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

Stocks, Matthew B.; Laycock, Stephen D.; Hayward, Steven

doi:10.1007/s10822-010-9410-0

Cited by 9 publications

(8 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The approach utilizes effectively the many-core processing capabilities of modern GPUs, the space partitioning properties of regular grids and octrees, and two efficient proximity querying algorithms based on these partition- in haptics for modelling flexibility is to use an elastic network model [47].…”

Section: Discussionmentioning

confidence: 99%

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Iakovou

Hayward

Laycock

2015

Journal of Molecular Graphics and Modelling

View full text Add to dashboard Cite

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 500Hz to 1kHz. 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 the 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 2ms 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 * Corresponding author Email addresses: sjh@cmp.uea.ac.uk (Steven Hayward), s.laycock@uea.ac.uk (Stephen D. Laycock) Graphics and Modelling June 8, 2015 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. Preprint submitted to Journal of Molecular

show abstract

Section: Discussionmentioning

confidence: 99%

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Iakovou

Hayward

Laycock

2015

Journal of Molecular Graphics and Modelling

View full text Add to dashboard Cite

show abstract

“…Molecular docking simulation [27] can make the observer feel the interaction force in the docking process, thereby increasing the understanding of it. HaptiMol ISAS software to explore water accessible biomolecular surfaces [28,29], HaptiMol ENM to simulate haptic feedback by applying forces to individual atoms [30], and HaptiMol RD to simulate haptic feedback in molecular docking [31][32][33][34] are haptic softwares created with the CHAI3D haptic framework that supports a grounded haptic devices with translational force feedback. More sophisticated devices with rotational force feedback also exist [35,36].…”

Section: Virtual Reality Simulationmentioning

confidence: 99%

Tensegrity representation of microtubule objects using unified particle objects and springs

Pramudwiatmoko

Gutmann

Ueno

et al. 2020

CBIJ

View full text Add to dashboard Cite

There are limitations in interactions with molecular objects in laboratory experiments due to the very small size of the objects. Common media to show the experimental results of molecular objects is still lack of observer interaction to understand it intuitively. In order to overcome this lack of interaction, this research takes tensegrity representation of molecular objects reproducing experimental results and creates interactive 3D objects to be presented in a virtual reality (VR) environment. The tensegrity representation enables us to enhance the interaction experience with the natural user interface with haptic technology and hand tracking controller. A particle simulation system that utilizes multiple GPUs resources is used to fulfill haptic VR requirements. We developed a unified particle object model using springs and particles which we call anchors which act as tensegrity structure of the object to support conformation of filament-type objects such as microtubules. Some object parameters can be set to match the flexural rigidity of the object with some experimental results. The bending shape of the object is evaluated using the classic bending equation and the results show high compatibility. Viscoelastic behavior also shows similarities with the viscosity reported in other studies. The object's flexural rigidity can be adjusted to match the target value with the direction of the prediction equation. The object model provides a better insight about molecular objects with natural and real-time interactions to provide a more intuitive understanding with the molecular objects presented. The results show that this model can also be applied to any filament-type or rod-like molecular object.

show abstract

“…14,15 (3) Molecular substituents, where the user can pinpoint particular atoms or functional groups and manipulate them with an external force, thereby 'steering' the simulation program's internal propagation, similar to the sort of manipulations which are possible using atomic force microscopy (AFM) experiments. 16 Keyboard and mouse interfaces are utilized in such systems, 5,17 but the most popular interface has been haptic devices, 3,4,7,[18][19][20][21][22][23][24][25][26][27][28] which offer up to six degrees of freedom (compared to two for a mouse). As such, they are well suited to facilitating user interaction with 3D molecular simulations.…”

Section: Introductionmentioning

confidence: 99%

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

et al. 2014

View full text Add to dashboard Cite

A GPU-accelerated immersive audiovisual framework for interaction with molecular dynamics using consumer depth sensors. Faraday Discussions, 169. pp. 63-87. ISSN 1359-6640 Available from: http://eprints.uwe.ac.uk/23115We recommend you cite the published version. The publisher's URL is: http://dx.doi.org/10.1039/C4FD00008K Refereed: Yes First published online 19 Mar 2014Disclaimer UWE has obtained warranties from all depositors as to their title in the material deposited and as to their right to deposit such material. UWE makes no representation or warranties of commercial utility, title, or fitness for a particular purpose or any other warranty, express or implied in respect of any material deposited. UWE makes no representation that the use of the materials will not infringe any patent, copyright, trademark or other property or proprietary rights.UWE accepts no liability for any infringement of intellectual property rights in any material deposited but will remove such material from public view pending investigation in the event of an allegation of any such infringement. PLEASE SCROLL DOWN FOR TEXT.A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors † With advances in computational power, the rapidly growing role of computational/ simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360 spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360 atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

show abstract

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

Cited by 9 publications

References 39 publications

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics

Tensegrity representation of microtubule objects using unified particle objects and springs

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

Contact Info

Product

Resources

About