A formal approach to the modeling, simulation and analysis of nano-devices.
type: Dataset
description: Nano-devices are molecular machines synthesized from molecular subcomponents whose functions are combined in order to perform the func- tion of the machine. It frequently results of relative motions of subcomponents triggered by chemical events such as excitement induced by light, acidity or tem- perature changes. Thus the function consists in the transformation of a chemical event into a mechanical event. An important and characteristic feature of these devices is their intrinsic compositional nature. Therefore process-algebra for- malisms are natural candidates for their modeling. To this aim we introduce a dialect of the -calculus, the nano calculus. It is a rule-based language, the basic agents are molecules, with explicit representa- tion of molecular complexations and internal states. Its stochastic semantics is governed by rules which correspond to chemical reactions. The stochastic rate of the rule, possibly in nite, corresponds to the kinetic rate of the reaction. We illustrated its relevance for the modeling and simulation of nano-devices with an example stemming from the collaboration with the chemistry department of bologna: the [2]RaH rotaxane. We modeled it in nano and simulated its behaviour under various conditions of concentration: rst we validate our model by checking its correspondance with the experimental data and then we investi- gate extreme conditions not observable in practice. We were able to show that some classical assumption about kinetic rates were not correct any longer in this setting. The calculus has many advantages for the modelling of biochemical sys- tems. It is in particular compact, easily reusable and modi able and maybe more importantly much biological-like and thus easier to learn for biochemists. On the other hand the -calculus, also often used to model biochemical sys- tems, has a much more developed theory and more available tools. We present an encoding from the nano calculus to the stochastic -calculus. It satis es a ve…
issued: 2026-05-14T22:55:54.117147
language: fr
modified: 2026-05-14T22:55:54.117152
contact point: Organization
  fn: CCSD
keyword: backward-bisimulation
keyword: infoeu-reposemanticsdoctoralthesis
keyword: infoinfo-bicomputer-science-csbioinformatics-q-bioqm
keyword: nano-devices
keyword: process-calculi
keyword: sdvbibslife-sciences-q-bioquantitative-methods-q-bioqm
keyword: theses
landing page: https://pastel.hal.science/tel-00780567

A formal approach to the modeling, simulation and analysis of nano-devices.
type: Distribution
format: HTML
issued: 2026-05-14T22:55:54.150110
modified: 2026-05-14T22:55:54.099001
access URL: https://pastel.hal.science/tel-00780567

test_moissonnage_selune
type: Agent