MEAM Seminar Series Summer 2014

Seminars are held on Tuesday mornings, with coffee at 10:30 am in the Towne Building and the seminar beginning at 10:45 am in Towne Building, room 337 (unless otherwise noted).

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Tuesday, May 27: MEAM Special Seminar, 10:45 a.m., Wu and Chen Auditorium

Armin Knoll, Researcher, IBM Research, Zurich Research Laboratory, Zurich, Switzerland
"Thermal Probe Nanolithography: What You See is What You Get"

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Abstract:

Progress in nanotechnology depends critically on the capability to fabricate, position, and interconnect nanometer-scale structures. While optical lithography still dominates large volume production, so called mask-less methods such as electron beam lithography or scanning probe methods are needed to create prototype devices and drive nanotechnology research. In this seminar I will present a short overview of the nanofabrication landscape.

In recent years thermal Scanning Probe Lithography (tSPL) has been developed at the IBM Research lab in Zurich. tSPL is a novel nano-patterning technique based on Scanning Probe Microscopy. A heated tip with an apex-radius of merely 5 nanometers is used to locally evaporate organic resists and thereby create arbitrary patterns. Recently, the technology has demonstrated several key achievements towards technical readiness and has become commercially available via the startup company SwissLitho.

A particular strength of scanning probe lithography methods is their potential to nondestructively image a surface with up to atomic resolution. We exploit this feature to implement a closed-loop control scheme which enables an autonomous and precise operation of the tool. Nanometer scale accurate reproduction of absolute depth values is demonstrated for 3D relief data. In addition, the scheme allows for a nanometer precise and marker-less overlay process of the next patterning level relative to existing nanostructures. These novel capabilities provide an intuitive and visually accessible platform for researchers to perform future challenges in nanofabrication.

iBio:

Armin W. Knoll - IBM Zurich Research Laboratory, Saeumerstr. 4, 8803 Rueschlikon, Switzerland (ark@zurich.ibm.com). Armin Knoll received a Master's degree in experimental physics from the University of Wuerzburg, Germany (1998) and the Ph.D. in Physical Chemistry from the University of Bayreuth, Germany, in 2004. After a postdoctoral fellowship with the University of Basel for 15 months (2003-2004) he joined the Advanced Media Concepts group of the Millipede project (2005-2006) at the IBM Zurich Research Laboratory as a Visiting scientist. Armin Knoll joined the Science & Technology department in April 2006 as research staff member. In 2012 he received an ERC Starting Grant from the European Commission. Currently he is leading the probe based nanofabrication effort at IBM Research - Zurich.

Thursday, May 29: MEAM PhD Defense, 10:00 a.m., Towne Building, Room 337

David Argudo, Ph.D. Candidate, University of Pennsylvania
"DNA conformational changes and phase transitions induced by tension and twist"

Advisor: Dr. Prashant Purohit

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Abstract:
DNA is a double stranded helical molecule with an intrinsic right handed twist. Its structure can be changed by applying forces and torques in single molecule experiments. In these experiments DNA has been seen to form super-helical structures (supercoils), collapse into tightly condensed states (toroids) and undergo structural changes (phase transitions). Our work focuses on studying all these phenomena by accounting for DNA elasticity, entropic effects due to thermal fluctuations and electrostatics. First, we study the DNA compaction problem in super-helices and toroidal structures. To do so we combine a fluctuating elastic rod model of DNA with electrostatic models for
DNA-DNA interactions where the choice for the electrostatic description varies depending on the presence of monovalent or multivalent ions. Our models are able to predict the onset of the transition to supercoils and toroids under a wide range of experimental conditions. Next, we address DNA phase changes in the presence of mechanical loads.
A phenomenon well known from experiments is the overstretching transition associated with the sudden change of DNA extension at high tensions. Depending on the ionic concentration, temperature and pulling rate, DNA can either transform into a melted state (inner strand separation) or S-DNA. Motivated by this, we study the equilibrium
and kinetics of the DNA overstretching transitions making use of a quartic potential and non-gaussian integrals to evaluate the free energy of the system. We find that the cooperativity of the transition is a key variable that characterizes the overstretched state.
In a separate study we make use of a heterogeneous fluctuating rod model to examine the hypothesis that a newly discovered left-handed form called L-DNA is a mixture of two relatively well-characterized DNA phases - S-DNA and Z-DNA. L-DNA is stable at high tensions and negative twist. We show that if the idea of a mixed state is correct, then
the content of S-DNA and Z-DNA varies as a function of the ionic concentration. Finally, we also use our fluctuating rod model to study the mechanical properties of drug-DNA complexes. We show that our methods can predict the results of experiments from various labs if we use only one set of experiments to fit the data to our model.

