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At least 19 recordsLinked to original sources
arXiv2025

Event-Based Simulation of Stochastic Memristive Devices for Neuromorphic Computing

In this paper, we build a general modelling framework for memristors, suitable for the simulation of event-based systems such as hardware spiking neural networks, and more generally, neuromorphic computing systems composed of three independent components: i) an event-based modelling approach, extending and generalising an existing general model of memristors - the Generalised Metastable Switch Model (GMSM) - eliminating errors associated with discrete time approximation, as well as offering potential improvements in terms of suitability for neuromorphic memristive system simulations; ii) a volatility state variable to allow for the unified understanding of disparate non-linear and volatile phenomena, including state relaxation, structural disruption, Joule heating, and non-linear drift in different memristive devices; and iii) a readout equation that separates the latent state variable evolution from explicit variables of interest such as an instantaneous resistance. We exhibit an illustrative implementation of this framework, fit to a resistive drift dataset for titanium dioxide memristors, based on a proposed linear conductance model for resistive drift in the devices. Finally, we highlight the application of the model to neuromorphic computing, through demonstrating the contribution of the volatility state variable to switching dynamics, resulting in frequency-dependent switching (for stable memristors acting as programmable synaptic weights) and the generation of action potentials (for unstable memristors, acting as spike-generators).

cs.ET↗
arXiv2007

Checking Equivalence of Quantum Circuits and States

Quantum computing promises exponential speed-ups for important simulation and optimization problems. It also poses new CAD problems that are similar to, but more challenging, than the related problems in classical (non-quantum) CAD, such as determining if two states or circuits are functionally equivalent. While differences in classical states are easy to detect, quantum states, which are represented by complex-valued vectors, exhibit subtle differences leading to several notions of equivalence. This provides flexibility in optimizing quantum circuits, but leads to difficult new equivalence-checking issues for simulation and synthesis. We identify several different equivalence-checking problems and present algorithms for practical benchmarks, including quantum communication and search circuits, which are shown to be very fast and robust for hundreds of qubits.

quant-ph↗
arXiv2008

On the CNOT-cost of TOFFOLI gates

The three-input TOFFOLI gate is the workhorse of circuit synthesis for classical logic operations on quantum data, e.g., reversible arithmetic circuits. In physical implementations, however, TOFFOLI gates are decomposed into six CNOT gates and several one-qubit gates. Though this decomposition has been known for at least 10 years, we provide here the first demonstration of its CNOT-optimality. We study three-qubit circuits which contain less than six CNOT gates and implement a block-diagonal operator, then show that they implicitly describe the cosine-sine decomposition of a related operator. Leveraging the canonicity of such decompositions to limit one-qubit gates appearing in respective circuits, we prove that the n-qubit analogue of the TOFFOLI requires at least 2n CNOT gates. Additionally, our results offer a complete classification of three-qubit diagonal operators by their CNOT-cost, which holds even if ancilla qubits are available.

quant-ph↗
arXiv2009

Steering plasmodium with light: Dynamical programming of Physarum machine

A plasmodium of Physarum polycephalum is a very large cell visible by unaided eye. The plasmodium is capable for distributed sensing, parallel information processing, and decentralized optimization. It is an ideal substrate for future and emerging bio-computing devices. We study space-time dynamics of plasmodium reactiom to localised illumination, and provide analogies between propagating plasmodium and travelling wave-fragments in excitable media. We show how plasmodium-based computing devices can be precisely controlled and shaped by planar domains of illumination.

nlin.PS↗
arXiv2013

Fast Equivalence-checking for Quantum Circuits

We perform formal verification of quantum circuits by integrating several techniques specialized to particular classes of circuits. Our verification methodology is based on the new notion of a reversible miter that allows one to leverage existing techniques for circuit simplification of quantum circuits. For reversible circuits which arise as runtime bottlenecks of key quantum algorithms, we develop several verification techniques and empirically compare them. We also combine existing quantum verification tools with the use of SAT-solvers. Experiments with circuits for Shor's number-factoring algorithm, containing thousands of gates, show improvements in efficiency by 3-4 orders of magnitude.

quant-ph↗
arXiv2013

High-performance Energy Minimization with Applications to Adiabatic Quantum Computing

Energy minimization of Ising spin-glasses has played a central role in statistical and solid-state physics, facilitating studies of phase transitions and magnetism. Recent proposals suggest using Ising spin-glasses for non-traditional computing as a way to harness the nature's ability to find min-energy configurations, and to take advantage of quantum tunneling to boost combinatorial optimization. Laboratory demonstrations have been unconvincing so far and lack a non-quantum baseline for definitive comparisons. In this work we (i) design and evaluate new computational techniques to simulate natural energy minimization in spin glasses and (ii) explore their application to study design alternatives in quantum adiabatic computers. Unlike previous work, our algorithms are not limited to planar Ising topologies. In one CPU-day, our branch-and-bound algorithm finds ground states on 100 spins, while our local search approximates ground states on 1, 000, 000 spins. We use this computational tool as a simulator to study the significance of hyper-couplings in the context of recently implemented adiabatic quantum computers.

