Quality and Capacity Analysis of Molecular Communications in Bacterial Synthetic Logic Circuits

Synthetic logic circuits have been proposed as potential solutions for theranostics of biotechnological problems. One proposed model is the engineering of bacteria cells to create logic gates, and the communication between the bacteria populations will enable the circuit operation. In this paper, we analyze the quality of bacteria-based synthetic logic circuit through molecular communications that represent communication along a bus between three gates. In the bacteria-based synthetic logic circuit, the system receives environmental signals as molecular inputs and will process this information through a cascade of synthetic logic gates and free diffusion channels. We analyze the performance of this circuit by evaluating its quality and its relationship to the channel capacity of the molecular communications links that interconnect the bacteria populations. Our results show the effect of the molecular environmental delay and molecular amplitude differences over both the channel capacity and circuit quality. Furthermore, based on these metrics, we also obtain an optimum region for the circuit operation resulting in an accuracy of 80% for specific conditions. These results show that the performance of synthetic biology circuits can be evaluated through molecular communications, and lays the groundwork for combined systems that can contribute to future biomedical and biotechnology applications.

Related papers:

title: Bioinspired and biomimetic systems for advanced drug and gene delivery
abstract: Natural nanocarriers found in biological frameworks have motivated the scientists to fabricate new structures that help to build characteristic systems mimicking the natural processes. Furthermore, these bioinspired and biomimetic systems improve biocompatibility during drug and gene delivery applications. The success of such a drug delivery system depends on parameters like shape, surface, texture, movement, and preparation methods. To date, various bioinspired and biomimetic drug delivery systems are available. Bacteria‐inspired, virus‐inspired, fungus‐inspired and mammalian cell‐inspired systems are presently in the spotlight. Bioinspired or biomimetic macromolecular and nanoparticle‐based drug and gene delivery systems are well studied. The bioinspired and biomimetic systems find great application in biomedicine. Drug delivery, gene delivery, theranostic, and biosensing applications are major among the biomedical applications of these versatile systems. These systems have great influence on the biological systems owing to their high biocompatibility, less toxicity, and significant interaction. Bioinspired and biomimetic systems have a bright future ahead with a lot of potentials to resolve any obstacles encountered in drug and gene delivery.

title: Engineering bacteria for diagnostic and therapeutic applications
abstract: Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.

title: Advancing therapeutic applications of synthetic gene circuits.
abstract: Synthetic biology aims to introduce new sense-and-respond capabilities into living cells, which would enable novel therapeutic strategies. The development of regulatory elements, molecular computing devices, and effector screening technologies has enabled researchers to design synthetic gene circuits in many organisms, including mammalian cells. Engineered gene networks, such as closed-loop circuits or Boolean logic gate circuits, can be used to program cells to perform specific functions with spatiotemporal control and restoration of homeostasis in response to the extracellular environment and intracellular signaling. In addition, genetically modified microbes can be designed as local delivery of therapeutic molecules. In this review, we will discuss recent advances in therapeutic applications of synthetic gene circuits, as well as challenges and future opportunities for biomedicine.

title: Finding alternatives to antibiotics
abstract: The spread of antibiotic‐resistant pathogens requires new treatments. As the rate of development of new antibiotics has severely declined, alternatives to antibiotics must be considered in both animal agriculture and human medicine. Products for disease prevention are different from those for disease treatment, and examples of both are discussed here. For example, modulating the gut microbial community, either through feed additives or fecal transplantation, could be a promising way to prevent certain diseases; for disease treatment, non‐antibiotic approaches include phage therapy, phage lysins, bacteriocins, and predatory bacteria. Interestingly, several of these methods augment antibiotic efficacy by improving bacterial killing and decreasing antibiotic resistance selection. Because bacteria can ultimately evolve resistance to almost any therapeutic agent, it is important to continue to use both antibiotics and their alternatives judiciously.

title: Biological Signal Processing with a Genetic Toggle Switch
abstract: Complex gene regulation requires responses that depend not only on the current levels of input signals but also on signals received in the past. In digital electronics, logic circuits with this property are referred to as sequential logic, in contrast to the simpler combinatorial logic without such internal memory. In molecular biology, memory is implemented in various forms such as biochemical modification of proteins or multistable gene circuits, but the design of the regulatory interface, which processes the input signals and the memory content, is often not well understood. Here, we explore design constraints for such regulatory interfaces using coarse-grained nonlinear models and stochastic simulations of detailed biochemical reaction networks. We test different designs for biological analogs of the most versatile memory element in digital electronics, the JK-latch. Our analysis shows that simple protein-protein interactions and protein-DNA binding are sufficient, in principle, to implement genetic circuits with the capabilities of a JK-latch. However, it also exposes fundamental limitations to its reliability, due to the fact that biological signal processing is asynchronous, in contrast to most digital electronics systems that feature a central clock to orchestrate the timing of all operations. We describe a seemingly natural way to improve the reliability by invoking the master-slave concept from digital electronics design. This concept could be useful to interpret the design of natural regulatory circuits, and for the design of synthetic biological systems.

title: Cellular Biosensors with Engineered Genetic Circuits.
abstract: An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.