Friday, May 30: MEAM Special Seminar, 11:00 a.m., Towne Building, Room 337

Mahmut Selman Sakar, Senior Research Scientist, Institute of Robotics and Intelligent Systems
"Microrobotic Platforms in Biotechnology: From Minimally Invasive Biomanipulation to Biological Robots"

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Abstract:

In recent years several mobile microrobots have been proposed for the use in biomedical applications where minimally invasive and targeted procedures are required. These untethered, wirelessly controlled and powered devices can enable new procedures never before possible. In this talk, I will go through the technological state of the art in biomedical microrobots by giving examples primarily from my own research experience. In the first part of my talk, I will describe how we improved the functionality and effectiveness of these devices by selecting appropriate materials and robot designs. In parallel to the advances in microscale engineering, extensive research has been conducted to construct biological machines. In the second part of my talk, I will describe the development of soft robots actuated by a multitude of spatiotemporally coordinated 3D skeletal muscle microtissues and describe several strategies to optimize their performance. These platforms provide critical mechanistic insight on the generation, transmission and coordination of cellular forces during tissue development, function and regeneration.

Bio:

Mahmut Selman Sakar received the Bachelor of Science degree from the Department of Electrical and Electronics Engineering, Bogazici University in 2005 and the Ph.D. from the Department of Electrical and Systems Engineering, University of Pennsylvania in 2010. During his doctoral studies, he worked on bacteria-powered microrobots and single cell manipulation using magnetic microrobots under the supervision of Prof. George J. Pappas and Prof. Vijay Kumar. Before joining Institute of Robotics and Intelligent Systems in 2012, he worked as a postdoctoral associate with Prof. Harry Asada in the Department of Mechanical Engineering, Massachusetts Institute of Technology on optogenetic control of engineered skeletal muscle bioactuators. Currently he is a senior research scientist in Prof. Bradley Nelson’s lab and he is working on the development of microrobotic platforms for several bioengineering applications.

June 3

Barukyah Shaparenko, Ph.D. Student, University of Pennsylvania
"Thermal Dielectrophoretic Force on a Dielectric Particle"

Advisor: Dr. Howard Hu

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Abstract:

Many microfluidic devices use an applied electric field to control and manipulate particles immersed in a fluid through the electrostatic force caused by dielectrophoresis (DEP). Additionally, electrothermal flow in the fluid can be caused by the effects of nonuniform temperature and the temperature-dependent electrical permittivity and conductivity material properties. We examine the effects on a particle immersed in a fluid subjected simultaneously to an electric and a nonuniform temperature field and find that the particle experiences an electrostatic force given by not only classical dielectrophoresis, but also an additional force, which we term thermal DEP. Assuming the change in the background electric field across the particle is small, and the relative change of temperature-dependent electric properties across the particle is also small, we develop a linearized model to solve the electric field analytically and integrate the Maxwell stress tensor to find an expression for the thermal DEP force. This thermal DEP force is proportional to the temperature gradient, the square of the electric field strength, and the particle’s volume. We solve two special cases, one where the electric field and temperature gradient are aligned, and a second case where they are perpendicular to each other. The general case for an arbitrary angle can be found simply by a superposition of these two cases. We compute the fully-coupled system in COMSOL to determine a range of validity for our linearized model and show a practical way to superimpose the classical DEP and thermal DEP forces to find the total electrostatic force on the particle relative to the fluid. Due to the high electrical conductivity of common biological buffers, the thermal DEP force can play an important role when an electric field is used to control and manipulate cells or bacteria. The thermal DEP force may also modify the heat transfer rates in nucleate boiling applications, where large temperature gradients are present.

