MEAM Seminar Series Summer 2008

Seminars are held on Thursdays at 2:00 p.m. in 337 Towne Building (220 South 33rd Street), unless otherwise noted. Click the date of each seminar to find out additional information about the speaker and topic.

June 12
David Cappelleri, PhD Candidate
"Flexible automation for micro- and meso-scale manipulation tasks with applications to manufacturing and biotechnology"

Speaker: David Cappelleri
PhD Candidate
Advisor: Vijay Kumar
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
This talk will present the design and implementation of a flexible automation system developed for micro and meso-scale manipulation tasks in the manufacturing and biotechnology industries. I will begin with an overview and introduction of the state-of-the-art in micro and meso-scale manipulation and precision robotic systems. Then I will discuss my work on the development of a robotic system for use in micro and meso-scale manipulation and assembly and show experimental results for the canonical peg-in-the-hole problem at the meso-scale. The next part of the talk will focus on tools and automation for biotechnology. Single cell manipulation and characterization studies will be presented as well as the design of a MEMS, compliant mechanism, computer vision based force sensor to sense forces at the micro-Newton level. I will also talk about work on automating the process of phototransfection on neuron and fibroblast cells along with quantifying morphological changes in the cells before and after the process.

June 19
Rahul Sampath, PhD Candidate
"Dendro: A parallel geometric multigrid method for finite element calculations on octree meshes with billions of unknowns"

Speaker: Rahul Sampath
PhD Candidate
Advisor: George Biros
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
We present Dendro, a suite of parallel algorithms for the discretization and numerical solution of second-order elliptic partial differential equations using octree meshes. A characteristic of octree meshes is that they contain 'hanging' nodes. Dendro uses a novel technique to handle these 'hanging' nodes and construct conforming trilinear finite element discretizations. To our knowledge, Dendro is the first parallel, octree-based, matrix-free, geometric multigrid solver for finite element discretizations. We present fixed-size and iso-granular scalability results for solving a Poisson problem and a linear elastostatics problem on up to 4096 CPUs on the Cray XT3 ("BigBen'') at the Pittsburgh Supercomputing Center (PSC) and the Intel 64 system ("Abe'') at the National Center for Supercomputing Applications (NCSA). We are able to solve problems with billions of elements on thousands of processors in less than 10 minutes. Although we do not discuss adaptive mesh refinement here, the proposed method can be used toward that goal as it has very low setup costs.

June 26
Hui Zhao, PhD Candidate
"Modeling electrokinetics with applications to micro and nano fluidic systems"

Speaker: Hui Zhao
PhD Candidate
Advisor: Haim H. Bau
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
With the rapid growth in lab-on-a-chip technology, the prospects of detecting viruses on a microfluidic diagnostic device or immobilizing single bio-molecules have become more and more promising. This imposes a big challenge for fluid manipulation such as propulsion, mixing and particle manipulation, which are far from trivial due to the low Reynolds number of the flow. Electrokinetics provides an opportunity to fulfill this task, with advantages as easily fabricated inexpensive devices that consume minimal power. After briefly discussing the fundamentals of electrokinetics, this talk will focus on two applications of the phenomena in micro/nano systems. First, a novel active chaotic stirrer is proposed to enhance mixing. The stirrer consists of a conducting cylinder and four electrodes. The conducting cylinder generates an induced charged electro-osmotic flow under the action of the electric field and stirring is achieved by systematically alternating the electric field in time. I also extend the application of electrokinetics to chromatography. I derive a mathematical model to calculate the dispersion coefficient in the presence of secondary flow. Also, a novel dispersion reduction strategy is realized by imposing a secondary or transverse flow, driven by DC electro-osmosis or AC electro-osmosis, that is independent from the primary flow. This work will guide the design of an efficient liquid chromatography device.

