2008-09

09/11/2008: Tethered Vesicle Assembly as Monitored by QCM-D by Professor Curtis Frank, Department of Chemical Engineering, Stanford University

Abstract

One of the stable forms of assemblies that amphiphilic phospholipids can generate in an aqueous solution is that of the vesicle or liposome, which consists of a spherical “sack” encapsulating a liquid (buffer or water) and having a lipid bilayer as the enclosing membrane. In a highly reductionist view, this structure may be able to mimic the cell membrane to some extent. Our research objective has been to develop assembly protocols such that an array of such vesicles could be used as a substrate for a bioanalytical device. The key to such potential devices is that the vesicles be localized at a solid substrate, and we accomplish this through use of a biotin-streptavidin-biotin tethering scheme. Moreover, this tethering protocol permits use of surface-sensitive tools to monitor the array fabrication. In this presentation, we will describe the use of the quartz crystal microbalance with dissipation monitoring to follow the lipid assembly process. We will show how the build-up of the tethered vesicle array may be followed quantitatively, and we will give one example of an antibody-antigen recognition experiment based on the tethered vesicle platform.

10/09/2008: New vistas in dispersion science and engineering, by Darsh Wasan, Department of Chemical and Biological Engineering, Illinois Institute of Technology

Abstract

Colloidal suspensions are used in a variety of technological contexts. For example, their spreading and adhesion behavior on solid surfaces can yield materials with desirable structural and optical properties. The structure and stability of colloidal dispersions depend highly on the interaction forces between colloidal particles and the confining geometries. This is especially the case in a concentrated colloidal dispersion when particles are more likely to come in close contact with one another and become more ordered in the confines of their restricted environment. In recent years, due to the advent of new instrumentation for measuring interaction forces in colloidal suspensions, novel forces, such as the structural force arising from the energy barrier caused by particle microstructuring and the attractive depletion force caused by the excluded volume effect, have been characterized. This lecture will highlight the role of structural forces in stabilizing dispersions and especially point out their importance in a variety of technological contexts, such as particle sedimentation, wetting, spreading and adhesion of such systems on solid surfaces and nanostructured material synthetics.

11/13/2008: Semiconductor Nanomembranes, by Max Lagally, University of Wisconsin, Madison

03/12/2009: Opportunities and Challenges in the Pursuit of Energy Savings Using Membranes for Large Scale Chemical Processes, by William Koros, Geogia Institute of Technology

04/02/2009: Reservoir Characterization by Production Data, by Larry W. Lake, The University of Texas at Austin

Abstract

The history of reservoir characterization has been based on and currently rests on static data. Indeed, entire technologies academic majors, and even commercial enterprises have sprung up to gather, interpret, and use core data, logs, geology and seismic data. The saturations, porosities, permeabilities, relative permeabilitiies, to name a few, from these technologies form the basis of volumetric calculations (original hydrocarbon in place), and recovery estimates (recoverable hydrocarbon).

Ironically, it is dynamic data or data from flowing wells that are of commercial interest because revenue streams are directly proportional to it. But, aside from use in pressure transient analysis and as targets in simulation history matching, these data are little used in characterization.

This situation is about the change. The large-scale use of near-continuous (real-time) surface and downhole measurements of rates (all fluids), pressures and temperatures will augment\ and in some cases supplant reliance on static measurements. Such measurements are common now on new production facilities. Indications are that they are cost-effective on existing or legacy production. But these measurements will only be useful if there are means to interpret them. The objective of this presentation is to discuss a set of models that will use the coming "tsunami" of data to be generated by production sensor technology too characterize reservoirs.

04/09/2009: Microfluidic Actuation by Thermocapillary Forces: Fundamentals, Devices and Sensing Arrays by Professor Sandra Troian, Laboratory of Interfacial & Small Scale Transport (LIS2T), Department of Applied Physics, California Institute of Technology

Abstract

Liquid elements with dimensions in the micron to nanometer range manifest exceedingly large surface to volume ratios and are therefore highly susceptible to flow induced by surface stresses. This feature has been used to direct the motion of small, free surface liquid structures for micro-, bio- and optofluidic applications. Both normal and tangential stresses can be used to steer, mix, meter or shape liquid structures on demand. When such structures exhibit an effective zero Reynolds number and small aspect ratio, then inertial forces and phase lag are negligible and the liquid responds instantaneously to boundary stresses. Any time dependence of the flow is then strictly due to actuation of the bounding surfaces. These limits constitute the so-called slender gap approximation used here to investigate thermocapillary actuation of liquid elements with the potential for direct-write of 3D nanostructures. This possibility arises from analysis of several experiments conducted during the past decade in which molten nanoscale polymer films subject to an ultra large transverse gradient undergo spontaneous formation of nanopillar arrays. The formation of these self-assembling protrusions has been attributed to a Casimir-like radiation pressure caused by interfacial reflections of acoustic phonons. We demonstrate instead that thermocapillary stresses play a crucial if not dominant role in this formation process. Simulations of the governing interface equation, used to specify the pillar spacing and time-dependent height, are used to explore construction of nanoscale components for optical and photonic applications.

