Programmability of Chemical Reaction Networks

Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri Nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior

A Survey on Continuous Time Computations

We provide an overview of theories of continuous time computation. These theories allow us to understand both the hardness of questions related to continuous time dynamical systems and the computational power of continuous time analog models. We survey the existing models, summarizing results, and point to relevant references in the literature

Applying Formal Methods to Networking: Theory, Techniques and Applications

Despite its great importance, modern network infrastructure is remarkable for the lack of rigor in its engineering. The Internet which began as a research experiment was never designed to handle the users and applications it hosts today. The lack of formalization of the Internet architecture meant limited abstractions and modularity, especially for the control and management planes, thus requiring for every new need a new protocol built from scratch. This led to an unwieldy ossified Internet architecture resistant to any attempts at formal verification, and an Internet culture where expediency and pragmatism are favored over formal correctness. Fortunately, recent work in the space of clean slate Internet design---especially, the software defined networking (SDN) paradigm---offers the Internet community another chance to develop the right kind of architecture and abstractions. This has also led to a great resurgence in interest of applying formal methods to specification, verification, and synthesis of networking protocols and applications. In this paper, we present a self-contained tutorial of the formidable amount of work that has been done in formal methods, and present a survey of its applications to networking.Comment: 30 pages, submitted to IEEE Communications Surveys and Tutorial

Assessing and augmenting SCADA cyber security: a survey of techniques

SCADA systems monitor and control critical infrastructures of national importance such as power generation and distribution, water supply, transportation networks, and manufacturing facilities. The pervasiveness, miniaturisations and declining costs of internet connectivity have transformed these systems from strictly isolated to highly interconnected networks. The connectivity provides immense benefits such as reliability, scalability and remote connectivity, but at the same time exposes an otherwise isolated and secure system, to global cyber security threats. This inevitable transformation to highly connected systems thus necessitates effective security safeguards to be in place as any compromise or downtime of SCADA systems can have severe economic, safety and security ramifications. One way to ensure vital asset protection is to adopt a viewpoint similar to an attacker to determine weaknesses and loopholes in defences. Such mind sets help to identify and fix potential breaches before their exploitation. This paper surveys tools and techniques to uncover SCADA system vulnerabilities. A comprehensive review of the selected approaches is provided along with their applicability

Elementary gates for quantum computation

We show that a set of gates that consists of all one-bit quantum gates (U(2)) and the two-bit exclusive-or gate (that maps Boolean values $(x,y)$ to $(x,x \oplus y)$) is universal in the sense that all unitary operations on arbitrarily many bits $n$ (U($2^n$)) can be expressed as compositions of these gates. We investigate the number of the above gates required to implement other gates, such as generalized Deutsch-Toffoli gates, that apply a specific U(2) transformation to one input bit if and only if the logical AND of all remaining input bits is satisfied. These gates play a central role in many proposed constructions of quantum computational networks. We derive upper and lower bounds on the exact number of elementary gates required to build up a variety of two-and three-bit quantum gates, the asymptotic number required for $n$-bit Deutsch-Toffoli gates, and make some observations about the number required for arbitrary $n$-bit unitary operations.Comment: 31 pages, plain latex, no separate figures, submitted to Phys. Rev. A. Related information on http://vesta.physics.ucla.edu:7777