title: Construction of a genetic toggle switch in Escherichia coli
abstract: It has been proposed that gene-regulatory circuits with virtually any desired property can be constructed from networks of simple regulatory elements. These properties, which include multistability and oscillations, have been found in specialized gene circuits such as the bacteriophage λ switch and the Cyanobacteria circadian oscillator. However, these behaviours have not been demonstrated in networks of non-specialized regulatory components. Here we present the construction of a genetic toggle switch—a synthetic, bistable gene-regulatory network—in Escherichia coli and provide a simple theory that predicts the conditions necessary for bistability. The toggle is constructed from any two repressible promoters arranged in a mutually inhibitory network. It is flipped between stable states using transient chemical or thermal induction and exhibits a nearly ideal switching threshold. As a practical device, the toggle switch forms a synthetic, addressable cellular memory unit and has implications for biotechnology, biocomputing and gene therapy.

title: Computing with biological switches and clocks
abstract: The complex dynamics of biological systems is primarily driven by molecular interactions that underpin the regulatory networks of cells. These networks typically contain positive and negative feedback loops, which are responsible for switch-like and oscillatory dynamics, respectively. Many computing systems rely on switches and clocks as computational modules. While the combination of such modules in biological systems leads to a variety of dynamical behaviours, it is also driving development of new computing algorithms. Here we present a historical perspective on computation by biological systems, with a focus on switches and clocks, and discuss parallels between biology and computing. We also outline our vision for the future of biological computing.

title: Plug-and-Play Multicellular Circuits with Time-Dependent Dynamic Responses.
abstract: Synthetic biology studies aim to develop cellular devices for biomedical applications. These devices, based on living instead of electronic or electromechanic technology, might provide alternative treatments for a wide range of diseases. However, the feasibility of these devices depends, in many cases, on complex genetic circuits that must fulfill physiological requirements. In this work, we explored the potential of multicellular architectures to act as an alternative to complex circuits for implementation of new devices. As a proof of concept, we developed specific circuits for insulin or glucagon production in response to different glucose levels. Here, we show that fundamental features, such as circuit's affinity or sensitivity, are dependent on the specific configuration of the multicellular consortia, providing a method for tuning these properties without genetic engineering. As an example, we have designed and built circuits with an incoherent feed-forward loop architecture (FFL) that can be easily adjusted to generate single pulse responses. Our results might serve as a blueprint for future development of cellular devices for glycemia regulation in diabetic patients.

title: Using computational modeling and experimental synthetic perturbations to probe biological circuits.
abstract: This chapter describes approaches for using computational modeling of synthetic biology perturbations to analyze endogenous biological circuits, with a particular focus on signaling and metabolic pathways. We describe a bottom-up approach in which ordinary differential equations are constructed to model the core interactions of a pathway of interest. We then discuss methods for modeling synthetic perturbations that can be used to investigate properties of the natural circuit. Keeping in mind the importance of the interplay between modeling and experimentation, we next describe experimental methods for constructing synthetic perturbations to test the computational predictions. Finally, we present a case study of the p53 tumor-suppressor pathway, illustrating the process of modeling the core network, designing informative synthetic perturbations in silico, and testing the predictions in vivo.

title: Recent advances in synthetic biology of cyanobacteria
abstract: Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO2. Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO2, diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this “green” chassis.

title: Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’
abstract: Computation underlies the organization of cells into higher-order structures, for example during development or the spatial association of bacteria in a biofilm. Each cell performs a simple computational operation, but when combined with cell–cell communication, intricate patterns emerge. Here we study this process by combining a simple genetic circuit with quorum sensing to produce more complex computations in space. We construct a simple NOR logic gate in Escherichia coli by arranging two tandem promoters that function as inputs to drive the transcription of a repressor. The repressor inactivates a promoter that serves as the output. Individual colonies of E. coli carry the same NOR gate, but the inputs and outputs are wired to different orthogonal quorum-sensing ‘sender’ and ‘receiver’ devices. The quorum molecules form the wires between gates. By arranging the colonies in different spatial configurations, all possible two-input gates are produced, including the difficult XOR and EQUALS functions. The response is strong and robust, with 5- to >300-fold changes between the ‘on’ and ‘off’ states. This work helps elucidate the design rules by which simple logic can be harnessed to produce diverse and complex calculations by rewiring communication between cells.

title: Molecular Communication: Index
abstract: This paper describes research challenges in Molecular Communication, a new and interdisciplinary research area that spans the nanotechnology, biotechnology, and communication technology. Molecular communication allows nanomachines to communicate using molecules as a communication carrier. Key research challenges include controlled propagation of carrier molecules, encoding/ decoding of information onto information molecules, and transmission/reception systems for carrier/information molecules. The authors of this paper are currently investigating the feasibility of molecular communication.

title: Applications of molecular communications to medicine: A survey
abstract: In recent years, progresses in nanotechnology have established the foundations for implementing nanomachines capable of carrying out simple but significant tasks. Under this stimulus, researchers have been proposing various solutions for realizing nanoscale communications, considering both electromagnetic and biological communications. Their aim is to extend the capabilities of nanodevices, so as to enable the execution of more complex tasks by means of mutual coordination, achievable through communications. However, although most of these proposals show how devices can communicate at the nanoscales, they leave in the background specific applications of these new technologies. Thus, this paper shows an overview of the actual and potential applications that can rely on a specific class of such communications techniques, commonly referred to as molecular communications. In particular, we focus on health-related applications. This decision is due to the rapidly increasing interests of research communities and companies to minimally invasive, biocompatible, and targeted health-care solutions. Molecular communication techniques have actually the potentials of becoming the main technology for implementing advanced medical solution. Hence, in this paper we provide a taxonomy of potential applications, illustrate them in some details, along with the existing open challenges for them to be actually deployed, and draw future perspectives.