2007-08

05/01/2008: Can the Earth Produce the Biomass We Demand? by Professor Tadeusz Patzek, Department of Civil and Environmental Engineering, University of California, Berkeley

Abstract

To demonstrate the utter impossibility of sustained, industrial-scale production of biofuels anywhere and from and source, I consider the local, field-scale sustainability of a productive industrial maize agrosystem that has replaced a fertile grassland ecosystem. Using the revised Second Law approach of Svirezhev, I show that currently this agrosystem is unsustainable in the US (and anywhere else), with or without tilling the soil.    The calculated average erosion rates of soil necessary to dissipate the entropy produced by US maize agriculture, 23 -- 45 t/ha-yr, are bounded from above by an experimental estimate of mean soil erosion by conventional agriculture worldwide, 47 t/ha-yr. Between 1982 and 1997, US agriculture caused an estimated 7 -- 23 t/ha-yr of average erosion with the mean of 15 t/ha-yr. The lower mean erosion rate of no till agriculture, 1.5 t/ha-yr, necessitates the elimination of weeds and pests with field chemicals -- with the ensuing chemical and biological soil degradation, and chemical runoff -- to dissipate the produced entropy. The increased use of field chemicals that replace tillers is equivalent to the killing or injuring of up to 300 kg/ha-yr of soil flora and fauna. Additional soil degradation, not discussed here, occurs by acidification, buildup of insoluble metal compounds, and buildup of toxic residues from field chemicals.  The degree of unsustainability of an average US maize field is high, requiring 6 -- 13 times more energy to remediate soil degradation, etc., than the direct energy inputs to maize agriculture. This additional energy, if spent, would not increase maize yields. The calculated  ``critical yield'' of ``organic'' maize agriculture that does not use field chemicals and fossil fuels is only 30 percent lower than the average maize yield of 8.7 tons per hectare (140 bushel/acre) assumed here. Immediate attention should be devoted in the US to more sustainable alternatives to the current industrial agriculture.  I will also discuss the implications of my findings to the current wholesale destruction of the tropical ecosystems.

04/10/2008: Development of a biomimetic lung surfactant, by Associate Professor Annelise Barron, Department of Bioengineering, Stanford University

Abstract

We are developing a new family of amphipathic peptide mimics for a synthetic lung surfactant (LS) replacement. Presently used exogenous LS replacements are extracted from animal lungs and used to treat respiratory distress sydrome in premature infants. The hydrophobic lung surfactant proteins SP-B and SP-C are necessary constituents of an effective surfactant replacement for the treatment of respiratory distress. As there are concerns and limitations associated with animal-derived surfactants, much recent work has focused on synthetic peptide analogues of SP-B and SP-C. However, creating an accurate peptide mimic of SP-C that retains good biophysical surface activity is challenging, given this lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One approach that overcomes these difficulties is the use of helical poly-/N/-substituted glycines, or "peptoids," to mimic SP-C. We discuss advances in the design and characterization of peptoid-based SP-C mimics, which recently have led to the creation of our most biomimetic surfactant replacements to date.
Peptoid sequences were systemically varied in order to study surface activity effects of varying peptoid helicity,/ N/-terminal side chain chemistry and sequence length, as well as the side chain structures used within the hydrophobic C-terminal helix. The secondary structures of the peptoid SP-C mimics are analyzed in organic solution by CD spectroscopy. Langmuir-Wilhelmy surface balance experiments, epifluorescence videomicroscopy studies, and pulsating bubble surfactometry are used to characterize the surface activity and surface film morphology of the mimics in combination with a biomimetic phospholipid formulation. These results provide us with the first comprehensive structure-function relationships for peptoid-based analogues of surfactant protein C, as well as strong evidence that they offer significant promise for use in a synthetic replacement for animal-derived surfactants. There are several other potential applications for a safe and non-immunogenic surfactant formulation with these properties, other than treating respiratory distress, including protection against ventilator-induced lung injury, drug delivery to the lungs, and treatment of ear infections.

03/13/2008: Innovative Bioreactors for Contaminated Air and Water Treatment: From Nano to Field Demonstration, by Marc A. Deshusses, Department of Chemical and Environmental Engineering, University of California Riverside

Abstract

Biological systems have a fantastic potential for the biotransformation of a wide range of substances including treatment of numerous man made pollutants. This provides opportunities for the development of novel and environmentally friendly bioprocesses for pollution control. In this seminar, recent research in the area of bioreactors for air and groundwater pollution control conducted in Deshusses' group will presented and discussed. This will includes the simple synthesis of reactive nanomaterials for environmental application, the use of molecular methods and establishment of relationships between pollutant removal and DNA or RNA fingerprints, high performance biotrickling filters treating H2S at a gas contact time as low as 1.5 seconds, and the treatment of perchlorate contaminated groundwater by bacteria deriving energy from iron particles on which they are attached. The discussion will include lab and field data and a brief assessment of the sustainability of some of these novel developments.

02/14/2008: Optimization of Oil and Gas Recovery by Closer Reservoir Monitoring, by Roland Horne, Standford University

Abstract

The permanent downhole pressure gauge is a class of tool recently harnessed in the industry. These tools are installed during the well completion and provide a continuous record of pressure changes during production. Permanent downhole gauges have the potential to provide more information than the traditional well test, which is carried out for a relatively short duration. Permanent downhole gauges may provide useful information regarding changes in reservoir properties or well condition with time as reservoir is produced.

However interpretation of permanent downhole gauge data is a new problem. Firstly, unlike the traditional well test where "disturbances" in reservoir (i.e. rates) are created and pressure and rates are both known, in the record from the permanent downhole gauge the changes in rates may not be properly known. Moreover, the dynamic changes in the reservoir, along with changes in the flowing temperature or in the gauge itself, make the data more complicated to interpret.

