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

Computer Aided Verification

The open access two-volume set LNCS 12224 and 12225 constitutes the refereed proceedings of the 32st International Conference on Computer Aided Verification, CAV 2020, held in Los Angeles, CA, USA, in July 2020.* The 43 full papers presented together with 18 tool papers and 4 case studies, were carefully reviewed and selected from 240 submissions. The papers were organized in the following topical sections: Part I: AI verification; blockchain and Security; Concurrency; hardware verification and decision procedures; and hybrid and dynamic systems. Part II: model checking; software verification; stochastic systems; and synthesis. *The conference was held virtually due to the COVID-19 pandemic

On Affine Reachability Problems

We analyze affine reachability problems in dimensions 1 and 2. We show that the reachability problem for 1-register machines over the integers with affine updates is PSPACE-hard, hence PSPACE-complete, strengthening a result by Finkel et al. that required polynomial updates. Building on recent results on two-dimensional integer matrices, we prove NP-completeness of the mortality problem for 2-dimensional integer matrices with determinants +1 and 0. Motivated by tight connections with 1-dimensional affine reachability problems without control states, we also study the complexity of a number of reachability problems in finitely generated semigroups of 2-dimensional upper-triangular integer matrices

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications

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

Timing properties in real-time systems

This dissertation proposes a formalism for the specification and verification of timing properties of real-time systems. Reasoning about properties of a real-time system requires one to consider both relative and absolute timing of events. Relative timing concerns the order in which events occur, such as mutual exclusion and precedence constraint properties. Absolute timing concerns the stringent timing restrictions imposed on a system, such as a response time deadline or a minimum elapsed time between occurrences of two events. The approach is based on Real Time Logic (RTL), a logic invented primarily for the specification of both relative and absolute timing of events. The notion of an event occurrence is central to RTL; an event occurrence marks a point in time which is of significance to the behavior of a system. Hence, concurrency is modeled as a partial ordering of the event occurrences in the system. A system specification and a property to be verified can be expressed as arithmetical relations on algebraic expressions involving the event occurrences. To verify the property with respect to the system specification, we prove that the property is a theorem derivable from the specification. Relationship of RTL to Presburger Arithmetic is discussed and a verification technique based on inequality provers is explored. The dissertation also introduces a specification language, Modechart, for real-time systems. The semantics of Modechart is described in terms of RTL formulas. In Modechart, we make use of the concept of modes which can be thought of as partitioning the state space of a system. Intuitively, modes can be viewed as control information that impose structure on the operation of a system. Modes are arranged hierarchically. Furthermore, modes at the same level of hierarchy can be related in one of two ways: in series or in parallel. A transition can be specified between two modes in series, but no transition is allowed between modes in parallel. The language allows sporadic/periodic actions in modes as well as constructs for specifying timing constraints such as delays and deadlines on mode transitions. Verification procedures are introduced for showing a Modechart specification satisfies a property expressed as an RTL formula.Computer Science

Tools and Algorithms for the Construction and Analysis of Systems

This open access two-volume set constitutes the proceedings of the 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, which was held during March 27 – April 1, 2021, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg and changed to an online format due to the COVID-19 pandemic. The total of 41 full papers presented in the proceedings was carefully reviewed and selected from 141 submissions. The volume also contains 7 tool papers; 6 Tool Demo papers, 9 SV-Comp Competition Papers. The papers are organized in topical sections as follows: Part I: Game Theory; SMT Verification; Probabilities; Timed Systems; Neural Networks; Analysis of Network Communication. Part II: Verification Techniques (not SMT); Case Studies; Proof Generation/Validation; Tool Papers; Tool Demo Papers; SV-Comp Tool Competition Papers