Mahmut Selman Sakar

Cell-mediated fibre recruitment drives extracellular matrix mechanosensing in engineered fibrillar microenvironments

To investigate how cells sense stiffness in settings structurally similar to native extracellular matrices (ECM), we designed a synthetic fibrous material with tunable mechanics and user-defined architecture. In contrast to flat hydrogel surfaces, these fibrous materials recapitulated cell-matrix interactions observed with collagen matrices including stellate cell morphologies, cell-mediated realignment of fibers, and bulk contraction of the material. While increasing the stiffness of flat hydrogel surfaces induced mesenchymal stem cell spreading and proliferation, increasing fiber stiffness instead suppressed spreading and proliferation depending on network architecture. Lower fiber stiffness permitted active cellular forces to recruit nearby fibers, dynamically increasing ligand density at the cell surface and promoting the formation of focal adhesions and related signaling. These studies demonstrate a departure from the well-described relationship between material stiffness and spreading established with hydrogel surfaces, and introduce fiber recruitment as a novel mechanism by which cells probe and respond to mechanics in fibrillar matrices.

Three-dimensionally printed biological machines powered by skeletal muscle

Significance Cell-based soft robotic devices could have a transformative impact on our ability to design machines and systems that can dynamically sense and respond to a range of complex environmental signals. We demonstrate innovative advancements in biomaterials, tissue engineering, and 3D printing, as well as an integration of these technologies, to forward engineer a controllable centimeter-scale biological machine capable of locomotion on a surface in fluid. Due in part to their elastic nature and the living components that can permit a dynamic response to environmental and applied stimuli, these biological machines can have diverse applications and represent a significant advancement toward high-level functional control over soft biorobotic systems. Combining biological components, such as cells and tissues, with soft robotics can enable the fabrication of biological machines with the ability to sense, process signals, and produce force. An intuitive demonstration of a biological machine is one that can produce motion in response to controllable external signaling. Whereas cardiac cell-driven biological actuators have been demonstrated, the requirements of these machines to respond to stimuli and exhibit controlled movement merit the use of skeletal muscle, the primary generator of actuation in animals, as a contractile power source. Here, we report the development of 3D printed hydrogel “bio-bots” with an asymmetric physical design and powered by the actuation of an engineered mammalian skeletal muscle strip to result in net locomotion of the bio-bot. Geometric design and material properties of the hydrogel bio-bots were optimized using stereolithographic 3D printing, and the effect of collagen I and fibrin extracellular matrix proteins and insulin-like growth factor 1 on the force production of engineered skeletal muscle was characterized. Electrical stimulation triggered contraction of cells in the muscle strip and net locomotion of the bio-bot with a maximum velocity of ∼156 μm s−1, which is over 1.5 body lengths per min. Modeling and simulation were used to understand both the effect of different design parameters on the bio-bot and the mechanism of motion. This demonstration advances the goal of realizing forward-engineered integrated cellular machines and systems, which can have a myriad array of applications in drug screening, programmable tissue engineering, drug delivery, and biomimetic machine design.

Single Cell Manipulation using Ferromagnetic Composite Microtransporters

For biomedical applications, such as single cell manipulation, it is important to fabricate microstructures that can be powered and controlled wirelessly in fluidic environments. In this letter, we describe the construction and operation of truly micron-sized, biocompatible ferromagnetic microtransporters driven by external magnetic fields. Microtransporters were fabricated using a simple, single step fabrication method and can be produced in large numbers. We demonstrate that they can be navigated to manipulate single cells with micron-size precision without disturbing the local environment.

An Integrated Microrobotic Platform for On‐Demand, Targeted Therapeutic Interventions

The presented microrobotic platform combines together the advantages of self-folding NIR light sensitive polymer bilayers, magnetic alginate microbeads, and a 3D manipulation system, to propose a solution for targeted, on-demand drug and cell delivery. First feasibility studies are presented together with the potential of the full design.