01/17/2008: Geological Storage as a Carbon Mitigation Option, by Professor and Chair Michael Celia, Department of Civil and Environmental Engineering, Princeton University

Abstract

The most promising approach to solve the carbon problem involves widespread implementation of zero-emission power plants. One promising option is to use fossil fuel-based plants with carbon capture and storage (CCS) technology. While a variety of storage options are being studied, geological storage appears to be most viable. Injection of captured CO2 into deep geological formations leads to a fairly complex flow system involving multiple fluid phases, a range of potential geochemical reactions, and mass transfer across phase interfaces. General models of this system are computationally demanding, with the problem made more difficult by the large range of spatial scales involved, and the importance of local features for both fluid flow and geochemical reactions. An especially important local feature involves leakage pathways, with one example being abandoned wells associated with the century-long legacy of oil and gas exploration and production. Such pathways also have large uncertainties associated with their properties. Therefore, inclusion of leakage in the storage analysis requires resolution of multiple scales, and incorporation of large uncertainties. Taken together, these render standard numerical simulators ineffective
due to their excessive computational demands. A series of simplifications to the governing equations can reduce computational demands, and ultimately render the system solvable by analytical or semi-analytical methods. These solutions, while restrictive in their assumptions, allow for large-scale analysis of leakage in a probabilistic framework. An example from Alberta, Canada will be used to demonstrate the utility of these solutions.

12/06/2007: Environmentally Friendly Energy Solutions, by Rakesh Agrawal, School of Chemical Engineering, Purdue University

Abstract

The recent rise in oil prices again reminds us that the world’s supply of fossil fuels is finite. Roughly 85% of current energy use is being met by fossil fuels. Alternate primary energy sources are being identified and developed to permit the continued functioning of the world economy. The first part of this presentation will survey some of these alternative sustainable primary energy sources: solar, wind, nuclear, and bio-based sources. It will also review the particular challenges associated with various end uses of energy.

Common energy carriers, such as electricity, are used to move energy from several primary sources to many different end uses. Recently, the possibility of an alternate energy system using H2 as a common energy carrier has been proposed and widely debated. In such a system, H2 would first have to be produced from a primary source. It would then need to be transported, delivered and stored at the point of end use. The second part of this presentation will briefly highlight the challenges associated with H2 supply chain that is currently being considered for fuel cell vehicles.

Finally, some new and novel solutions to sustain the current transportation sector will be presented. These solutions provide a feasible framework for a fossil fuel-free world. Also they provide exciting possibilities for chemical engineers to apply their expertise and contribute to the grand challenge of energy.

11/08/2007: Proteomics on a Supported Membrane Chip, by Paul Cremer, Department of Chemistry, Texas A&M

Abstract

Supported phospholipid bilayers (SPBs) offer a promising environment to mimic many properties of native cell membranes. As such, these systems hold great promise for creating highly selective biosensors as well as for the design of nanoscale architectures in which membrane proteins may be separated without denaturation. Two important hurdles exist, however, before these systems can be widely exploited in applications. First, SPBs are generally unstable upon exposure to air. Second, there is typically insufficient space between the lower leaflet of the supported bilayer and an underlying planar support to allow full mobility for membrane proteins. In this presentation I will describe recent advances in our laboratory for creating air stable SPBs as well as a novel "double cushion" platform that allows transmembrane proteins to retain lateral mobility.

10/11/2007: Elucidating the Control Mechanism for DNA damage repair with the p53-Mdm2 system: Single Cell Data Analysis and Ensemble Modeling, by Babatunde A. Ogunnaike, Chemical Engineering Department, Univ. of Delaware

Abstract

The p53-Mdm2 system, which plays a crucial role in DNA damage repair, is one of the best-studied of the “negative feedback motifs” known to be present in human cells (see for example, Piette, et al, 1997; Vogelstein et al, 2000; and Michael and Oren, 2003). Such studies typically involve perturbing cell populations with appropriate stimuli and monitoring total population response with immunoblots. Often such measurements of ensemble behavior are sufficient for understanding the molecular mechanism underlying the phenomenon in question. In the case of DNA damage repair using the p53-Mdm2 system however, Lahav et al, (2004), recently published experimental evidence that the dynamic behavior of the ensemble is fundamentally different from that of individual cells, creating a dilemma about the underlying control system mechanism.

Specifically, in response to DNA damage, the observed ensemble response is a damped oscillation in p53 levels whose amplitude increases with increased DNA damage. This behavior is consistent with “analog” control and a model by Bar-Or et al., (2000), predicts it reasonably well. However, the data in Lahav, et al., (2004) shows that at the single cell level, the response to DNA damage is rather a series of discrete pulses in p53; furthermore, with increase in DNA damage, neither the mean height nor the duration of the pulses changed, but the mean number of pulses increased. In addition, genetically identical cells each showed a different number of pulses of p53. Taken together, the observed single cell behavior is consistent with “digital” control (Lahav et al., 2004), raising the obvious question: how can “digital” behavior at the single cell level appear “analog” at the ensemble level? The more fundamental issue concerning the underlying DNA damage response mechanism is captured by the following challenge stated by Lahav, et al.:

What is the mechanism for digital oscillations in this system? Digital undamped oscillatory behavior is a challenge to modelers because the simplest theoretical models of this negative feedback loop show damped analog oscillations.

