Graduate Seminars

2013

2012

2015

Professor David Sholl
Georgia Tech

“Using High Throughput Computation to Accelerate
Development of Materials for Scalable Energy Technologies”

Abstract

Computational modeling of materials can be a powerful complement to experimental methods when models with useful levels of predictive ability can be deployed more rapidly than experiments. Achieving this goal involves judicious choices about the level of modeling that is used and the key physical properties of the materials of interest that control performance in practical applications. I will discuss two examples of using high throughput computations to identify new materials for scalable energy applications: the use of metalorganic frameworks in membranes and gas storage and the selection of metal hydrides for high temperature nuclear applications. These examples highlight the challenges of generating sufficiently comprehensive material libraries and the potential advantages and difficulties of using computational methods to examine large libraries of materials.
Wednesday, October 14, 2015
12:30 pm, HED 116

2014

Professor Amy Karlsson
Department of Chemical and Biomolecular Engineering
University of Maryland

“Engineering Peptides and Proteins to Combat Human Disease”

Abstract

Rational design and directed evolution are both powerful approaches for engineering proteins and peptides. Our lab applies these approaches to exploit the power of proteins and peptides in studying and combatting human disease, and I will discuss applications of protein engineering in fungal disease and cancer. We applied a rational design approach to engineer non-natural antimicrobial β-peptides that exhibit antifungal activity against the fungal pathogen Candida albicans. Through this work, we developed a deeper understanding of the properties of β-peptides that contribute to their toxicity towards fungal cells and fungal biofilms, and we are currently working on ways to apply this understanding to designing improved antifungal agents. We have also used directed evolution to engineer antibodies that can fold and function inside cells, which has broad applications in human diseases, including cancer. The reducing environment inside cells prevents formation of the disulfide bonds normally required for proper antibody folding, but we have developed a bacterial inner membrane display system that harnesses the cytoplasmic folding quality control mechanisms of the Escherichia coli twin-arginine translocation pathway to engineer proteins able to fold in the cytoplasmic environment. We used this method to display and screen a combinatorial library of single-chain variable fragment (scFv) antibodies and isolated scFvs with dramatic improvements in both antigen-binding and intracellular solubility. We are now using our display method to engineer scFvs for studying and treating cancer and fungal disease.

Bio

Dr. Amy J. Karlsson received her bachelor’s degree in chemical engineering from Iowa State University in 2003 and then joined Prof. Sean Palecek’s group at the University of Wisconsin, where she received her PhD in chemical engineering in 2009. Following her doctoral work, she was an NIH Ruth L. Kirschstein Postdoctoral Fellow in Prof. Matt DeLisa’s lab at Cornell University. Dr. Karlsson joined the Department of Chemical and Biomolecular Engineering at the University of Maryland as an assistant professor in 2012. Her group’s research lies at the interface of biology and engineering and uses protein engineering strategies to improve the understanding of human diseases and develop tools for drug design and disease diagnosis.
Thursday, May 1, 2014
12:45 pm, ZHS 159
The scientific community is cordially invited.

 

2011

Dr. Yvonne Chen
California Institute of Technology 
Pasadena, CA

“Genetic Control of T-Cell Proliferation with Synthetic RNA Regulatory Systems”

Abstract

Adoptive T-cell therapy seeks to harness the precision and efficacy of the immune system against diseases that escape the body’s natural surveillance. Clinical trials have demonstrated the use of cytolytic T cells (CTLs) genetically engineered to express disease-specific antigen receptors as a promising treatment option for opportunistic diseases, virus-associated malignancies, and cancers. However, the safety and efficacy of T-cell therapies depend, in part, on the ability to regulate the fate and function of CTLs with stringency and flexibility. The emerging field of synthetic biology provides powerful conceptual and technological tools for the construction of regulatory systems that can interface with and reprogram complex biological processes such as cell growth. Here, we present the development of synthetic RNA-based regulatory systems and their applications in advancing cellular therapies. Rationally designed, drug-responsive ribozyme switches are linked to the proliferative cytokines IL-2 and IL-15 to construct cis-acting regulatory systems capable of T-cell proliferation control in both mouse and primary human T cells. We further demonstrate the ability of our synthetic controllers to effectively modulate T-cell growth rates in response to drug input in animal models. In addition, we report the development of rationally designed, miRNA-based regulatory devices capable of drug-responsive control over the expression of endogenous cytokine receptor chains. The RNA-based regulatory systems exhibit unique properties critical for translation to therapeutic applications, including adaptability to diverse ligand inputs and regulatory targets, tunable regulatory stringency, and rapid response to input availability. By providing tight gene expression control with customizable ligand inputs, RNA-based regulatory systems can greatly improve cellular therapies and advance broad applications in health and medicine.

 

 Friday, April 22, 2011
3:30 pm, HED 116
The scientific community is cordially invited.

2011

Dr. Hong Shen
Department of Chemical Engineering 
University of Washington

“Biomaterial-engineering the Immune System”

Abstract

Our research interfaces biomaterials, the immune system and engineering design. We use materials with defined properties to probe how the immune system interacts with biomaterials at both cellular and molecular levels. Built upon our understanding, we design biomaterials to exploit intracellular pathways of immune cells for safe and effective therapeutics, such as tissue implants, non-viral gene delivery systems and vaccines. These biomaterials also provide an excellent tool for us to further dissect the cellular and molecular mechanisms by which immune responses are triggered and sustained. A challenge of current vaccines is to achieve a spectrum of immune responses in a single construct. In this talk, I will mainly discuss how we bring together the aforementioned research interests to address this challenge.

 

 Monday, February 28, 2011
12:45 pm, HED 116
The scientific community is cordially invited.

2011

Dr. Andrew Peterson
Stanford University
Stanford, CA

Catalysis Design for Sustainable Fuels

Abstract

Quantum mechanics-based tools have advanced to the point where the computational design of catalysts from first principles is becoming possible. In concert with experiments, these tools can be used for improving catalytic processes for sustainable fuel synthesis. First, I will describe how we are employing density functional theory (DFT) to understand the (photo-)electrocatalytic activity of materials to reduce CO2 to hydrocarbons (solar fuels). We have identified the elementary mechanisms that make this transformation possible and have shown that the protonation of adsorbed CO dictates the overall efficiency of the transformation. By using computational screening tools, we are discovering new candidate materials that can reduce the overpotential of this step, which may help to make solar fuels technologically and economically feasible. In the second part of the talk, I will show how creative catalyst design can enable the development of an efficient and adaptable biorefinery that produces the light end (C0-C3) product spectrum of a conventional refinery. The design of catalysts that can perform decarboxylation reactions without being subject to CO fouling will be key in this development, as will the design of catalysts for the selective synthesis of gasoline-range hydrocarbons from light-end feedstocks. These advances can lead to flexible biorefineries that are adaptable to changing market dynamics.

 

  Thursday, February 17, 2011
11:00 am, ZHS 159
The scientific community is cordially invited.

2010


Dr. Lofti Zadeh
Professor and Director of the Berkeley Initiative in Soft Computing (BISC)

“Computing with Words”

Abstract

Computing with Words (CW or CWW) is a system of computation which offers an important capability that traditional systems of computation do not have a capability to compute with information described in a natural language. In the main, CW is concerned with solution of problems which are stated in a natural language. The importance of CW derives from the fact that much of human knowledge is perception-based and is described in a natural language.
CW has important applications to decision analysis, question-answering systems, system modeling, specification and optimization, and mechanization of natural language understanding. Basically, CW opens the door to a wide-ranging enlargement of the role of natural languages in scientific theories.

 

Bio

Lofti A. Zadeh is an alumnus of the University of Tehran, MIT and Columbia University. His earlier work was concerned in the main with systems analysis, decision analysis and information systems. His current research is focused on fuzzy logic, computing with words and soft computing, which is a coalition of fuzzy logic, neurocomputing, evolutionary computing, probabilistic computing and parts of machine learning. Lotfi Zadeh is a Fellow of the IEEE, AAAS, ACM, AAAI, and IFSA. He is a member of the National Academy of Engineering and a Foreign Member of the Finnish Academy of Sciences, the Polish Academy of Sciences, Korean Academy of Science & Technology, the Bulgarian Academy of Sciences, the International Academy of Systems Studies, Moscow and the Azerbaijan National Academy of Sciences. He is a recipient of many medals and awards as well as twenty –five honorary doctorates. He has published extensively on a wide variety of subjects relating to the conception, design and analysis of information/intelligent systems, and is serving on the editorial boards of over seventy journals.

