2013 Spring Seminar Series

Monday, June 10, 2013

On Tactical and Strategic Decision Making under Uncertainty
Selen Cremaschi
University of Tulsa, Department of Chemical Engineering


11:00 AM
Monday, June 10, 2013
CEB 218 (810 South Clinton Street)
Most tactical and strategic decisions in process industries, such as research & development (R&D), capital, and infrastructure investments, are made in highly uncertain environments. The explosion of the alternatives with increasing uncertainty prohibits the generation of a comprehensive search space for such problems, and limits the applicability of existing tools and methods. This talk will give an overview of our research activities on developing novel methods to optimize the operation and design of a wide range of applications under uncertainty: (1) surrogate model generation and derivative-free optimization for process synthesis and design of multi-scale processes, (2) systematic procedures for uncertainty propagation and reduction for robust design of chemical processes, (3) efficient solution algorithms for optimization under endogenous uncertainty for strategic decision making. Superstructure optimization is, in theory, a very powerful approach to address tactical problems such as process synthesis for energy applications. However, the resulting mathematical program is difficult, and in some cases impossible, to solve. Surrogate models, simpler functional representations of the underlying complex system, can be used to simplify the problem. We developed three sequential design algorithms to construct accurate surrogate models to be used in optimization problems. These algorithms scale well to problems in high dimensions, and investigate the trade-off between space-filling and adaptive nature of sampling methods. Our results reveal that an adaptive sampling approach is required in order to accurately model strong nonlinearities. Whether we are able to use the fundamental models or surrogate models to define our systems, there are many sources of uncertainty in these models, which in turn leads to uncertainties in the outputs such as plant throughput, and environmental impacts. Our group successfully demonstrated that the unique combination of a novel data clustering approach to identify the relevant experimental data with model fine-tuning and evaluation techniques reduces the prediction uncertainty from up to five orders of magnitude to the same order of magnitude. Although this approach is powerful for systems with uncertainties that are independent of decisions, optimization problems with decision-dependent, i.e., endogenous, uncertainty are commonly observed in process industry, e.g., synthesis of process networks with uncertain process yields, and biomass-to-commodity chemicals investment planning. Despite this, mostly due their challenging nature, the research community strayed away from these problems. Our analysis using simulation-based optimization (SIMOPT) approach revealed the importance of endogenous uncertainties on the overall cost and the resulting decision tree for these problems along with the significant computational cost of SIMOPT. As a new direction to solve these problems, we have recently developed a novel heuristic approach that decomposes the original multi-period multi-stage stochastic program into a series of two-stage stochastic programs, which are then solved rolling through the stages and periods. This approach is highly-parallelizable, and our preliminary results suggest that the solutions obtained are close to the true solution.

Tuesday, May 2, 2013

Graphene, a 2D Network of Carbon Atoms: Properties and Applications of Graphene Quantum materials and Graphene-Encased Biological Cells
Prof. Vikas Berry
Kansas State University
William H. Honstead Professor of Chemical Engineering&
Associate Professor


11:00 AM
Tuesday, May 2, 2013
CEB 218 (810 South Clinton Street)
This presentation will outline the extraordinary properties of graphene and will then discuss the results of two recently completed projects: (A) graphene nanostructures for energy and semiconducting applications, and (B) graphene encasement for liquid-phase imaging under electron microscopy conditions. (A) Due to electronic ‘edge states’ and quantum confinement, graphene nano-ribbons (GNRs) and graphene quantum dots (GQDs) – single-atom-thick nanostructures of sp2 hybridized carbon atoms – exhibit shape and size dependent electrical, magnetic, optical and chemical properties. These properties can be tuned over a wide range by controlling the nanostructure of GNRs and GQDs. However, large-scale synthesis of these graphene nanostructures (GNs) with predetermined shape/size has remained a challenge. This talk will demonstrate a route to produce GNs with predetermined shapes (square, rectangle, triangle and ribbon) and controlled dimensions (published in Nature Communications). This is achieved by diamond-edge-induced nanotomy (nanoscale-cutting) of graphite into graphite nanoblocks, which are then exfoliated (overall yield ~ 80 %). The edges of these graphene nanostructures are straight and relatively smooth with a Raman ID/IG ratio of 0.22–0.28 (roughness < 1 nm). Further, thin films of GNRs exhibit a bandgap evolution with width reduction (0, 10 and ~35 meV for 50, 25 and 15 nm, respectively). The nanotomy process may be applied to other 2D nano¬materials (BN, MoS2 and NbSe2 ) to produce unique 2D nanostruc¬tures, which can significantly expand the scope of their applications and fundamental studies. The presentation will also demonstrate a humidity sensor based on electron-tunneling modulation between GQDs. (B) Imaging of hygroscopic, permeable, and electron-absorbing biological cells under transmission electron microscopy (TEM) at high vacuum and fixed electron beam has been a challenge due to the resultant volumetric-shrinkage, electrostatic charging, and structural degradation of cells. The second part of the seminar will demonstrate that bacterial cells can be encased within graphenic chambers to preserve their dimensional and topological characteristics under high vacuum (10-5 Torr) and beam current (150 A/cm2) (published in Nano Letters). The strongly-repelling clouds in the interstitial sites of graphene’s lattice reduces the graphene-encased-cell’s permeability from 7.6 - 20 nm/s to 0 nm/s. The C-C bond flexibility enables conformal encasement of cells. Additionally, graphene’s high Young’s modulus retains cell’s structural integrity under TEM conditions, while its high electrical and thermal conductivity significantly abates electrostatic-charging. Further, a novel process to wrap liposomes with liquid samples will be shown. We envision that the graphenic encasement approach will facilitate real-time TEM imaging of fluidic samples and potentially obtain snapshots of live biochemical activities.

