Metropolis Integration Schemes for Self-Adjoint Diffusions

We present explicit methods for simulating diffusions whose generator is self-adjoint with respect to a known (but possibly not normalizable) density. These methods exploit this property and combine an optimized Runge-Kutta algorithm with a Metropolis-Hastings Monte-Carlo scheme. The resulting numerical integration scheme is shown to be weakly accurate at finite noise and to gain higher order accuracy in the small noise limit. It also permits to avoid computing explicitly certain terms in the equation, such as the divergence of the mobility tensor, which can be tedious to calculate. Finally, the scheme is shown to be ergodic with respect to the exact equilibrium probability distribution of the diffusion when it exists. These results are illustrated on several examples including a Brownian dynamics simulation of DNA in a solvent. In this example, the proposed scheme is able to accurately compute dynamics at time step sizes that are an order of magnitude (or more) larger than those permitted with commonly used explicit predictor-corrector schemes.Comment: 54 pages, 8 figures, To appear in MM

When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Electron spin resonance of nitrogen-vacancy centers in optically trapped nanodiamonds

Using an optical tweezers apparatus, we demonstrate three-dimensional control of nanodiamonds in solution with simultaneous readout of ground-state electron-spin resonance (ESR) transitions in an ensemble of diamond nitrogen-vacancy (NV) color centers. Despite the motion and random orientation of NV centers suspended in the optical trap, we observe distinct peaks in the measured ESR spectra qualitatively similar to the same measurement in bulk. Accounting for the random dynamics, we model the ESR spectra observed in an externally applied magnetic field to enable d.c. magnetometry in solution. We estimate the d.c. magnetic field sensitivity based on variations in ESR line shapes to be ~50 microTesla/Hz^1/2. This technique may provide a pathway for spin-based magnetic, electric, and thermal sensing in fluidic environments and biophysical systems inaccessible to existing scanning probe techniques.Comment: 29 pages, 13 figures for manuscript and supporting informatio

Fluigi: an end-to-end software workflow for microfluidic design

One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications with implications in health, materials, and sensing. Computational design methodologies allow for increased performance and reliability of these circuits. Major challenges that remain include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of “specify-design-build-test.” I summarize the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow for genetic circuits. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. However, adoption of microfluidics for synthetic biology has been slow due to the expert knowledge and equipment needed to fabricate and control devices. I present an end-to-end workflow for a computer-aided-design (CAD) tool, Fluigi, for designing microfluidic devices and for integrating biological Boolean genetic circuits with microfluidics. The workflow starts with a ``netlist" input describing the connectivity of microfluidic device to be designed, and proceeds through placement, routing, and design rule checking in a process analogous to electronic computer aided design (CAD). The output is an image of the device for printing as a mask for photolithography or for computer numerical control (CNC) machining. I also introduced a second workflow to allocate biological circuits to microfluidic devices and to generate the valve control scheme to enable biological computation on the device. I used the CAD workflow to generate 15 designs including gradient generators, rotary pumps, and devices for housing biological circuits. I fabricated two designs, a gradient generator with CNC machining and a device for computing a biological XOR function with multilayer soft lithography, and verified their functions with dye. My efforts here show a first end-to-end demonstration of an extensible and foundational microfluidic CAD tool from design concept to fabricated device. This work provides a platform that when completed will automatically synthesize high level functional and performance specifications into fully realized microfluidic hardware, control software, and synthetic biological wetware

From Microbial Communities to Distributed Computing Systems

A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tool

Bio- und Umweltsensorik basierend auf organischer Optoelektronik

The integration of organic light emitting diodes (OLEDs) and organic photodetectors (OPDs) promises compact and low-cost hybrid integrated sensors for optical detection. The thermal evaporation-based device fabrication technique allows for all optical sensing elements being permanently aligned with a high degree of miniaturization, creating more portable, energy-efficient and multiplexing-capable devices; these may be easily combined with microfluidic units resulting in a minimal sample and reagent volume demand of the sensor. This dissertation deals in particular with the system design, development, characterization and deployment of a monolithic integrated sensor unit with 8 OLED and 8 OPD pixel pairs for different applications. The following work provides an extensive study of the system efficiency via ray tracing simulations, investigating crucial boundary conditions for efficient analyte detection. The proposed sensing unit contains OLED and OPD devices with an individual pixel size of 0.5mm × 0.5mm fabricated on a 12.5mm × 12.5mm glass substrate. The developed sensor system was successfully characterized and applied in a biosensing application by detecting fluorescence labelled single-stranded DNA (ssDNA) after forming the Förster resonance energy transfer (FRET) upon the hybridization of two ssDNA strands. This optoelectronic sensor has the potential to enable compact and low-cost fluorescence point-of-care (POC) devices for decentralised multiplex biomedical testing. Additionally, this sensing platform was deployed in environmental and agricultural applications to detect nutrients such as nitrite and nitrate. In this colorimetric application the popular Griess reaction was utilized to form the nitrite concentration dependent amount of azo dye, which absorbs light around 540nm