quant-ph↗
arXiv2010

Rule-Based Optimization of Reversible Circuits

Reversible logic has applications in various research areas including low-power design and quantum computation. In this paper, a rule-based optimization approach for reversible circuits is proposed which uses both negative and positive control Toffoli gates during the optimization. To this end, a set of rules for removing NOT gates and optimizing sub-circuits with common-target gates are proposed. To evaluate the proposed approach, the best-reported synthesized circuits and the results of a recent synthesis algorithm which uses both negative and positive controls are used. Our experiments reveal the potential of the proposed approach in optimizing synthesized circuits.

quant-ph↗
arXiv2011

How to build a DNA search engine like Google?

This paper proposed a new method to build the large scale DNA sequences search system based on web search engine technology. We give a very brief introduction for the methods used in search engine first. Then how to build a DNA search system like Google is illustrated in detail. Since there is no local alignment process, this system is able to provide the ms level search services for billions of DNA sequences in a typical server.

q-bio.GN↗
arXiv2010

Block-based quantum-logic synthesis

In this paper, the problem of constructing an efficient quantum circuit for the implementation of an arbitrary quantum computation is addressed. To this end, a basic block based on the cosine-sine decomposition method is suggested which contains $l$ qubits. In addition, a previously proposed quantum-logic synthesis method based on quantum Shannon decomposition is recursively applied to reach unitary gates over $l$ qubits. Then, the basic block is used and some optimizations are applied to remove redundant gates. It is shown that the exact value of $l$ affects the number of one-qubit and CNOT gates in the proposed method. In comparison to the previous synthesis methods, the value of $l$ is examined consequently to improve either the number of CNOT gates or the total number of gates. The proposed approach is further analyzed by considering the nearest neighbor limitation. According to our evaluation, the number of CNOT gates is increased by at most a factor of $\frac{5}{3}$ if the nearest neighbor interaction is applied.

quant-ph↗
arXiv2011

Artificial Immune Privileged Sites as an Enhancement to Immuno-Computing Paradigm

The immune system is a highly parallel and distributed intelligent system which has learning, memory, and associative capabilities. Artificial Immune System is an evolutionary paradigm inspired by the biological aspects of the immune system of mammals. The immune system can inspire to form new algorithms learning from its course of action. The human immune system has motivated scientists and engineers for finding powerful information processing algorithms that has solved complex engineering problems. This work is the result of an attempt to explore a different perspective of the immune system namely the Immune Privileged Site (IPS) which has the ability to make an exception to different parts of the body by not triggering immune response to some of the foreign agent in these parts of the body. While the complete system is secured by an Immune System at certain times it may be required that the system allows certain activities which may be harmful to other system which is useful to it and learns over a period of time through the immune privilege model as done in case of Immune Privilege Sites in Natural Immune System.

cs.CR↗
arXiv2012

Hybrid CMOS-MQCA Logic Architectures using Multi-Layer Spintronic Devices

We present a novel hybrid CMOS-MQCA architecture using multi-layer Spintronic devices as computing elements. A feasibility study is presented with 22nm CMOS where new approaches for spin transfer torque induced clocking and read-out scheme for variability-tolerance are introduced. A first-of-its-kind Spintronic device model enables circuit simulation using existing CAD infrastructure. Approximately 70% reduction in energy consumption is observed when compared against conventional field-induced clocking scheme.

cs.ET↗
arXiv2011

ReveR: Software Simulator of Reversible Processor with Stack

A software model of a reversible processor ReveR with the stack is discussed in this paper. An architecture, the minimal set of elementary reversible operations together with an implementation of the basic control flow structures and procedures calls using simple assembler language are described.

cs.ET↗
arXiv2011

Simulating Spiking Neural P systems without delays using GPUs

We present in this paper our work regarding simulating a type of P system known as a spiking neural P system (SNP system) using graphics processing units (GPUs). GPUs, because of their architectural optimization for parallel computations, are well-suited for highly parallelizable problems. Due to the advent of general purpose GPU computing in recent years, GPUs are not limited to graphics and video processing alone, but include computationally intensive scientific and mathematical applications as well. Moreover P systems, including SNP systems, are inherently and maximally parallel computing models whose inspirations are taken from the functioning and dynamics of a living cell. In particular, SNP systems try to give a modest but formal representation of a special type of cell known as the neuron and their interactions with one another. The nature of SNP systems allowed their representation as matrices, which is a crucial step in simulating them on highly parallel devices such as GPUs. The highly parallel nature of SNP systems necessitate the use of hardware intended for parallel computations. The simulation algorithms, design considerations, and implementation are presented. Finally, simulation results, observations, and analyses using an SNP system that generates all numbers in $\mathbb N$ - {1} are discussed, as well as recommendations for future work.

