Related papers: Molecular Model Checking a Temporal Logic

We propose a modular method for proving termination of general logic programs (i.e., logic programs with negation). It is based on the notion of acceptable programs, but it allows us to prove termination in a truly modular way. We consider…

Particle-style token machines are a way to interpret proofs and programs, when the latter are defined according to the principles of linear logic. In this paper, we show that token machines also make sense when the programs at hand are…

Quantified CTL (QCTL) extends the temporal logic CTL with quantifications over atomic propositions. This extension is known to be very expressive: QCTL allows us to express complex properties over Kripke structures (it is as expressive as…

Theory evaluation is a key problem in many areas: machine learning, scientific discovery, inverse engineering, decision making, software engineering, design, human sciences, etc. If we have a set of theories that are able to explain the…

Recently, large language models (LLMs) have shown significant progress, approaching human perception levels. In this work, we demonstrate that despite these advances, LLMs still struggle to reason using molecular structural information.…

This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…

This paper revisits the classical notion of sampling in the setting of real-time temporal logics for the modeling and analysis of systems. The relationship between the satisfiability of Metric Temporal Logic (MTL) formulas over…

Parse trees are fundamental syntactic structures in both computational linguistics and compilers construction. We argue in this paper that, in both fields, there are good incentives for model-checking sets of parse trees for some word…

Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…

Quantum computers promise to efficiently solve not only problems believed to be intractable for classical computers, but also problems for which verifying the solution is also considered intractable. This raises the question of how one can…

Model checking is a powerful technique for software verification. However, the approach notably suffers from the infamous state space explosion problem. To tackle this, in this paper, we introduce a novel symbolic method for encoding Petri…

We introduce a method of verifying termination of logic programs with respect to concrete queries (instead of abstract query patterns). A necessary and sufficient condition is established and an algorithm for automatic verification is…

The termination problem of a logic program can be addressed in either a static or a dynamic way. A static approach performs termination analysis at compile time, while a dynamic approach characterizes and tests termination of a logic…

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one…

Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…

Quantum logic (QL) is a non-classical logic for analyzing the propositions of quantum physics. Modal logic MB, which is a logic that handles the value of the inner product that appears in quantum mechanics, was constructed with the…

We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic…

We propose a model-based approach to the model checking problem for recursive schemes. Since simply typed lambda calculus with the fixpoint operator, lambda-Y-calculus, is equivalent to schemes, we propose the use of a model of…

In this paper we consider the problem of certified static checking of module-like constructs of programming languages. We argue that there are algorithms and properties related to modules that can be defined and proven in an abstract way.…

We propose a formal proof of the undecidability of the model checking problem for alternating- time temporal logic under imperfect information and perfect recall semantics. This problem was announced to be undecidable according to a…