 Friday, October 22, 2010
3:00 pm, MHP Auditorium
The scientific community is cordially invited.

2010

Dr. Jongseung Yoon
Beckman Institute for Advanced Science and Technology
 UIUC

“Printed Assembly of Micro/Nanomaterials with Silicon and Gallium Arsenide Based Compound Semiconductors for High Performance Photovoltaics and Optoelectronics”

Abstract

In the first part of my talk, I will present our recent work that explores techniques to exploit silicon for unusual photovoltaic module designs. Silicon, in amorphous or various crystalline forms, is used in >90% of all installed photovoltaic (PV) capacity. The high natural abundance of silicon, with the excellent reliability and good efficiency of solar cells made with it, suggest its continued use, on massive scales, for the foreseeable future. As a result, although there is significant promise for organics, nanocrystals, nanowires and other new materials for photovoltaics, many opportunities continue to exist for research into unconventional means for using silicon in advanced PV systems. We developed new approaches to exploit printed arrays of ultrathin, monocrystalline Si solar microcells for unconventional photovoltaic modules. The resulting devices can offer many useful features, including high degrees of mechanical flexibility, user-definable levels of transparency, ultra-thin form factor micro-optic concentrator designs, together with the potential for high efficiency and low cost.

In the second part of my presentation, I will discuss about releasable epitaxial multilayer assemblies of gallium arsenide (GaAs) based compound semiconductors for high performance photovoltaics and optoelectronics. Compound semiconductors such as GaAs provide unmatched performance in photovoltaic and optoelectronic devices. Current methods for growing and fabricating these materials are incompatible with the most important modes of use, particularly in photovoltaics, where large quantities of material must be distributed over large areas on low cost, amorphous foreign substrates. We developed new methods that address many of these challenges, through cost effective production of bulk quantities of high quality functional films of GaAs from thick, epitaxial assemblies formed in a single deposition sequence on a growth wafer. Specialized designs enabled separation, release and assembly of individual active layers in these stacks to create devices on substrates ranging from glass, to silicon and plastic, in quantities and over areas that exceed possibilities with conventional approaches.

 Thursday, March 4, 2010
12:45 pm, HED 116
The scientific community is cordially invited.

2010

Dr. Tina Salguero
HRL Laboratories, LLC
Malibu, CA 

“Molecules and Materials for 21st Century Needs”

Abstract

With our perspective at the beginning of a new decade, it seems clear that the 21st century will be an age when custom-tailored molecules and materials will reach an unprecedented level of importance. In this talk, I will describe several examples of custom-tailored molecules and materials that range across the fields of organometallic chemistry and materials science and have applications in catalysis, chemical synthesis, and energy production.

 Tuesday, March 2, 2010
1:15 pm, HED 116
The scientific community is cordially invited.

2010

Dr. Rusen Yang
School of Materials Science and Engineering
 Georgia Institute of Technology
 Atlanta, GA

“Nanogenerators for Self-Powered Nanosystems”

Abstract

A self-powered nanosystem that harvests its operating energy from the environment is an attractive proposition for sensing, medical science, defense technology, and even personal electronics. Therefore, it is essential to explore innovative nanotechnologies for converting mechanical energy (such as body movement), vibration energy (such as acoustic/ultrasonic wave), and hydraulic energy (such as blood flow) into electric energy that will be used to power nanodevices without using battery. Piezoelectric zinc oxide nanowire (NW) arrays have been successfully demonstrated to convert nano-scale mechanical energy into electric energy. The operation mechanism of the electric generator relies on the unique coupling of piezoelectric and semiconducting dual properties of ZnO as well as the elegant rectifying function of the Schottky barrier formed between the metal electrode and the NW. This mechanism resulted in the DC nanogenerator driven by ultrasonic wave. Recently we achieved a new breakthrough with laterally-packaged single wire generator, which solved the transient contact issue in DC nanogenerator and produced power output from low frequency and irregular mechanical disturbance, such as finger tapping and running hamster. This presentation will introduce the fundamental principle of nanogenerator and its potential applications.

 Monday, February 22, 2010
12:45 pm, HED 116
The scientific community is cordially invited.

2010

Professor Yu-Shu Wu
Department of Petroleum Engineering
Colorado School of Mines
Golden CO 80401 USA

“Unconventional Reservoir Simulation”

Abstract

Unconventional hydrocarbon resources from low-permeability formation, i.e., tight sands and shales, are currently received great attention because of their potential to supply the entire world with sufficient energy for the decades to come. In the past few years, as a result of industry-wide R&D effort, progresses are being made towards commercial development of gas and oil from such unconventional resources. However, studies, understandings, and effective technologies needed for development of unconventional reservoirs are far behind the industry needs. Unconventional reservoir dynamics is characterized by highly nonlinear behavior of multiphase flow in extremely low-permeability rock, coupled by many co-existing, processes, e.g., non-Darcy flow and rock-fluid interaction within tiny pores or microfractures. Quantitative characterization of unconventional reservoirs has been a significant scientific challenge currently. Because of complicated flow behavior, strong interaction between fluid and rock as well as multi-scaled heterogeneity, the traditional Darcy-law-and-REV-based model may not be applicable for describing flow phenomena in unconventional reservoirs. In this presentation, we will discuss a general mathematical model proposed for unconventional reservoir simulation. We will present a unified framework model to incorporate various nonlinear flow and transport processes using a multi-domain, multi-continuum concept to handle multi-scaled heterogeneity of unconventional formation. Specifically, we will use extended or modified Darcy law to include the following processes: (2) non-Newtonian behavior (i.e., threshold pressure gradient for flow to occur); (3) non-Darcy flow with inertial effects; (3) adsorption and other reaction effect; and (4) rock deformation. The proposed modeling methodology has been implemented into a general reservoir simulator and will be demonstrated for its application in analyzing well tests in fractured vuggy reservoirs, non-Darcy flow, and non-Newtonian flow in porous and fractured reservoirs.

Friday, January 29, 2010
12:45 pm, HED 116
The scientific community is cordially invited.

2009

Ajit Yoganathan
Wallace H. Coulter Distinguished Faculty Chair 
Biomedical Engineering
Georgia Institute of Technology Atlanta, Georgia

“Surgical Planning of the Total Cavopulmonary Connection Using MRI, Experimental and Computational Fluid Mechanics”

Lecturer’s Webpage

http://www.bme.gatech.edu/facultystaff/faculty_record.php?id=5

Monday, February 23, 2009
12:30 – 1:30 pm, OHE 132
The scientific community is cordially invited.

2009

Dr. Denis Grebenkov 
Laboratoire de Physique de la Matiere Condensee CNRS
Ecole Polytechnique, France

“Diffusion-Weighted and NMR Imaging of Porous Media”

Abstract

A non-invasive study of translational dynamics requires a kind of “marking” or “labeling” of the traveling atoms or molecules for tracing their displacements. Magnetic field is a superb experimental tool for encoding the motion of spin-bearing particles. Moreover, since a geometrical confinement considerably affects diffusive motion, the geometry of porous media can be indirectly accessed by measuring the signal attenuation due to restricted diffusion in inhomogeneous magnetic fields. In this talk, we focus on some theoretical and numerical aspects of this problem. Starting from the classical Bloch-Torrey equation, we obtain the NMR signal in a compact matrix form. Each attenuation mechanism (restricted diffusion, gradient dephasing, surface or bulk relaxation) is represented by a matrix which is constructed from the Laplace operator eigenbasis and thus depending only on the geometry of the confinement. In turn, the physical parameters (free diffusion coefficient, gradient intensity, surface or bulk relaxivity) characterize the “strengths” of the underlying attenuation mechanisms and naturally appear as coefficients in front of these matrices. We illustrate the use of this matrix technique by considering restricted diffusion in simple domains: a slab, a cylinder, and a sphere. Further investigation of irregularly-shaped confinements is discussed.

Lecturer’s Webpage

http://pmc.polytechnique.fr/pagesperso/dg/

Thursday, February 12, 2009
11:00 am, HED 116
The scientific community is cordially invited.