In this seminar we present a comprehensive, systems engineering model that uses the Lahav data to elucidate this mechanism and resolve the dilemma. First, we develop a simple model of the p53-Mdm2 effector system that reproduces the single non-oscillatory response to a stress signal experimental observed by Lahav et al. Next, from a careful analysis of the Lahav data we develop a probabilistic model of the distribution of pulses observed in a cell population. Finally, we combine the two with the simplest possible digital control algorithm to show how oscillatory responses whose amplitudes grow with DNA damage can arise from single cell behavior in which each single pulse response is independent of the extent of DNA damage.

09/13/2007: Old Dogs and New Tricks: Will Biotechnology Actually Revolutionize the Oil Industry This Time Around?, by Steven Bryant, Center for Subsurface Modeling, University of Texas at Austin

Abstract

The idea of using microbes to increase recovery from oil reservoirs is more than fifty years old. Proponents of microbial enhanced oil recovery (MEOR) have long championed its advantages, but field applications have never lived up to the promise implied by those claims. In the current era of sustained high oil prices and increasing demand for hydrocarbons, operators have renewed their interest in all forms of EOR. Meanwhile, techniques for genomic engineering, metabolic engineering and biotechnology in general have developed rapidly. Can the potential of MEOR – in essence, the possibility of implementing EOR for the same price as a waterflood – be realized this time around?

To answer that question, it is instructive to review the reasons for the failure of MEOR in the past. An important lesson from that review is that a multidisciplinary perspective is absolutely necessary for this application. We then consider an example of MEOR that works and has yielded an economic success in the field. Here the lesson is a common one in engineering: simpler processes are more robust. However, efforts to establish a mechanistic understanding of the successful process raise more questions than they answer. These questions turn out to relate to a much broader theme: how life forms have managed to adapt to an extraordinary range of conditions on this planet. Recognizing these issues provides insight into what is feasible and what is improbable for oilfield applications of biotechnology.

2006-07

03/08/2007: Influence of Materials Technology on the Fuel Efficiency of Aeroturbines, by A. G. Evans, Materials Department, University of California, Santa Barbara

Abstract

The fuel efficiency of aero-turbines has been improved systematically during recent decades. The trend is strongly correlated with the increase in achievable temperature in the hot sections of the turbine. In turn, this temperature increase is attributed to combined advances in materials and active cooling technologies. This presentation examines the materials innovations that continue to be implemented due to advancements at the frontiers of materials and mechanics. The most recent advances have been enabled by multilayer coatings that impart thermal and oxidation protection. The former is provided by an oxide with exceptionally low thermal conductivity. The latter is achieved using alloy coatings that form alumina. For continued performance enhancement using such multilayer concepts a systems-level methodology is needed. The materials and mechanics formulations that have been devised for this purpose are described.

02/08/2007: Modeling Chemical Reactivity: Effects of Confinement, by Keith E. Gubbins, Center for High Performance Simulation (CHiPS) and Department of Chemical Engineering, North Carolina State University

Abstract

A goal of theory is to predict chemical reactivity – equilibrium composition, reaction mechanisms and reaction rates, as well as diffusion limitations – from first principles. At present our ability to achieve this is quite limited, for a number of reasons. First, ab initio methods are necessary, since electrons are rearranged, but these are computationally very demanding, and with current supercomputers we are quite limited in the length and time scales that can be accessed; moreover, the scaling of the computational burden with the number of electrons is poor. Second, reaction events are rare, and so even if we have the energy landscape for the reaction conventional molecular dynamics simulations are insufficient. A brief review of the most widely used methods to model chemical reactions, at both the electronic and atomistic levels will be presented, with comments on their applicability and a description of their strengths and weaknesses1. In many applications a combination of ab initio and semi-classical atomistic simulations will be needed. Specialized atomistic simulation methods are usually necessary, since the reactions are themselves rare events, and the free energy landscape for the reaction is often rugged with many possible reaction paths.

Chemical reactions are often carried out in nano-structured materials, which can enhance reactions due to their large specific surface area, their interactions with the reacting mixture and confinement effects. An experimental investigation of the role of each possible catalytic effect is challenging, since experimental measurements reflect an integration over multiple catalytic effects. In this talk several of the different factors that can influence a chemical reaction in confinement will be considered. We first consider the influence of steric hindrance on the equilibrium and kinetics for the rotational isomerizations of several small hydrocarbons. These examples illustrate how reaction rates can vary doubly exponentially with the dimensions of the confining material (the 'shape-catalytic' effect). As a second example, we consider the unimolecular decomposition of formaldehyde on graphitic carbon pores of various sizes . These results illustrate the influence of electrostatic interactions with the supporting material on the reaction mechanism and equilibrium yield for reactions involving a charge transfer. As a final example, we consider the interaction of a water molecule with a defective carbon substrate as an example of a chemical interaction that can be enhanced through a shape-catalytic effect. We show using ab initio calculations how a vacancy site on a carbon surface can induce the thermal splitting of water at relatively low temperatures . We also examine the dissociation on a vacancy site on a nanotube surface, which shows the shape-catalytic effect of the surface curvature. These results are a first step toward the design of catalytic materials that take advantage of different enhancing effects simultaneously.