June 10

Michael Norton, Ph.D. Student, University of Pennsylvania
"Capillary Surfaces on Non-Uniform Substrates at the Micro- and Nano- Scale"

Advisor: Dr. Haim Bau

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Abstract:

Droplets and bubbles are ubiquitous motifs found in natural and industrial processes. In the absence of significant external forces, liquid-liquid and gas-liquid interfaces form constant mean curvature surfaces that locally minimize the free energy of a given system subject to constraints. In this talk, such minimal-energy or capillary surfaces will be discussed in the context of two systems. First, the wetting of micron-sized ellipsoidal particles will be considered. We find that, even in the space of axially symmetric interfaces, multiple constant mean curvature surfaces can satisfy volume and contact angle constraints. Partial encapsulation may be preferred (has a lower free energy) even when the droplet's volume is sufficient to fully engulf the particle. The co-existence of multiple equilibrium states suggests possible hysteretic encapsulation behavior. Secondly, motivated by our observations of sub-micron bubbles in a liquid cell using electron microscopy, a small mobile and growing bubble confined between two non-parallel plates is considered theoretically. By including contact line slipping, several features of observations including directional motion and anisotropic growth are corroborated. The implications these observations have for gaining deeper insights into nanoscale interfacial phenomena, such as measuring surface tension in-situ and understanding the mass transfer of bubble growth, are discussed.

June 17

Nicholas Schneider, Ph.D. Student, University of Pennsylvania
“In Situ Liquid Cell Electron Microscopy with the NanoAquarium: A Study in Electrochemistry and Radiation Chemistry”

Advisor: Dr. Haim Bau

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Abstract:

The advent of Electron Microscopy has fostered major advances in a broad spectrum of disciplines. The required vacuum of standard electron microscopy precludes imaging of process and objects suspended in liquid media. Many important processes, such as the potentially catastrophic formation of dendrites during battery cycling, take place in liquid systems. The recent development of liquid cells like the NanoAquarium overcomes this limitation, enabling imaging of temporally evolving processes in liquid systems with nanoscale resolution. I will describe the use of the NanoAquarium to investigate the morphological evolution of the electrode-electrolyte interface during electroplating and stripping of electrodes, nanoparticle growth and assembly, and the fundamentals of beam-irradiated medium interactions (Radiation Chemistry). The results of my work are applicable to battery technology and to nanomanufacturing.

June 20: MEAM/GRASP Seminar, 12:00 p.m., Towne Building, Rm 337

Jun Seo, Ph.D. Student, University of Pennsylvania
"Grasping and Assembling with Modular Robots"

Advisors: Dr. Vijay Kumar and Dr. Mark Yim

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Abstract:
In this talk, I will present my research on robotic grasping and assembling: how to enable robots to grasp objects and assemble target structures autonomously. They are fundamental problems in robotic manipulation where we have robots rearrange our environment; they can be applied to a wide range of scenarios such as manufacturing, disaster response, space exploration, and assisted living. Modular robot platforms can facilitate the problems with versatility and robustness. In the first part, I will discuss grasping/fixturing objects with customized effectors and implementing the ideas with modular arm links and end-effectors. In the second part, I will focus on assembly planning for target structures of the common brick wall pattern with rectangular, modular robots, which is a part of collective efforts for realizing a swarm of autonomous boats in the Modular Robotics Lab at Penn.

Bio:
Jun Seo is a Ph.D. candidate working in the GRASP Laboratory at the University of Pennsylvania. He is advised by Dr. Vijay Kumar and Dr. Mark Yim. Jun's research interests include robotic grasping/manipulation and robotic self-assembly/reconfiguration; he has been investigating theoretical and practical issues relating to the design of software and hardware for the problems. He received the B.S. degree from the Department of Mechanical and Aerospace Engineering at Seoul National University, Seoul, Korea.