title: Fundamentals of Molecular Information and Communication Science
abstract: Molecular communication (MC) is the most promising communication paradigm for nanonetwork realization since it is a natural phenomenon observed among living entities with nanoscale components. Since MC significantly differs from classical communication systems, it mandates reinvestigation of information and communication theoretical fundamentals. The closest examples of MC architectures are present inside our own body. Therefore, in this paper, we investigate the existing literature on intrabody nanonetworks and different MC paradigms to establish and introduce the fundamentals of molecular information and communication science. We highlight future research directions and open issues that need to be addressed for revealing the fundamental limits of this science. Although the scope of this development encompasses wide range of applications, we particularly emphasize its significance for life sciences by introducing potential diagnosis and treatment techniques for diseases caused by dysfunction of intrabody nanonetworks.

title: Ca2+-signaling-based molecular communication systems: Design and future research directions
abstract: Nanomedicine is revolutionizing current methods for diagnosing, treatment and prevention of diseases with the integration of molecular biology, biotechnology as well as nanotechnology for sensing and actuation capabilities at the molecular scale using nanoscale devices, namely nanomachines. While numerous examples of these applications have been tested in vivo , the real deployments are far from reality. Limitations in controlling, monitoring, miniaturization, and computing inhibit access and manipulation of information at the nano-scale. Integrating communication and networking functionalities provide new opportunities for such challenges with the newly introduced Molecular Communications. These natural communication systems are found with plurality inside the human body. The current challenge is to utilize these natural systems to create artificial biocompatible communication networks that can interconnect multiple nanomachines in multiple parts of the body and connected to the cloud, is defined as the Internet of Bio-Nano Things ( IoBNT ). Nanonetworks inside cellular tissues perform communication using a signaling process such as Ca 2+ . This specifically signaling process is very important for many regulatory functions in tissues and its control and communication is crucial to allow nanomedicine capabilities towards diagnosis and treatments of diseases at the nano-scale. This paper presents a review of techniques that enable the design of the Ca 2+ -signaling-based molecular communication system for cellular tissues, essential tools for its deployment, application and, lastly, the research future direction in this field. In the end, one must acquire the sufficient knowledge to understand both biological and telecommunication concepts that encompass this technology to bring it further.

title: Molecular communication for drug delivery systems: A survey
abstract: Drug delivery systems (DDS) are engineered methods to enable the targeted delivery of therapeutic agents at the right rate and location while minimizing the undesired side effects. The recent advances in bioengineering and nanotechnology make it possible to design molecular compounds with specific sizes, shapes, structures and chemical properties to improve the drug uptake and minimize its side effects. Despite all of this progress, overcoming the biological barriers to drug delivery remains challenging. Observing the parallels between the delivery of drugs and the delivery of data, a new paradigm in communication systems research, called molecular communication (MC), has been devised to approach this problem. This paper presents the state-of-the-art, challenges and research opportunities in studying DDS through the MC paradigm. First, the constituting elements of a DDS are presented, highlighting the contributions from MC research. Second, an overview is given of the novel modeling approaches based on communication theory and several simulation platforms applicable to the study of drug delivery systems are presented. Finally, lessons are drawn from the efforts of the MC community on this research topic and future research opportunities and challenges are discussed.

title: On the Interaction between a Nanoparticulate System and the Human Body in Body Area Nanonetworks
abstract: In this work, we investigate the interaction of a nanoparticulate system for nanomedicine applications with the biological environment, i.e., the human body. Following the molecular communication paradigm, we assess how our nanoparticulate system model is suitable for coexistence in a biological environment. Specifically, we assume the presence of the human immune system that can affect the optimal behavior of nanoparticles, aiming to locally deliver drug inside the human body. When a flow of nanoparticles is injected into the blood, the interference due to the immune system can provide a strong decrease of the nanoparticle concentration, by means of “humoral immunity”, the phagocytosis process, etc. As a consequence, the correct drug delivery will occur with a lower probability. Since the mechanism behind the biological immune system is very complicated, in this paper, we start from a simplistic nanoparticulate model, where the nanoparticles and the cells of the immune system are subject to the diffusion laws. Finally, we derive the end-to-end physical model of our nanoparticulate nanomedicine system with the presence of the human immune system cells. The error analysis is then investigated in terms of how these errors can affect the performance of the system, i.e., nanoparticle survival probability.

title: Molecular Communication and Networking: Opportunities and Challenges
abstract: The ability of engineered biological nanomachines to communicate with biological systems at the molecular level is anticipated to enable future applications such as monitoring the condition of a human body, regenerating biological tissues and organs, and interfacing artificial devices with neural systems. From the viewpoint of communication theory and engineering, molecular communication is proposed as a new paradigm for engineered biological nanomachines to communicate with the natural biological nanomachines which form a biological system. Distinct from the current telecommunication paradigm, molecular communication uses molecules as the carriers of information; sender biological nanomachines encode information on molecules and release the molecules in the environment, the molecules then propagate in the environment to receiver biological nanomachines, and the receiver biological nanomachines biochemically react with the molecules to decode information. Current molecular communication research is limited to small-scale networks of several biological nanomachines. Key challenges to bridge the gap between current research and practical applications include developing robust and scalable techniques to create a functional network from a large number of biological nanomachines. Developing networking mechanisms and communication protocols is anticipated to introduce new avenues into integrating engineered and natural biological nanomachines into a single networked system. In this paper, we present the state-of-the-art in the area of molecular communication by discussing its architecture, features, applications, design, engineering, and physical modeling. We then discuss challenges and opportunities in developing networking mechanisms and communication protocols to create a network from a large number of bio-nanomachines for future applications.

