies.

October 12, 2020
10:30 AM
Via Zoom
Dr. Sarah Perry
University of Massachusetts, Amherst

Electrostatic interactions and polyelectrolyte complexation can be used in the self-assembly of a wide range of responsive, bioinspired soft materials ranging from dehydrated thin films, fibers, and bulk solids to dense, polymer-rich liquid complex coacervates, as well as more complex hierarchical structures such as micelles and hydrogels. This responsiveness can include swelling and dissolution or solidification, which can be harnessed to facilitate encapsulation and the subsequent fabrication of functional materials. In particular, we draw inspiration from biomolecular condensates, or membraneless organelles, which utilize liquid-liquid phase separation to create transient compartments in cells. These condensates are commonly formed due to weak, multivalent interactions involving intrinsically disordered proteins, and have been shown to enable the selective uptake of specific proteins, DNA/RNA, and small molecule drugs. We utilize polypeptides as model sequence-controlled polymers to study how the patterning or presentation of charges and other chemical functionalities can modulate the potential for liquid-liquid phase separation via complex coacervation. We further examine how the distribution of charge on globular proteins can be used to facilitate selective uptake into coacervate phases, and how such materials can be used to stabilize proteins and viruses against denaturation. This molecular-level understanding of polyelectrolyte complexation is further enhanced by detailed rheological and thermodynamic examinations of the molecular nature of the various material transitions present in these systems. Our experimental efforts are supported by the parallel development of computational approaches for modeling and predicting the phase behavior of patterned polymeric materials. Our goal is to establish molecular-level design rules to facilitate the tailored creation of materials based on polyelectrolyte complexation that can both illuminate self-assembly phenomena found in nature, and find utility across a wide range of real-world applications.

October 19, 2020
10:30 AM
Via Zoom
Dr. Pierre-Thomas Brun

The talk is concerned with the directed control of fluidic instabilities to program shapes. While instabilities are traditionally regarded as a route towards failure in engineering, I aim to follow a different path; taming fluidic instabilities and harnessing the patterns and structures they naturally form. This methodology capitalizes on the inherent periodicity, scalability, versatility, and robustness of mechanical instabilities. This new design paradigm – building with instabilities – calls for an improved understanding of instabilities and pattern formation in complex media. While stability analysis is a classic topic in mechanics, little is known on the so called inverse problem: finding the optimal set of initial conditions and interactions that will be transmuted into a target shape without direct external intervention. While the epicenter of the research is fundamental, utilizing instabilities to structure soft materials opens new research directions in the study of the behavior and deformations of architected soft materials, inspired by natural soft-materials that self-assemble into well defined structures to display remarkable properties. More broadly, the talk is rooted on the basis of recognizing model experiments as a valuable and powerful tool for discovery and exploration, in turn seeding the development of formal and predictive models.

November 2, 2020
10:30 AM
Via Zoom
Dr. Claire S. Adjiman
Imperial College London

The performance of separation processes depends on the flowsheet structure, the design of the equipment and the operating conditions, as well as on the choice of processing materials such as solvents, sorbents or membranes. In practice, processing materials are often selected in the early stages of process development and considered as fixed for the purpose of process/equipment design. This can lead to sub-optimal designs: for example, a solvent which leads to the best absorption capacity may incur significant recovery costs and therefore not be cost-effective from a process-wide perspective. It is thus desirable to extend the boundary of process design to include processing materials in the set of design variables.

In this seminar, we explore how better designs can be obtained by integrating molecular and process design decisions. Given the number of potential solutions to this extended design problem, and the complexity of the task, computer-aided design can play an important role in identifying promising areas of the solution space. A key objective is thus to identify candidate molecules and/or mixtures that should be investigated experimentally, thereby providing focus for experimental studies and reducing their cost.

The methodology presented here to achieve this objective offers a general blueprint the integrated computer-aided design of molecules and processes. The approach rests on two key features. First, we need predictive property prediction techniques that enable us to establish a quantitative link between molecular structure and process performance. Second, we treat the design problem as a single optimisation problem, in which all decision variables are considered simultaneously. The application of the proposed approach to the design of chemical processes is presented.

November 9, 2020
10:30 AM
Via Zoom
Dr. Rong Li
National University of Singapore / John Hopkins University