2008

Malancha Gupta
Harvard University
Cambridge, MA 

“Fabrication Methods for the Production of Polymer Films: Initiated Chemical Vapor Deposition
 and 
Templated Formation of Ionotropic Gels Using Patterned Paper ”

Abstract

This talk will describe two methods for the production of polymer films. The first method focuses on the use of initiated chemical vapor deposition to make a wide variety of polymer coatings such as poly(2-(perfluoroalkyl)ethyl methacrylate), poly(glycidyl methacrylate), and poly(furfuryl methacrylate). Vapor deposition has the environmental benefit of using no solvents and the process can be used to conformally coat substrates with complex geometries such as fabrics and wires since there are no surface tension problems. Deposition rates as high as 300 nm/min can be achieved. The proposed polymerization mechanism is the classical free radical polymerization mechanism of vinyl monomers. Monomer and initiator gases are fed into a vacuum chamber where resistively heated wires are used to thermally decompose the initiator molecules into free radicals. The free radicals then attack the vinyl bonds of the monomer molecules. Propagation occurs on the surface of a cooled substrate. We have demonstrated that the process can be used to modify the surfaces of high-aspect-ratio (~100) polymeric membranes and electrospun fiber mats. The second method focuses on the use of paper templates to fabricate shaped films of ionotropic hydrogels. Solutions of polymers such as alginic acid, carrageenan, and carboxymethyl cellulose form films with defined shapes when brought into contact with patterned templates of paper wetted with aqueous solutions of multivalent cations. This method allows the production of topographically and topologically complex 3D shapes, such as interlocking rings and Möbius strips. The shaped films can be made magnetically responsive by using paramagnetic ions like holmium as the cross-linking ions or by suspending ferrite microparticles in the hydrogels. Heterogeneous films of ionotropic hydrogels can be fabricated through the use of multiple templates. These heterogeneous structures include single films where a pattern of one hydrogel is surrounded by another hydrogel (“gel-in-gel” structures) and hydrogels that contain a gradient in the concentration of cross-linking agent.

Thursday, December 11, 2008
1:00 pm, HED 116
The scientific community is cordially invited.

2008

Rafael Verduzco
Oak Ridge National Laboratory Oak Ridge, TN 

“Novel Liquid Crystal Networks”

Abstract

The combination of liquid crystals and polymers results in fascinating materials in which the elasticity of polymers is coupled to the liquid crystal (LC) order. In this work, we present three qualitatively different types of LC gels and elastomers and explore their electro-optical response, mechanical actuation, and flexoelectric behavior. Using block copolymer self-assembly, we prepare LC physical gels that exhibit fascinating texture transitions with temperature and multiple director relaxation modes, in contrast to covalent gels which show a single relaxation mode. Next, covalent networks with a controlled molecular weight between cross-links were prepared by “click” cross-linking of telechelic polymers produced by ring-opening metathesis polymerization. These networks swell readily in a small molecular LC solvent, 5CB, to form LC gels with high swelling ratios that exhibit a fast, reversible, and low-threshold electro-optic response. Finally, a series of bent-core liquid crystals were synthesized and used to swell calamitic monodomain liquid crystal elastomers (LCE). Nematic bent-core liquid crystals show enhanced flexoelectricity, and bent-core elastomers represent a potential method for incorporating flexoelectricity into a robust polymeric device. These LC networks and gels provide insight into the connection between physical properties and network structure and also demonstrate the broad range of materials accessible with different synthetic approaches.

Lecture Webpage:

http://www.ornl.gov/~vgh/ 

Tuesday, Dec 8th, 2008
1:00 pm, HED 116
The scientific community is cordially invited.

2008

Sridevi Sarma 
Massachusetts Institute of Technology
Harvard Medical School

“Improving Deep Brain Stimulation in Parkinson’s Disease Using Feedback Control”

Abstract

An estimated 3 to 4 million people in the United States have Parkinson’s Disease (PD), a chronic progressive neural disease that occurs when specific neurons in the midbrain degenerate, causing movement disorders such as tremor, rigidity, and bradykinesia. Currently, there is no cure to stop disease progression. However, surgery and medications are available to relieve some of the symptoms in the short term. A highly promising treatment is deep brain stimulation (DBS). DBS is a surgical procedure in which an electrode is inserted through a small opening in the skull and implanted in a targeted area of the brain. The electrode is connected to a neurostimulator (sits inferior to the collar bone), which injects current back into the brain to regulate the pathological neural activity. Although DBS is virtually a breakthrough for PD, it is necessary to search for the optimal stimulation signal postoperatively. This calibration often takes several weeks or months because the process is trial-and- error. During a post-operative visit, the neurologist asks the patient to perform various motor tasks and makes subjective observations. Based on these, he/she tweaks the stimulation parameters and asks the patient to return in hours, days or even weeks. The difficulty is that there are millions of stimulation parameters to choose from, though experience has reduced this to roughly 1000 options. My current research efforts are to 1. reduce calibration time down to days by developing a systematic testing paradigm using feedback control principles, and to 2. develop a new stimulation paradigm that allows for broader classes of DBS signals to be administered. Despite the fact that DBS is simply a control signal applied to a neural system to achieve desirable motor behavior from a patient, investigators are only beginning to approach these problems from a control systems engineering perspective.

Bio

Sridevi V. Sarma received a BS (1994) from Cornell University and an MS (1997) and PhD (2006) from Massachusetts Institute of Technology in Electrical Engineering and Computer Science. Sri is now a postdoctoral fellow jointly at Harvard Medical School and MIT. Her research interests include control of constrained and defective systems (applications in neuroscience) and large-scale optimization. Sri is president and cofounder of Infolenz Corporation, a Marketing Analytics company. She is a recipient of the GE faculty for the future scholarship, a National Science Foundation graduate research fellow, and a recipient of the Burroughs Wellcome Fund Careers at the Scientific Interface Award.

Thursday, March 6, 2008
10:30-11:30 am, EEB 248
The scientific community is cordially invited.

2008

Professor Thomas Marlin
Department of Chemical Engineering
McMaster University
Ontario, Canada

“A Robust Control Approach to Optimizing
Production, Inventory and Transportation”

Abstract

Recently, advances in computing and optimization algorithms have lead to a renewed interest in analyzing logistics systems with the recognition that (1) substantial uncertainties exist in their dynamic behavior and (2) periodic re-optimization (rolling horizon optimization) affects the future behavior. The Model-Predictive Control (MPC) structure is ideal for modeling these closed-loop logistics systems. This talk will introduce the concept of robust model-predictive control of uncertain systems and how it can be implemented in real-time. Challenges in formulation and computation will be introduced, and proposals for a computationally tractable approach presented.

Application to a simple (but real) industrial logistics problem will be presented. The problem has several manufacturing steps with intermediate inventory and transportation to regional distribution outlets. Uncertainty occurs in manufacturing times, transportation times, and customer demands. The goal is to reduce holding (inventory) costs while preventing backorders, where possible. The behavior of the system under various control approaches will be compared, and the advantages of a robust approach quantified.

This work has been performed in conjunction with Adam Warren and Xiang Li at McMaster University.

Thursday, February 21, 2008
12:45 pm, OHE 122
The scientific community is cordially invited.

2008

Oscar D. Dubón, Jr.
Department of Materials Science and Engineering University of California Berkeley 
and 
Lawrence Berkeley National Laboratory Berkley, CA

“Pulsed-laser processing of ferromagnetic semiconductors”

Abstract

Because of their unique combination of magnetic and semiconducting properties and their potential as both injection sources and filters for spin-polarized carriers, ferromagnetic semiconductors have attracted much attention for spin-based electronics, or spintronics. These novel materials are formed by the substitution of a relatively small fraction of host atoms—a few atomic percent—with a magnetic species such as Mn. In the prototypical ferromagnetic semiconductor Ga1-xMnxAs, inter-Mn exchange is known to be mediated by holes in extended or weakly localized states; however, the fundamental nature of exchange across the Ga-Mn-pnictide series is less clear. Unfortunately, challenges in materials synthesis have obstructed both the further understanding of these materials and their application in practical devices. Even the relatively low alloying levels necessary for ferromagnetism require the application of non-equilibrium growth strategies, in particular low-temperature molecular beam epitaxy (LT-MBE).

At Berkeley we have undertaken investigations on the synthesis of ferromagnetic semiconductors using a combination of Mn ion implantation and pulsed-laser melting (II-PLM). By this simple process we have produced epitaxial, single crystalline films of ferromagnetic GaxMn1-xAs. These epilayers display the essential magnetic and electrical properties observed in films grown by LT-MBE. We have used II-PLM to produce new Ga-Mn-pnictide alloys including ferromagnetic Ga1-xMnxP. This material represents an intriguing system in which strongly localized carriers in a detached impurity band stabilize ferromagnetism. The possibility of introducing more than one species by ion implantation into a semiconductor host opens further opportunities to study quaternary alloys and probe chemical trend in the ferromagnetic Curie temperature. I will present results from our studies of these novel ferromagnetic semiconductors as well as efforts to develop laser patterning techniques for the realization of planar spintronic structures.