title: Miniature Devices in the Wild: Modeling Molecular Communication in Complex Extracellular Spaces
abstract: Miniature devices voyaging inside the human body for diagnostic and drug delivery purposes is no longer a wild dream. At the very heart of such an endeavor lies the capability of miniature devices like synthetic cells and microrobots to achieve complex tasks collectively by exchanging information molecules. Towards this end, we model the spatiotemporal dynamics of the molecular transport process in complex extracellular spaces (ECSs) such that the signaling delay can be accurately predicted. More precisely, we use parameters like ECS volume fraction, tortuosity, and cross-section area of diffusion paths to capture the physicochemical features of the ECS. Based on these parameters, we propose a new algorithm to calculate the directional diffusion coefficient, which is then used in an effective diffusion equation to describe the molecular transport process across the region of interest. Our modeling results show good agreement with detailed 3D simulations in complex ECSs, while the classical diffusion and previous approaches fail to capture the heterogeneity and directionality of the transport process. Consequently, the proposed approach represents a major step towards characterizing the interaction of cooperative miniature devices that can achieve complex tasks via diffusion-based molecular communication.

title: Shannon Meets Fick on the Microfluidic Channel: Diffusion Limit to Sum Broadcast Capacity for Molecular Communication
abstract: Molecular communication (MC) over a microfluidic channel with flow is investigated based on Shannon’s channel capacity theorem and Fick’s laws of diffusion. Specifically, the sum capacity for MC between a single transmitter and multiple receivers (broadcast MC) is studied. The transmitter communicates by using different types of signaling molecules with each receiver over the microfluidic channel. The transmitted molecules propagate through microfluidic channel until reaching the corresponding receiver. Although the use of different types of molecules provides orthogonal signaling, the sum broadcast capacity may not scale with the number of the receivers due to physics of the propagation (interplay between convection and diffusion based on distance). In this paper, the performance of broadcast MC on a microfluidic chip is characterized by studying the physical geometry of the microfluidic channel and leveraging the information theory. The convergence of the sum capacity for microfluidic broadcast channel is analytically investigated based on the physical system parameters with respect to the increasing number of molecular receivers. The analysis presented here can be useful to predict the achievable information rate in microfluidic interconnects for the biochemical computation and microfluidic multi-sample assays.

title: TCP-Like Molecular Communications
abstract: In this paper, we present a communication protocol between a pair of biological nanomachines, i.e., a transmitter and a receiver, built upon molecular communications in an aqueous environment. In our proposal, the receiver, acting as a control node, sends a connection setup signal to the transmitter, which stokes molecules, to start molecule transmission. The molecules transmitted by the transmitter propagate in the environment and are absorbed by the receiver through its receptors. When the receiver absorbs the desired quantity of molecules, it releases a tear-down signal to notify the transmitter to stop the transmission. The proposed protocol implements a bidirectional communication by using a number of techniques originally designed for the TCP. In fact, the proposed protocol is connection-oriented and uses the TCP-like probing to find a suitable transmission rate between the transmitter and the receiver to avoid receiver congestion. Unlike the TCP, however, explicit acknowledgments are not used since they would degrade the communication throughput due to the large delay, which is a characteristic feature of molecular communications. Thus, the proposed protocol uses implicit acknowledgments, and feedback signals are sent by the receiver to throttle the transmission rate at the transmitter, i.e., explicit negative feedback. We also present the results of an extensive simulation campaign, used to validate the proposed protocol and to properly dimension the main protocol parameters.

title: In-Body Network Biomedical Applications: From Modeling to Experimentation
abstract: Innovative diagnostic approaches and therapies are more and more based on the use of injections or oral delivery of nanoparticle sized substances. For a better understanding of the overall phenomena, aiming to facilitate a safe application at large scale, the development of accurate models and analysis techniques are required. These techniques take into consideration different aspects of the overall process: accurate numerical modeling of the different phases of the nanoparticles in the body, and knowledge of the local environment, that can be varying very fast within a short-range in the body itself. Such aspects should be taken into account to correctly predict the amount of drug and its timely release for the specific disease. Deep and accurate analysis of the interaction between the nanoparticles and the biological fluid where the nanoparticles are immersed is mandatory for an efficient correlation of all these aspects. Because of their biocompatibility, in this paper, we focus our attention on systems of Titanium (Ti), and its oxide (e.g., TiO2), given their specific features in terms of density, lack of cytotoxic effects, etc. Specifically, we present the study and design of an in-body system by characterizing each of the emission, diffusion, and reception processes with a proper realistic model. The theoretical investigation is further supported by experimental study of the morphology and other important characteristics (e.g., the pH of the particles, and thermal stability) of TiO2 systems when immersed in a Ringer solution, in order to derive important information related to their potential toxicity inside the human body.