01/11/2007: Smart Surfactants and Ligands in Pharmaceutical, Environmental, and Energy Applications, by Professor Keith P. Johnston, Department of Chemical Engineering, University of Texas at Austin

Abstract

Smart surfactants and ligands are being designed to (1) perform multiple functions, (2) achieve targeted activity at particular interfaces, and (3) be active at unusual interfaces, for example, in CO2. In pharmaceutical science, one of the key challenges is particle engineering of poorly water soluble drugs to achieve high bioavailability for oral and pulmonary administration. Increasingly, two goals are being pursued simultaneously: (1) control of particle nucleation and growth to achieve the desired particle morphology and (2) rapid wetting and dissolution, and in some cases high levels of supersaturation. Studies of fundamental thermodynamic, transport and interfacial mechanisms are leading to improvements in bioavailability in vivo. Environmentally benign carbon dioxide-based emulsions may replace toxic organic solvents for pharmaceutical, chemical, materials, and microelectronics processing applications. Surfactants stabilize CO2-in-water emulsions or foams needed to control mobility in CO2-enhanced oil recovery, for producing 60 billion barrels of oil (approximately $6 trillion value). Nonionic methylated branched hydrocarbon surfactants emulsify up to 90% CO2 in water with polyhedral cells smaller than 10 microns, with the potential for excellent mobility control. An emerging understanding of the role of surfactants in charging and stabilization mechanisms for colloids in low-permittivity solvents (dielect. const. < 5) will help advance a variety of applications including electrophoretic displays and electrophoretic deposition of nanocrystals to form superlattices. On the basis of novel experimental measurements for both hydrophilic and hydrophobic TiO2, a general mechanism is presented to describe particle charging in terms of preferential partitioning of cations and surfactant anions between the particle surface and reverse micelles in the bulk solvent. The design of smart surfactants and ligands for nano- and micron-sized emulsions and particle dispersions is in its infancy, and many new concepts will be developed for pharmaceutical, environmental, and energy applications.

12/14/2006: Rheology and Fluid Mechanics of Polymer Solutions Undergoing Rapid Elongational Deformations, by Professor Robert E. Armstrong, Department of Chemical Engineering, MIT

Abstract

Bead-spring kinetic theory models, which we illustrate in this talk by elastic dumbbells, have proven to be very useful in describing the rheological behavior of polymeric liquids and for understanding the response of these liquids in complex flows. In this talk we consider two experiments in which simple bead-spring models have failed to capture key physical observations, and we discuss improvements to the models motivated by these failures. The first experiment is filament stretching, which consists of the sudden startup of uniaxial elongational flow followed by stress relaxation. When stress is plotted against birefringence in this experiment, hysteresis is observed between the growth and relaxation parts of the experiment. Simple bead-spring models do not capture this hysteretic behavior. We analyze the Kramers chain, a fine-scale model for polymer dynamics, in order to assess the validity of the coarser-grained bead-spring models in these deformations. Whereas the spring force is a simple function of the dumbbell length for customary nonlinear elastic springs, we find that the relationship between the ensemble averaged end-to-end force and the extension for a Kramers chain depends on the kinematic history to which it has been subjected. We find that it is essential for a dumbbell model to have an end-to-end force that depends upon the deformation history in order to capture hysteresis in the filament stretching experiment.

We then turn to a discussion of a complex flow, namely flow around a linear, periodic array of cylinders. Viscoelastic liquids in this flow undergo a transition from steady, two-dimensional flow to a spatially periodic, threedimensional flow at a critical flow rate. Simple bead-spring models do not correctly capture this flow transition, and we believe that this shortcoming is due to the failure of these models to describe well the rapid elongational flow in the wake behind the cylinders. In order to address this problem we construct a new bead-spring model that is simple enough to be used in finite element simulations, and yet captures correctly the dynamics of hysteresis observed in the first experiment. The new model describes a polymer molecule as a set of identical segments where each segment represents a fragment of the polymer that is short enough so that it can sample its entire configuration space on the time scale of the deformation and therefore stretches reversibly. As the molecule unravels, the number of segments decreases but the maximum length of each segment increases so that the model accounts for the constant maximum contour length of the parent molecule. The behavior of this new model in the flow around cylinders will be presented.

10/12/2006: "Molecular Engineering of Stem Cell and Gene Therapies", by Professor David Schaffer, Department of Chemical Engineering and The Helen Wills Neuroscience Institute, UC Berkeley

Abstract

New molecular therapies based on gene delivery and stem cells have significant potential for tissue engineering and repair for numerous diseases. Before these approaches can succeed, however, a number of fundamental engineering challenges must be overcome, particularly in the nervous system, our tissue of interest.

Gene therapy, the introduction of genetic material to the cells of a patient for therapeutic benefit, has the potential to directly translate the basic knowledge derived from the Human Genome Project into therapeutic benefit. However, the vehicles or vectors that deliver therapeutic genes still require engineering for enhanced efficiency and safety. Our efforts are focused on modifying these vehicles at the molecular level to overcome the common dilemma faced by all: they did not evolve in nature to perform the therapeutic endeavors we ask of them. We have developed novel approaches to engineer already promising gene delivery vehicles, the adeno-associated viral vector and lentiviral vector. Specifically, we are applying directed evolution approaches to overcome several challenges in vector performance, including its mass transport through tissue and cells and interactions with the immune system.

