Applying forces to elastic network models of large biomolecules using a haptic feedback device

Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version

Impact of haptic 'touching' technology on cultural applications

No abstract available

Asynchronous haptic simulation of contacting deformable objects with variable stiffness

International audienceAbstract--This paper presents a new asynchronous approach for haptic rendering of deformable objects. When stiff nonlinear deformations take place, they introduce important and rapid variations of the force sent to the user. This problem is similar to the stiff virtual wall for which a high refresh rate is required to obtain a stable haptic feedback. However, when dealing with several interacting deformable objects, it is usually impossible to simulate all objects at high rates. To address this problem we propose a quasi-static framework that allows for stable interactions of asynchronously computed deformable objects. In the proposed approach, a deformable object can be computed at high refresh rates, while the remaining deformable virtual objects remain computed at low refresh rates. Moreover, contacts and other constraints between the different objects of the virtual environment are accurately solved using a shared Linear Complementarity Problem (LCP). Finally, we demonstrate our method on two test cases: a snap-in example involving non-linear deformations and a virtual thread interacting with a deformable object

Articular human joint modelling

Copyright @ Cambridge University Press 2009.The work reported in this paper encapsulates the theories and algorithms developed to drive the core analysis modules of the software which has been developed to model a musculoskeletal structure of anatomic joints. Due to local bone surface and contact geometry based joint kinematics, newly developed algorithms make the proposed modeller different from currently available modellers. There are many modellers that are capable of modelling gross human body motion. Nevertheless, none of the available modellers offer complete elements of joint modelling. It appears that joint modelling is an extension of their core analysis capability, which, in every case, appears to be musculoskeletal motion dynamics. It is felt that an analysis framework that is focused on human joints would have significant benefit and potential to be used in many orthopaedic applications. The local mobility of joints has a significant influence in human motion analysis, in understanding of joint loading, tissue behaviour and contact forces. However, in order to develop a bone surface based joint modeller, there are a number of major problems, from tissue idealizations to surface geometry discretization and non-linear motion analysis. This paper presents the following: (a) The physical deformation of biological tissues as linear or non-linear viscoelastic deformation, based on spring-dashpot elements. (b) The linear dynamic multibody modelling, where the linear formulation is established for small motions and is particularly useful for calculating the equilibrium position of the joint. This model can also be used for finding small motion behaviour or loading under static conditions. It also has the potential of quantifying the joint laxity. (c) The non-linear dynamic multibody modelling, where a non-matrix and algorithmic formulation is presented. The approach allows handling complex material and geometrical nonlinearity easily. (d) Shortest path algorithms for calculating soft tissue line of action geometries. The developed algorithms are based on calculating minimum ‘surface mass’ and ‘surface covariance’. An improved version of the ‘surface covariance’ algorithm is described as ‘residual covariance’. The resulting path is used to establish the direction of forces and moments acting on joints. This information is needed for linear or non-linear treatment of the joint motion. (e) The final contribution of the paper is the treatment of the collision. In the virtual world, the difficulty in analysing bodies in motion arises due to body interpenetrations. The collision algorithm proposed in the paper involves finding the shortest projected ray from one body to the other. The projection of the body is determined by the resultant forces acting on it due to soft tissue connections under tension. This enables the calculation of collision condition of non-convex objects accurately. After the initial collision detection, the analysis involves attaching special springs (stiffness only normal to the surfaces) at the ‘potentially colliding points’ and motion of bodies is recalculated. The collision algorithm incorporates the rotation as well as translation. The algorithm continues until the joint equilibrium is achieved. Finally, the results obtained based on the software are compared with experimental results obtained using cadaveric joints

deForm: An interactive malleable surface for capturing 2.5D arbitrary objects, tools and touch

We introduce a novel input device, deForm, that supports 2.5D touch gestures, tangible tools, and arbitrary objects through real-time structured light scanning of a malleable surface of interaction. DeForm captures high-resolution surface deformations and 2D grey-scale textures of a gel surface through a three-phase structured light 3D scanner. This technique can be combined with IR projection to allow for invisible capture, providing the opportunity for co-located visual feedback on the deformable surface. We describe methods for tracking fingers, whole hand gestures, and arbitrary tangible tools. We outline a method for physically encoding fiducial marker information in the height map of tangible tools. In addition, we describe a novel method for distinguishing between human touch and tangible tools, through capacitive sensing on top of the input surface. Finally we motivate our device through a number of sample applications

Design and development of a VR system for exploration of medical data using haptic rendering and high quality visualization

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Haptic Rendering of Hyperelastic Models with Friction

International audience— This paper presents an original method for inter-actions' haptic rendering when treating hyperelastic materials. Such simulations are known to be difficult due to the non-linear behavior of hyperelastic bodies; furthermore, haptic constraints enjoin contact forces to be refreshed at least at 1000 updates per second. To enforce the stability of simulations of generic objects of any range of stiffness, this method relies on implicit time integration. Soft tissues dynamics is simulated in real time (20 to 100 Hz) using the Multiplicative Jacobian Energy Decomposition (MJED) method. An asynchronous preconditioner, updated at low rates (1 to 10 Hz), is used to obtain a close approximation of the mechanical coupling of interactions. Finally, the contact problem is linearized and, using a specific-loop, it is updated at typical haptic rates (around 1000 Hz) allowing this way new simulations of prompt stiff-contacts and providing a continuous haptic feedback as well