title: Bacteria-based communication in nanonetworks
abstract: a b s t r a c t This paper describes a Bacteria-based Nanonetwork for communication between eukaryotic cell sized nano devices. The communication is achieved by the exchange of DNA molecules which are transported by bacteria guided by chemotaxis. First, the modules of the network are described and all the biological phenomena that support the basic communication steps are explained in detail. Then an analytical model is developed to assess the communication range and the network performance in terms of capacity and end-to-end delay by considering the available information about the biological mechanisms used. As there are no appropriate estimates of the propagation delay introduced by bacterial chemotaxis, our newly developed simulator is introduced which helps us to obtain the statistics on bacteria propagation. Finally, by combining the analytical model with the simulation results, a network performance in terms of end-to-end delay, capacity and end-to-end throughput is obtained which is 4 orders of magnitude higher than the other molecular communication approaches.

title: Design and Analysis of Wireless Communication Systems Using Diffusion-Based Molecular Communication Among Bacteria
abstract: The design of biologically-inspired wireless communication systems using bacteria as the basic element of the system is initially motivated by a phenomenon called Quorum Sensing. Due to high randomness in the individual behavior of a bacterium, reliable communication between two bacteria is almost impossible. Therefore, we have recently proposed that a population of bacteria in a cluster is considered as a bio node in the network capable of molecular transmission and reception. This proposition enables us to form a reliable bio node out of many unreliable bacteria. In this paper, we study the communication between two nodes in such a network where information is encoded in the concentration of molecules by the transmitter. The molecules produced by the bacteria in the transmitter node propagate through the diffusion channel. Then, the concentration of molecules is sensed by the bacteria population in the receiver node which would decode the information and output light or fluorescent as a result. The uncertainty in the communication is caused by all three components of communication, i.e., transmission, propagation and reception. We study the theoretical limits of the information transfer rate in the presence of such uncertainties. Finally, we consider M-ary signaling schemes and study their achievable rates and corresponding error probabilities.

title: Molecular Communications Pulse-Based Jamming Model for Bacterial Biofilm Suppression
abstract: Studies have recently shown that the bacteria survivability within biofilms is responsible for the emergence of superbugs. The combat of bacterial infections, without enhancing its resistance to antibiotics, includes the use of nanoparticles to quench the quorum sensing of these biofilm-forming bacteria. Several sequential and parallel multi-stage communication processes are involved in the formation of biofilms. In this paper, we use proteomic data from a wet lab experiment to identify the communication channels that are vital to these processes. We also identified the main proteins from each channel and propose the use of jamming signals from synthetically engineered bacteria to suppress the production of those proteins. This biocompatible technique is based on synthetic biology and enables the inhibition of biofilm formation. We analyze the communications performance of the jamming process by evaluating the path loss for a number of conditions that include different engineered bacterial population sizes, distances between the populations, and molecular signal power. Our results show that sufficient molecular pulse-based jamming signals are able to prevent the biofilm formation by creating lossy communications channels (almost −3 dB for certain scenarios). From these results, we define the main design parameters to develop a fully operational bacteria-based jamming system.

title: Programmable full-adder computations in communicating three-dimensional cell cultures
abstract: Synthetic biologists have advanced the design of trigger-inducible gene switches and their assembly into input-programmable circuits that enable engineered human cells to perform arithmetic calculations reminiscent of electronic circuits. By designing a versatile plug-and-play molecular-computation platform, we have engineered nine different cell populations with genetic programs, each of which encodes a defined computational instruction. When assembled into 3D cultures, these engineered cell consortia execute programmable multicellular full-adder logics in response to three trigger compounds.

title: Bacteria-based AND logic gate: a decision-making and self-powered biosensor.
abstract: We developed a bacteria-based AND logic gate using a Pseudomonas aeruginosa lasI/rhlI double mutant with two quorum-sensing signaling molecules as the input signals. We showed a distinct electrical output signal, despite the complexity and continuous regulation of metabolic reactions of living cells.

title: Programming the quorum sensing-based AND gate in Shewanella oneidensis for logic gated-microbial fuel cells.
abstract: An AND logic gate based on a synthetic quorum-sensing (QS) module was constructed in a Shewanella oneidensis MR-1 mtrA knockout mutant. The presence of two input signals activated the expression of a periplasmic decaheme cytochrome MtrA to regenerate the extracellular electron transfer conduit, enabling the construction of AND-gated microbial fuel cells.

title: Modeling the "Effective capacitance" for the RC interconnect of CMOS gates
abstract: With finer line widths and faster switching speeds, the resistance of on-chip metal interconnect is having a dominant impact on the timing behavior of logic gates. Specifically, the gates are switching faster and the interconnect delays are getting longer due to scaling. This results in a trend in which the RC interconnect delay is beginning to comprise a larger portion of the overall logic stage delay. This shift in relative delay dominance from the gate to the RC interconnect is increased by resistance shielding. That is, as the gate "resistance" gets smaller and the metal resistance gets larger, the gate no longer "sees" the total net capacitance and the gate delay may be significantly less than expected. This trend complicates the timing analysis of digital circuits, which relies upon simple, empirical gate delay equations for efficiency. In this paper, we develop an analytical expression for the "effective load capacitance" of a pc interconnect. In addition, when there is significant shielding, the response waveforms at the gate output may have a large exponential tail. We show that this waveform tail can strongly influence the delay of the RC interconnect. Therefore, we propose an extension of the effective capacitance equation that captures the complete waveform response accurately, with a two-piece gate-output-waveform approximation.

