Related papers: A Process Calculus for Molecular Interaction Maps
Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always…
We present an algorithm turning any term of a linear quantum $\lambda$-calculus into a quantum circuit. The essential ingredient behind the proposed algorithm is Girard's geometry of interaction, which, differently from its well-known uses…
In exploring the simulation of human rhythmic perception and synchronization capabilities, this study introduces a computational model inspired by the physical and biological processes underlying rhythm processing. Utilizing a reservoir…
Complex systems often involve higher-order interactions which require us to go beyond their description in terms of pairwise networks. Triadic interactions are a fundamental type of higher-order interaction that occurs when one node…
Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited…
A statistical model is a mathematical representation of an often simplified or idealised data-generating process. In this paper, we focus on a particular type of statistical model, called linear mixed models (LMMs), that is widely used in…
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and…
Mathematical reasoning in large language models (LMs) has garnered significant attention in recent work, but there is a limited understanding of how these models process and store information related to arithmetic tasks within their…
Artifact-centric process models aim to describe complex processes as a collection of interacting artifacts. Recent development in process mining allow for the discovery of such models. However, the focus is often on the representation of…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
This paper proposes a communication model for multiuser multiple-input multiple-output (MIMO) systems based on large intelligent surfaces (LIS), where the LIS is modeled as a collection of tightly packed antenna elements. The LIS system is…
These course notes are about computing modular forms and some of their arithmetic properties. Their aim is to explain and prove the modular symbols algorithm in as elementary and as explicit terms as possible, and to enable the devoted…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
We propose a process calculus, named AbC, to study the behavioural theory of interactions in collective-adaptive systems by relying on attribute-based communication. An AbC system consists of a set of parallel components each of which is…
Quantum communication and cryptographic protocols are well on the way to becoming an important practical technology. Although a large amount of successful research has been done on proving their correctness, most of this work does not make…
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x…
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…
In this demonstration, we will present the world's first molecular multiple-input multiple-output (MIMO) communication link to deliver two data streams in a spatial domain. We show that chemical signals such as concentration gradients could…
Refinement calculus is a powerful and expressive tool for reasoning about sequential programs in a compositional manner. In this paper we present an extension of refinement calculus for reactive systems. Refinement calculus is based on…
Modeling processes are the activities of capturing and representing processes and control of their dynamic behavior. Desired features of the model include capture of relevant aspects of a real phenomenon, understandability, and completeness…