Tuesday, April 30, 2013

Electrochemical Oxidation in Wastewater Treatment
Prof. Brian P. Chaplin
Villanova University


11:00 AM
Tuesday, April 30, 2013
CEB 218 (810 South Clinton Street)
Electrochemical oxidation is an emerging advanced oxidation process with many applications in water treatment, including organic compound oxidation, pathogen inactivation, and on-site generation of oxidants. The recent surge in research activity in these areas has been facilitated by the development of stable electrode materials, namely boron-doped diamond (BDD) and Ti4O7 electrodes. Several important advantages of BDD and Ti4O7 electrodes over traditional electrode materials have stimulated this growing scientific interest. These advantages include high stability under anodic polarization, suppression of water electrolysis reactions, and chemical inertness. However, a detailed understanding of oxidation processes at the electrode/solution interface is still lacking. In this talk I will discuss our ongoing research efforts aimed at understanding the mechanisms of electrochemical oxidation at the electrode/solution interface. A combination of electrochemical oxidation experiments, electrochemical measurements, and density functional theory (DFT) modeling was used to develop a mechanistic understanding of the oxidation of compounds at the electrode surface. Results from this work are used to develop new electrodes will high reactivity towards water contaminants, while limiting undesirable byproduct formation. Additional work will also be presented on recent efforts focused on the development of reactive electrochemical membranes. The goal of this work is to develop a new technology that combines filtration and advanced oxidation into a single technology. The various applications of this new technology will be discussed in the context of water treatment..

Thursday, April 25, 2013

Thermodynamics of protein folding and stability: a quasichemical perspective
Prof. Dilip Asthagiri
Johns Hopkins University
Baltimore, Maryland


11:00 AM
Thursday, April 25, 2013
CEB 218 (810 South Clinton Street)
The stability of a folded protein against unfolding is usually small, being only about a few times the typical strength of a hydrogen bond in water. This modest stability arises from a balance of large competing hydration effects and intra-molecular interactions in the protein. Nature provides examples of both cases where this balance is specifically altered, as happens in the metal-induced folding of an otherwise unstructured peptide, and where the balance is preserved by changing solvent conditions using osmolytes, as happens in the face of extremes of temperature or pressure or presence of solutes that can denature the protein. Elucidating the physics underlying such protein-solvent adaptation is a fundamental challenge in biology and the principal focus of our research efforts. In seeking a molecular scale understanding of the thermodynamics of the protein in the solvent milieu, we deal with a many-body system characterized by many different scales of length and of interaction energies. Acknowledging these challenges, we have developed a theoretical and computational framework that allows, for the first time, a clear examination of the excess free energy of the protein in a given solvent. I will present the main ideas behind this framework and illustrate it with examples on the hydration of the Ca(2+) ion and the protein cytochrome C. Then I will consider in detail the role of trimethylamine-n-oxide, an osmolyte, and urea in the coil to helix transition of a deca-alanine peptide. As part of our research on thermodynamics of protein folding, we are also studying metal-induced folding of unfolded peptides. Time permitting, I will present our studies on metal selectivity in a zinc finger protein, a system where metal binding and folding are coupled.

--+++ Thursday, April 11, 2013

Theory and Simulation of Biomolecular Systems: Surmounting the Challenge of Bridging the Scales
Prof. Greg Voth
University of Chicago
Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute


2:30 PM
Thursday, April 11, 2013
CEB 218 (810 South Clinton Street)
A multiscale theoretical and computational methodology will be discussed for studying biomolecular systems across multiple length and time scales. The approach provides a systematic connection between all-atom molecular dynamics, coarse-grained modeling, and mesoscopic phenomena. At the heart of the approach is a method for deriving coarse-grained models from protein structures and their underlying molecular-scale interactions. This particular aspect of the work has strong connections to the theory of renormalization, but it is more broadly developed and implemented for heterogeneous biomolecular systems. A critical component of the methodology is also its connection to experimental structural data such as cryo-EM or x-ray, thus making it “hybrid” in its character. Important applications of the multiscale approach to study key features of large multi-protein complexes such as the HIV-1 virus capsid, actin filaments, and protein-mediated membrane remodeling will be presented as time allows..