title: Performance computation for precharacterized CMOS gates with RC loads
abstract: For efficiency, the performance of digital CMOS gates is often expressed in terms of empirical models. Both delay and short-circuit power dissipation are sometimes characterized as a function of load capacitance and input signal transition time. However, gate loads can no longer be modeled by purely capacitive loads for high performance CMOS due to the RC metal interconnect effects. This paper presents a methodology for interfacing empirical gate models to reduced order RC interconnect models in terms of a nonlinear iteration procedure. The delay and power are calculated with errors on the same order as those for the original empirical equations. Moreover, a linear equivalent gate model is generated which accurately captures the delays at the interconnect fan-out nodes.

title: Controlling the contents of microdroplets by exploiting the permeability of PDMS.
abstract: A microfluidic device capable of exploiting the permeability of small molecules through polydimethylsiloxane (PDMS) has been fabricated in order to control the contents of microdroplets stored in storage wells. We demonstrate that protein precipitation and crystallization can be triggered by delivery of ethanol from a reservoir channel, thus controlling the protein solubility in microdroplets. Likewise quorum sensing in bacteria was triggered by delivery of the auto-inducer N-(3-oxododecanoyl)-l-homoserine lactone (OdDHL) through the PDMS membrane of the device.

title: Kinetics of bacterial growth: relationship between population density and specific growth rate of continuous cultures.
abstract: Results from studies of continuous cultures of Aerobacter aerogenes growing in chemically denned media indicate that specific growth rate (R) is a function of population density (P) as well as the concentration of the limiting nutrient (S). From these observations, and those of others, the following model for bacterial growth is derived: mic-21-1-40-si1.gif where um and B are growth parameters that are constants under defined conditions. This model is believed to have general applicability and to account for bacterial growth in both batch and continuous cultures.

title: The Theory of Bacterial Constant Growth Apparatus
abstract: Recent work in bacterial genetics has emphasised the usefulness of apparatus whose purpose is to maintain a constant population of bacteria in a state of active growth. Several such devices have been described for example by Monod (1950), Novick and Szilard (1950), and Perret (1954). It seems worthwhile to give a short account of the underlying theory as a guide to the problems of design likely to be encountered with organisms of different growth characteristics; or under various conditions of culture. Mathematically the problem may be stated as follows:-Consider an organism growing freely in a limited, conistant volume of nutrient. After some period of growth factors come into play which depress the power of the organism, to divide and eventually stop it growing altogether. These factors may be of several different kinds: for example, exhaustion of nutrient, insufficiency of oxygen, or production of some toxic metabolite, the general effect however, is that the growth rate of the population at any time is a function of its size (n) so that

title: A physical end-to-end model for molecular communication in nanonetworks
abstract: Molecular communication is a promising paradigm for nanoscale networks. The end-to-end (including the channel) models developed for classical wireless communication networks need to undergo a profound revision so that they can be applied for nanonetworks. Consequently, there is a need to develop new end-to-end (including the channel) models which can give new insights into the design of these nanoscale networks. The objective of this paper is to introduce a new physical end-to-end (including the channel) model for molecular communication. The new model is investigated by means of three modules, i.e., the transmitter, the signal propagation and the receiver. Each module is related to a specific process involving particle exchanges, namely, particle emission, particle diffusion and particle reception. The particle emission process involves the increase or decrease of the particle concentration rate in the environment according to a modulating input signal. The particle diffusion provides the propagation of particles from the transmitter to the receiver by means of the physics laws underlying particle diffusion in the space. The particle reception process is identified by the sensing of the particle concentration value at the receiver location. Numerical results are provided for three modules, as well as for the overall end-to-end model, in terms of normalized gain and delay as functions of the input frequency and of the transmission range.

title: Closed-form expressions for interconnection delay, coupling, and crosstalk in VLSIs
abstract: A closed-form formula for a waveform of the RC interconnection line with practical boundary conditions is derived. Expressions are also derived for the voltage slope and transition time of the RC interconnection and for coupling capacitance and crosstalk voltage height, which can be used in VLSI designs. Using the expressions, the optimum linewidth that minimizes RC delay and the trend of RC delay in the scaled-down VLSIs are discussed.

title: Probabilistic transfer matrices in symbolic reliability analysis of logic circuits
abstract: We propose the probabilistic transfer matrix (PTM) framework to capture nondeterministic behavior in logic circuits. PTMs provide a concise description of both normal and faulty behavior, and are well-suited to reliability and error susceptibility calculations. A few simple composition rules based on connectivity can be used to recursively build larger PTMs (representing entire logic circuits) from smaller gate PTMs. PTMs for gates in series are combined using matrix multiplication, and PTMs for gates in parallel are combined using the tensor product operation. PTMs can accurately calculate joint output probabilities in the presence of reconvergent fanout and inseparable joint input distributions. To improve computational efficiency, we encode PTMs as algebraic decision diagrams (ADDs). We also develop equivalent ADD algorithms for newly defined matrix operations such as eliminate_variables and eliminate_redundant_variables, which aid in the numerical computation of circuit PTMs. We use PTMs to evaluate circuit reliability and derive polynomial approximations for circuit error probabilities in terms of gate error probabilities. PTMs can also analyze the effects of logic and electrical masking on error mitigation. We show that ignoring logic masking can overestimate errors by an order of magnitude. We incorporate electrical masking by computing error attenuation probabilities, based on analytical models, into an extended PTM framework for reliability computation. We further define a susceptibility measure to identify gates whose errors are not well masked. We show that hardening a few gates can significantly improve circuit reliability.

