Sakar, M Selman
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Publication MicroBioRobots for Single Cell Manipulation(2010-11-22) Sakar, Mahmut SelmanOne of the great challenges in nano and micro scale science and engineering is the independent manipulation of biological cells and small man-made objects with active sensing. For such biomedical applications as single cell manipulation, telemetry, and localized targeted delivery of chemicals, it is important to fabricate microstructures that can be powered and controlled without a tether in fluidic environments. These microstructures can be used to develop microrobots that have the potential to make existing therapeutic and diagnostic procedures less invasive. Actuation can be realized using various different organic and inorganic methods. Previous studies explored different forms of actuation and control with microorganisms. Bacteria, in particular, offer several advantages as controllable micro actuators: they draw chemical energy directly from their environment, they are genetically modifiable, and they are scalable and configurable in the sense that any number of bacteria can be selectively patterned. Additionally, the study of bacteria inspires inorganic schemes of actuation and control. For these reasons, we chose to employ bacteria while controlling their motility using optical and electrical stimuli. In the first part of the thesis, we demonstrate a bio-integrated approach by introducing MicroBioRobots (MBRs). MBRs are negative photosensitive epoxy (SU8) microfabricated structures with typical feature sizes ranging from 1-100 μm coated with a monolayer of the swarming Serratia marcescens. The adherent bacterial cells naturally coordinate to propel the microstructures in fluidic environments, which we call Self-Actuation. First, we demonstrate the control of MBRs using self-actuation, DC electric fields and ultra-violet radiation and develop an experimentally-validated mathematical model for the MBRs. This model allows us to to steer the MBR to any position and orientation in a planar micro channel using visual feedback and an inverted microscope. Examples of sub-micron scale transport and assembly as well as computer-based closed-loop control of MBRs are presented. We demonstrate experimentally that vision-based feedback control allows a four-electrode experimental device to steer MBRs along arbitrary paths with micrometer precision. At each time instant, the system identifies the current location of the robot, a control algorithm determines the power supply voltages that will move the charged robot from its current location toward its next desired position, and the necessary electric field is then created. Second, we develop biosensors for the MBRs. Microscopic devices with sensing capabilities could significantly improve single cell analysis, especially in high-resolution detection of patterns of chemicals released from cells in vitro. Two different types of sensing mechanisms are employed. The first method is based on harnessing bacterial power, and in the second method we use genetically engineered bacteria. The small size of the devices gives them access to individual cells, and their large numbers permit simultaneous monitoring of many cells. In the second part, we describe the construction and operation of truly micron-sized, biocompatible ferromagnetic micro transporters driven by external magnetic fields capable of exerting forces at the pico Newton scale. We develop micro transporters using a simple, single step micro fabrication technique that allows us to produce large numbers in the same step. We also fabricate microgels to deliver drugs. We demonstrate that the micro transporters can be navigated to separate single cells with micron-size precision and localize microgels without disturbing the local environment.Publication Flagellar dynamics in viscous fluids(2009-09-11) Sakar, Mahmut-Selman; Arratia, Paulo E.; Lee, C.Publication Stochastic Modeling and Control of Biological Systems: The Lactose Regulation System of Escherichia Coli(2009-01-01) Julius, Agung; Halász, Ádám; Sakar, M Selman; Rubin, Harvey; Kumar, Vijay; Pappas, George JIn this paper, we present a comprehensive framework for stochastic modeling, model abstraction, and controller design for a biological system. The first half of the paper concerns modeling and model abstraction of the system. Most models in systems biology are deterministic models with ordinary differential equations in the concentration variables. We present a stochastic hybrid model of the lactose regulation system of E. coli bacteria that capture important phenomena which cannot be described by continuous deterministic models.We then show that the resulting stochastic hybrid model can be abstracted into a much simpler model, a two-state continuous-time Markov chain. The second half of the paper discusses controller design for a specific architecture. The architecture consists of measurement of a global quantity in a colony of bacteria as an output feedback and manipulation of global environmental variables as control actuation. We show that controller design can be performed on the abstracted (Markov chain) model and implementation on the real model yields the desired result.