THE UNIVERSITY OF TEXAS AT AUSTIN • COCKRELL SCHOOL OF ENGINEERING. DEPARTMENT OF CHEMICAL ENGINEERING

Host: Dr. Buddie Mullins

Abstract summary coming soon!!!

Dr. Christopher Bohn, National Research Council – Energy Research Group

Seminar Abstract

Chemical looping is a new energy approach that permits combustion of fossil fuels with inherent capture of carbon dioxide and can achieve thermal efficiencies >50 %. I present results on the development of iron-based oxygen carriers with excellent redox stability and rapid kinetics over repeated cycles. Using experimental and numerical techniques, I demonstrate that these carriers can also be used to generate high purity hydrogen from coal or biomass while simultaneously capturing carbon dioxide for sequestration.

Iron oxide is also one of the few binary oxides capable of exceeding a solar to hydrogen efficiency of 10 % in photoelectrochemical water splitting. I show that activating n-type dopants in iron oxide by thermal annealing improves conductivity and photocurrent by three orders of magnitude. Further strategies for enhancement including plasmonic electrodes and nanostructuring are also presented.

Biography

Christopher Bohn is a National Research Council (NRC) Postdoctoral Research Associate in the Energy Research Group. He received his B.S.E. degree with honors in Chemical Engineering from Princeton University, and a Ph.D. in Chemical Engineering and Biotechnology from the University of Cambridge, UK. His doctoral work, supported by a Gates Cambridge Scholarship (you could cut this), focused on the synthesis and characterization of iron-based materials for use in carbon dioxide capture and hydrogen production. At the National Institute of Standards and Technology Nanolab, Chris is working with Veronika Szalai on integrating new concepts from optics and catalysis to enhance the efficiency of photoelectrodes for solar water splitting.

Seminar Abstract

Dr. Cole DeForest, California institute of Technology

There is a growing interest in understanding how a cell senses its microenvironment and how these external cues influence important cellular functions.  Such information may be particularly important from a fundamental perspective (e.g., defining the stem cell niche), as well as from the applied viewpoint of regenerating functional tissue equivalents.  Though both chemical and mechanical signals have been implicated in dictating local cell behavior, isolated effects are difficult to assess in vivo due to the myriad of uncontrollable, ever-changing cues.  In addition, many of these cues are presented in spatiotemporally-complex patterns.  To better understand how cells receive instructive information from their extracellular niche, synthetic environments including hydrogels have proven beneficial at assaying cell function in well-defined systems where single cues can be introduced and subsequent effects can be individually elucidated.  Unfortunately, few 3D culture platforms allow the experimenter to recapitulate the heterogeneous and dynamic nature of the native tissue environment through 4D control of the material properties in both time and space.  In this work, we demonstrate that by utilizing multiple photoreactions that are each initiated with different wavelengths of light, we can independently induce changes to the local physical and chemical material properties at specific locations within a hydrogel culture platform to direct real-time changes in cell function.  This talk will detail the synthesis and characterization of these dynamically-tunable hydrogel materials and will highlight several examples where user-triggered alterations in the cellular niche can be used to both better understand and direct stem cell fate.

Biography

Cole A. DeForest is a postdoctoral scholar with Dr. David Tirrell in the Divisions of Chemistry and Chemical Engineering at the California Institute of Technology.  He received his B.S.E. degree from Princeton University in 2006, majoring in Chemical Engineering and minoring in Material Science Engineering and Bioengineering.  He obtained his Ph.D. degree under the guidance of Dr. Kristi Anseth from the University of Colorado in Chemical and Biological Engineering with an additional certificate in Molecular Biophysics.  He has authored and co-authored 18 articles in peer-reviewed journals including Nature Materials, Nature Chemistry, and Angewandte Chemie.  Dr. DeForest has received numerous research awards and honors including the Biomedical Engineering Society Student Fellow Award (2013), DSM Polymer Technology Award (2011), ACS Excellence in Graduate Polymer Research Award (2010), MRS Graduate Student Research Gold Award (2009), Society for Biomaterials Outstanding Achievement Award (2009), Princeton University Material Science Student of the Year (2006), Princeton University Most Approachable Resident Adviser (2005), and Boulder High School Valedictorian (2002).  He has been supported through fellowships from the National Institutes of Health and the US Department of Education.  Dr. DeForest’s research seeks to develop and optimize bioorthogonal chemistries to probe and better understand fundamental cell function through user-programmable biomaterials whose physical and chemical properties can be tuned in time and space.

Seminar Abstract

Dr. Tse Nga (Tina) Ng, Palo Alto Research Center

Solution-processed electronic materials have been developed to enable manufacturing platforms complementary to conventional silicon technology. These electronic inks can be deposited and patterned by low-cost printing tools such as inkjet printers and gravure presses. Notably, the printing process is compatible with many substrates ranging from plastics to fibers, to potentially integrate electronics on any surface. At Palo Alto Research Center, I have developed processes for printed electronics that enable new form factors and applications in flexible displays and sensors. Some examples include flexible medical x-ray imagers and integrated logic-memory arrays. These applications required development of both individual device components as well as system integration.

In this talk, I will present the advantages and limitations of printed devices, and then discuss how to integrate the individual components together by using complementary organic transistor circuits. I will show how to tackle the challenges of device variations and stability in the integrated systems. Device characterization and circuit simulations are carried out to achieve designs that tolerate the variations in printed devices, as well as to determine design rules for reliable thin-film electronic systems. Both device structures and system-level view of printing are considered, in order to improve the reliability of the processes and accelerate the development of flexible electronics.

Biography

Dr. Tse Nga (Tina) Ng is a Senior Research Scientist with the Electronic Materials and Device Laboratory at Palo Alto Research Center (PARC). She joined PARC in 2006, and since then her research has focused on flexible electronics. Her work on printed systems has received the 2012 Innovation Award from Flextech Alliance and has been named Runner-up for the Wall Street Journal Technology Innovation Award. Tina received her M.S. and Ph.D. in physical chemistry from Cornell University, NY, USA, working with Professor John Marohn on the development of force measurement techniques, such as cantilever magnetometry and electric force microscopy, to study nanoscale phenomena in organic semiconductors.

