Joshua D. Bishop

Programmable parts: a demonstration of the grammatical approach to self-organization

In this paper, we introduce a robotic implementation of the theory of graph grammars (Klavins et al., 2005), which we use to model and direct self-organization in a formal, predictable and provably-correct fashion. The robots, which we call programmable parts, float passively on an air table and bind to each other upon random collisions. Once attached, they execute local rules that determine how their internal states change and whether they should remain bound. We demonstrate through experiments how they can self-organize into a global structure by executing a common graph grammar in a completely distributed fashion. The system also presents a challenge to the grammatical method (and to distributed systems approaches in general) due to the stochastic nature of its dynamics. We conclude by discussing these challenges and our initial approach to addressing them.

Precision chemical heating for diagnostic devices

Decoupling nucleic acid amplification assays from infrastructure requirements such as grid electricity is critical for providing effective diagnosis and treatment at the point of care in low-resource settings. Here, we outline a complete strategy for the design of electricity-free precision heaters compatible with medical diagnostic applications requiring isothermal conditions, including nucleic acid amplification and lysis. Low-cost, highly energy dense components with better end-of-life disposal options than conventional batteries are proposed as an alternative to conventional heating methods to satisfy the unique needs of point of care use.

A disposable chemical heater and dry enzyme preparation for lysis and extraction of DNA and RNA from microorganisms

Sample preparation, including bacterial lysis, remains a hurdle in the realization of complete point-of-care tests for many pathogens. Here, we developed a sample preparation methodology for enzymatic lysis and sample heating for low-resource, point-of-care applications. We show an instrument-free chemical heater system for rapid lysis of a Gram-positive bacterium (Staphylococcus aureus) and an RNA virus (human respiratory syncytial virus) using a dried lysis enzyme mixture (achromopeptidase) for S. aureus. After a lysis step (<1 minute), lysis enzymes are heat deactivated (<5 minutes) using a simple disposable chemical heater. We demonstrated that both DNA and RNA in the heat-treated sample could be directly amplified without purification, even in the presence of a clinically-obtained human nasal sample. This simple approach to dry enzyme storage and sample heating is adaptable to many applications where samples need to be lysed, including use in low-resource laboratories and in single-use or cartridge-based point-of-care diagnostic devices.

Characterization of a biomolecular fuel delivery device under load

We describe the design, implementation, and characterization of a biomolecular RNA fuel delivery device under load. The device is based on genelet technology, and is capable of driving dynamic behavior in complex nucleic acid circuits. Here we closely examine the behavior of a system consisting of the device driving the operation of a simple, fluorescently-labeled DNA probe. We use a simple model to characterize the stability region of the system and the effect of changing load conditions. Finally, we validate these analytical observations with basic experiments.

Dynamics and control of biomolecules: Research venues and opportunities

The purpose of this session is to present to the CDC audience a set of molecular-level biological research venues in which dynamics and control is, or can be, of use. With the large and growing number of people within the control community interested in biology, experiment driven research at the interface of biology and control is enticing. In our session, four different research venues are presented: 1) feedback control of individual DNA molecules in a nanopore, with a goal of DNA sequencing; 2) DNA secondary structure kinetics, with the goal of improving design and synthesis of DNA logic circuits that may be used, for example, for in vivo feedback control of biological processes; 3) an artificial DNA nanomotor, for which feedback compensation improves robustness and performance; and, 4) cooperative protein interactions in muscle force generation, in which identification of feedback mechanisms can ultimately improve therapeutic methods for post-cardiac arrest rehabilitation.

Collective Sensing with Self-Organizing Robots

We introduce a way to compose two local rule sets to form an environmental sensor. Each set of local rules results in a different global behavior when interpreted by a set of interacting programmable particles. In the composed system, the particles choose which set of rules to use depending on whether or not a certain condition is true or false about the initial state of the system. The global behavior of the system eventually matches only one set of rules, signaling that the particles have collectively recognized the condition on the initial state. We demonstrate the composition method on our robotic testbed

Enabling lateral transport of genomic DNA through porous membranes for point-of-care applications

Paper-based nucleic acid diagnostics have the potential to translate laboratory assays to simple-to-use, point-of-care devices, but many prototypes of these systems still lack the ability to process realistic samples due to the inability of genomic-sized DNA to move through membranes with small pores. For applications involving pathogen or human gene identification, the ability to fragment and transport DNA would provide more options for device design and broaden the range of applications. To address this challenge, we have developed and characterized a method that combines cell lysis with DNA fragmentation to allow for lateral transport of genomic DNA through commonly-used porous membranes. Additionally, we demonstrate that varying heating time and temperatures allows for control of both lysis and fragmentation based on genome size. These data align with previously published models that describe both DNA denaturation and thermal scission. This level of control allows semi-selective transport of pathogenic DNA, which can reduce the amount of interference from non-target human DNA in downstream applications. This method can be easily automated and is rapid, occurring in less than 10 minutes with one user step.