Monday June 23rd: MEAM PhD Defense, 2:00 p.m., Levine Hall, Room 307

Matthew Turpin, Ph.D. Candidate, University of Pennsylvania
" Safe, Scalable, and Complete Motion Planning of Large Teams of Interchangeable Robots"

Advisor: Vijay Kumar

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Abstract:
Large teams of robots have been implemented to great success in Kiva's automated warehouses as well as UPenn's and KMel Robotics' swarms of quadrotors. In settings such as these, robots must plan paths which avoid collisions with other robots and obstacles in the environment. I propose two approaches to solve this problem.

First, I address the design of formation control techniques that maintain a specified shape and present novel decentralized formation control algorithm that is robust to failure and provides feasible trajectories for highly dynamic robots. An alternate approach is to plan for robots to move independently of one another. Unfortunately, trajectory planning for large teams of robots generally suffers from either the curse of dimensionality or lack of completeness. I will demonstrate that relaxing the assumption of labeling each robot and specifying a fixed assignment of robots to destinations in the trajectory generation problem yields a number of computational and performance benefits. My algorithm to solve this Concurrent Assignment and Planning of Trajectories (CAPT) problem has polynomial time complexity, preserves completeness, and tends to minimize effort exerted by any one robot. This algorithm generates solutions to variants of the CAPT problem in settings ranging from kinematic robots in an obstacle free environment to teams of robots with 4th order dynamics in a cluttered environment. Further extending this idea, it can be useful to use a team of robots to visit a very large number of goal locations for exploration, surveillance, and search and rescue. I present an approximation algorithm that yields a solution to this multi-robot routing problem with completion time no more than a constant factor times the optimal solution. Simulation and experimental verification demonstrates the validity of each algorithm.


June 24

Jinzhou Yuan, Ph.D. Student, University of Pennsylvania
"Microswimmers and Microfluidics: Understanding and Manipulating the Motion of Nematodes such as Caenorhabditis (C.) elegans"

Advisor: Dr. Haim Bau

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Abstract:
Nematodes are of great importance to agriculture, animal and human health, and fundamental biological research. The nematode Caenorhabditis (C.) elegans is widely used a model organism for medical studies. My work focuses on studying the locomotion of nematodes; their interactions with surfaces and each other; and developing new tools to facilitate nematode research.
In the first half of my talk, I will present the design, fabrication, characterization, and applications of two microfluidic devices for measuring the motility of C. elegans and for motility-based, high-throughput sorting of C. elegans. In the second half of the talk, I will focus on experimental and theoretical studies of the effect of a surface on the swimming of C. elegans. We find that low Reynolds number undulatory swimmers, such C. elegans, independent of genes required for mechanosensation, are attracted to and tend to swim along surfaces. Both our experimental observation and theory suggest the existence of a short-range hydrodynamic torque that steers the undulatory swimmer towards the surface. The interplay between the hydrodynamic torque and steric hindrance is responsible for surface following. Since the morphology and the swimming gait of the nematodes are highly conserved, our devices and results are also applicable to other nematode species.

July 1

Speaker, Institution
"Talk Title TBA"

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Content TBD

July 8

Xin Liu, Ph.D. Student, University of Pennsylvania
"Mechanisms Controlling Atomic-Scale Friction and Adhesion of Single-Asperity Contacts on Ideal Materials"