cs.DC↗
arXiv2011

Self-Assembly with Geometric Tiles

In this work we propose a generalization of Winfree's abstract Tile Assembly Model (aTAM) in which tile types are assigned rigid shapes, or geometries, along each tile face. We examine the number of distinct tile types needed to assemble shapes within this model, the temperature required for efficient assembly, and the problem of designing compact geometric faces to meet given compatibility specifications. Our results show a dramatic decrease in the number of tile types needed to assemble $n \times n$ squares to $Θ(\sqrt{\log n})$ at temperature 1 for the most simple model which meets a lower bound from Kolmogorov complexity, and $O(\log\log n)$ in a model in which tile aggregates must move together through obstacle free paths within the plane. This stands in contrast to the $Θ(\log n / \log\log n)$ tile types at temperature 2 needed in the basic aTAM. We also provide a general method for simulating a large and computationally universal class of temperature 2 aTAM systems with geometric tiles at temperature 1. Finally, we consider the problem of computing a set of compact geometric faces for a tile system to implement a given set of compatibility specifications. We show a number of bounds on the complexity of geometry size needed for various classes of compatibility specifications, many of which we directly apply to our tile assembly results to achieve non-trivial reductions in geometry size.

cs.CG↗
arXiv2012

Efficient Squares and Turing Universality at Temperature 1 with a Unique Negative Glue

Is Winfree's abstract Tile Assembly Model (aTAM) "powerful?" Well, if certain tiles are required to "cooperate" in order to be able to bind to a growing tile assembly (a.k.a., temperature 2 self-assembly), then Turing universal computation and the efficient self-assembly of $N \times N$ squares is achievable in the aTAM (Rotemund and Winfree, STOC 2000). So yes, in a computational sense, the aTAM is quite powerful! However, if one completely removes this cooperativity condition (a.k.a., temperature 1 self-assembly), then the computational "power" of the aTAM (i.e., its ability to support Turing universal computation and the efficient self-assembly of $N \times N$ squares) becomes unknown. On the plus side, the aTAM, at temperature 1, isn't only Turing universal but also supports the efficient self-assembly $N \times N$ squares if self-assembly is allowed to utilize three spatial dimensions (Fu, Schweller and Cook, SODA 2011). We investigate the theoretical "power" of a seemingly simple, restrictive class of tile assembly systems (TASs) in which (1) the absolute value of every glue strength is 1, (2) there's a single negative strength glue type and (3) unequal glues can't interact. We call these the \emph{restricted glue} TASs (rgTAS). We first show the tile complexity of producing an $N \times N$ square with an rgTAS is $O(\frac{\log n}{\log \log n})$. We also prove that rgTASs are Turing universal with a construction that simulates an arbitrary Turing machine. Next, we provide results for a variation of the rgTAS class, partially restricted glue TASs, which is similar except that the magnitude of the negative glue's strength can only assumed to be $\ge 1$. These results consist of a construction with $O(\log n)$ tile complexity for building $N \times N$ squares, and one which simulates a Turing machine but with a greater scaling factor than for the rgTAS construction.

cs.ET↗
arXiv2011

DNA Circuits Based on Isothermal Constrained Loop Extension DNA Amplification

In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a new variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement amplification (SDA). Then, we formalize this process in terms of the theory of formal languages and show, on the basis of this formulation, how to manage OR and AND gates. We then explain how to introduce negation, which allows us to prove that, in principle, it is possible to implement the computation of any boolean function on DNA strands using ICLEDA.

cs.ET↗
arXiv2011

Trans-Canada Slimeways: Slime mould imitates the Canadian transport network

Slime mould Physarum polycephalum builds up sophisticated networks to transport nutrients between distant part of its extended body. The slime mould's protoplasmic network is optimised for maximum coverage of nutrients yet minimum energy spent on transportation of the intra-cellular material. In laboratory experiments with P. polycephalum we represent Canadian major urban areas with rolled oats and inoculated slime mould in the Toronto area. The plasmodium spans the urban areas with its network of protoplasmic tubes. We uncover similarities and differences between the protoplasmic network and the Canadian national highway network, analyse the networks in terms of proximity graphs and evaluate slime mould's network response to contamination.

nlin.PS↗