Conferences, Lectures, & Seminars
Events for March
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Integrating Models and Experiments: Synthetic Ecosystems and Molecular Switches
Wed, Mar 01, 2006 @ 12:00 PM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
GRADUATE SEMINARIntegrating Models and Experiments: Synthetic Ecosystems and Molecular SwitchesDr. Xiaoxia (Nina) Lin
Harvard Medical SchoolABSTRACTIn 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.Wednesday, March 1, 2006
12 noon SGM 101
The Scientific Community is Cordially Invited
Location: Seeley G. Mudd Building (SGM) - 101
Audiences: Everyone Is Invited
Contact: Petra Pearce
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Process Systems Engineering in Semiconductor Processing
Tue, Mar 07, 2006 @ 12:00 PM - 01:00 PM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
GRADUATE SEMINARProfessor S. Joe Qin
Department of Chemical Engineering
University of Texas, AustinAbstract: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.Location: Hedco Pertroleum and Chemical Engineering Building (HED) - 116
Audiences: Everyone Is Invited
Contact: Petra Pearce
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Ensemble Kalman Filter For History Matching
Wed, Mar 08, 2006 @ 11:30 AM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
Speaker: Dr. Dean Oliver, Professor and Director,
Mewbourne School of Petroleum and Geology Engineering
The University of OklahomaThe 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.
Location: Hedco Pertroleum and Chemical Engineering Building (HED) - CO 116
Audiences: The Scientific Community is Cordially Invited
Contact: Takimoto Idania
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Lyman L. Handy Colloquium Series
Thu, Mar 09, 2006 @ 12:45 PM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
Professor Efthimios (Tim) Kaxiras Department of Applied Physics Harvard University
Location: Olin Hall of Engineering (OHE) - 122
Audiences: Everyone Is Invited
Contact: Petra Pearce
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Analytical Methods in Compositional Modeling
Fri, Mar 10, 2006 @ 11:00 AM - 12:00 PM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
Speaker: Dr. Tara LaForce
Stanford UniversitySubsurface 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.
Location: Hedco Pertroleum and Chemical Engineering Building (HED) - 116
Audiences: Everyone Is Invited
Contact: Takimoto Idania
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Opportunities in Nanomagnetism
Fri, Mar 10, 2006 @ 02:30 PM - 04:00 PM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
Samuel BaderSenior Scientist at Argonne National Laboratory and
Scientific Director of the Argonne Center for Nanoscale MaterialsOpportunities in NanomagnetismABSTRACTNanomagnetism is the discipline dealing with magnetic phenomena specific to structures having dimensions in the submicron range. This talk addresses the challenges and scientific problems in this emerging area, including its fabrication strategies, and describes experiments that explore new spin-related behaviors in metallic systems as well as theoretical efforts to understand the observed phenomena. As a subfield of nanoscience, nanomagnetism shares many of the same basic organizing principles such as geometric confinement, physical proximity, and chemical self-organization. These principles are illustrated by means of several examples drawn from the quests for ultrastrong permanent magnets, ultra-high-density magnetic recording media, and nanobiomagnetic sensing strategies. As a final example showing the synergetic relationships to other fields of science, the manipulation of viruses to fabricate magnetic nanoparticles is discussed.**ALL FIRST YEAR MATERIALS SCIENCE MAJORS ARE REQUIRED TO ATTEND**Location: Vivian Hall of Engineering (VHE) - 217
Audiences: Everyone Is Invited
Contact: Petra Pearce
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Cytomimicry: Fabrication of Biofunctionalized Materials Through Biotic-Abiotic Interfacing
Fri, Mar 24, 2006 @ 01:00 PM - 03:00 PM
Mork Family Department of Chemical Engineering and Materials Science
Conferences, Lectures, & Seminars
GRADUATE SEMINARDean 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 AngelesABSTRACTThe 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 endgroups 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.
Location: Hedco Pertroleum and Chemical Engineering Building (HED) - 116
Audiences: The Scientific Community is Cordially Invited
Contact: Petra Pearce