Furthermore, gene therapy has enormous potential to synergize with stem cells to repair damaged tissue. Neural stem cells are present throughout the adult nervous system, but we must learn at a quantitative, molecular level the signaling mechanisms that control these cells before we can harness them. We have identified novel signaling factors that regulate neural stem cells and are investigating the mechanisms by which the cells process these signals into functional decisions. Specifically, we are exploring the hypothesis that cell switching between multiple steady states in gene regulation networks can serve as a general mechanism for the critical fate choices these cells must make as they differentiate into specific cell types, such as neurons. We hope that this basic knowledge can be applied, in combination with improved gene delivery vehicles, to regenerate neural tissue from the effects of neurodegenerative disorders such as Alzheimer's, Parkinson's, and Lou Gehrig's Diseases.

09/14/2006: "Opportunities and Challenges in Nanostructured Materials", by Professor Jagdish (Jay) Narayan, Department of Materials Science and Engineering, North Carolina State University

Abstract

This talk addresses some of the fundamental issues and critical advantages in reducing the grain size/ feature size to the nanoscale regime. We find that as the grain size or feature size is reduced, there is a critical size below which the defect content can be frozen or reduced virtually to zero. This critical size for most defects in materials falls in the nanoscale regime. Thus, nanostructured materials offer a unique opportunity to realize the property of a perfect material. However, with this opportunity comes a great challenge in terms of engineering a large fraction of atoms near the surfaces/interfaces. Another challenge is to self-assemble nanounits with desired structure and orientation with respect to the matrix. This often requires thin film epitaxy across the misfit scale with lattice misfit ranging from about 1% to 50%. Using a new paradigm of domain matching epitaxy (DME), we are able to deal with thin film epitaxy across the misfit scale within the continuum ground state energy description of the strained system. The DME framework is based upon matching of integral multiples of lattice planes, where there is one dislocation in each domain corresponding to missing (compressive strain) or extra (tensile strain) half plane. According to the DME paradigm, 2.0% and 25% misfits correspond to 49/50 and 3/4 planar matching, respectively. The misfit in between the integral multiples of planes is accommodated by the principle of domain variation. The limiting factors in DME are associated with matching of interface interatomic potentials, lattice relaxation, overlapping of dislocation cores and bending of lattice planes. For large misfit systems, strain free energy often dominates over chemical free energy. We focus on integration of systems based on III-nitrides, II-oxides, and perovskites.

08/25/2006: Modeling Chemical Reactivity: Effects of Confinement, by Keith E. Gubbins, Center for High Performance Simulation (CHiPS) and Department of Chemical Engineering, North Carolina State University

Abstract

A goal of theory is to predict chemical reactivity – equilibrium composition, reaction mechanisms and reaction rates, as well as diffusion limitations – from first principles. At present our ability to achieve this is quite limited, for a number of reasons. First, ab initio methods are necessary, since electrons are rearranged, but these are computationally very demanding, and with current supercomputers we are quite limited in the length and time scales that can be accessed; moreover, the scaling of the computational burden with the number of electrons is poor. Second, reaction events are rare, and so even if we have the energy landscape for the reaction conventional molecular dynamics simulations are insufficient. A brief review of the most widely used methods to model chemical reactions, at both the electronic and atomistic levels will be presented, with comments on their applicability and a description of their strengths and weaknesses1. In many applications a combination of ab initio and semi-classical atomistic simulations will be needed. Specialized atomistic simulation methods are usually necessary, since the reactions are themselves rare events, and the free energy landscape for the reaction is often rugged with many possible reaction paths.

Chemical reactions are often carried out in nano-structured materials, which can enhance reactions due to their large specific surface area, their interactions with the reacting mixture and confinement effects. An experimental investigation of the role of each possible catalytic effect is challenging, since experimental measurements reflect an integration over multiple catalytic effects. In this talk several of the different factors that can influence a chemical reaction in confinement will be considered. We first consider the influence of steric hindrance on the equilibrium and kinetics for the rotational isomerizations of several small hydrocarbons. These examples illustrate how reaction rates can vary doubly exponentially with the dimensions of the confining material (the 'shape-catalytic' effect). As a second example, we consider the unimolecular decomposition of formaldehyde on graphitic carbon pores of various sizes . These results illustrate the influence of electrostatic interactions with the supporting material on the reaction mechanism and equilibrium yield for reactions involving a charge transfer. As a final example, we consider the interaction of a water molecule with a defective carbon substrate as an example of a chemical interaction that can be enhanced through a shape-catalytic effect. We show using ab initio calculations how a vacancy site on a carbon surface can induce the thermal splitting of water at relatively low temperatures . We also examine the dissociation on a vacancy site on a nanotube surface, which shows the shape-catalytic effect of the surface curvature. These results are a first step toward the design of catalytic materials that take advantage of different enhancing effects simultaneously.

08/23/2006: Smart Surfactants and Ligands in Pharmaceutical, Environmental, and Energy Applications, by Keith P. Johnston, Department of Chemical Engineering, University of Texas at Austin