Thursday, January 29, 2008
1:00 pm, OHE 122
The scientific community is cordially invited.

2008

 Dr. Jennifer N. Cha
IBM Almaden Research Center
 San Jose, CA

“Exploring the Bio-Nano Interface to Address Challenges in Nanoelectronics”

Abstract

As nanoelectronic device features shrink towards a critical limit, new research directions have been sought to resolve the resultant technological issues in a cost-effective manner.  The ability of Nature to synthesize and assemble materials with high fidelity and precision has provided a potential means of overcoming these formidable challenges. Over the past few years, there have been numerous and extensive efforts to both understand the biological mechanisms for building inorganic and organic architectures and use biological systems to assemble nanoscale materials.  New applications of current genetic engineering techniques have also been developed to overcome the difficulties of interfacing biology with non-biological substrates, enabling the use of biomolecular systems for addressing particular challenges in nanoelectronics.
The first part of this talk will highlight some of the mechanisms of biomineralization and will in particular focus on the way biosilicates are both synthesized and assembled in Nature. One of the inherent reasons to understand how inorganic materials are produced in living systems is that all of these processes occur under ambient conditions, even those materials that are produced industrially under high temperature and pressure or at extreme pH. I will describe the mechanism by which one biological organism synthesizes highly ordered silica structures at neutral pH and how one can apply these mechanisms to biomimetic approaches using synthetic block copolymers. The understanding of how to chemically control both nucleation and growth of oxides at the nanometer scale led to the synthesis of highly-ordered, two-dimensional nanopatterned ceramic thin films that were used as nanoscale etch masks for producing nanoparticles of phase change materials.
A significant amount of research at IBM has also been devoted to exploring nanowires and single walled carbon nanotubes (CNTs) as alternatives to silicon technology. Despite the unique electronic and physical properties of CNTs, however, there exist numerous technological challenges; in particular, the production of entirely semiconducting CNTs of a single or narrow range of band-gaps. The second part of this talk will focus on our recent efforts at the use of DNA to disperse CNTs and bio-combinatorial libraries to discover unique amino acid sequences that can bind a subset of dispersed CNTs. Specific biomolecular recognition of particular nanomaterials that demonstrate unique physical characteristics may impact applications ranging from nanoelectronics to nanomedicine.

 

Lecture Webpage

 

Thursday, January 24, 2008
12:45 pm, OHE 122
The scientific community is cordially invited.

2008

Mohammad El-Naggar
Professor, University of Southern California

“Living Conductors: The Nature and Implications of Electrical Transport in Bacterial Nanowires”

Abstract

Bacterial nanowires are conductive pilus-like appendages produced by bacteria, most notably some ‘metal-reducers’, in direct response to electron acceptor limitation. These recently discovered supramolecular assemblies represent a new paradigm in extracellular electron transfer, but the mechanism of electron transport remains unclear. This talk will feature quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium (DMRB) Shewanella oneidensis MR-1, whose electron transport system holds practical promise for renewable energy recovery and bioremediation. The Shewanella nanowires display a surprising non-linear electrical transport behavior, where the voltage dependence of the conductance reveals peaks indicating discrete energy levels with higher electronic density of states. These results indicate that the molecular constituents along the Shewanella nanowires possess an intricate electronic structure that plays a role in mediating the overall electron transport.  We will highlight the vast implications of signal transduction at the biological-inorganic interface as well as devices that exploit this interface, such as microbial fuel cells. We will also discuss our recent efforts to develop experimental and image analysis tools that target the interactions between the living and non-living worlds at this interface.

 

Lecture Webpage

 

Tuesday, January 22, 2008
12:45 pm, OHE 122
The scientific community is cordially invited.

2008

Dr. Liangfang Zhang 
Chemical Engineering Department, MIT

“Lipid-Polymer Hybrid Nanoparticles for Targeted Therapeutics”

Abstract

Nanotechnology is the understanding and the control of matter generally in 1-100 nm dimension range. The application of nanotechnology to medicine, known as nanomedicine, concerns the use of precisely engineered materials at this length scale to develop novel therapeutic and diagnostic modalities. In the past two decades, there has been a progressive increase in the number of commercially available nanoparticle-based therapeutics products. Among these products, liposomal drugs and polymer-based drugs are two dominant classes, accounting for more than 80% of the total amounts. However, both liposomes and polymeric nanoparticles (NPs) have their own drawbacks as drug carriers that limit their application potential in many medical areas.

Here I report a platform bionanotechnology that enables the formulation of targeted NPs which have merits of both lipid- and polymer-based NPs, while excluding some of their limitations. The NPs are comprised of: i) a biodegradable polymeric core which can carry bioactive drugs and release them at a sustained rate; ii) a lipid monolayer shell which can prevent the carried agents from freely diffusing out of the nanoparticle and reduce water penetration rate into the nanoparticle, thereby enhancing drug encapsulation efficiency and slowing drug release; iii) a stealth material that can allow the particles to evade recognition by immune system components and increase particle circulation half life; and iv) a targeting molecule that can bind to a unique molecular signature on cells, tissues, or organs of the body. The targeting therapeutic potential of these lipid-polymer hybrid NPs is demonstrated in treating prostate cancer and cardiovascular disease.

Lecture Webpage

 

Monday, Decenber 3, 2007
2:00 pm, SAL 101
The scientific community is cordially invited.

2007

Dr. Andrea Armani
California Institute of Technology

“Biophotonics: Lighting the Way ”

Abstract

For many biological and chemical experiments, a sensor must have high sensitivity, high specificity, and fast response time. There are many technologies which are able to achieve one or two of these three requirements, but many still face fundamental sensitivity or response limitations.

Silica optical resonators are able to overcome these limitations because of the high quality factor (Q). In their application as a single molecule sensor, the sensitivity is derived from the long photon lifetime inside the microcavity, and the specificity is derived from functionalization of the silica surface.   During the initial series of label-free detection experiments, pure Interleukin-2 (IL-2) solutions were injected into the volume surrounding the microtoroid. The microtoroid successfully detected step-like shifts in resonance wavelength from individual IL-2 molecules binding. Additional experiments have shown that even in the more complex environment of serum individual binding events of IL-2 are still resolved. Therefore, this single molecule sensor will enable research in new areas of biophysics and cell biology.

Lecture Webpage

 

Tuesday, November 27, 2007
3:00 pm, SAL 101
The scientific community is cordially invited.

2007

Dr. Michael McAlpine 
Post-Doctoral Researcher
Division of Chemistry and Chemical Engineering

“Integrated Nanowire Electronics and 
Sensors on Flexible Plastics Substrates”

Abstract

The introduction of an ambient-temperature route for integrating high performance materials on flexible plastic substrates could enable exciting avenues in fundamental research, and innovative electronic and medical devices. However, the temperature constraints imposed by these substrates restrict the use of high carrier mobility materials, such as polycrystalline silicon, generally limiting these devices to the modest computational capabilities of amorphous silicon and organic semiconductor thin film transistors. The development of new materials and novel materials processes for overcoming this restriction could impact a broad spectrum of applications.

Semiconductor nanowires represent unique, high performance building blocks for electronic, photonic, and sensing devices. In this talk, I will present my work demonstrating that single-crystal nanowires can be hierarchically assembled onto flexible plastic substrates under ambient conditions to create multi component, fully integrated devices, including field-effect transistors, light-emitting diodes, ring oscillators, and electronic noses. These devices all exhibit performance metrics which meet or exceed the state-of-the-art for flexible electronics.
The key to our approach is the separation of the high-temperature synthesis of single-crystal nanowires from room temperature assembly, thus enabling fabrication of high-performance devices on virtually any substrate. Silicon nanowire field-effect transistors on plastic substrates display mobilities ivaling those of single-crystal silicon and exceeding those of amorphous silicon and organic transistors currently used for plastic electronics. Furthermore, we show that these systems can be integrated into ring oscillators on plastic which generate frequencies approaching the microwave, the highest observed frequencies for circuits based on nanoscale materials.