Dr. Ardemis A. Boghossian, California Institute of Technology

Seminar Abstract

Plants have evolved highly sophisticated mechanisms of self-repair to regenerate proteins that become photo-damaged over time. In the absence of this self-repair cycle, plants demonstrate less than 5% of their photosynthetic yield, diminishing plant growth and lifetime. Key to this self-repair process is the reversible self-assembly of protein complexes, which is characterized by the molecular recognition of parts, kinetic trapping of meta-stable thermodynamic states, and chemical signaling to switch between states. In this seminar, we explore both biomimetic and natural regenerative mechanisms in an effort to develop biological light-harvesting devices with prolonged lifetimes.  We demonstrate the first synthetic photoelectrochemical cell capable of mimicking key aspects of the self-repair cycle. The dynamic photoelectrochemical complex consists of two recombinant proteins, phospholipids, and a single-walled carbon nanotube (SWCNT) that reversibly assemble into a particular configuration, forming an array of  lipid bilayers housing light-converting proteins. Surfactant addition and removal are used to signal between the disassembly and re-assembly of the photoactive complex, and a kinetic model reveals that the thermodynamically meta-stable complex can transition reversibly between free components and the assembled state at surfactant removal rates above 10^-5 sec^-1. Application of a biomimetic regeneration cycle increases photoconversion efficiency by more than 300% over 168 hours and extends the solar cell lifetime indefinitely. We also demonstrate the first intact, chloroplast-based biofuel cell.  Application of regenerative, reactive oxygen species (ROS) scavenging nanoceria (NC) particles is shown to enhance the natural regeneration cycle and fuel cell power output. Thus, the interface of nanotechnology with biological, light-harvesting components enables a new generation of dynamic, biological solar cells with enhanced natural and biomimetic self-repair mechanisms.

Biography

Ardemis A. Boghossian is currently a postdoctoral researcher in the Frances H. Arnold lab at the California Institute of Technology. She received her B.S. in Chemical Engineering from the University of Michigan in 2007. In 2012, she received her Ph.D. in Chemical Engineering from the Massachusetts Institute of Technology under the supervision of Michael S Strano. As a NDSEG fellow, Ardemis has contributed to the experimental and theoretical development of nanotube-based optoelectronic devices for both light-harvesting and sensing applications. Her current postdoctoral research focuses on using protein engineering and directed evolution to address the solar energy challenge.

Seminar Abstract

Dr. Qing Hua Wang, Massachusetts Institute of Technology

Graphene is a single atomic layer of carbon with extraordinary properties including exceptionally high electronic carrier mobilities, thermal conductivity, and mechanical strength

. Researchers are rapidly developing graphene-based applications in high-speed electronics, chemical and biological sensing, optoelectronics, and energy storage and conversion to take advantage of these behaviors. In all these applications, the chemical interaction of graphene with other materials plays a crucial role, and needs to be characterized and manipulated at the atomic level. The chemical functionalization of graphene via organic chemistry is actively being pursued for a variety of goals, including modifying its doping level and electronic structure, altering its affinity toward various organic, biological, and inorganic materials, and increasing its processability.

In this talk, I will describe my work on the chemical functionalization of graphene via two different approaches. First, I will discuss self-assembled monolayers of organic molecules that are physisorbed on the surface of graphene and characterized using atomic resolution scanning tunneling microscopy (STM). These monolayers, formed from perylene-based organic semiconductor molecules, have excellent long-range ordering with patterns that depend on intermolecular interaction forces that are not disrupted by surface defects in the graphene. These organic layers also serve as high quality seeding layers for the atomic layer deposition (ALD) of oxides, which play important roles in graphene electronics. Second, I will describe the direct covalent attachment of chemical groups onto the graphene lattice from diazonium salts. The chemical reactivity of graphene toward this reaction is found to depend strongly on the nature of the underlying substrate, as shown by Raman spectroscopic mapping. Covalent chemical schemes can also be exploited to robustly tether proteins to the graphene surface. Finally, I will also discuss the spatial micro- and nanopatterning of graphene chemistry in both covalent and noncovalent functionalization schemes via scanning probe lithography and reactivity imprint lithography, which will enable new applications in electronic devices and chemical sensors.

Biography

Dr. Qing Hua Wang is currently a postdoctoral researcher in Chemical Engineering at the Massachusetts Institute of Technology. She obtained her Ph.D. in Materials Science and Engineering at Northwestern University in 2010 and her B.A.Sc. in Engineering Science at the University of Toronto in 2005. Her research is focused on the synthesis, characterization, and application of 2D nanomaterials, in particular studying the interactions of graphene with molecules and materials. Her research interests also include scanning probe microscopy, optical spectroscopy, self-assembly, and nanofabrication.

Seminar Abstract

Dr. Ryan P. Lively, Algenol Biofuels

As corn-based biofuels reach their practical limits, advanced algae-based biofuels are poised to supply the rapidly increasing demand for renewable fuels.  Large energy costs in biorefineries using traditional separation techniques for dilute feedstocks are currently a hurdle, but also a major opportunity for innovation.  Advanced materials and their manufacturing into low-cost, energy-efficient separation devices to meet this challenge will be the focus of the talk.  First, post-combustion CO₂ capture will be discussed as an economical carbon source for the algae.  A highly scalable materials production technique—fiber spinning—is used to create high-flux polyimide hollow fiber membranes as well as multi-layer hollow fiber sorbents that function as integrated adsorbing heat exchanging devices.   Flexible zeolitic imidazolate frameworks (ZIFs) are identified as promising candidates for advanced filler materials in polymer-inorganic hybrids.  The versatility of the fiber sorbent platform is illustrated.  Materials synthesis, bench-scale module testing and technoeconomic analysis of these fiber-based systems will be presented.  Besides the CO₂ capture challenge, purification of dilute ethanol feeds must be addressed.  In this regard, a highly hydrophobic zeolite is a uniquely attractive candidate for dilute ethanol recovery.  Fundamental transport and thermodynamic characterizations of a suitable zeolite for this application are presented.  Exceptionally high ethanol/water selectivities are obtained for the neat zeolite.  Zeolite morphology control is demonstrated, as is the inclusion of high aspect ratio forms of the zeolite into hybrid materials. Routes forward for both separations are discussed.

