In this paper, we describe a general methodology for the realistic modelling and simulation of deformable objects. The system of particles is used for this purpose. The first main contribution of this work is in the modelling field. Multi-layer particle systems are used to obtain a geometric description of an existing object. The second contribution is in the domain of the simulation. The particle systems are physically-based models that allow a realistic simulation of movements and deformations. This implies the representation of physical characteristics of existing objects, and thus the control of a wide variety of behaviours (stiffness, elasticity, control of volume variation) interesting in various areas such as medical applications, reverse-engineering, prototyping... The second contribution of this paper is to put these physical constraints into the model. Moreover, this paper proposes some techniques for the animation and the rendering of the particle systems.