Finally, we exploit SiO2 surface chemistries to construct a “nano-electronic nose” library, which can distinguish acetone and hexane vapours via distributed responses. We also demonstrate that amide coupling of theoretically tailored peptide sequences to the arrays allows for selective discrimination of chemicals often found in the breath of sick patients. This excellent sensing performance coupled with biocompatible plastic could open up far-reaching opportunities in mobile computing, lightweight display, or even implantable monitoring applications.

 

Lecture Webpage

 

Thursday, November 15, 2007
12:45 pm, OHE 122
The scientific community is cordially invited.

2007

Dr. Shanfeng Wang 
Postdoctoral research fellow
Departments of Orthopedic Surgery and Biomedical Engineering
Mayo Clinic, Rochester, Minnesota

“The Role of Polymer Science in Designing and Understanding Novel Biomaterials for Tissue-Engineering Applications”

Abstract

The third-generation biomaterials currently investigated are cell- and gene-activating materials combining both resorbable and bioactive properties. In an effort to develop third-generation biomaterials with controllable physical properties for diverse tissue-engineering applications, we have developed a variety of novel crosslinkable and biodegradable polymers. In this talk, both fundamental and practical challenges in biomaterials and tissue engineering will be addressed and the solutions will be proposed using various polymeric biomaterials for bone and nerve regenerations.

In the first half of this talk, the importance of understanding microscopic chain dimensions, morphologies at different length scales, and macroscopic physical properties in rationally developing novel polymeric biomaterials will be elaborated on a series of multi-block copolymers poly(propylene fumarate-co-caprolactone) (PPF-co-PCL) as well as PPF. PPF-co-PCL can be either chemically crosslinked or photo-crosslinked, making it possible to fabricate 3D scaffolds using various techniques such as stereolithography. The physical properties of the crosslinked form can be modulated efficiently by the copolymer composition. Furthermore, the shape-memory effect has been revealed when the copolymer is semi-crystalline, offering a possibility for developing smart scaffolds.

The second half of this talk will be on the cell-material interactions and biological evaluations of 2D polymer substrates and 3D scaffolds. It is gradually accepted that cells can respond to the substrate stiffness as well as other chemical and topological cues. Without the need of being modified covalently with adhesive proteins, the role of surface stiffness can be reflected in regulating cell responses including attachment and proliferation in both cases of bone marrow stromal cells and SPL201 (Schwann cell precursor line) cells. Two PPF-co-PCL copolymers with distinct PCL compositions were used to fabricate flexible nerve tubes and stiff bone-tissue-engineering scaffolds. Histological analysis of in vivo implantation results showed that the nerve tubes are biocompatible and support axon growth. Rat femoral defect and subcutaneous models were used to evaluate biocompatibility of the scaffolds and bone ingrowth with or without the controlled delivery of recombinant human bone morphogenetic protein-2 (rhBMP-2).

Lecture Webpage

 

Tuesday, January 16, 2007
1:00 pm, HED 116
The scientific community is cordially invited.

2007

Dr. Susan Daniel
Department of Chemistry Texas A&M University

“Protein Mobility, Filtering, and Separation in Model Cell Membranes”

Abstract

Investigating how biomolecules behave in cell membranes gives us insight that can be used to create better assays, sensors, and devices that mimic the cell surface. Applications for these devices include rapid combinatorial analysis of drug targets, biosensors for toxin detection, and proteomics research. Solid-supported lipid bilayers (SLBs) are an excellent platform for mimicking the surface chemistry of cells. However, there are several drawbacks to these platforms. First, proteins can lose their mobility in these systems, impairing their function. Second, there is no good way to discriminate between analytes that bind to the same surface ligand within these platforms. Third, separation, purification, and formation of arrays of membrane species is difficult, impeding the progress of rapid combinatorial assaying of membrane proteins. Results will be presented on studies conducted to understand these issues and strategies to overcome them. By investigating the behavior of protein-protein interactions on SLBs, we found that protein-packing influences the point at which diffusion is arrested in these systems. To improve binding specificity, we devised a system for size-selective discrimination of protein analytes that bind to the same ligand, by incorporating poly(ethylene glycol) (PEG) lipopolymers into SLBs. Using our platform, we were able to achieve discrimination of several orders of magnitude. Finally, we developed a technique to separate membrane species within an SLB: bilayer chromatography. Results will be presented that show our separation method is sensitive enough to differentiate isomers of dye-labeled lipids and is currently being extended to the separation of membrane proteins.

Lecture Webpage

 

Friday, January 12, 2007

2006

Dr. Noah Malmstadt
Postdoctoral Scholar University of California at Los Angeles

“Engineered self-assembly for ion channel protein-based molecular sensors”

Abstract

There has been much recent interest in using channel proteins as the basis of new chemical detection technologies, including molecular sensing and single-molecule DNA sequencing; these proteins are also important drug targets. Ion channel measurements are performed by incorporating proteins into lipid bilayer membranes; however, these 5 nm-thick membranes are fragile, short-lived, and labor-intensive to fabricate. These shortcomings greatly limit the use of ion channel proteins in engineered devices. We have developed two novel technologies that address these shortcomings: In the first, we have encapsulated lipid bilayer membranes within a hydrogel network. This encapsulation process, in which a hydrogel is polymerized in situ around a self-assembled lipid bilayer, results in membranes that are robust to mechanical perturbation and that last over ten times longer than the previous state of the art. Hydrogel-encapsulated membranes can support extended measurements of ion channel proteins at the single-molecule level, and have the potential to enable long-lived ion channel sensors in portable devices. Our second novel technology is a microfluidic system for automated membrane fabrication and measurement. This system controls and automates the process of membrane self-assembly through material-driven solvent extraction from a multiphase droplet flow. Ion channel proteins can be incorporated in these membranes and measured with single-molecule resolution. This on-demand bilayer fabrication technology can form the basis of membrane arrays for high throughput sensing for chemical detection as well as drug discovery and screening. These technologies provide two complementary pathways to the development of devices in which channel proteins serve as active nanoscale sensing elements.

Lecture Webpage

 

Friday, December 01, 2006
11:00 am, HED 116
The Scientific Community is Cordially Invited to Attend.

2006

Dr. Karen Christman
Postdoctoral Scholar University of California at Los Angeles

“Polymers for Bionanotechnology”

Abstract

Over the past few decades, techniques to produce submicron and nanoscale features on surfaces have emerged. While such advances were initially applied to the electronics field, the fusion of biology and nanotechnology has begun to provide useful tools for biosensors, biomaterials, and tissue engineering applications. The ability to spatially orient and anchor proteins in particular affords many opportunities for biotechnology and medicine. Site-specifically immobilizing proteins, forming protein assemblies, and fabricating three dimensional biological nanostructures using various polymers and lithography techniques will be discussed.

Lecture Webpage

 

Monday, November 27, 2006
11:00 am, HED 116
The Scientific Community is Cordially Invited to Attend.

2006

Dr. Abolhassan Vafai
Professor, International & Scientific Cooperation Director of SUT Civil Engineering Department
Sharif University of Technology

“The Future and Challenges of Technology for the Prosperity and Well-Being of the World”

Abstract

In this seminar, an overview of the important role which technology plays in our everyday lives and in improving standards of living will be presented. Then, a few of the emerging technologies, which will change the way we live today, will be introduced. In addition, a close look at the economically fast developing countries, which will soon dominate the world market, will help us to understand the problems, which developed countries, may face in the future. Finally, those challenges which technology may face in the future in order to make its promises become true are examined.

Lecture Webpage

 

Monday, October 16, 2006
Refreshments will be served after the seminar in the HEDCO lobby
Everyone is Invited to Attend.

2006

Professor Wilfred Chen
Department of Chemical and Environmental Engineering University of California, Riverside

“Environmental Biotechnology: Challenges and Opportunities for Chemical Engineers”

Abstract

Environmental biotechnology refers to the utilization of biomolecules to improve environmental quality. Over the past three decades breakthroughs in molecular genetics have revolutionized our ability to analyze and manipulate the structures and properties of nucleic acids and proteins. However, a major limitation in the applications of biomolecules is the existence of a functional gap between naturally occurring biomolecules and those required by specific practical settings. Therefore, the ability to close this functional gap has become a première intellectual and engineering challenge. In this talk, I will attempt to highlight opportunities available for chemical engineers to make significant contributions in the area of environmental biotechnology and their future challenges. Specially, I will discuss our recent work on the development of new biomolecular engineering tools and their applications in the remediation and detection of toxic pollutants. Examples will include: (1) developing biocatalysts for the detoxification of organophosphorus pesticides, (2) engineering plant-microbe symbiosis for rhizoremediation of heavy metal and TCE, (3) engineering elastin biopolymers for heavy metal remediation and antibody array fabrication, and (4) real-time monitoring of infectious viruses.