Biography

Dr. Lively’s research seeks to revolutionize fluid separation processes critical to the global energy infrastructure via application of chemistry-inspired materials design. During his Ph.D. studies at Georgia Tech, he introduced a rapid temperature swing adsorption (RTSA) approach for post-combustion CO₂ capture. This concept was successfully demonstrated by adapting knowledge developed in membrane science to design unique nanoscale composite adsorbent/heat exchangers.  Through collaboration with faculty at Georgia Tech, Dr. Lively successfully guided this RTSA approach towards a new three million dollar research program at Georgia Tech funded by the Department of Energy, General Electric, Algenol Biofuels, and Southern Company.

Currently a post-doctoral fellow working for Algenol Biofuels, Dr. Lively is expanding his expertise in gas and liquid separations by designing new materials and processes for gas and liquid management in enclosed algal bioreactors. This position involves first-hand interaction with realistic separation challenges and requires workable solutions rooted in materials science. With an emphasis on materials research and a “top-down,” process-guided materials development strategy, Dr. Lively has created membranes and sorbents that are tailored specifically for the challenges in the biofuels industry. An array of readily tunable microporous materials, functional polymers, tunable copolymers, and a stable of commercially available polymers are the tools used in his work.  Dr. Lively has created composite materials (e.g., mixed matrix membranes, hollow fiber sorbents, micro-capillary heat exchangers, etc.) that can be integrated into demanding industrial systems.

Host: Dr. Brian Korgel

Abstract summary coming soon!!!

Host: Dr. Lea Hildebrandt Ruiz

Abstract summary coming soon!!!

Host: Dr. Gyeong Hwang

Abstract summary coming soon!!!

Texas Distinguished Faculty Lectureship

(Reception to follow in CPE 2.802F)

Hosts: Drs. Lydia Contreras & Hal Alper

Abstract summary coming soon!!!

Dr. Shaoyi Jiang, University of Washington

Seminar Abstract:

An important challenge in many applications, ranging from biomedical devices to ship hulls, is the prevention of nonspecific biomolecular and microorganism attachment on surfaces. For example, nonspecific protein adsorption degrades the performance of surface-based diagnostic devices and causes an adverse effect on the healing process around implanted biomaterials. To address this challenge, our goals are twofold. First, we strive to provide a fundamental understanding of nonfouling mechanisms at the molecular level using an integrated experimental and simulation approach. Second, we aim to develop biocompatible and environmentally benign ultra low fouling materials based on the molecular principles we have learned. Over the last few years, we have demonstrated that zwitterionic and mixed charge materials and surfaces are highly resistant to nonspecific protein adsorption, cell adhesion and bacteria adhesion/biofilm formation from complex media. Both simulation and experimental results show that the strong hydration of zwitterionic materials is responsible for their excellent nonfouling properties. In addition to their excellent nonfouling properties, zwitterionic carboxybetaine-based materials have functional groups for direct ligand immobilization while the cationic precursors of zwitterionic materials have self-sterilizing capabilities. Superhydrophilic zwitterionic materials are also shown to have unique advantages for stealth nanoparticles over their amphiphilic poly(ethylene glycol) (PEG) counterparts. At present, zwitterionic materials have already been applied to a number of applications, including implantable medical devices, early cancer diagnostics, drug/gene delivery, antimicrobial coatings, and marine coatings.

Seminar Abstract:

Dr. Rangaramanujam Kannan, Johns Hopkins School of Medicine

Neuroinflammation, caused by activated microglia and astrocytes, plays a key role in the pathogenesis of cerebral palsy (CP), retinal degeneration, and other debilitating neurodegenerative disorders. Engineering and reprogramming the microglial response, to achieve targeted attenuation of neuroinflammation, can be a potent therapeutic strategy. However, drug delivery to the central nervous system is strongly restricted for most drugs by the blood-brain-barrier, making treatment of diffuse neuroinflammation a challenge. We take advantage of the unique, intrinsic, pathology-dependent, biodistribution patterns of dendrimers (with no targeting moieties) in diseases models of neurodegeneration. For example, dendrimers are transported to the periventricular region of the brain of newborn rabbit kits with cerebral palsy (CP), whereas little brain uptake is seen in healthy animals. Interestingly, they further localize selectively in activated microglia and astrocytes in animals with CP. Such selective localization in activated microglia is also seen in retinal degeneration models, upon intravitreal administration.¹ Building on these findings, we have designed and synthesized dendrimer-drug nanodevices, taking advantage of their rich surface functionality using appropriate linking chemistry. They can deliver and release the drug in the targeted tissue in a tailored and sustained manner. Two examples of this approach of targeting neuroinflammation the retina (intravitreal administration)² and the brain (intravenous administration)² will be presented. We show that a single intravenous dose of dendrimer-drug conjugate, administered after birth to rabbit kits with CP, results in significant improvement in motor function along with decrease in neuroinflammation and oxidative/neuronal injury, followed by improved myelination, by 5 days of age.¹ These studies suggest that attenuation of ongoing neuroinflammation, achieving by appropriate engineering of the glial response, can have significant positive consequences in these and other debilitating neurodegenerative diseases. Application of this approach to designing dendrimer-based targeted therapeutic platforms is being explored in a variety of systemic inflammation and neuroinflammation-associated disorders.

References:

1. S Kannan, H Dai, RS Navath, B Balakrishnan, A Jyoti, J Janisse, R Romero, RM Kannan (2012). ‘Dendrimer-based postnatal therapy for neuroinflammation and cerebral palsy in a rabbit model’. Science Translational Medicine, 4(130), p. 130ra46. Highlighted in Nature, Science, Nature Review Drug Discovery.

2. R Iezzi, B Raja Guru, I Glybina, M Mishra, A Kennedy, RM Kannan (2012). ‘Dendrimer-based targeted intravitreal therapy for sustained attenuation of neuroinflammation in retinal degeneration’. Biomaterials, 33(3), 979-988.

Dr. Karen Winey, University of Pennsylvania

Seminar Abstract:

Nanoparticles, particularly carbon nanotubes and metal nanowires, provide new routes for engineering the electrical properties of polymers.  This lecture will focus on two aspects of this expanding field, namely electrical conductivity and resistive switching.  With regard to electrical conductivity, Winey’s group has demonstrated the importance of nanotube orientation both via simulation and by melt processing the nanocomposite to align carbon nanotubes and using X-ray scattering to quantify the extent of orientation.  To better compare simulations and experimental results, Winey’s group has made silver nanowires of well-defined aspect ratios (L/D < 50) and the experimental thresholds for electrical percolation compare favorably with both their simulations and analytical models as a function of aspect ratio.  Most recently, Winey’s group has extended the simulations to polydisperse systems and thin films.  The study of electrical percolation in polymer nanocomposites presumes that two states dominate such that below and above the critical concentration the electrical conductivity is dominated by the insulating matrix and by the conductive fillers, respectively.  In contrast, Winey and her group have found resistive switching in nanocomposites of silver nanowires and polystyrene, wherein these bulk materials can reversibly transform from high to low resistance as a function of applied voltage.  Cyclic voltammetry measurements at 10K are consistent with the hypothesis that applied voltage can form conductive silver filaments between neighboring nanowires.  Dynamic electrical properties in bulk polymer nanocomposites may enable new applications for polymer nanocomposites as functional materials.