July 3
Santi Swaroop Adavani, PhD Candidate
"Fast algorithms for inverse problems with elliptic and parabolic PDE constraints: applications to cardiac electrophysiology"

Speaker: Santi Swaroop Adavani
PhD Candidate
Advisor: George Biros
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
The main goal of this project is to design and implement fast algorithms to solve inverse problems that arise in cardiac electrophysiology. We investigate the computational challenges involved in solving inverse electrophysiology problems and propose numerical techniques to address them. We consider the following two formulations : 1) a source identification problem with an elliptic PDE constraint, and 2) an inverse medium problem with a parabolic PDE constraint. We use L2 Tikhonov regularization in both the problems for stability. We use a reduced space approach in which we eliminate the state and the adjoint variables and we iterate in the inversion parameter space using Conjugate Gradients (CG). We propose SVD based preconditioners to accelerate the convergence of CG to solve the source identification problem. The overall complexity of reconstructing the source is O(N logN), where N is the number of grid points. We propose multigrid based preconditioners to accelerate the convergence of CG to solve the inverse medium problem. The overall complexity of recovering the medium properties is O(NtN +N log^2 N), where N is the number of grid points and Nt is the number of time steps. We present numerical experiments to show mesh-independent convergence of our algorithms-even in the case of no regularization. This feature makes these methods algorithmically robust to the value of the regularization parameter, and thus, useful for the cases in which we seek high-fidelity reconstructions.

July 10
Haizhen Pan, PhD Candidate
"Plastic flow rules with microstructural evolution and effects on strain localization"

Speaker: Haizhen Pan
PhD Candidate
Advisor: John L. Bassani
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
In this lecture, we consider a class of elastic-plastic materials that possess local orthotropic symmetry which is naturally represented in terms of second-order orientation tensors that can evolve with deformation. Applications include textured polycrystals, oriented polymers, and composite materials. At finite strain, the standard multiplicative elastic-plastic decomposition is adopted, and the flow rule is defined in the intermediate configuration. The spin of the orthotropic axes, i.e. the microstructural spin, is defined to be the difference between the material and plastic spin. The theory of invariants coupled with representations for tensor-valued functions are utilized to develop phenomenological constitutive relations, including an equation for plastic spin. The classical normality flow rule leads to generators for the plastic part of the rate of deformation that only depend linearly on the stress tensor. In constructing a constitutive equation for plastic spin in the intermediate configuration, we assume similar dependencies on stress tensor in addition to nonlinear dependencies on the invariants of stress and orientation tensors. Comparisons with experimental data for textured polycrystals under uniaxial tension and simple shear loading are promising. Significant effects of microstructural evolution on limits to ductility are predicted. Sheet necking and shear banding are considered in this paper. The effects of microstructural evolution can increase or delay the tendency for localization from uniform states of deformation, depending upon parameters in the equation for plastic spin that determine the direction and degree of rotations as well as the initial degree of anisotropy and the orientation of orthotropic axes relative to the loading direction.

July 17
Alan Rosenwinkel, PhD Candidate
"Understanding stress at the atomic scale"

Speaker: Alan Rosenwinkel
PhD Candidate
Advisor: John L. Bassani
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
The ability to construct and manipulate nanoscale structures has renewed interest in understanding the concept of stress at the atomic scale. In particular, in the setting of molecular dynamics, one would like to compute stress given a description of interatomic potentials along with atomic coordinates and momenta as a function of time. Key concepts leading to the so-called Virial Stress were introduced by Clausius in 1870 in a study of the "effective force of heat" and has been adopted, more or less consistently, since then. Nevertheless, a rigorous derivation of atomic-level stress and a clear demonstration of its validity has been somewhat elusive. Of particular interest is the extent to which the atomistic expression can be localized in time and space while maintaining a meaningful connection to the continuum definition of stress.

Using the principle of virtual work we present a derivation of stress in a discrete, dynamical medium that yields an expression comprising three terms: the two well known terms of the Virial Stress and one that vanishes by the virial theorem. To understand the significance of each term and to establish the validity of this atomic-level stress, we have carried out a series of molecular dynamics simulations for heating of both harmonic and anharmonic crystals, with and without constraint. The calculated stresses are shown to agree both with physical intuition and continuum limits. Localization of the atomic stress is also investigated, both from a theoretical perspective and by molecular dynamics simulation of both space- and time-varying stress fields.