Development of methods for combinational approaches to cis-regulatory module interactions

The complexity and size of the higher animal genome and relative scarcity of DNA-binding factors with which to regulate it imply a complex and pleiotropic regulatory system. Cisregulatory modules (CRMs) are vitally important regulators of gene expression in higher animal cells, integrating external and internal information to determine an appropriate response in terms of gene expression by means of direct and indirect interactions with the transcriptional machinery. The interaction space available within systems of multiple CRMs, each containing several sites where one or more factors could be bound is huge. Current methods of investigation involve the removal of individual sites or factors and measuring the resulting effect on gene expression. The effects of investigations of this type may be masked by the functional redundancy present in some of these regulatory systems as a result of their evolutionary development. The investigation of CRM function is limited by a lack of technology to generate and analyse combinatorial mutation libraries of CRMs, where putative transcription factor binding sites are mutated in various combinations to achieve a holistic view of how the factors binding to those sites cooperate to bring about CRM function. The principle work of this thesis is the generation of such a library. This thesis presents the development of microstereolithography as a method for making microfluidic devices, both directly and indirectly. A microfluidic device was fabricated that was used to generate oligonucleotide mixtures necessary to synthesise combinatorial mutants of a CRM sequence from the muscle regulatory factor MyoD. In addition, this thesis presents the development of the optimisation algorithms and assembly processes necessary for successful sequence assembly. Furthermore, it was found that the CRM, in combination with other CRMs, is able to synergistically regulate gene expression in a position and orientation independent manner in three separate contexts. Finally, by testing a small portion of the available combinatorial mutant library it was shown that mutation of individual binding sites within of the CRM is not sufficient to show a significant change in the level of reporter gene expression

Exploring topological phonons in different length scales: microtubules and acoustic metamaterials

The topological concepts of electronic states have been extended to phononic systems, leading to the prediction of topological phonons in a variety of materials. These phonons play a crucial role in determining material properties such as thermal conductivity, thermoelectricity, superconductivity, and specific heat. The objective of this dissertation is to investigate the role of topological phonons at different length scales. Firstly, the acoustic resonator properties of tubulin proteins, which form microtubules, will be explored The microtubule has been proposed as an analog of a topological phononic insulator due to its unique properties. One key characteristic of topological materials is the existence of edge modes within the energy gap. These edge modes allow energy to be transferred at specific frequencies along the edges of the material, while the bulk remains unaffected. In the case of microtubules, its ability to store vibrational energy at its edges and the sensitivity to changes in local bulk structure align with the properties of topological insulators. Furthermore, the appearance of edge modes in topological phononic insulators is determined by the local interactions of the bulk material. Even small changes in the local structure can shift the resonant frequency of the edge mode or completely extinguish it. Similarly, the ability of microtubules to shorten or overcome energy barriers is greatly affected by changes in their local bulk structure. This suggests a parallel between the impact of local bulk structure on both topological insulators and microtubules. This similarity has led to the proposal that microtubules could serve as an analog of topological phononic insulators, providing insights into their dynamics and potential applications in fields such as chemotherapy drug development and nanoscale materials. Secondly, the application of topological phonons in the realm of acoustic metamaterials will be examined. Acoustic waves have recently become a versatile platform for exploring and studying various topological phases, showcasing their universality and diverse manifestations. The unique properties of topological insulators and their surface states heavily rely on the dimension and symmetries of the material, making it possible to classify them using a periodic table of topological insulators. However, certain combinations of dimensions and symmetries can impede the achievement of topological insulation. It is of utmost importance to preserve symmetries in order to maintain the desired topological properties, which necessitates careful consideration of coupling methods. In the context of discrete acoustic resonant models, efficiently coupling resonators while simultaneously preserving symmetry poses a challenging question. In this part, a clever experimental approach is proposed and discussed to couple acoustic crystals. This modular platform not only supports the existence of topologically protected edge and interface states but also offers a convenient setup that can be easily assembled and disassembled. Furthermore, inspired by recent theoretical advancements that draw on techniques from the field of C*-algebras for identifying topological metals, the present study provides direct observations of topological phenomena in gapless acoustic crystals. Through these observations, a general experimental technique is realized and developed to demonstrate the topology of such systems. By employing the method of coupling acoustic crystals, the investigation unveils robust boundary-localized states in a topological acoustic metal and presents a reinterpretation of a composite operator as a new Hamiltonian. This reinterpretation enables the direct observation of a topological spectral flow and facilitates the measurement of topological invariants. Through these investigations, the aim of this dissertation is to deepen our understanding of the significance and potential applications of topological phonons in diverse systems