Related papers: Hybrid Calculus of Wrapped Compartments
The hazard function represents one of the main quantities of interest in the analysis of survival data. We propose a general approach for parametrically modelling the dynamics of the hazard function using systems of autonomous ordinary…
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…
We propose a hybrid process calculus for modelling and reasoning on cyber-physical systems (CPS{s}). The dynamics of the calculus is expressed in terms of a labelled transition system in the SOS style of Plotkin. This is used to define a…
We develop a stochastic calculus that makes it easy to capture a variety of predictable transformations of semimartingales such as changes of variables, stochastic integrals, and their compositions. The framework offers a unified treatment…
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the…
Modeling the dynamics of probability distributions from time-dependent data samples is a fundamental problem in many fields, including digital health. The goal is to analyze how the distribution of a biomarker, such as glucose, changes over…
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
Self-organizing systems demonstrate how simple local rules can generate complex stochastic patterns. Many natural systems rely on such dynamics, making self-organization central to understanding natural complexity. A fundamental challenge…
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…
While distributed systems with transfer of processes have become pervasive, methods for reasoning about their behaviour are underdeveloped. In this paper we propose a bisimulation technique for proving behavioural equivalence of such…
Metamodeling of complex numerical systems has recently attracted the interest of the mathematical programming community. Despite the progress in high performance computing, simulations remain costly, as a matter of fact, the assessment of…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
Predictive dynamical models for marine ecosystems are used for a variety of needs. Due to sparse measurements and limited understanding of the myriad of ocean processes, there is however significant uncertainty. There is model uncertainty…
Hybrid systems are characterized by the hybrid evolution of their state: A part of the state changes discretely, the other part changes continuously over time. Typically, modern control applications belong to this class of systems, where a…
Stochastic evolution underpins several approaches to the dynamics of open quantum systems, such as random modulation of Hamiltonian parameters, the stochastic Schrodinger equation (SSE), and the stochastic Liouville equation (SLE). These…
Complex systems are composed of many particles or agents that move and interact with one another. The underlying mathematical framework to model many of these systems must incorporate the spatial transport of particles and their…
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each…