July 24
Richard M. Springman, PhD Candidate
"Mechano-chemical coupling in the adhesion of thin structures to surfaces with topography"

Speaker: Richard M. Springman
PhD Candidate
Advisor: John L. Bassani
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
The mechanical and chemical equilibrium fields of adhered cells in both in-vivo and in-vitro microenvironments are coupled through interactions that depend on the local concentrations of certain chemical species (e.g. integrins) and on the local separation of the cell-cell or cell-substrate interface. An adhesive law capturing these dependencies in the presence of mobile species of both strengthening and weakening type is used to study the adhesion of shells to a rigid substrate with surface topography, which is the model system for cell adhesion in 3D micro-environments. The adhesive species, which are confined to the shell surface, are assumed to form an ideal solution with spatially-varying concentrations at equilibrium. Nonlinear shell kinematics accounting for finite rotations of both closed spherical shells and open spherical caps are coupled with the equilibrium equations for axisymmetric deformations and with linearly elastic material response. Changes in the adhesive state under applied load are investigated and pull-off is demonstrated to depend on the chemical fields and loading rate, in addition to the geometry and material properties. Surface topography results in configurations that bridge over low surface features or that conform to the substrate, depending on both the spacing and depth of the features. Equilibrium traction and chemical fields develop patterns that are controlled by the topography. In addition to understanding in-vivo cell adhesion, which almost always involves 3D surface topography, understanding how surface features affect equilibrium is crucial for the engineering of scaffolds used to support cell growth.

July 28
Andy Perrin, PhD Candidate
"Explicit finite difference schemes for particulate flows"

Speaker: Andy Perrin
PhD Candidate
Advisor: Howard H. Hu
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
Many implicit schemes have been proposed for direct numerical simulation of particles in fluids, but they can be quite complicated and require a lot of memory when the concentration of particles is high. Explicit finite difference schemes on a regular grid are one way around these issues. The fluid velocity and density can be marched in time without inverting any matrices, and the particles can be moved according to Newton's laws. Enforcing the no-slip condition on the spherical particle's surfaces as they move on a Cartesian grid is not so easy, however, so we have proposed a spectral expansion method that exactly satisfies no-slip to deal with the problem. This method allows a grid as coarse as ten grid spacings per particle diameter to give smooth forces and accurately resolved pressure distributions on the particle surface. The method has been validated by comparison to a finite element particle solver, and by direct comparison to experiment. Up to 1035 particles have been simulated on a PC, and the effective viscosity of a sheared particulate suspension has been calculated up to a particle concentration of 25%.

July 31
Michael Park, PhD Candidate
"Configuration recognition, self-reassembly, and distributed fault tolerance studies with CKBot, a modular robotic system"

Speaker: Michael Park
PhD Candidate
Advisor: Mark Yim
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
We present developments in automating control for CKBot, our modular robotic system. In particular, we discuss an implementation of an isomorphic configuration recognition algorithm for an arbitrary cluster of modules. Applying basic concepts from graph theory, we introduce a centralized approach that allows a configuration of modules to detect its shape. If a structure corresponds to a known shape (e.g., a particular configuration in a library of configurations), an on-board controller determines the exact permutation to execute the overall coordinated motion of the system. We will also discuss the modular self-reassembly after explosion experiments. This section will include information about the system's hardware, hierarchical control architecture, and software state machine algorithm implemented in these experiments. Lastly, we present a distributed, fault-tolerant control scheme based on a collective decision of modules in the presence of a minority of faulty members. In this approach, all modules receive an infrared signal from a broadcaster; in certain cases a few modules may not see the signal, or may have faulty IR detectors. We demonstrate that when a sub-critical number of modules are erroneous, a correct decision can still be made.