Dr. Christopher Roberts, University of Delaware

Seminar Abstract:

Protein aggregation is a ubiquitous concern during biopharmaceutical product formulation and process development. The process of nonnative aggregation has also attracted long-standing interest in fundamental disease studies due to its potential role in a growing number of chronic ailments such as Huntington’s Disease, Alzheimer’s Disease, and prion diseases. In both cases, there is evidence that the size, structure, and/or morphology of aggregates are important factors in the biological response(s) to aggregates in vivo. Aggregation of native or folded proteins is also a long-standing area of research, both as a possible approach for bio-separations, as well as its implications for limiting drug dosage or delivery options. This seminar focuses on experimental, modeling, and protein engineering approaches to control or predict the effects of mutations and solvent conditions on aggregation and self-assembly of therapeutic and model proteins. The importance of electrostatic interactions is highlighted by a number of examples, including aggregation mechanisms, phase behavior of aggregates (as opposed to monomers), and structural perturbations to the native state.  These provide insights into rational formulation design, as well as different design paradigms to arrest or drive aggregation.  A different approach to interpreting laser light scattering and related experiments is also proposed, that allows one to easily deal with both low and high concentration protein conditions, but highlights that “low” and “high” concentrations are not as simple a definition as conventionally accepted.

Dr. Cato Laurencin, University of Connecticut Health Center

2012-2013 Pirkey Lectureship

(Reception to follow in CPE 2.802F, food provided by Dine by Design)

Seminar Abstract:

The next ten years will see unprecedented strides in regenerating musculoskeletal tissues. We are moving from an era of advanced prosthetics, to what I term regenerative engineering. In doing so, we have the capability to begin to address grand challenges in musculoskeletal regeneration.  Tissues such as bone, ligament, and cartilage can now be understood from the cellular level to the tissue level.  We now have the capability to produce these tissues in clinically relevant forms through tissue engineering techniques. Our improved ability to optimize engineered tissues has occurred in part due to an increased appreciation for stem cell technology and nanotechnology, two relatively new tools for the tissue engineer.

Critical parameters impact the design of novel scaffolds for tissue regeneration. Cellular and intact tissue behavior can be modulated by these designs. Design of systems for regeneration must take place with a holistic and comprehensive approach, understanding the contributions of cells, biological factors, scaffolds and morphogenesis.

Seminar Abstract:

This seminar topic concerns fundamental issues of cell growth and development as they relate to human disease and therapeutic intervention.  Efforts are directed towards understanding human cancer as a disease of uncontrolled cell growth and development.  A common theme within this biology is a rewiring of metabolism to support and drive these processes.  At the core of this effort lies the utilization of computational modeling and high throughput technologies.  Using these tools, I have studied the effects of an alternative glycolytic pathway observed in proliferating cells that I recently identified.  These efforts have enumerated several principles of glycolytic regulation in growing cells.  Towards this end, I have defined and characterized a metabolic pathway that is genetically selected for and drives the development of human cancer.  This pathway involves the diversion of glycolytic flux into de novo serine metabolism through phosphoglycerate dehydrogenase (PHGDH).  This direction has also led to the study of problems in stem cell biology and cell fate determination that I will discuss.  Together, these findings define a systems biology approach through combining these mathematical tools with an integration of genetics, biochemistry, and cell biology along with high-throughput technologies such as mass spectrometry.  Investing such effort I believe has the potential to fundamentally alter our understanding of disease biology and lead to innovative therapies.

Seminar Abstract:

An important notion that is emerging in post-genomic biology is that cellular components can be visualized as a network of interactions between different molecules like proteins, RNA, DNA and metabolites. This has led to the application of network theory to a wide range of biological problems including understanding regulation of gene expression, function prediction, host-microbe associations and drug discovery settings. While in transcriptional networks, typically trans-acting elements like TFs and sigma factors form one set of nodes and their target genes, of which they control the activity, form the other set of nodes. The links between them which have directionality from the trans-acting elements to their target genes, controlled by their cis-regulatory elements, form a complex and directional network of interactions. In the first half of my talk, I will focus on our recent understanding of the structure of the transcriptional regulatory networks in prokaryotic and eukaryotic organisms. I will then present evidence that transcriptional regulation plays a significant role in shaping the organization of genes on chromosomes in both the major domains of life, bacteria and eukarya. In the second half, I will present our efforts to systematically dissect the expression dynamics of RNA-binding proteins (RBPs) in post-transcriptional networks formed by RBPs and their target RNAs in the model eukaryote, S. cerevisiae. Our analysis shows that RBPs generally exhibit high protein stability, translational efficiency and protein abundance but their encoding transcripts tend to have low half-life. Analysis of the RBP-RNA interaction network revealed that the number of distinct targets bound by an RBP (connectivity) is strongly correlated with its protein stability, translational efficiency and abundance. We also note that RBPs show less noise in their expression in a population of cells, with highly connected RBPs showing significantly lower noise indicating that highly connected RBPs are likely to be tightly regulated at the protein level as significant changes in their expression may bring about large-scale changes in global expression levels by affecting their targets. Towards the end, I will briefly introduce the notion of Drug-Target networks and present some of the problems, which are being addressed using this framework.

