SOFA: A Multi-Model Framework for Interactive Physical Simulation

International audienceSOFA (Simulation Open Framework Architecture) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, \sofa{} can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.Comment: 25 pages, 1 table, 7 figures; preprint submitted to Biophysical Journa

The application of three-dimensional mass-spring structures in the real-time simulation of sheet materials for computer generated imagery

Despite the resources devoted to computer graphics technology over the last 40 years, there is still a need to increase the realism with which flexible materials are simulated. However, to date reported methods are restricted in their application by their use of two-dimensional structures and implicit integration methods that lend themselves to modelling cloth-like sheets but not stiffer, thicker materials in which bending moments play a significant role. This thesis presents a real-time, computationally efficient environment for simulations of sheet materials. The approach described differs from other techniques principally through its novel use of multilayer sheet structures. In addition to more accurately modelling bending moment effects, it also allows the effects of increased temperature within the environment to be simulated. Limitations of this approach include the increased difficulties of calibrating a realistic and stable simulation compared to implicit based methods. A series of experiments are conducted to establish the effectiveness of the technique, evaluating the suitability of different integration methods, sheet structures, and simulation parameters, before conducting a Human Computer Interaction (HCI) based evaluation to establish the effectiveness with which the technique can produce credible simulations. These results are also compared against a system that utilises an established method for sheet simulation and a hybrid solution that combines the use of 3D (i.e. multilayer) lattice structures with the recognised sheet simulation approach. The results suggest that the use of a three-dimensional structure does provide a level of enhanced realism when simulating stiff laminar materials although the best overall results were achieved through the use of the hybrid model