Advisor: Dr. Robert Carpick

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Abstract:
A gap in our understanding of the fundamental mechanisms governing nanoscale adhesion and friction exists, resulting in ongoing challenges as technologically-relevant devices are miniaturized. For example, there is much excitement about a new generation of devices based on graphene. While recent studies have shown that graphene has promising friction-reducing properties, even at thicknesses of one atomic layer [1-3], the mechanisms controlling friction and adhesion for graphene-covered substrates are not yet well understood. In the first part of the talk, I will discuss the frictional properties of fluorinated graphene studied by atomic force microscopy (AFM). Friction on fluorinated graphene increases substantially with increasing degree of fluorination. As evidenced by molecular dynamics (MD) simulations, performed through collaboration with Shenoy group at Penn, this strong dependence is attributed to the fact that attachment of fluorine atoms to graphene scaffold greatly enhances the corrugation of the interfacial potential energy, thus the local energy barrier for sliding is significantly increased. These observations provide new insights into the atomic-scale effects of functionalization on frictional properties of graphene. In addition, they suggest a potential approach to sensitively probe the local chemistry and structure of functionalized graphene.

For the second part, I will discuss the speed dependence of atomic friction between AFM tips and atomically-flat gold surfaces. There is evidence from experiments, simulations, and theory indicating that friction can be significantly affected by the sliding speed, in accordance with the Prandtl-Tomlinson model with thermal activation (termed the “PTT model”) [4]. However, full understanding of this phenomenon is hindered since atomic-scale friction experiments have not yet achieved sliding speeds comparable to those in atomistic simulations. We have conducted matched AFM experiments and molecular dynamics (MD) simulations to bridge this gap. All controllable parameters, including tip geometry, tip and sample materials (silica and gold respectively), applied load, mechanical stiffnesses, ultrahigh vacuum environment, and most importantly, sliding speeds, are matched between experiment and simulation. Sliding speeds significantly higher than typical AFM experiments are enabled by fast data acquisition methods and by a custom-designed high speed scanning apparatus. Sliding speeds slower than typical MD simulations are attained by using accelerated MD methodology performed by Martini group at U.C. Merced. For the first time, both experiments and simulations are performed at overlapping scanning speeds. Using the PTT model to compare and contrast experiment and simulation data, we have made the first experimental observation of the saturation of the friction force above a critical scanning speed, as predicted by the PTT model and seen in MD simulations. Furthermore, comparison of the energetic parameters extracted from fits of the PTT model to experimental and simulation data agree within uncertainty. However, the physical parameter connected to dynamic processes at the contact, essentially and effective attempt frequency, differs by orders of magnitude between experiment and theory. We propose that this results from the different degrees of inertia in the two systems.

[1] Lee, C., et al., Frictional Characteristics of Atomically Thin Sheets. Science, 2010. 328(5974): p. 76.
[2] Filleter, T., et al., Friction and Dissipation in Epitaxial Graphene Films. Physical Review Letters, 2009. 102(8): p. 086102.
[3] Kim, K.-S., et al., Chemical Vapor Deposition-Grown Graphene: The Thinnest Solid Lubricant. ACS Nano, 2011: p. 5107–5114.
[4] Li et al., Speed Dependence of Atomic Stick-Slip Friction in Optimally Matched Experiments and Molecular Dynamics Simulations, Phys. Rev. Lett. 106 (2011) 126101.

July 15, 10:45 A.M., Towne Building, Raisler Lounge

Heather Culbertson, Ph.D. Student, University of Pennsylvania
"Modeling and Rendering of Virtual Haptic Textured Surfaces"

Advisor: Dr. Katherine Kuchenbecker

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Abstract:

The human sense of touch excels at sensing and interpreting vibrations experienced when touching real objects with a tool. These vibrations allow you to gather information about the physical world, even though you are not directly touching objects. Unfortunately, the richness of these interaction cues is missing from many virtual environments, leading to a less satisfying and immersive experience. We can create the perceptual illusion of touching a real surface by displaying appropriate tool vibrations during virtual interactions. This talk presents my work in creating haptic models of textured surfaces from acceleration, force, and speed data recorded during physical interactions. We use these texture model sets to render synthetic vibration signals in real time as a person interacts with our TexturePad system, which includes a Wacom tablet and a stylus augmented with a voice-coil actuator. We evaluated the realism of the resulting virtual textures using a human subject study to test the strengths and weaknesses of our modeling and rendering approach. The results indicated that our virtual textures accurately capture and recreate the roughness of real textures, but other modeling and rendering approaches are required to completely match surface hardness and slipperiness. I will conclude by discussing the new rendering system we are developing to address these limitations.