Recent selected references :
1) Martinez-Antonio A, Janga SC, Thieffry D, Functional organisation of Escherichia coli transcriptional regulatory network, Journal of Molecular Biology, 2008
2) Janga SC, Collado-Vides J, Babu MM, Transcriptional regulation constrains the organization of genes on eukaryotic chromsomes, Proc Natl Acad Sci U S A, 2008
3) Janga, SC, Salgado H, Martinez-Antonio A, Transcriptional regulation shapes the organization of genes on bacterial chromosomes, Nucleic Acids Research, 2009
4) Mittal N, Roy N, Babu MM, Janga SC, Dissecting the expression dynamics of RNA-binding proteins in post-transcriptional regulatory networks, Proc Natl Acad Sci U S A, 2009
5) Scherrer T, Mittal N, Janga SC, Gerber AP, A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes PLoS One. 2010
6) Mittal N, Scherrer T, Gerber AP, Janga SC, Interplay between post-transcriptional and post-translational interactions of RNA-binding proteins, Journal of Molecular Biology, 2011
7) Janga SC, Mittal N Construction, structure and dynamics of post-transcriptional regulatory network directed by RNA-binding proteins Adv Exp Med Biol. 2011
8) Janga SC, Tzakos A, Structure and organization of drug-target networks: insights from genomic approaches for drug discovery, Mol. Biosyst, 2009

Texas Distinguished Faculty Lectureship

Seminar Abstract:

G.V. Rex Reklaitis

Gedge Distinguished Professor

School of Chemical Engineering

Purdue University

West Lafayette, IN

Launched in July 2006 with support from the NSF, over 30 industrial partners, and the four hosting universities, the Center aspires to be the national focal point for science-based development of structured organic particle-based products and their manufacturing processes. Such products, which are comprised of multi-component organic systems whose performance depends on microstructure, are widely used to deliver active substances at predetermined rate and in specific environments. This family of products is manufactured using similar processes across a number of industries, including pharmaceuticals, nutraceuticals, agricultural agents, detergents, and foods. The engineering of such products encounters common technical limitations:

• Solid state physics that is poorly understood
• “Soft” materials that are delicate – High shear/high temperature conditions must be avoided
• Constitutive behaviour has a hierarchy of scale and substantial complexity

The manufacturing of these products has been largely carried out in batch mode, with limited on-line sensing and automation, and limited availability of reliable engineering predictive models to support process design, scale-up and operation.

In this presentation, we will outline the technical objectives and organization of the research plan under which the Center has been operating. Highlights will be given of representative research projects in ares such as understanding of material properties, predictive modeling of key unit operations, knowledge management, on-line sensing (PAT) and real time process management. Progress on the realizization of the three test beds specifically targeted for production of solid oral dosage pharmaceuticals and the steps taken towards the commercialization of one of these, a continuous automated tableting line, will be reviewed.

Seminar Abstract:

In the current talk we will present our recent results on the development of alternative catalysts for H₂ production.  The main objective of our research is to identify catalysts to substantially reduce or replace Platinum-group metals.  Our research approaches involve parallel efforts in density functional theory (DFT) calculations, surface science experiments on model systems, and synthesis and characterization of supported catalysts under thermochemical or electrochemical conditions.

We will first use water electrolysis to demonstrate the feasibility of using monolayer Pt on tungsten carbide (WC) to achieve the same activity as bulk Pt [1].  We will present DFT calculations of similar electronic and chemical properties between monolayer Pt/WC and Pt, synthesis and characterization of monolayer Pt/WC films, and electrochemical evaluation of the activity and stability of Pt/WC for water electrolysis.  Comparing to the leading Pt electrocatalyst, the monolayer Pt/WC represents a reduction by a factor of ten in Pt loading [2].  We will then use the thermochemical production of H₂ to illustrate the advantages of using bimetallic catalysts.  Bimetallic catalysts often show unique activity and selectivity over their parent metals due to the electronic modification and strain effect.  We will present our results of using Ni/Pt bimetallic surfaces and catalysts for H₂ production from polyols [3,4] and ammonia [5], further highlighting the importance of using the combined approaches of DFT calculations, surface science experiments, and reactor evaluations.

[1]  D.V. Esposito, S.T. Hunt, K.D. Dobson, B.E. McCandless, R.W. Birkmire and J.G. Chen, “Low-Cost Hydrogen Evolution Catalysts Based on Monolayer Platinum on Tungsten Monocarbide (WC) Substrates”, Angewandte Chemie International Edition, 49 (2010) 9859-9862

[2]  D.V. Esposito and J.G. Chen, “Monolayer Platinum Supported on Tungsten Carbides as Low-Cost Electrocatalysts: Opportunities and Limitations”, Energy & Environmental Science, 4 (2011) 3900-3912.

[3]  M. Salciccioli, W. Yu, M.A. Barteau, J.G. Chen, D.G. Vlachos, “Differentiation of O-H and C-H Bond Scission Mechanisms of Ethylene Glycol on Pt and Ni/Pt Using Theory and Isotopic Labeling Experiments”, Journal of the American Chemical Society, 133 (2011) 7996-8004.

[4]  W. Yu, M.A. Barteau and J.G. Chen, “Glycolaldehyde as a Probe Molecule for Biomass-derivatives: Reaction of C-OH and C=O Functional Groups on Monolayer Ni Surfaces”, Journal of the American Chemical Society, 133 (2011) 20528-20535.

[5]  D.A. Hansgen, D.G. Vlachos and J.G. Chen, “Using First Principles to Predict Bimetallic Catalysts for the Ammonia Decomposition Reaction”, Nature Chemistry, 2 (2010) 484-489.

Seminar Abstract:

Block copolymer directed self assembly continues to make advances that place this technology as a potential candidate for sub-20nm lithography.  The naturally periodic features found in block copolymer films display superior size uniformity at ultra-high densities, making them ideal lithographic masks to define the highly periodic data bits in the data sectors of hard disk drives for bit patterned media (BPM) technology at densities beyond 1Tbit/in^2.

Nanofabrication challenges towards bit patterned media, however, reach far beyond pattern formation at small length scales. We explore two potential architectures amenable to directed self assembly: arrays of hexagonal close packed (hcp) circular dots and arrays of rectangular bits with a high aspect ratio. On the one hand, hcp patterns maximize feature density for a given lithographic dimension while, on the other hand, rectangular patterns support wider write head poles in order to achieve the high write fields needed to write high-coercivity media. In both cases a combination of e-beam lithography with block copolymer self assembly ensures the small dimensions required for high density media together with the flexibility to achieve accurate translational placement over circular tracks with constant angular pitch. We review the benefits and implications of using block copolymer thin films as lithographic masks. We will show that, even though it represents a major departure from the semiconductor lithography roadmap, a combination of e-beam lithography with block copolymer assembly stands as one of the most viable candidates to nanoimprint templates for BPM technology.