August 1
David Cappelleri, PhD Candidate
"Flexible automation for micro- and meso-scale manipulation tasks with applications to manufacturing and biotechnology"

Speaker: David Cappelleri
PhD Candidate
Advisor: Vijay Kumar
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
This talk will present the design and implementation of a flexible automation system developed for micro and meso-scale manipulation tasks in the manufacturing and biotechnology industries. I will begin with an overview and introduction of the state-of-the-art in micro and meso-scale manipulation and precision robotic systems. Then I will discuss my work on the development of a robotic system for use in micro and meso-scale manipulation and assembly and show experimental results for the canonical peg-in-the-hole problem at the meso-scale. The next part of the talk will focus on tools and automation for biotechnology. Single cell manipulation and characterization studies will be presented as well as the design of a MEMS, compliant mechanism, computer vision based force sensor to sense forces at the micro-Newton level. I will also talk about work on automating the process of phototransfection on neuron and fibroblast cells along with quantifying morphological changes in the cells before and after the process.

August 7
Mark Arselault, PhD Candidate
"The manipulation and mechanical studies of nano filaments and nano motors"

Speaker: Mark Arselault
PhD Candidate
Advisor: Haim H. Bau
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
When an AC electric field was applied across a small gap between two metal electrodes elevated above a surface, rhodamine-phalloidin-labeled actin filaments were attracted to the gap and became suspended between the two electrodes. We estimated the tension using a linear, Brownian dynamic model. Our experimental method provides a novel means for trapping and manipulating biological filaments and for probing the surface conductance and mechanical properties of single polymers. Additionally, optical tweezers were used to bring a motor protein-coated bead into close proximity to a pre-selected, suspended actin filament, facilitating the myosin-mediated bead attachment to the filament. The clearance beneath the filament allowed the bead to move freely along and around its filamentous track, unhindered by solid surfaces. The bead's three-dimensional position was tracked as a function of time to obtain its trajectory. Variants of this technique will enable types of higher complexity found in cells to be addressed with in vitro experiments.

August 12
M.A.  Alves
"Extensional rheometry on a chip"

Speaker: M.A. Alves
Department of Chemical Engineering, Faculty of Engineering
University of Porto, Portugal

Abstract:
Rheological characterization of complex fluids in extensional flow is still a remarkable challenge, particularly for dilute polymeric solutions. In the last decade a number of groups have suggested the use of microfluidic devices for characterization of dilute polymeric solutions, since the reduction of the geometry dimension enhances viscoelastic effects. Other advantages of using microfluidic devices include the use of microlitre samples and the possibility of achieving very large deformation rates under low Reynolds number flows.

Converging dies (abrupt or hyperbolic contractions) or cross-slot devices are typically used for extensional viscosity measurements. As we will show the flow kinematics in classical cross-slot devices and hyperbolic contractions deviates significantly from the idealized purely extensional flow, and the strain rate may vary significantly, an important limitation if meaningful rheometric measurements are sought.

We have devised an automatic procedure for optimal shape design, which allows us to search for the geometry of a microfluidic device with optimal performance. We demonstrate, based on numerical simulations with a finite-volume method, that a purely extensional flow can be achieved in a specially designed cross-slot geometry. The proposed optimization methodology is general, fully automated, and applicable to laminar flows of Newtonian and viscoelastic fluids.

Interestingly, we found that purely elastic instabilities arise in extensionally-dominated viscoelastic flows, which lead to the onset of steady asymmetric flows at high deformation rates. A similar instability was found by Arratia et al. [1] in their experiments at the microscale and was later predicted numerically by Poole et al. [2] Although these instabilities are undesirable in terms of the performance of the microfluidic extensional rheometer, this type of flows offer a rich variety of phenomena that we also address in this talk. We illustrate that similar elastic instabilities arise in a variety of extensionally dominated flows, and discuss the benefits of using them in order to promote mixing at the microscale.

References
[1] P. E. Arratia, C. C. Thomas, J. D. Diorio and J. P. Gollub, “Elastic instabilities of
polymer solutions in cross-channel flow”, Phys. Rev. Lett. 96, 144502 (2006).
[2] R. J. Poole, M. A. Alves and P. J. Oliveira, “Purely-elastic flow asymmetries”, Phys.
Rev. Lett. 99, 164503 (2007).