Lecture Webpage

 

Monday, April 17, 2006
12:30 pm, THH 116
The Scientific Community is Cordially Invited

2006

Dean Ho, Ph.D.
Research Associate Departments of Bioengineering and Electrical Engineering California Institute of Technology and Mechanical and Aerospace Engineering Department University of California, Los Angeles

“Cytomimicry: Fabrication of Biofunctionalized Materials Through Biotic-Abiotic Interfacing”

Abstract

The concept of biotic-abiotic interfacing has enabled the assembly of structures that integrate synthetic and biological components towards functional micro/nano engineering systems. This talk will highlight our recent applications of biomolecule-functionalized thin films as a platform for converting light energy into electrical energy, as well as a platform of modifying cell patterning through cellular mechano-sensors. These thin films possess the advantages of configurable characteristics based upon desired functionality. In order to develop the films as the platform for the nano/micro energy system and cell-film interaction study, we need to be able to understand and control its material and chemical properties. For example, block lengths, compositions, and stiffness properties can be altered, and UV-reactive end groups can be added to undergo free-radical polymerization to increase membrane mechanical stability which can in turn enhance protein stability and resistance to a wide range of environments (pH, temp., etc.).

We have recently demonstrated the use of composite thin film vesicles functionalized with embedded membrane proteins (BR/COX) to generate light-dependent currents with no applied voltage. Our configuration has enabled each vesicle to serve as a dedicated energy producing unit which serves as an optimized failure management system. In addition, characterization of the mechanical properties of these biofunctional thin films has revealed their dramatic increase in robustness over conventional lipid systems towards the development of devices driven by inherent biomolecular activity. Furthermore, this talk will highlight a myriad of achievements in vectorial orientation of proteins in polymers for device engineering purposes. In addition, integrating the membrane with cell matrix proteins such as collagen serves as a powerful modality for studying cell patterning process. The cellular mechano-sensors can detect the relative Young’s modulus variation of the film which can then induce the formation of various patterns and architectures. The understanding and control of these mechano-sensing and cell system responses to the received signal will provide us with a powerful pathway towards tissue engineering through next generation devices engineered at the biotic-abiotic interface.

Lecture Webpage

 

Friday, March 24, 2006

2006

Dr. Tara LaForce 
Stanford University

“Analytical Methods in Compositional Modeling”

Abstract

Subsurface flow of several phases occurs in enhanced oil recovery (EOR), geological carbon dioxide storage, coal-bed methane production, and surfactant enhanced remediation of non-aqueous phase liquid contaminants in aquifers. The thermodynamic processes that allow for efficient flow of multiple fluids simultaneously are poorly understood, yet this knowledge is the key to developing a successful hydrocarbon production strategy. Using the method of characteristics (MOC) it is possible to construct analytical solutions to the conservation laws governing dispersion-free multicomponent, multiphase flow in one dimension. Analytical solutions provide insight into the behavior of multiphase flow and can also be used in streamline simulators and as benchmarks for traditional simulators.

The first analytical solutions presented are for an analogue ternary system modeling gas injection into an oil reservoir. Three components are present and up to three phases may form. In this study the analytical solutions are compared to core flood data. The analytical solutions accurately predict core flood effluents for most of the experiments. A single set of relative permeability parameters is insufficient to model all of the experiments, indicating hysteresis in the relative permeabilities.

Analytical solutions are also constructed to model surfactant enhanced remediation of a contaminated aquifer. Like the previous example up to three phases may form. Three realistic sets of relative permeability parameters are studied. The phase relative permeabilities have a substantial impact on the recovery efficiency. In some cases the recovery of oil declines with increasing surfactant in the injection mixture.

Current research on four-component three-phase flow will be discussed. This extension of MOC theory is critical because at least four components are needed in order to accurately model CO2 or WAG injection into a water-flooded reservoir. Future analytical and numerical research into multiphase flow with adsorption and hysteresis and discuss further applications of MOC theory to coal-bed methane production, CO2 sequestration and EOR will also be proposed.

Friday, March 10, 2006

2006

Dr. Dean Oliver, Professor and Director, 
Mewbourne School of Petroleum and Geology Engineering The University of Oklahoma

“Ensemble Kalman Filter For History Matching”

Abstract

The problem of reservoir characterization through automatic history matching has been extensively studied in recent years. Efficient applications have, however, required either an adjoint or a gradient simulator method to compute the gradient of the objective function or a sensitivity coefficient matrix for the minimization. Both computations are expensive when the number of model parameters or the number of observation data is large. The codes for gradient-based history matching methods are also complex and time-consuming to write.

This talk reports the use of the Ensemble Kalman Filter (EnKF) for automatic history matching. EnKF is a Monte Carlo method, in which a collection of reservoir models is used to estimate various relationships for history matching. An estimate of uncertainty in future reservoir performance can also be obtained from the ensemble.

Unlike traditional history matching, the source code of the reservoir simulator is not required, which allows this method to be used with any reservoir simulator. Also, the assimilation of the data in EnKF is done sequentially rather than simultaneously as in traditional history matching. By so doing the reservoir models are always kept up-to-date, which may be important when the frequency of data is fairy high.

In this talk, the application of the EnKF to the problem of history matching the PUNQ-S3 test modelwill be described. It is a small (19x28x5) three-phase reservoir engineering model that was developed by research units in the European Union to compare methods for quantifying uncertainty assessment in history matching. The model is also tested on a synthetic problem in which the locations of geologic facies must be determined. In both cases, the EnKF provided satisfactory history matching results while requiring less computation than traditional methods.

Lecture Webpage

 

Wednesday, March 8, 2006

2006

Professor S. Joe Qin
Department of Chemical Engineering University of Texas, Austin

“Process Systems Engineering in Semiconductor Processing”

Abstract

The semiconductor industry is in the midst of a technology transition from 200mm to 300mm wafers to gain manufacturing efficiency and reduce manufacturing cost per chip. These technological changes present a unique opportunity to optimally design the control systems to achieve fab-wide control.

In this seminar we introduce systems engineering approaches to semiconductor manufacturing and present a hierarchical optimization and control framework for semiconductor fab control. The equipment level control involves real-time feedback control of tool parameters. The next level run-to-run control involves sharing information from multiple steps to achieve feedforward and predictive control. The top level of the hierarchy is the fab-wide control which is the highest level optimization to achieve desired electrical properties by recalculating the optimal targets for the lower level. Challenges due to multiple, different tools in each module and multiple products being processed in the same module of tools are discussed. Stability analysis results are given for single product runs and mixed product runs. Fault detection and process monitoring needs at various levels are discussed as well. In summary, various systems engineering issues and opportunities are demonstrated in the large scale but nano-sized semiconductor manufacturing processes.

Lecture Webpage

 

Tuesday, March 7, 2006

2006

Dr. Xiaoxia (Nina) Lin 
Harvard Medical School

“Integrating Models and Experiments: Synthetic Ecosystems and Molecular Switches”

Abstract

In this talk, I will focus on two of my current projects that aim to advance our understanding of important biological processes through a systems biology and synthetic biology approach. 1. Construction and evolution of synthetic microbial symbiotic systems. Mutualistic symbiosis exists widely in nature. It is of fundamental importance to understand its origin, evolution, and the principles of its working. A synthetic system would be ideal for such study, as it would allow us to focus on relevant features by simplifying the system and make precise measurements that are difficult for much more complicated natural mutualistic ecosystems. We engineered a microbial symbiotic system that consists of two cross-feeding E. coli amino acid auxotrophs and investigated its evolutionary adaptation in minimal medium in serial batch cultures. We observed that different lineages all showed an overall trend of improving fitness. Interestingly, the growth rate did decrease occasionally. To identify the genetic basis for the observed mutualistic adaptation, we utilized new polony based whole-genome sequencing technology to analyze an isolated clone of one of the auxotrophs after 40 rounds of passaging in the evolution and pindowned a number of relevant mutations. We also developed an ordinary differential equation (ODE) model to investigate the dynamics of the system, which has provided important insights into the interactions between the two auxotrophs. 2. Mechanisms of biological switching through multi-site modifications of single molecules. A widespread feature of biological systems is their switch-like response to external or internal signals, also termed ultrasensitivity, which is crucial for the regulation of numerous biological processes. Multi-site modifications of single molecules have been known to contribute to ultrasensitivity. However, the underlying mechanism has largely remained unclear. We proposed a new mathematical model that describes how ultrasensitivity can emerge at a system level through multi-site modifications of a single protein. The fundamental features include: i) a chain of different phosphorylation states of the substrate protein caused by not-fully processive kinase/phosphatase; and ii) change of substrate protein activities along the phosphorylation chain. We have further quantitatively characterized how the degree of ultrasensitivity is affected by various properties of a multi-site system. The proposed model is capable of explaining mechanistically the switch-like behavior of many biological systems and the revealed mechanism may constitute a major paradigm for achieving biological switching. Finally, I will discuss my future research plan. The directions in which I would like to continue and expand my current research include: 1) mechanisms of multi-site based ultrasensitivity; 2) engineering of genetic circuits; and 3) system-level modeling and engineering of micro-organisms.