Seminar Abstract:

With the advent of high throughput biomolecular engineering techniques, it has become possible to isolate short peptides that bind to a variety of targets ranging from inorganic materials to proteins.  The application of peptides as therapeutics has been hampered by the inherent susceptibility of peptides to proteases present throughout the human body.  One strategy to overcome this protease susceptibility is to fortify peptides via cyclization or other conformational constraints.  Indeed, nature uses this strategy in several classes of peptides such as cyclotides and defensins which are stabilized by networks of disulfide bonds and in some cases head-to-tail cyclization.  My group studies a class of peptides termed lasso peptides because of their unique slipknot-like structure.  This highly entropically disfavored fold endows the peptides with tremendous stability; some lasso peptides can retain their structure and function even after boiling in 8 M urea.  Lasso peptides are also resistant to proteolysis by digestive proteases such as pepsin and chymotrypsin.  In this talk I will describe our efforts in understanding the biosynthesis of lasso peptides with a particular focus on the role of the leader peptide in lasso peptide biosynthesis.  I will also describe our efforts in lasso peptide engineering including a directed evolution study aimed at improving the antimicrobial efficacy of the lasso peptide microcin J25.  Finally I will describe new work on the biosynthesis of “designer” lasso peptides in which we graft an arbitrary peptide sequence onto the hyperstable lasso peptide scaffold.

Cockrell School of Engineering Lectureship

Seminar Abstract:

The pathological hallmark of more than twenty neurodegenerative diseases, like Alzheimer’s, Parkinson’s and the prion diseases, is the presence within the brain of plaques containing ordered protein aggregates called fibrils. It is not yet known why these structures form in some individuals and not in others, or whether the plaques are toxic or Nature’s way of sequestering toxic species. Dr. Hall will describe current thinking on the scientific underpinnings for this phenomenon, and her computational efforts to contribute to our knowledge of how and why proteins assemble into fibrils.

Seminar Abstract:

Energy efficiency and sustainability are major factors towards mitigating the depletion of fossil fuel reserves and the environmental impact of their consumption. Tight integration is a key enabler towards achieving these goals, both in existing chemical plants, but also in emerging technologies for power generation and for production of fuels and chemicals from renewable resources.

The first part of the talk will focus on the dynamics and control of tightly integrated process networks. The efficient transient operation of such networks is essential, as the current economic environment dictates frequent changes in operating states and a tight coordination between the optimization and supervisory control levels. Recent results will be discussed which establish that tight integration, achieved through large material and / or energy recycle, leads to multi-time-scale dynamics, with individual units evolving in a fast time scale with weak connections, which become significant over slower time scales giving rise to a slow evolution of the entire process network. A model reduction framework will be described which enables obtaining a hierarchy of low-order nonlinear models valid in the different time scales. The analysis lends itself naturally to a hierarchical control framework which allows for the development of robust nonlinear supervisory control strategies for effective network transitions. The efficacy of the proposed hierarchical controller design framework will be illustrated through case studies on reaction-separation networks, reactor – heat exchanger networks, heat integrated and thermally coupled distillation columns, and hybrid power production systems.

The second part of the talk will focus on the emerging concept of biorefinery, which aims at the production of fuels and chemicals from renewable resources (biomass). Although considerable emphasis has been given so far to the “upstream” conversion of biomass to intermediate platforms (sugars or syngas), progress in “downstream” conversion to chemicals and intermediates is still lagging. Due to the oxygen present in biomass and the diversity of raw materials derived from biomass, the necessary downstream reaction and separation processes are different from existing ones based on fossil fuels. Furthermore, there is limited data available on physical properties of such molecules, and on their full array of chemical transformations, and their kinetics and thermodynamics. These challenges lead to several emerging opportunities for systems research that can have a major impact on the realization of the ambitious concept of an integrated biorefinery. The talk will highlight such opportunities and will discuss recent results on: i) the elucidation of the chemical transformations involved in biomass conversion, and ii) the design and optimization of novel reaction-separation processes for biomass-based chemical synthesis.

Seminar Abstract:

Plasmonic nanostructures have long been known to manipulate light to yield unique optical properties.  In this essence, my talk will discuss how optical properties of plasmonic nanostructures can be harnessed to understand fundamental physical processes directly relevant for biomedical and energy applications.  First I will show how metal nanoshells, plasmonic nanostructures consisting of a silica core wrapped in a gold shell, when coupled to fluorophores in their vicinity give rise to remarkable distant-dependent enhancements in their emissive properties. I will particularly describe the fluorescence enhancement of clinically relevant and FDA-approved near-infrared fluorophore, Indocyanine green.  Then I will describe the use of these enhanced fluorescent nanoshells combined with iron oxide nanoparticles and targeting moieties for multi-modal MRI and fluorescence imaging, and targeted photothermal therapy of cancer cells both in vitro and in vivo.  I will show in situ tracking of these multifunctional nanoshells in vivo providing detailed information regarding the distribution and fate of complex nanoparticles designed for specific diagnostic and therapeutic functions.

In the next part of my talk I will discuss the use of plasmonic nanostructures as probes for the design of next-generation hydrogen storage systems. Currently, experimental understanding of how nanoparticle size controls the kinetics and thermodynamics of metal-hydride formation and decomposition is limited due to challenges both in directly probing these events at the nanoscale, and preparing uniform samples over a series of sizes.  By developing a sensitive optical technique to monitor the luminescence of metal nanocrystals in-situ, I will present experimental results detailing the thermodynamics and kinetics of hydride phase transformations within a size-series of monodisperse palladium nanocrystals. This in situ optical approach enables a detailed understanding of how nanocrystal surfaces impact the energy barriers to hydride nucleation which directly impacts the design of practical high-performance hydrogen storage materials.

Seminar Abstract:

Zeolites are crystalline inorganic oxides that contain microporous channels, cages and pockets that are typically sub-nanometer in dimension. They are indispensable catalysts in the petrochemical industry because their microporous voids can select molecules and reactions using size exclusion criteria. In many cases, the choice of zeolites to meet specific catalytic targets has relied on phenomenological concepts of shape selectivity. This reflects, in part, our incomplete understanding of confinement effects in zeolite catalysis, which has been limited by the combined effects of active site and surrounding environment properties to reaction rates and by the presence of different void structures within a given microporous solid. A more fundamental understanding of acid strength and confinement effects in zeolite catalysis is required to improve existing processes for petroleum-based fuel and chemical production. More importantly, this knowledge is also relevant to the development of new catalytic technologies for the selective conversion of renewable carbon sources (lignocellulosic biomass) that differ markedly from petroleum in terms of thermal stability, chemical functionality and oxygen content.

