Computer Science

Although many exciting applications of molecular communication (MC) systems are envisioned to be at microscale, the MC testbeds reported so far are mostly at macroscale. To link the macroworld to the microworld, we propose and demonstrate a biological signal conversion interface that can also be seen as a microscale modulator. In particular, the proposed interface transduces an optical signal, which is controlled using an LED, into a chemical signal by changing the pH of the environment. The modulator is realized using E. coli bacteria as microscale entity expressing the light-driven proton pump gloeorhodopsin from Gloeobacter violaceus. Upon inducing external light stimuli, these bacteria locally change their surrounding pH level by exporting protons into the environment. To verify the effectiveness of the proposed optical-to-chemical signal converter, we analyze the pH signal measured by a pH sensor, which serves as receiver. We develop an analytical parametric model for the induced chemical signal as a function of the applied optical signal. Using this model, we derive a training-based channel estimator which estimates the parameters of the proposed model to fit the measurement data. We further derive the optimal maximum likelihood detector and a suboptimal low-complexity detector to recover the transmitted data from the measured received signal. It is shown that the proposed parametric model is in good agreement with the measurement data. Moreover, for an example scenario, we show that the proposed setup is able to successfully convert an optical signal representing a sequence of binary symbols into a chemical signal with a bit rate of 1 bit/minute and recover the transmitted data from the chemical signal using the proposed estimation and detection~schemes. The proposed modulator may form the basis for future MC testbeds and applications at microscale.

Neuromorphic networks of artificial neurons and synapses can solve computational hard problems with energy efficiencies unattainable for von Neumann architectures. For image processing, silicon neuromorphic processors outperform graphic processing units (GPUs) in energy efficiency by a large margin, but they deliver much lower chip-scale throughput. The performance-efficiency dilemma for silicon processors may not be overcome by Moore's law scaling of complementary metal-oxide-semiconductor (CMOS) field-effect transistors. Scalable and biomimetic active memristor neurons and passive memristor synapses form a self-sufficient basis for a transistorless neural network. However, previous demonstrations of memristor neurons only showed simple integrate-and-fire (I&F) behaviors and did not reveal the rich dynamics and computational complexity of biological neurons. Here we show that neurons built with nanoscale vanadium dioxide active memristors possess all three classes of excitability and most of the known biological neuronal dynamics, and are intrinsically stochastic. With the favorable size and power scaling, there is a path toward an all-memristor neuromorphic cortical computer.

Quantum computing is greatly advanced in recent years and is expected to transform the computation paradigm in the near future. Quantum circuit simulation plays a key role in the toolchain for the development of quantum hardware and software systems. However, due to the enormous Hilbert space of quantum states, simulating quantum circuits with classical computers is extremely challenging despite notable efforts have been made. In this paper, we enhance quantum circuit simulation in two dimensions: accuracy and scalability. The former is achieved by using an algebraic representation of complex numbers; the latter is achieved by bit-slicing the number representation and replacing matrix-vector multiplication with symbolic Boolean function manipulation. Experimental results demonstrate that our method can be superior to the state-of-the-art for various quantum circuits and can simulate certain benchmark families with up to tens of thousands of qubits.

Biologically inspired recurrent neural networks, such as reservoir computers are of interest in designing spatio-temporal data processors from a hardware point of view due to the simple learning scheme and deep connections to Kalman filters. In this work we discuss using in-depth simulation studies a way to construct hardware reservoir computers using an analog stochastic neuron cell built from a low energy-barrier magnet based magnetic tunnel junction and a few transistors. This allows us to implement a physical embodiment of the mathematical model of reservoir computers. Compact implementation of reservoir computers using such devices may enable building compact, energy-efficient signal processors for standalone or in-situ machine cognition in edge devices.

Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representations that are faithful, efficient, and practical remains challenging. This paper introduces CRN++, a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler translating CRN++ programs into chemical reactions, thereby laying the foundation of a comprehensive framework for molecular programming. Our language addresses the key challenge of embedding familiar imperative constructs into a set of chemical reactions happening simultaneously and manipulating real-valued concentrations. Although some deviation from ideal output value cannot be avoided, we develop methods to minimize the error, and implement error analysis tools. We demonstrate the feasibility of using CRN++ on a suite of well-known algorithms for discrete and real-valued computation. CRN++ can be easily extended to support new commands or chemical reaction implementations, and thus provides a foundation for developing more robust and practical molecular programs.

Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical reaction networks (CRNs) which formalizes coupled chemical reactions in a well-mixed solution. CRNs are pivotal for our understanding of biological regulatory and metabolic networks, as well as for programming engineered molecular behavior. Although it is clear that small CRNs are capable of complex dynamics and computational behavior, it remains difficult to explore the space of CRNs in search for desired functionality. We use Alloy, a tool for expressing structural constraints and behavior in software systems, to enumerate CRNs with declaratively specified properties. We show how this framework can enumerate CRNs with a variety of structural constraints including biologically motivated catalytic networks and metabolic networks, and seesaw networks motivated by DNA nanotechnology. We also use the framework to explore analog function computation in rate-independent CRNs. By computing the desired output value with stoichiometry rather than with reaction rates (in the sense that X→Y+Y computes multiplication by 2 ), such CRNs are completely robust to the choice of reaction rates or rate law. We find the smallest CRNs computing the max, minmax, abs and ReLU (rectified linear unit) functions in a natural subclass of rate-independent CRNs where rate-independence follows from structural network properties.

In this position paper, we present a discussion on neuromorphic computing and especially the learning/training algorithm to design a series of brains with different memristive values to solve complex ill-posed inverse problems based on a Finite Element(FE) method. First, the neuromorphic computing is addressed and we focus on a type of memristive circuit computing that falls into the scope of neuromorphic computing. Secondly based on reference [1] in which the complex dynamics of the complex memristive circuit was studied, we design a method and an approach to train the memristive circuit so that the memristive values are optimally obtained.

The emerging field of living technologies aims to create new functional hybrid materials in which living systems interface with artificial ones. Combining research into living technologies with emerging developments in computing architecture has enabled the generation of organic electronics from plants and slime mould. Here, we expand on this work by studying capacitive properties of a substrate colonised by mycelium of grey oyster fungi, Pleurotus ostreatus. Capacitors play a fundamental role in traditional analogue and digital electronic systems and have a range of uses including sensing, energy storage and filter circuits. Mycelium has the potential to be used as an organic replacement for traditional capacitor technology. Here, were show that the capacitance of mycelium is in the order of hundreds of pico-Farads. We also demonstrate that the charge density of the mycelium `dielectric' decays rapidly with increasing distance from the source probes. This is important as it indicates that small cells of mycelium could be used as a charge carrier or storage medium, when employed as part of an array with reasonable density.

We implement a capacitorless model of a VO2 oscillator by introducing into the circuit of a field-effect transistor and a VO2 thermal sensor, which provide negative current feedback with a time delay. We compare the dynamics of current and voltage oscillations on a switch in a circuit with a capacitor and without a capacitor. The oscillation period in the capacitorless model is controlled in a narrow range by changing the distance between the switch and the sensor. The capacitorless model provides the possibility of significant miniaturization of the oscillator circuit, and it is important for the implementation of large arrays of oscillators in oscillatory neural networks to solve the problem of classification and pattern recognition.

Reservoir computing is a subfield of machine learning in which a complex system, or 'reservoir,' uses complex internal dynamics to non-linearly project an input into a higher-dimensional space. A single trainable output layer then inspects this high-dimensional space for features relevant to perform the given task, such as a classification. Initially, reservoirs were often constructed from recurrent neural networks, but reservoirs constructed from many different elements have been demonstrated. Elementary cellular automata (CA) are one such system which have recently been demonstrated as a powerful and efficient basis which can be used to construct a reservoir. To investigate the feasibility and performance of a monolithic reservoir computing circuit with a fully integrated, programmable read-out layer, we designed, fabricated, and tested a full-custom reservoir computing circuit. This design, the cellular memristive-output reservoir (CMOR), is implemented in 65-nm CMOS technology with integrated front-end-of-the-line (FEOL) resistive random-access memory (ReRAM) used to construct a trainable output layer. We detail the design of this system and present electrical test results verifying its operation and capability to carry out non-linear classifications.