August 12
Yucun Lou, PhD Candidate
"Guided assembly of nanostructures"

Speaker: Yucun Lou
PhD Candidate
Advisor: John L. Bassani
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
This work is an investigation of the effects of elastic fields on diffusive phase separation and aggregation.  A phase field model is de! veloped that incorporates chemical, interfacial, and elastic energies and couples naturally to externally-imposed mechanical fields to study aggregation in bulk and in thin films under patterned external load.  The kinetics and morphology of aggregation depend significantly upon elastic properties of the system, which include the transformation strain and elastic heterogeneous moduli. Eshelby-type asymptotic estimates for interaction energies provide very useful guidelines to understand the trends observed from simulations.

August 14
Nathan Michael, PhD Candidate
"Planning and control for teams of robots in complex environments"

Speaker: Nathan Michael
PhD Candidate
Advisor: Vijay Kumar
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
We address the challenge of controlling a team of robots through a complex environment, which is relevant to applications such as environmental monitoring or surveillance. The difficulty of the problem lies in the design of individual control laws for each of the agents that account for inter-agent interactions while preserving convergence properties of the control law and drive the system to a desired state. We introduce an abstract representation that reduces the complexity of the control law and is invariant to the number of robots in two and three dimensions. Further, the control requires minimal global state information, resulting in decentralized control laws at the agent level, and permits the inclusion of a supervisory agent such as an aerial robot. We define energy metrics based on the abstract representation that reduce the complexity of the planning problem to designing trajectories for the abstract representation of the system. We review an experimental infrastructure developed to validate these multi-robot planning and control strategies and provide experimental verification on teams of nonholonomic robots. We conclude by discussing limitations of the work and propose future work to address these limitations.

August 21
Michael G. Schrlau, PhD Candidate
"Carbon-based nanoprobes and their applications to cell physiology"

Speaker: Michael G. Schrlau
PhD Candidate
Advisor: Haim H. Bau
Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Abstract:
There is a need in medical and biological research to probe cells with minimal intrusion and high spatial resolution. Since the discovery of carbon nanotubes and the fabrication of nanoscale carbon pipes, we and others have sought to create carbon-based, one-dimensional cellular probes for, among other uses, intracellular delivery, probing, sensing, and nanosurgery. We have developed a method of integrating nanoscale carbon pipes into glass micropipettes to form carbon nanopipettes (CNPs) in large quantities and without the need for cumbersome assembly. CNPs have been used with standard cell physiology equipment to simultaneously provide a nanoscale channel for mass transport and a conductive pathway for electrical measurements. In this seminar, I will first present the fabrication method of CNPs and their resultant properties. I will then show how CNPs can probe and inject fluids into cells without compromising cell viability or hindering their growth and proliferation. Finally, I will demonstrate the utility of CNPs in cell physiology by using them to inject calcium-mobilizing, second messengers into cells to identify cell signaling pathways. I will conclude by briefly discussing additional applications being explored for CNPs.

August 21
Adam P. Hitchcock
"Chemical imaging at 30 nm spatial resolution in 2-d and 3-d with scanning transmission x-ray microscopy"

Speaker: Adam P. Hitchcock
Brockhouse Institute for Materials Research, McMaster University
Hamilton, Ontario

Abstract:
Soft X-ray scanning transmission X-ray microscopy (STXM) is a powerful tool for materials analysis, with particular strengths in quantitative chemical mapping in two and three dimensions of fully hydrated biological and polymer systems. In addition to chemical identification and mapping via the intrinsic X-ray absorption spectral contrast, dichroic mapping using variable orientation of linear polarized light provides useful information on molecular alignment which can be important in characterizing natural and synthetic fibers and carbon nanotube systems.  The STXM technique will be described and illustrated using examples from recent work at the Advanced Light Source (Berkeley, CA) and the Canadian Light Source (Saskatoon, SK).