In this talk, I will discuss how kinetic and mechanistic studies of Brønsted acid-catalyzed reactions of hydrocarbons (alkanes, alkenes) and oxygenates (alkanols, ethers) can be used to independently assess acid strength and solvation effects in catalysis. These studies show how turnover rates and selectivities depend on specific catalyst and reactant properties, such as acid site deprotonation energies and reactant gas-phase proton affinities. They show that zeolites can behave as catalytically diverse materials, in some cases with enzyme-like reaction specificity, for reasons beyond simple considerations of shape selectivity. This diversity arises from the stabilization of reactive intermediates and transition states by dispersion forces upon confinement and prevails even for Brønsted acid-mediated reactions, which is remarkable in light of the similar acid strengths among aluminosilicate zeolites. These insights have clarified enduring controversies regarding the effects of thermal, chemical and cation-exchange treatments on the catalytic reactivity of faujasite zeolites used in fluid catalytic cracking. These concepts and findings give predictive guidance about which void environments provide the right fit for certain reactions and represent progress toward the design of catalytic materials that convert alternative feedstocks to fuels and chemicals derived historically from petroleum.

Seminar Abstract:

Sun provides more than 150,000 TW of incident radiation on earth which can easily provide us a carbon neutral source of renewable energy to meet our current needs (~15 TW). However, energetically broad distribution of the emitted electromagnetic radiation from the sun poses significant scientific challenges to harvest this energy economically. Conventionally, a semiconductor photocell absorbs this incident radiation generating electron-hole pairs across its energy bandgap, which are then collected at different electrodes to get useful electric power. However, material challenges of collecting these charge carriers before they recombine, along with fundamental challenges of utilizing the excess energy from “hot” carriers (generated by photons with energy higher than semiconductor bandgap), need to be addressed to develop clean energy sources.

Here, I will discuss my recent results on progress made in developing efficient thermophotovoltaic emitters and infrared photocells to achieve above mentioned goals. Thermophotovoltaics (TPV) is a less-studied alternative to the photovoltaic (PV), or light-to-electric, energy conversion method described above. In TPV, a secondary emitter re-emits all the incident power as an energetically narrow beam of infrared light matched to the photocell bandgap. This incident light can then be converted efficiently into electricity without incurring losses from hot-carriers. However, emission from real materials has impeded study in this area. I will show how refractory materials, like tungsten, can be easily molded into desired nanophotonic or plasmonic metamaterials to selectively tailor the glow and directionality of the emitted light. Moreover, this energy-conversion process requires using this tailored light source (or incident sunlight for PV) to generate electricity using a cheap photocell module. I will discuss my recent results in understanding charge transport and tuning recombination dynamics in thin film semiconductor devices, specifically semiconductor nanocrystals, for development of solution processable, inexpensive, infrared photocell modules. I will also discuss some fundamental advances made in thin-film plasmonics which can be beneficial not only for development of thinner solar cells, but also for developing next-generation of medical sensors, faster computer chips etc.

Seminar Abstract:

Heterogeneous catalysts form the bedrock of industrial processes, yet little is understood in terms of structure-activity relationships. This is complicated by the fact that heterogeneous catalysts are not structurally identical, and that the catalysts change over the course of the reaction. Comprehensive characterization is necessary in order to determine the catalytic sites and hence mechanisms. In the first part of the talk, I present an amorphous molybdenum sulfide catalyst active for hydrogen evolution, photo-sensitized by semiconductor nanorods to produce solar fuel. The uniformity and large surface area of these molybdenum sulfide coated cadmium chaldogenide nanocrystals facilitate the structural and electronic characterization of the catalytically active species. In the second part of the talk, hydrogen uptake is monitored at the single particle level using darkfield spectroscopy. This non-invasive, in situ technique reveals that the hydrogen storage trajectories of plasmonic particles are shape dependent. Single particle studies of catalytic events allow measurements that would otherwise be obscured by ensemble averaging.

Seminar Abstract:

Reducing the cost of solar energy has been named one of the grand challenges for the 21st century by the National Academy of Engineering. Solution processed plastic solar cells are one path toward achieving this goal and have already demonstrated solar power conversion efficiencies as high at 10% in the lab and it is believed that more than 15% should be possible in tandem devices. While this level of performance is lower than has been achieved with conventional semiconductors, the ability to print from low cost inks onto plastic substrates at low temperatures and avoid the expenses associated with rare earth or monocrystalline semiconductors results in low costs per watt and rapid energy payback times. While the technology is still developing and thus the current modules are relatively low performance and expensive, the ability to fabricate semi-transparent and colored solar panels has enabled a range of niche applications inaccessible to inorganic solar cells.

While there has been remarkable success over the last several years at developing new materials and device structures to increase the efficiency of lab-scale organic solar cells, there is still a great deal that is not well understood about the underlying physics and materials science of these devices. After a brief introduction to the field, this talk will discuss our research in two areas of critical importance to the large scale commercialization of organic solar cells. The first topic will be the origin of non-langevin recombination kinetics in certain bulk heterojunction solar cell materials. Non-langevin recombination is an important enabling property for the low cost manufacturing of polymer solar cells. The second topic will discuss the use of ultrafast spectroscopy to identify the minimum driving force for electron transfer in polymer/fullerene blends, which is one of the primary factors determining the upper limit of efficiency for single junction organic solar cells. Our progress in both these areas has resulted from cross-disciplinary collaboration between researchers in academia, industry, and the national labs to better understand the underlying science and the ultimate potential of this emerging photovoltaic technology.

