114 research outputs found
Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics
Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500 Hz to 1 kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2 ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates
Haptic Interaction with 3D oriented point clouds on the GPU
Real-time point-based rendering and interaction with virtual objects is gaining popularity
and importance as di�erent haptic devices and technologies increasingly provide the basis
for realistic interaction. Haptic Interaction is being used for a wide range of applications
such as medical training, remote robot operators, tactile displays and video games. Virtual
object visualization and interaction using haptic devices is the main focus; this process
involves several steps such as: Data Acquisition, Graphic Rendering, Haptic Interaction
and Data Modi�cation. This work presents a framework for Haptic Interaction using the
GPU as a hardware accelerator, and includes an approach for enabling the modi�cation
of data during interaction. The results demonstrate the limits and capabilities of these
techniques in the context of volume rendering for haptic applications. Also, the use
of dynamic parallelism as a technique to scale the number of threads needed from the
accelerator according to the interaction requirements is studied allowing the editing of
data sets of up to one million points at interactive haptic frame rates
Simulating molecular docking with haptics
Intermolecular binding underlies various metabolic and regulatory processes of the
cell, and the therapeutic and pharmacological properties of drugs. Molecular docking
systems model and simulate these interactions in silico and allow the study of the
binding process. In molecular docking, haptics enables the user to sense the interaction
forces and intervene cognitively in the docking process. Haptics-assisted docking
systems provide an immersive virtual docking environment where the user can interact
with the molecules, feel the interaction forces using their sense of touch, identify
visually the binding site, and guide the molecules to their binding pose. Despite a
forty-year research e�ort however, the docking community has been slow to adopt this
technology. Proprietary, unreleased software, expensive haptic hardware and limits
on processing power are the main reasons for this. Another signi�cant factor is the
size of the molecules simulated, limited to small molecules.
The focus of the research described in this thesis is the development of an interactive
haptics-assisted docking application that addresses the above issues, and enables
the rigid docking of very large biomolecules and the study of the underlying interactions.
Novel methods for computing the interaction forces of binding on the CPU
and GPU, in real-time, have been developed. The force calculation methods proposed
here overcome several computational limitations of previous approaches, such as precomputed
force grids, and could potentially be used to model molecular
exibility
at haptic refresh rates. Methods for force scaling, multipoint collision response, and
haptic navigation are also reported that address newfound issues, particular to the
interactive docking of large systems, e.g. force stability at molecular collision. The
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result is a haptics-assisted docking application, Haptimol RD, that runs on relatively
inexpensive consumer level hardware, (i.e. there is no need for specialized/proprietary
hardware)
New Geometric Data Structures for Collision Detection
We present new geometric data structures for collision detection and more, including: Inner Sphere Trees - the first data structure to compute the peneration volume efficiently. Protosphere - an new algorithm to compute space filling sphere packings for arbitrary objects. Kinetic AABBs - a bounding volume hierarchy that is optimal in the number of updates when the objects deform. Kinetic Separation-List - an algorithm that is able to perform continuous collision detection for complex deformable objects in real-time. Moreover, we present applications of these new approaches to hand animation, real-time collision avoidance in dynamic environments for robots and haptic rendering, including a user study that exploits the influence of the degrees of freedom in complex haptic interactions. Last but not least, we present a new benchmarking suite for both, peformance and quality benchmarks, and a theoretic analysis of the running-time of bounding volume-based collision detection algorithms
Surface collision detection for virtual prototyping
This paper presents an efficient collision detection algorithm designed to support assembly and maintenance simulation of complex assemblies. This approach exploits the surface knowledge, available from CAD models, to determine intersecting surfaces. It proposes a novel combination of Overlapping Axis-Aligned Bounding Box (OAABB) and R-tree structures to gain considerable performance improvements. This paper also shows an efficient traversal algorithm based on the R-tree structure of Axis-Aligned Bounding Boxes to determine intersecting objects and intersecting surfaces between three-dimensional components, for supporting the recognition of constraints in assembly and disassembly operations in virtual prototyping environments.
The implementation of the proposed collision detection algorithm performs well against moderately complex industrial case studies. Current experimental results show that this implementation is effective in determining intersecting surfaces at interactive rates with moderately complex real case studies.info:eu-repo/semantics/publishedVersio
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