Electrokinetic and optical control of bacterial microrobots

One of the great challenges in microscale science and engineering is the independent manipulation of cells and man-made objects on the micron scale. For such work, motile microorganisms are integrated with engineered systems to construct microbiorobots (MBRs). MBRs are negative photosensitive epoxy (SU-8) microfabricated structures with typical feature sizes ranging from 1 to 100 µm coated with a monolayer of swarmer cells of the bacterium Serratia marcescens. The adherent cells naturally coordinate to propel the microstructures in fluidic environments. In this study, ultraviolet light is used to control rotational motion and direct current electric fields are used to control the two-dimensional movement of MBRs. They are steered in a fully automated fashion using computer-controlled visual servoing, used to transport and manipulate micron-sized objects, and employed as cell-based biosensors. This work is a step toward in vitro mechanical or chemical manipulation of cells as well as controlled assembly of microcomponents.

Automated biomanipulation of single cells using magnetic microrobots

Transport of individual cells or chemical payloads on a subcellular scale is an enabling tool for the study of cellular communication, cell migration, and other localized phenomena. We present a magnetically actuated robotic system capable of fully automated manipulation of cells and microbeads. Our strategy uses autofluorescent robotic transporters and fluorescently labeled microbeads to aid tracking and control in optically obstructed environments. We demonstrate automated delivery of microbeads infused with chemicals to specified positions on neurons. This system is compatible with standard upright and inverted light microscopes and is capable of applying forces less than 1 pN for precision positioning tasks.

Soft micromachines with programmable motility and morphology

Nature provides a wide range of inspiration for building mobile micromachines that can navigate through confined heterogenous environments and perform minimally invasive environmental and biomedical operations. For example, microstructures fabricated in the form of bacterial or eukaryotic flagella can act as artificial microswimmers. Due to limitations in their design and material properties, these simple micromachines lack multifunctionality, effective addressability and manoeuvrability in complex environments. Here we develop an origami-inspired rapid prototyping process for building self-folding, magnetically powered micromachines with complex body plans, reconfigurable shape and controllable motility. Selective reprogramming of the mechanical design and magnetic anisotropy of body parts dynamically modulates the swimming characteristics of the micromachines. We find that tail and body morphologies together determine swimming efficiency and, unlike for rigid swimmers, the choice of magnetic field can subtly change the motility of soft microswimmers.

Modeling, control and experimental characterization of microbiorobots

In this paper, we describe how motile microorganisms can be integrated with engineered microstructures to develop a micro-bio-robotic system. SU-8 microstructures blotted with swarmer cells of Serratia Marcescens in a monolayer are propelled by the bacteria in the absence of any environmental stimulus. We call such microstructures with bacteria MicroBioRobots (MBRs) and the uncontrolled motion in the absence of stimuli self actuation. Our paper has two primary contributions. First, we demonstrate the control of MBRs using self actuation and DC electric fields, and develop an experimentally validated mathematical model for the MBRs. This model allows us to use self actuation and electrokinetic actuation to steer the MBR to any position and orientation in a planar micro channel. Second, we combine our experimental setup and a feedback control algorithm to steer robots with micrometer accuracy in two spatial dimensions. We describe the fabrication process for MBRs and show experimental results demonstrating actuation and control.

Stochastic Modeling and Control of Biological Systems: The Lactose Regulation System of Escherichia Coli

In 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.

Stochastic Source Seeking by Mobile Robots

We consider the problem of designing controllers to steer mobile robots to the source (the minimizer) of a signal field. In addition to the mobility constraints, e.g., posed by the nonholonomic dynamics, we assume that the field is completely unknown to the robot and the robot has no knowledge of its own position. Furthermore, the unknown field is randomly switching. In the case where the information of the field (e.g., the gradient) is completely known, standard motion planning techniques for mobile robots would converge to the known source. In the absence of mobility constraints, convergence to the minimum of unknown fields can be pursued using the framework of numerical optimization. By considering these facts, this paper exploits an idea of the stochastic approximation for solving the problem mentioned in the beginning and proposes a source seeking controller which sequentially generates the next waypoints such that the resulting discrete trajectory converges to the unknown source and which steers the robot along the waypoints, under the assumption that the robot can move to any point in the body fixed coordinate frame. To this end, we develop a rotation-invariant and forward-sided version of the simultaneous-perturbation stochastic approximation algorithm as a method to generate the next waypoints. Based on this algorithm, we design source seeking controllers. Furthermore, it is proven that the robot converges to a small set including the source in a probabilistic sense if the signal field switches periodically and sufficiently fast. The proposed controllers are demonstrated by numerical simulations.