Related papers: A Calculus of Looping Sequences with Local Rules
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect…
The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the…
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems.…
The lefthanded Lov\'asz local lemma (LLLL) is a generalization of the Lov\'asz local lemma (LLL), a powerful technique from the probabilistic method. We prove a computable version of the LLLL and use it to effectivize a collection of…
One-dimensional cellular automata are discrete dynamical systems that operate on an infinite lattice of sites and are characterized by the locality and uniformity of their update rule. Permutations of the state set and isometric…
We study non-terminating graph rewriting models, whose local rules are applied non-deterministically -- and yet enjoy a strong form of determinism, namely space-time determinism. Of course in the case of terminating computation it is…
Existing formalisms for the algebraic specification and representation of networks of reversible agents suffer some shortcomings. Despite multiple attempts, reversible declensions of the Calculus of Communicating Systems (CCS) do not offer…
Background: Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cy-cles (TICs) causing unbounded metabolic flux ranges…
The characterisation of termination using well-founded monotone algebras has been a milestone on the way to automated termination techniques, of which we have seen an extensive development over the past years. Both the semantic…
Linear temporal logic (LTL) is a specification language for finite sequences (called traces) widely used in program verification, motion planning in robotics, process mining, and many other areas. We consider the problem of learning LTL…
Although random cell complexes occur throughout the physical sciences, there does not appear to be a standard way to quantify their statistical similarities and differences. The various proposals in the literature are usually motivated by…
A Cellular Automata (CA) rule is presented that can generate "loop patterns" in a 2D grid under fixed boundary conditions. A loop is a cyclically closed path represented by one-cells enclosed by zero-cells. A loop pattern can contain…
We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may…
A cell lists method based on doubly linked lists and with complexity O(N) is developed for particle deletion and insertion in reaction ensemble Monte Carlo simulation. Because the random move in Metropolis algorithm can be reduced to…
Constraint Handling Rules is an effective concurrent declarative programming language and a versatile computational logic formalism. CHR programs consist of guarded reactive rules that transform multisets of constraints. One of the main…
A small-world cellular automaton network has been formulated to simulate the long-range interactions of complex networks using unconventional computing methods in this paper. Conventional cellular automata use local updating rules. The new…
We define a bi-directional embedding between hypersequent calculi and a subclass of systems of rules (2-systems). In addition to showing that the two proof frameworks have the same expressive power, the embedding allows for the recovery of…
Diagram chasing is not an easy task. The coherence holds in a generalized sense if we have a mechanical method to judge whether given two morphisms are equal to each other. A simple way to this end is to reform a concerned category into a…
Windowed recurrences are sliding window calculations where a function is applied iteratively across the window of data, and are ubiquitous throughout the natural, social, and computational sciences. In this monograph we explore the…
Real-time coupled cluster (CC) methods have several advantages over their frequency-domain counterparts, namely, response and equation of motion CC theories. Broadband spectra, strong fields, and pulse manipulation allow for the simulation…