July 22, 10:45 A.M., Towne Building, Raisler Lounge

Sean Anderson, Ph.D. Student, University of Pennsylvania
“Carbon Nanopipettes for Advanced Cellular Probing and Microinjection”

Advisor: Dr. Haim Bau

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Abstract:
Carbon nanopipettes (CNPs) consist of a pulled-quartz micropipette with a thin layer of amorphous carbon deposited along its entire interior surface via chemical vapor deposition. The micropipette maintains a continuous fluidic pathway from its nanoscopic tip to its distal macroscopic end, while the insulated carbon film provides an electrical path to the tip that can be used as a working electrode. The quartz at the tip of the CNP can be chemically etched to expose a desired length of a carbon pipe to control the size and characteristics of the electrode. CNPs are inexpensive, batch-fabricated, and can be made hollow or solid. They can be used as nanoelectrodes, nanoinjectors, or both simultaneously, with improved durability and biocompatibility compared with glass micropipettes. This talk will describe recent advances in CNP technology, including an impedimetric AC technique for detecting cellular and nuclear penetration during microinjection and cellular probing, development of a Matlab-based automated injection system, and the use of CNPs for fast-scan cyclic voltammetry to measure neurotransmitter concentrations in the brain of the Drosophila melanogaster (fruit fly). As a target biological application of microinjection, we are using microinjection of fluorescently labeled tRNA to monitor subcellular tRNA dynamics in real time.

July 29, 10:45 A.M., Levine Hall, Wu and Chen Auditorium

Rebecca Pierce, Ph.D. Student, University of Pennsylvania
"Talk Title TBA"

Advisor: Dr. Katherine Kuchenbecker

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Content TBD

Friday, August 1, MEAM/ GRASP PhD Defense, 11:00 a.m., MEAM Conference Room, Towne Building, Room 227

Jun Seo, Ph.D. Candidate, University of Pennsylvania
"Grasping and Assembling with Modular Robots"

Advisors: Dr. Mark Yim, Dr. Vijay Kumar

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Content TBD

August 5

Michael Wald, Ph.D. Student, University of Pennsylvania
"Talk Title TBA"

Advisor: Dr. Kevin Turner

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Content TBD

Friday, August 11, MEAM Special Seminar, 11:00 a.m., Towne Building, Room 337

Moeketsi Mpholo, National University of Lesotho and Teboho Nchaba, University of Cape Town
"Solar and Wind Resource Assessment in Lesotho"

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Content TBD

August 12

Mehdi Bakhshi Zanjani, Ph.D. Student, University of Pennsylvania
"Talk Title TBA"

Advisor: Dr. Jennifer Lukes

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Content TBD

August 19

Nick Eckenstein, Ph.D. Student, University of Pennsylvania
"Talk Title TBA"

Advisor: Dr. Mark Yim

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Content TBD

Friday, August 22: 12:00 P.M. Towne Building, Room 337

Matthew Piccoli, Ph.D. Student, University of Pennsylvania
"Talk Title TBA"

Advisor: Dr. Mark Yim

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Thursday, August 28, MEAM PhD Defense, 9:30 a.m. Levine, Room 307

Reza Avazmohammadi, Ph.D. Candidate, University of Pennsylvania
"Talk Title TBA"

Advisor: Pedro Ponte Castañeda

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Friday, August 29, MEAM PhD Defense, 10:00 a.m., Levine, Room 307

Morteza Hakimi Siboni, Ph.D. Candidate, University of Pennsylvania
"Talk Title TBA"

Advisor: Pedro Ponte Castañeda

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Friday, August 29: 12:00 P.M. Towne Building, Room 337

Yi Yang, Ph.D. Student, University of Pennsylvania
"Talk Title TBA"

Advisor: Talid Sinno

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Content TBD