title: Information processing and signal integration in bacterial quorum sensing
abstract: Bacteria communicate using secreted chemical signaling molecules called autoinducers in a process known as quorum sensing. The quorum‐sensing network of the marine bacterium Vibrio harveyi uses three autoinducers, each known to encode distinct ecological information. Yet how cells integrate and interpret the information contained within these three autoinducer signals remains a mystery. Here, we develop a new framework for analyzing signal integration on the basis of information theory and use it to analyze quorum sensing in V. harveyi. We quantify how much the cells can learn about individual autoinducers and explain the experimentally observed input–output relation of the V. harveyi quorum‐sensing circuit. Our results suggest that the need to limit interference between input signals places strong constraints on the architecture of bacterial signal‐integration networks, and that bacteria probably have evolved active strategies for minimizing this interference. Here, we analyze two such strategies: manipulation of autoinducer production and feedback on receptor number ratios.

title: Parity-Check Coding Based on Genetic Circuits for Engineered Molecular Communication Between Biological Cells
abstract: Synthetic biology, through genetic circuit engineering in biological cells, is paving the way toward the realization of programmable man-made living devices, able to naturally operate within normally less accessible domains, i.e., the biological and the nanoscale. The control of the information processing and exchange between these engineered-cell devices, based on molecules and biochemical reactions, i.e., molecular communication (MC), will be enabling technologies for the emerging paradigm of the Internet of Bio-Nano Things, with applications ranging from tissue engineering to bioremediation. In this paper, the design of genetic circuits to enable MC links between engineered cells is proposed by stemming from techniques for information coding and inspired by recent studies favoring the efficiency of analog computation over digital in biological cells. In particular, the design of a joint encoder-modulator for the transmission of binary-modulated molecule concentration is coupled with a decoder that computes the a-posteriori log-likelihood ratio of the information bits from the propagated concentration. These functionalities are implemented entirely in the biochemical domain through activation and repression of genes, and biochemical reactions, rather than classical electrical circuits. Biochemical simulations are used to evaluate the proposed design against a theoretical encoder/decoder implementation taking into account impairments introduced by diffusion noise.

title: Maximum Likelihood Detection With Ligand Receptors for Diffusion-Based Molecular Communications in Internet of Bio-Nano Things
abstract: Molecular Communication (MC) is a bio-inspired communication technique that uses molecules as a method of information transfer among nanoscale devices. MC receiver is an essential component having profound impact on the communication system performance. However, the interaction of the receiver with information bearing molecules has been usually oversimplified in modeling the reception process and developing signal detection techniques. In this paper, we focus on the signal detection problem of MC receivers employing receptor molecules to infer the transmitted messages encoded into the concentration of molecules, i.e., ligands. Exploiting the observable characteristics of ligand-receptor binding reaction, we first introduce a Maximum Likelihood (ML) detection method based on instantaneous receptor occupation ratio, as aligned with the current MC literature. Then, we propose a novel ML detection technique, which exploits the amount of time the receptors stay unbound in an observation time window. A comprehensive analysis is carried out to compare the performance of the detectors in terms of bit error probability. In evaluating the detection performance, emphasis is given to the receptor saturation problem resulting from the accumulation of messenger molecules at the receiver as a consequence of intersymbol interference. The results reveal that detection based on receptor unbound time is quite reliable even in saturation, whereas the reliability of detection based on receptor occupation ratio substantially decreases as the receiver gets saturated. Finally, we also discuss the potential methods of implementing the detectors.

title: Noise Analysis in Ligand-Binding Reception for Molecular Communication in Nanonetworks
abstract: Molecular communication (MC) will enable the exchange of information among nanoscale devices. In this novel bio-inspired communication paradigm, molecules are employed to encode, transmit and receive information. In the most general case, these molecules are propagated in the medium by means of free diffusion. An information theoretical analysis of diffusion-based MC is required to better understand the potential of this novel communication mechanism. The study and the modeling of the noise sources is of utmost importance for this analysis. The objective of this paper is to provide a mathematical study of the noise at the reception of the molecular information in a diffusion-based MC system when the ligand-binding reception is employed. The reference diffusion-based MC system for this analysis is the physical end-to-end model introduced in a previous work by the same authors, where the reception process is realized through ligand-binding chemical receptors. The reception noise is modeled in this paper by following two different approaches, namely, through the ligand-receptor kinetics and through the stochastic chemical kinetics. The ligand-receptor kinetics allows to simulate the random perturbations in the chemical processes of the reception, while the stochastic chemical kinetics provides the tools to derive a closed-form solution to the modeling of the reception noise. The ligand-receptor kinetics model is expressed through a block scheme, while the stochastic chemical kinetics results in the characterization of the reception noise using stochastic differential equations. Numerical results are provided to demonstrate that the analytical formulation of the reception noise in terms of stochastic chemical kinetics is compliant with the reception noise behavior resulting from the ligand-receptor kinetics simulations.