Abstract

Smart surfactants and ligands are being designed to (1) perform multiple functions, (2) achieve targeted activity at particular interfaces, and (3) be active at unusual interfaces, for example, in CO2. In pharmaceutical science, one of the key challenges is particle engineering of poorly water soluble drugs to achieve high bioavailability for oral and pulmonary administration. Increasingly, two goals are being pursued simultaneously: (1) control of particle nucleation and growth to achieve the desired particle morphology and (2) rapid wetting and dissolution, and in some cases high levels of supersaturation. Studies of fundamental thermodynamic, transport and interfacial mechanisms are leading to improvements in bioavailability in vivo.
Environmentally benign carbon dioxide-based emulsions may replace toxic organic solvents for pharmaceutical, chemical, materials, and microelectronics processing applications. Surfactants stabilize CO2-in-water emulsions or foams needed to control mobility in CO2-enhanced oil recovery, for producing 60 billion barrels of oil (approximately $6 trillion value). Nonionic methylated branched hydrocarbon surfactants emulsify up to 90% CO2 in water with polyhedral cells smaller than 10 microns, with the potential for excellent mobility control.
An emerging understanding of the role of surfactants in charging and stabilization mechanisms for colloids in low-permittivity solvents (dielect. const. < 5) will help advance a variety of applications including electrophoretic displays and electrophoretic deposition of nanocrystals to form superlattices. On the basis of novel experimental measurements for both hydrophilic and hydrophobic TiO2, a general mechanism is presented to describe particle charging in terms of preferential partitioning of cations and surfactant anions between the particle surface and reverse micelles in the bulk solvent. The design of smart surfactants and ligands for nano- and micron-sized emulsions and particle dispersions is in its infancy, and many new concepts will be developed for pharmaceutical, environmental, and energy applications.

08/21/2006: Influence of Materials Technology on the Fuel Efficiency of Aeroturbines, by A. G. Evans, Materials Department, UCSB

Abstract

The fuel efficiency of aero-turbines has been improved systematically during recent decades. The trend is strongly correlated with the increase in achievable temperature in the hot sections of the turbine. In turn, this temperature increase is attributed to combined advances in materials and active cooling technologies. This presentation examines the materials innovations that continue to be implemented due to advancements at the frontiers of materials and mechanics. The most recent advances have been enabled by multilayer coatings that impart thermal and oxidation protection. The former is provided by an oxide with exceptionally low thermal conductivity. The latter is achieved using alloy coatings that form alumina. For continued performance enhancement using such multilayer concepts a systems-level methodology is needed. The materials and mechanics formulations that have been devised for this purpose are described.

2005-06

04/13/2006: A Personal Perspective Of The Changing Nuclear Threat, by Dr. Siegfried Hecker, Stanford/Los Alamos National Laboratory

Abstract

Presidents Reagan and Gorbachev ushered in the end of the Cold War with a summit meeting at Reykjavik in October 1986. The political changes unleashed altered the nuclear threat from one that could end civilization as we know it to one of securing "loose nukes" in chaotic Russia and other states of the former Soviet Union. Whereas during the Cold War nuclear deterrence brought an uneasy global peace, the dissolution of the Soviet Union resulted in a resurgence of regional and ethnic conflicts, troubling nuclear proliferation developments, and the emergence of international megaterrorism. The gravity of these developments was demonstrated on 9/11. Now, we face the most difficult challenge of how to avoid a nuclear 9/11, which will not only cause horrific destruction, but will also threaten international order and our way of life. Plutonium is a key component of nuclear deterrence and today's nuclear threat. I will touch on what makes plutonium the most complex and fascinating element in the periodic table.

03/09/2006: Professor Efthimios (Tim) Kaxiras, Harvard University

02/09/2006: Measurement of Molecular and Thermal Diffusion Coefficients in Multicomponent Mixtures, by Dr. Abbas Firoozabadi, Yale University/RERI

Abstract

Molecular, pressure, and thermal diffusion processes are important in a variety of disciplines including a vast number of problems related to the exploitation and production of hydrocarbons and improved oil recovery in fractured petroleum reservoirs. The combined effect of these diffusions can result in the unusual floatation of a stable heavy fluid on the top of a light fluid in certain mixtures of interest in hydrocarbon reservoirs. The study of diffusion processes in mixtures with three and higher species has been a challenge. Multicomponent diffusion is much more complicated than diffusion in binaries; there are some inherent differences between binary and ternary mixtures. Few measurements of molecular diffusion coefficients for multicomponent mixtures have been reported in the literature, even for ternaries. Current techniques are relatively slow and it takes several days to conduct a single measurement. Since the early twentieth century, a variety of methods have been developed to measure thermal diffusion coefficients. The two main methods are:1) the thermogravitational column technique and 2) the optical methods. There is only one report of measurements in a ternary mixture by a thermogravitational method. All the optical techniques have only been used to determine molecular and thermal diffusion coefficients for binary mixtures. In this talk, I will present a theory and derive working equations for determining thermal and molecular diffusion coefficients in multicomponent mixtures. An analytical model will be presented for the unsteady state behavior of multicomponent mixtures in a thermogravitational column and in an optical diffusion cell using laser beams. In the past, a major drawback with the beam deflection technique has been its limitation to binary mixtures. This is because the measured quantity is the components' net effect on the deflection of the beam rather than the concentration of each individual component. The beam deflection technique can only provide 2(n-1) coefficients, while n(n-1) diffusion coefficients define an n-component mixture. We have solved this problem by using beams of different wavelengths and have developed the mathematical solution to the general problem of multiple wavelengths. In order to determine all the diffusion coefficients of an n-component mixture, (n-1) beams of different wavelengths are required. Therefore, we can determine all the diffusion coefficients from the transient beam deflection measurements.