Seminar Abstract:

Crystalline silicon and thin-film technologies have ruled the photovoltaic landscape for several decades with continual efficiency improvements and cost reductions.  One recent trend has been to use thinner semiconductors, which reduces both materials cost and losses associated with bulk recombination.  Light management for these and more advanced multi-junction structures becomes critical in order to maximize absorption in the active layer and minimize parasitic loss in the electrodes.  This talk will first discuss our work using periodic arrays of vertical silicon nanowires to improve light absorption in thin films of crystalline silicon.  By forming a photonic crystal structure we can control the propagation of light through the material leading to path length enhancements above the randomized scattering limit.  Increased surface recombination losses due to the nanowire geometry can be minimized by coating the structure with a hole conducting polymer, which simultaneously forms a junction for charge carrier extraction and helps to passivate the surface leading to improved solar cell photocurrent.  The talk will then detail how we exploit the plasmonic field enhancements in small gaps between silver nanowires self-assembled from solution to locally heat and weld them together only at junction points, forming excellent transparent electrodes.  Since the heat generation is strongly dependent on the gap size, it self-limits after welding occurs, preventing further heating that could break apart nanowire networks or damage heat-sensitive materials underneath.  Finite element method simulations show that at each junction the top nanowire focuses light and generates heat selectively in the bottom nanowire while electron microscopy confirms that the bottom nanowire always recrystallizes epitaxially onto the top nanowire at the junction.  We have watched this welding process evolve in time using dark-field scattering and electrical resistance measurements on single junctions and connected the microscopic changes to results in macroscopic interconnected networks of silver nanowire transparent electrodes.  The highly local nature of the heating enables this plasmonic welding process to be used for metal nanowire mesh electrodes on heat-sensitive substrates like Saran Wrap and polymer photovoltaics that are destroyed using a standard hotplate treatment.  These studies lay the foundation for a metal nanowire top electrode self-assembled from solution that simultaneously acts as an active optical element to increase light absorption and a high-performance transparent electrode to collect current.

Seminar Abstract:

New applications in electronics and optics require methods of forming micro- and nanostructures in ways that are applicable to different classes of materials and substrates. These methods should also be simple, inexpensive, and amenable to manufacturing. This seminar describes several unconventional methods of forming micro- and nanostructures for electronic, optical, and optoelectronic applications. These methods all have a mechanical process as a key step. The first part of the seminar focuses on nanoskiving and several supporting techniques. Nanoskiving is a process of fabrication and replication that combines soft lithographic molding and the deposition of thin films (by physical or chemical means) with ultrathin mechanical sectioning with an ultramicrotome. This seminar describes the constraints on the materials applicable to nanoskiving, and then describes several applications, including nanowire chemical sensors, addressable nanowire electrodes for electrodeposition, organic photodetectors, plasmonic waveguides, and near-IR filters. Supporting techniques developed include mechanical and magnetic methods to manipulate the structures produced by nanoskiving and transfer them to optical fibers and other optical structures. The first part of the seminar also discusses two additional forms of unconventional fabrication: shadow evaporation, and fabrication using a commercial nanoindentation system. Proof-of-principle applications demonstrated using shadow evaporation include field-effect transistors and logic gates produced using a single step of photolithography, and applications of nanoindentation include substrates for surface-enhanced Raman spectroscopy.

The second part of the seminar describes two applications of elastic micro- and nanostructured devices: a stretchable “rubber” solar cell, and a stretchable sensor of pressure and strain. A stretchable organic solar cell was fabricated by spin-coating the transparent electrode and active layer on a pre-strained elastomeric membrane. Upon release of the pre-strain, the films formed topographic waves that imparted elasticity to the device when strained (up to 27%). The device exhibited similar photovoltaic properties when both stretched and unstretched. This seminar also describes the fabrication and properties of a transparent, elastic, skin-like sensor of pressure and strain comprising transparent patterns of spray-deposited films of carbon nanotubes, which were rendered stretchable by an application of strain and release along each axis. This action produced spring-like structures in the nanotubes, which accommodated strains up to 70% with little change in resistance. When embedded in elastomeric membranes, the nanotube films functioned as electrodes in arrays of transparent, stretchable capacitors, which manifest applications of pressure or tension as increases in capacitance.

2011-2012 Pirkey Lectureship

Seminar Abstract:

Our increasing concerns on limited fossil resources and environmental problems including climate change are urging us to develop sustainable systems for the production of chemicals, fuels and materials from renewable resources. Microorganisms have been and will be playing crucial roles in such bioprocesses. When they are isolated from nature, however, their performance is not good enough to be employed for industrially competitive processes. That is why metabolic engineering is employed to enhance their performance. Metabolic engineering can be defined as purposeful modification of cellular characteristics and performance by employing various tools. Over the last decade, metabolic engineering has become more powerful through the integration with systems biology and synthetic biology. In this lecture, I will present the general strategies for systems metabolic engineering of microorganisms. Several key examples on the production of succinic acid, diamines, butanol, polyesters, and metal nanoparticles by metabolically engineered microorganisms will be presented. It is believed that systems metabolic engineering will be an essential strategy for making any bioprocess competitive. [This work was supported by the Korean Systems Biology Research Grant, Advanced Biomass Research Center, Intelligent Biodesign Research Center, Center for Systems and Synthetic Biotechnology from the Korean Ministry of Education, Science and Technology.]

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Sang Yup Lee received B.S. in Chem. E. from Seoul National University in 1986, and Ph.D. in Chem. E. from Northwestern University in 1991. Currently, he is Distinguished Professor and Dean of College of Life Science and Bioengineering at KAIST. He is also the Director of Center for Systems and Synthetic Biotechnology, Director of BioProcess Engineering Research Center, and Director of Bioinformatics Research Center. He has published more than 390 journal papers, and numerous patents. He received many awards, including the National Order of Merit, Citation Classic Award, Elmer Gaden Award, and Merck Metabolic Engineering Award. He is currently Fellow of AAAS, Fellow of American Academy of Microbiology, Fellow of Society for Industrial Microbiology, Fellow of Korean Academy of Science and Technology, Fellow of National Academy of Engineering of Korea, Foreign Associate of National Academy of Engineering USA, Editor-in-Chief of Biotechnology Journal, and editor and board member of many journals. His research interests are metabolic engineering, systems biology and biotechnology, synthetic biology, industrial biotechnology and biorefineries, and nanobiotechnology.

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Contact Info:

Sang Yup Lee

Metabolic and Biomolecular Engineering National Research Laboratory

Department of Chemical and Biomolecular Engineering and Department of BioSystems

BioProcess Engineering Research Center and Bioinformatics Research Center

Center for Systems and Synthetic Biotechnology, Institute for the BioCentury

Korea Advanced Institute of Science and Technology (KAIST)

Daejeon 305-701, Korea (leesy@kaist.ac.kr)