title: Amplifying Genetic Logic Gates
abstract: Biological Transistor A transistor is a device that amplifies and switches electronic signals. Bonnet et al. (p. 599,  see the Perspective by Benenson) engineered a genetic circuit to behave like a transistor in individual living cells. Instead of regulating messenger RNA levels, which has been used previously in designing such systems, the approach relied on changing the state of double-stranded DNA. Six basic logic gates were designed and constructed that were based on the activity of two serine recombinases. A genetic circuit architecture resembling a transistor can be engineered into individual live cells.  Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulates transcription rates. We realized permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic-gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.

title: Analysis of noise in quorum sensing.
abstract: Noise may play a pivotal role in gene circuit functionality, as demonstrated for the genetic switch in the bacterial phage lambda. Like the lambda switch, bacterial quorum sensing (QS) systems operate within a population and contain a bistable switching element, making it likely that noise plays a functional role in QS circuit operation. Therefore, a detailed analysis of the noise behavior of QS systems is needed. We have developed a set of tools generally applicable to the analysis of gene circuits, with an emphasis on investigations in the frequency domain (FD), that we apply here to the QS system in the marine bacterium Vibrio fischeri. We demonstrate that a tight coupling between exact stochastic simulation and FD analysis provides insights into the structure/function relationships in the QS circuit. Furthermore, we argue that a noise analysis is incomplete without consideration of the power spectral densities (PSDs) of the important molecular output signals. As an example we consider reversible reactions in the QS circuit, and show through analysis and exact stochastic simulation that these circuits make significant and dynamic modifications to the noise spectra. In particular, we demonstrate a "whitening" effect, which occurs as the noise is processed through these reversible reactions.

title: Frequency domain analysis of noise in autoregulated gene circuits
abstract: We describe a frequency domain technique for the analysis of intrinsic noise within negatively autoregulated gene circuits. This approach is based on the transfer function around the feedback loop (loop transmission) and the equivalent noise bandwidth of the system. The loop transmission, T, is shown to be a determining factor of the dynamics and the noise behavior of autoregulated gene circuits, and this T-based technique provides a simple and flexible method for the analysis of noise arising from any source within the gene circuit. We show that negative feedback not only reduces the variance of the noise in the protein concentration, but also shifts this noise to higher frequencies where it may have a negligible effect on the noise behavior of following gene circuits within a cascade. This predicted effect is demonstrated through the exact stochastic simulation of a two-gene cascade. The analysis elucidates important aspects of gene circuit structure that control functionality, and may provide some insights into selective pressures leading to this structure. The resulting analytical relationships have a simple form, making them especially useful as synthetic gene circuit design equations. With the exception of the linearization of Hill kinetics, this technique is general and may be applied to the analysis or design of networks of higher complexity. This utility is demonstrated through the exact stochastic simulation of an autoregulated two-gene cascade operating near instability.

title: N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks
abstract: Diffusion-based molecular communication is a promising bio-inspired paradigm to implement nanonetworks, i.e., the interconnection of nanomachines. The peculiarities of the physical channel in diffusion-based molecular communication require the development of novel models, architectures and protocols for this new scenario, which need to be validated by simulation. N3Sim is a simulation framework for nanonetworks with transmitter, receiver, and harvester nodes using Diffusion-based Molecular Communication (DMC). In DMC, transmitters encode the information by releasing molecules into the medium, thus varying their local concentration. N3Sim models the movement of these molecules according to Brownian dynamics, and it also takes into account their inertia and the interactions among them. Harvesters collect molecules from the environment to reuse them for later transmissions. Receivers decode the information by sensing the particle concentration in their neighborhood. The benefits of N3Sim are multiple: the validation of channel models for DMC and the evaluation of novel modulation schemes are just a few examples.

title: Advanced Data Mining Techniques
abstract: This book covers the fundamental concepts of data mining, to demonstrate the potential of gathering large sets of data, and analyzing these data sets to gain useful business understanding. The book is organized in three parts. Part I introduces concepts. Part II describes and demonstrates basic data mining algorithms. It also contains chapters on a number of different techniques often used in data mining. Part III focusses on business applications of data mining.Methods are presented with simple examples, applications are reviewed, and relativ advantages are evaluated.

title: Intrinsic noise in gene regulatory networks
abstract: Cells are intrinsically noisy biochemical reactors: low reactant numbers can lead to significant statistical fluctuations in molecule numbers and reaction rates. Here we use an analytic model to investigate the emergent noise properties of genetic systems. We find for a single gene that noise is essentially determined at the translational level, and that the mean and variance of protein concentration can be independently controlled. The noise strength immediately following single gene induction is almost twice the final steady-state value. We find that fluctuations in the concentrations of a regulatory protein can propagate through a genetic cascade; translational noise control could explain the inefficient translation rates observed for genes encoding such regulatory proteins. For an autoregulatory protein, we demonstrate that negative feedback efficiently decreases system noise. The model can be used to predict the noise characteristics of networks of arbitrary connectivity. The general procedure is further illustrated for an autocatalytic protein and a bistable genetic switch. The analysis of intrinsic noise reveals biological roles of gene network structures and can lead to a deeper understanding of their evolutionary origin.