Lecture Webpage

 

Wednesday, March 1, 2006
12:00 pm, SGM 101
The Scientific Community is Cordially Invited

2006

Dr. Kristian Jessen 
Stanford University

“High-Resolution Compositional Simulation of Multicontact Miscible Displacements”

Abstract

A significant portion of the existing hydrocarbon reserves are candidates for enhanced recovery processes. Miscible/near-miscible gas injection or water alternating gas injection processes hold the potential for significant improvement of recoveries relative to primary production and water flooding. The ultimate recovery of a miscible and near-miscible gas injection scheme is a complex function of the local displacement efficiency and global sweep efficiency. Successful performance evaluation of recovery processes based on numerical calculations requires, in part, high resolution in permeability heterogeneity and appropriate representation of the phase behavior and transport properties of the fluid system. Numerical simulation of these processes is challenging because the predicted displacement efficiency is very sensitive to numerical diffusion. In this talk, I address the challenges related to compositional simulation of multicomponent multiphase flows. First, I demonstrate the shortcomings of conventional finite difference/volume (FD) simulation approaches in one dimension (1D), using a mix of analytical solutions, standard FD calculations and high order accurate FD calculations. I show that numerical artifacts have a fluid system specific impact on the prediction of the local displacement efficiency. This behavior is a direct result of the strong nonlinear coupling between flow and phase behavior. Next, I extend the analysis to 2D and 3D displacement processes. Physical dispersion is included in the model to delineate the grid resolution required to resolve the physics at a given simulation length scale. I present calculation examples for multicontact miscible gas/oil displacements and enhanced condensate recovery processes by gas injection/cycling. Finally, I conclude with a discussion of the future challenges and research directions in the field of compositional simulation.

Lecture Webpage

 

Monday, February 27, 2006
1:00 pm, VKC 207
The Scientific Community is Cordially Invited

2006

Dr. Huimin Zhao 
Departments of Chemical and Biomolecular Engineering, Chemistry, and Bioengineering, Institute for Genomic Biology, and Center for Biophysics and Computational Biology, University of Illinois, Urbana

“Biomolecular Engineering for Fun and Profit”

Abstract

Biomolecules such as nucleic acids and proteins have been increasingly exploited for applications in medical, chemical, agricultural, and food industries. However, a major limitation in the applications of biomolecules is the existence of a functional gap between naturally occurring biomolecules and those required by specific practical settings. Thus, how to close this functional gap has become a première intellectual and engineering challenge. In this talk, I will discuss our recent work on the development of new biomolecular engineering tools and their applications. Specifically, I will discuss: (1) developing estrogen receptor based genetic switches for human gene therapy; (2) engineering a novel phosphite-dehydrogenase based NAD(P)H cofactor regeneration system, and (3) designing new biosynthetic pathways for synthesis of thermally stable energetic compounds.

Lecture Webpage

 

Thursday, February 23, 2006
12:45 pm, OHE 122
The Scientific Community is Cordially Invited

2006

Professor Bahman Anvari 
Department of Bioengineering Rice University

“Biomolecular Engineering for Fun and Profit”

Abstract

The ability of cellular membranes to perform useful work is often ignored because they are relatively delicate and under many conditions deform easily. Yet, the membranes of living cells are poised to utilize the intense electric fields (> 10 MV/m) generated by the electrochemical gradients across them. For example, the ability of membranes to generate electrically-induced force is demonstrated in cochlear outer hair cells (OHCs) that are capable of producing rapid (> 50 kHz) movements, known as electromotility, a process required for normal hearing. Using a novel experimental approach that combines optical trapping with voltage-clamping and fluorescence imaging, we have demonstrated that native biological membranes are capable of electrically-induced pico-Newton level force generation over a broad range of electrical excitation frequency (> 3 kHz). This electromechanical force is: (1) enhanced in presence of a specialized transmembrane protein, prestin, found in the OHCs; (2) affected by the amplitude and polarity of the transmembrane electrical potential; and (3) diminished in the presence of a specific anionic amphipathic agent, salicylate. Our long-term objectives are to understand the molecular basis of electromotility, and investigate how membrane-based electromechanical coupling can be modulated in a controlled manner through changes in membrane physical properties and membrane-protein interactions. Characterizing the nanoelectromechanical properties of plasma membranes has the potential to not only lead to a better understanding of the hearing process and development of therapeutics for specific types of hearing loss, but also has relevance to a broad range of biological processes where membranes harness the energy in the transmembrane electric field, and to the development of biological nano-electromechanical systems with diagnostics and therapeutic applications.

Lecture Webpage

 

Thursday, February 16, 2006
12:45 pm, OHE 122
The Scientific Community is Cordially Invited

2006

Jin Wang,
Ph.D., P.E. Advanced Micro Devices, Inc

“Subspace Identification Using the Parity Space”

Abstract

Subspace identification methods (SIMs) have been one of the main streams of research in system identification. Compared to the prediction error methods (PEMs), SIMs have a better numerical reliability and a modest computational complexity, particularly when the number of outputs and states is large. However, most of the SIMs, like other more traditional PEMs, consider output errors only and assume the input variables are noise-free. Therefore, under the errors-in-variables (EIV) situation, most of the existing SIMs gives biased estimates. Besides, due to the correlation between the input and the unmeasured disturbance under feedback control, many subspace algorithms do not work on closed-loop data, even though the data satisfy identifiability conditions for prediction error methods. In this talk, I will present a new subspace identification method using the parity space employed in fault detection in the past. The basic algorithm, known as subspace identification method via principal component analysis (SIMPCA), gives consistent estimation of the deterministic part and stochastic part of the system, for both closed-loop and errors-in-variables situation. Two modifications, SIMPCA with column weighting and SIMPCA with modified instrumental variables, are developed to further improve the efficiency/accuracy of SIMPCA. Simulation examples are given to illustrate the performance of the proposed algorithms.

 

Tuesday, January 24, 2006
12:00 pm, SGM 101
The Scientific Community is Cordially Invited

2005

Medhat M. Kamal
Technology Project Manager, Chevron Energy Technology Company, San Ramon, California

“Numerical Well Testing– A Method to Use Transient Testing Results in Reservoir Simulation”

Abstract

Transient testing is facing a challenge to have the information it provides incorporated in numerical simulators used to predict reservoir performance. The main reason for the problem is that transient testing technology, developed largely via analytical solutions, provides average reservoir parameters not suited to the numerically discretized environment of current reservoir simulators. Previous efforts to include transient testing data in numerical reservoir simulation studies focused on history matching the pressure behavior during the test on a Cartesian-type plot just like matching stabilized production rates and pressures. Such approach neglects the wealth of information contained in the transient behavior of the tests.

A method called Numerical Well Testing (NWT) is proposed in this talk to preserve the information obtainable from traditional well test analysis and deliver it in a form suitable for direct use in numerical reservoir simulation. NWT is a systematic method that consists of five steps starting with traditional well test analysis, locally refining grids based on the analysis results, modifying full field numerical models, upscaling the results, and predicting future reservoir performance.

Two field examples are used to illustrate the method. The talk concludes by describing the software developments needed to make NWT a routine analysis method.