Thursday, March 14, 2013

Engineering Biologically-Inspired Materials
Prof. Szu-Wen Wang
University of California at Irvine
Department of Chemical Engineering and Materials Science


11:00 AM
Thursday, March 14, 2013
CEB 218 (810 South Clinton Street)
New materials that can be programmed to elicit desired biological responses have enormous potential in therapeutic applications. Our research group uses a biomimetic approach to design such materials. We apply tools of genetic engineering to produce precisely-structured protein-based materials which cannot be fabricated using conventional chemical synthesis. By redesigning architecture and self-assembly behavior at the molecular and nanoscale levels, one can customize these biomaterials to yield novel properties and biological interactions. One example is a self-assembling protein nanoparticle, based on the E2 subunit of pyruvate dehydrogenase. By truncating this complex down to its structural core, we obtain a highly-stable, 25-nm dodecahedron with a hollow cavity. We have demonstrated that this nanoparticle can be designed to accommodate drug molecules, exhibit pH-triggered assembly and drug release, target cancer cells, and modulate immunological responses. In another example, we have developed a versatile platform to fabricate a new class of biomimetic polymers which has previously been elusive to create. Since these polymers are based on the extracellular matrix protein collagen, this gives us the potential to control cellular processes by specifically tailoring the underlying matrix material. These biomimetic polymers are expressed in yeast, contain precisely-defined cell interaction sites and chemical linkage sites, and are structurally comparable to the natural material. We show that cellular responses to these biopolymers can be modulated by altering specific cell interaction sites. These studies collectively reveal the tremendous potential of using natural protein scaffolds as a departure point for creating new types of biomaterials.

Thursday, March 7, 2013

Developing New Materials for Energy and Environmental Applications via Molecular Simulation
Prof. Edward J. Maginn
University of Notre Dame
Dept. of Chemical and Biomolecular Engineering


11:00 AM
Thursday, March 7, 2013
CEB 218 (810 South Clinton Street)
The term “molecular simulation” refers to the use of computational methods to describe the behavior of matter at the atomistic level. Driven by advances in computational speed, parallelization and algorithms, molecular simulations are able to address increasingly relevant problems at a fraction of the computational cost required just a few years ago. In this seminar, I will highlight some recent results from our group where molecular simulations have played a key role in the development of new materials used in energy and environmental applications. In particular, I will focus on our efforts at developing new ionic liquids for CO2 capture and other gas separations as well as phase equilibria simulations in support of the development of new fluids for heating and cooling applications that are both environmentally friendly and energy efficient..

Thursday, February 21, 2013

From Rheology to Biology: The Application of Polymer Hydrodynamics to Problems in Biology
Prof. Ronald Larson
University of Michigan
Dept. of Chemical Engineering


11:00 AM
Thursday, February 21, 2013
CEB 218 (810 South Clinton Street)
Using Stokeslets, elastic elements, and Langevin dynamics, we develop meso-scale “bead-spring” methods to simulate the dynamics of polymer molecules in flow fields, and the self-propulsion of micron-sized bacterial swimmers. These methods allow us to predict the unraveling of long polymer molecules in shear and extensional flow, and in a droplet drying flow used for creating DNA micro arrays. In extensional flow, the unraveling is dominated by highly out-of-equilibrium “dumbbell” and “fold” configurations that produce a highly heterogeneous population of conformations. In shearing flow, the dynamics are dominated by tumbling of molecular configurations, due to vorticity. The results are successfully compared with experiments using single fluorescently stained DNA molecules, including DNA deposited during drying of a droplet. We apply these methods to study the hydrodynamics of swimming of multi-flagellated bacteria, such as Escherichia coli. Finally, we use microfluidic methods to determine the kinetics of target search of proteins along DNA molecules and the rates of transcription of DNA into RNA..

Thursday, January 31, 2013

Integrating Engineering and Biology in Cancer Research
Prof. Konstantinos Konstantopoulos
The Johns Hopkins University
Dept. of Chemical and Biomolecular Engineering


11:00 AM
Thursday, January 31, 2013
CEB 218 (810 South Clinton Street)
Cancer metastasis is a highly orchestrated multistep process, in which cancerous cells separate from a primary tumor and migrate across blood vessel walls into the circulatory system where they interact extensively with host cells before they lodge and colonize the target organ. This seminar will provide an example of a multidisciplinary approach integrating engineering fundamentals with concepts and techniques from biochemistry, biophysics and cell biology in order to better understand two key steps of the metastatic cascade: (a) the adhesive interactions of tumor cells in the circulation and (b) their migration through tissues. Specifically, it will emphasize the importance of the fluid dynamic environment in regulating the adhesion process of metastatic cancerous cells to host cells. In view of the critical role of a family of adhesion molecules called selectins in metastasis, the seminar will discuss our approach for the identification and functional characterization of selectin-binding molecules on tumor cells, and also outline how this information could lead to the development of novel diagnostic and therapeutic strategies. The seminar will also challenge the conventional wisdom regarding the mechanisms of cell migration, which has primarily been derived from studies on unconfined 2-dimensional (2D) extracellular matrices, and discuss how physical confinement alters the molecular machinery for tumor cell migration.

 
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