01/12/2006: Aberration Corrected Electron Microscopy: What are the New Perspectives for Materials Sciences? by Dr. C. Kisielowski, LBNL Berkeley, CA

Abstract

Ongoing technological advancements of electron microscopy will reshape the way electron scattering is utilized to investigate structure and composition of materials down to the atomic level. It foreseeable (and partly established) that electron microscopes will have the ability to image single atoms of most elements of the periodic table of elements and to tie the spatial information to spectroscopy, which probes for chemical constituents and local bonding. Therefore, a three-dimensional materials characterization can reach towards atomic resolution and it is feasible to solve the long-standing problem of information loss that comes from projecting the 3D materials structure into a 2D image plane. This talk highlights how much materials science already benefits from recent advancement of instrumentation. Application examples include a characterization of a dislocation in GaAs in terms of displacement fields and impurity segregation, investigations of strain relaxation processes in FePt nanoparticles, and investigations of local band gap fluctuations that are induced by indium clusters in GaN/InGaN/GaN quantum wells. The given examples also point to current limitations that will be removed by the next generation of fully aberration corrected microscopes, which are currently developed within the DoE s TEAM-Project.

12/08/2005: Future Prospects of Solid State Lighting, by Professor Shuji Nakamura, Department of Materials Science, UCSB

Abstract

Semipolar/Nonpolar GaN have been developed for the growth of blue LEDs to minimize the piezoelectric field. The hole concentration of p-type GaN was an order of 1018cm-3. The emission of the blue LEDs showed the strong polarization. The Microcavity (MC)-LEDs with Photonic Crystal (PC) have been developed to increase the light extraction efficiency. The Micro-Cone LEDs were also developed to improve the light extraction efficiency.

11/10/2005: Crystal Engineering for Product & Process Design, by Professor Michael F. Doherty, UCSB

Abstract

Crystalline organic solids are ubiquitous as either final products or as intermediates in the specialty chemical, pharmaceutical, and home & personal care industries. Virtually all small molecular weight drugs are isolated as crystalline materials, and over 90% of all pharmaceutical products are formulated in particulate, generally crystalline form. Crystalline chemical intermediates, such as adipic acid, are produced in large amounts to make polymers and specialty products. Skin creams and other personal care product formulations contain crystalline solids. In most cases the properties of the crystalline solid have a major impact on the functionality of the product as well as the design and operation of the manufacturing process. A novel method for modeling the shape evolution of 3-dimensional faceted crystals has been developed in which the normal distances to each face from an origin inside the crystal are represented by a system of ordinary differential equations. The model is initialized from an arbitrary initial seed shape and size, but known polymorph. The growth model for the crystal faces is based on surface integration kinetics as the rate determining step. The key variables on which the model depends are (1) properties of the solid state, such as unit cell, space group, intermolecular potentials, charge distribution, etc, and (2) surface free energy at the crystalsolution interface. At each time step, the entire family of possible discrete shape evolution events (e.g., vertices bifurcating into edges or faces, etc.) are exhaustively enumerated and investigated using a new set of simple testable conditions. The evolving crystal shape is then determined from the evolving set of normal distances and the corresponding crystallographic planes. The model has been successfully applied to a selection of complex molecular crystals of interest in pharmaceutical and specialty chemical products. In this presentation we discuss the interactions between crystal engineering and crystallization process & product design. We assess the current status of knowledge in this field and identify critical areas for future research and development.

10/13/2005: "Doped oxides as catalysts, why gold clusters are reactive, and electronic manipulation of catalysis", by Prof. Horia Metiu, Department of Chemistry and Biochemistry, UCSB

Abstract

"Doped oxides as catalysts, why gold clusters are reactive, and electronic manipulation of catalysis" I will talk about three distinct subjects, all connected to catalysis. In the first I will explore whether doped oxides (for example, AuxCe1-xO2) might provide us with a new class of oxidation catalysts. We do this by using density functional calculations, to determine the binding energies of various compounds and the activation energies of the possible reactions. We use CO oxidation as a test of the oxidizing power of the doped oxides. In the second topic I discuss experiments done in collaboration with Moskovits and Kolmakov in which we test whether manipulating the number of electrons in a nano-catalyst can affect the catalytic activity. The experiments study CO oxidation by a SnO2 nanowire, which is part of an electric circuit and sits on top of a gate. We find that we can manipulate the reaction rate by changing (with the gate) the number of electrons in the wire. Finally, if there is any time left I will discuss a possible reason why small Au clusters are good catalysts, while large clusters are not. We and others have proposed that the clusters are reactive because they have many low coordination sites on the surface. Here I want to amend that picture and propose that the reactivity depends on what I call "orbital roughness", not on geometrical (low coordination) roughness.

09/15/2005: Programmable molecular sensors and switches: applications in metabolic engineering, intelligent therapeutics, and biosensors, by Professor Christina D. Smolke, Division of Chemistry and Chemical Engineering, Caltech

Abstract

Cells employ a variety of different sensor biomolecules to dynamically evaluate their environments and trigger appropriate metabolic responses. The ability to program cells with engineered molecules that can sense structural and chemical events is a critical technology for many of the challenges that face us in biotechnology and medical research. Recent progress in the design of tailor-made molecular switches and sensors is rapidly advancing our ability to engineer smart systems that will perform information processing or signal integration within cells or complex biological samples. I will discuss our work in the design a new class of nucleic acid-based molecular sensors that transform different types of informational input into biological function and their application in regulating complex cellular behavior. In particular, the application of these devices to metabolic engineering strategies for microbial alkaloid synthesis, targeted molecular therapies, and diagnostic devices will be addressed.

**All first year materials science graduate students are required to attend**