Bio

Medhat M. Kamal is a Technology Project Manager with Chevron Energy Technology Company in San Ramon, California. Prior to that he worked for ARCO, Schlumberger and Amoco. Kamal has 32 years of industry experience in well testing, reservoir description, and production and reservoir engineering and has published repeatedly in various SPE journals. He holds a BS degree from Cairo U. and MS and PhD degrees from Stanford U. all in petroleum engineering. Kamal has served SPE sections in Stanford, Tulsa, Houston, Dallas and San Francisco in various capacities since 1970, including chairing the Dallas section in 1993. A distinguished SPE member since 1983, Kamal has served as member and chairman of SPE’s Textbook, Monograph and Cultural Diversity Committees. He received the SPE 1977 Cedric K. Ferguson Medal. and was a distinguished lecturer in 1998. He also received the SPE Formation Evaluation Award, 2004; SPE Distinguished Service Award, 2004; SPE Regional Service Award in North, East and Central Texas Region, 1998 and was selected as the Texas Society of Professional Engineers Petroleum Engineer of the year for 1994.

Kamal is the current Co-Executive editor of SPEREE and the Editor of the upcoming monograph on Well Testing.

 

Thursday, December 15, 2005

2005

Dr. U. (Balu) Balachandran 
Argonne National Laboratory Argonne, IL

“Hydrogen Economy: Status of Science & Technology and R&D Opportunities”

Abstract

Hydrogen is considered the fuel of choice for both the electric power and transportation industries because of concerns over global climate change. Dependence on depleting oil reserves found in politically unstable regions of the world is forcing many nations to look into the so-called hydrogen economy – a solution that holds the potential to provide sustainable clean, secure, affordable, and reliable energy. At present, petroleum refining and the production of ammonia and methanol collectively consume ≈95% of all deliberately produced hydrogen in the U.S. Most of the demands for hydrogen are currently met by fossil-based technologies such as steam reforming of methane, naphtha reforming, and coal gasification. New cost-efficient production pathways will be needed as we move into the hydrogen-based transportation system. Present needs include economically viable and environmentally benign sources for hydrogen, safe and efficient storage, infrastructure for delivery, and utilization technologies. Also needed are establishment of safety codes and standards, and public training/acceptance. Materials science will play a major role in addressing the challenges of the hydrogen economy. The current status of the hydrogen production, storage, distribution, and utilization technologies will be reviewed. Topics addressed will include membranes for hydrogen production/separation, thermo-chemical water splitting, and technical barriers/research opportunities.

*Work supported by the U.S. Department of Energy.

 

Monday, December 12, 2005
1:00 pm, HED 116
The Scientific Community is Cordially Invited

2005

Dr. Maghsood Abbaszadeh 
Innovative Petrotech Solutions, Inc.

“Multiscale Data Integration for Reservoir Characterization and Identification of Sweet Spots for Well Placement”

Abstract

Data for reservoir characterization comes from a variety of sources at different scales and with different qualities. These data carry various types of useful information for reservoir modeling. The statistical methodology of multiscale multivariate Gaussian is presented to integrate data sources of seismic, geology and peterophysics into a single super secondary data for static reservoir descriptions. The theoretical aspects of the method are discussed and analyzed in comparison to the commonly advocated geostatistical method of block cokriging. The usefulness of the method as a means to quantify the value of information of various data sources is also discussed. The applicability of the technique is illustrated in reservoir characterization of a heterogeneous turbidite field in the Gulf of Mexico. A workflow for a comprehensive geostatistical reservoir characterization is then briefly presented, utilizing results of integrated data.

One of the main tasks of any reservoir development plan is to decide where to drill wells based on multiple geostatistical reservoir models. The concept of dynamic sweet spots regarding well placement and field development is introduced. Sweet spots refer to connected high-quality reservoir rock volumes with good flow capability. The technique for identification of dynamic sweet spots requires optimized calibration of reservoir flow response with simplified proxy functions. Proxy functions offer measure of drainable rock volumes combined with the fundamentals of flow in porous media. Details of the dynamic sweet spot method are presented and demonstrated on the same heterogeneous turbidite reservoir for well placement and subsequent water and gas injection pilots.

 

Wednesday, December 7, 2005
1:00 pm, HED 116
The Scientific Community is Cordially Invited

2005

Dr. Hugh Stitt
Johnson Matthey

“What flow visualisation can teach us about reactor design (What? Flow visualisation can teach us about reactor design?)”

Abstract

Reactor design in industry is still dominated by empirical methods and the use of design margins. Flow visualisation techniques such as tomography and velocimetry are extensively used as research tool for, especially multiphase, reactors. While the images and movies can be impressive, they do not in themselve give us quantitative guidance in reactor design. How should and can we use these to improve reactor design in practice? The use of these techniques to improve uderstanding of reactor hydrodynamics and their use to underpin and validate phenomenological models that can potentially used in design will be briefly reviwed. The question then is how can these techniques benefit scale up, design and operation of commercial reactors. Examples will be presented of using flow visualisation in scale up studies and in diagnostic studies of commercial reactors, and the different demands of flow visualisation in lab, pilot and commercial reactors discussed.

Lecture Webpage

 

Thursday, November 17, 2005
1:00 pm, HED 116
The Scientific Community is Cordially Invited

2005

Dr. Kaveh Dehghani 
Chevron

“Integration of Laboratory, Modeling and Field Studies to Evaluate a Waterflooded Vuggy Carbonate Reservoir for Application of Improved Oil Recovery Methods”

Abstract

A waterflooded vuggy carbonate reservoir in Permian Basin was considered for application of Improved Oil Recovery (IOR) methods. An integrated laboratory, modeling and field study was used for the evaluation process. The following shows different parts of the evaluation process:

A methodology was developed to model and successfully history match the primary and waterflood phases in a 15 well, 100 acre vuggy portion of the field. This method is based on a derived log trace of secondary porosity calculated by subtracting sonic porosity (matrix only) from a core calibrated total porosity transformed from Density and Neutron-logs. Log signatures of vugular intervals were developed recognizing significant differences in matrix and total porosity. A detailed geostatistical distribution of total porosity was first generated and permeability was assigned using a cloud transform of core data from nearby wells. Two geostatistical distributions of secondary porosity with different correlation lengths were then generated using the developed secondary porosity trace. Vugular zones were assumed to have a secondary porosity of 8% or greater. These models were superimposed on the permeability cube by assigning exceptional high permeability values to the vuggy zones.

Using a general scale up method, the detailed permeability cubes were scaled-up for simulation studies. The models incorporating vuggy permeability distributions showed a far superior history match of primary and waterflood performance than those without vuggy permeability distributions. Good history match was also obtained on individual well basis. Sensitivity of the match to vuggy zone permeability and correlation length was analyzed. Results from these simulation runs provide insight into the spatial distribution and permeabilities of the vuggy zones.

During the process of this examination it was recognized that this reservoir was a potential candidate for the steam injection process. Thin zones of vuggy high porosity and high permeability within the main pay interval have threatened the effectiveness of waterflood, leaving a major portion of oil by-passed in the lower permeability matrix. Feasibility of increasing recovery by steam injection in this part of the field was investigated using thermal compositional models. The analysis of the results from this modeling practice showed that primary recovery produced 14% of OOIP and waterflood added a 12% incremental recovery. The results also showed that combining a short steamflood cycle followed by a blow-down cycle from all wells (including the injectors) resulted in a big kick in both oil production rate and cumulative oil production curves (e.g., 2.5 years of flood followed by 2.5 years of production). The best scenario of well configuration was 10 acre 5 spots with incremental oil recovery of 18% of OOIP. A preliminary economic calculation showed steam injection to be economically feasible.

We also conducted laboratory experiments on a core sample from this reservoir in order to quantify the recovery mechanisms. These comprise thermal expansion, thermally enhanced solution gas drive, vaporization, and in-situ steam drive. Computed Tomography (CT) imaging of a miscible flood was used to characterize the connectivity of the vugs and matrix rock. A series of blow-down tests were then conducted by heating the core to 300 â—� F. The backpressure regulator on the system was set just above the bubble point of the oil at 300 â—� F. The pore pressure was then reduced at a constant rate from one end of the core sample. The first blow-down test was with the core at initial oil saturation with pressure reduction from the top of the sample; the second at initial oil saturation with pressure reduction from the bottom; and the third at residual oil saturation to water with pressure reduction from the top. The volumes and compositions of the produced fluids were measured in all the blow-down tests. The initial and final oil saturation distribution for the second blow-down experiment was also CT imaged.

The CT images reveal that the core sample contains vugs, high permeability matrix, and low permeability matrix rock; and that the vugs are connected through the high permeability matrix. The blow-down experiments show that 50-68% of the oil is recovered; with 8-20% due to thermal expansion, 20-24% due to thermally enhanced solution gas drive, 12-16% due to dry distillation, and 8-10% due to in-situ steam drive.

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Friday, October 28, 2005
1:45 pm, HED 116
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