Generation of Potential Energy Surfaces in High Dimensions and Their Haptic Exploration

Haag, Moritz P.; Marti, Konrad H.; Reiher, Markus

doi:10.1002/cphc.201100539

Cited by 34 publications

(45 citation statements)

References 47 publications

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“…The seamless integration of complex quantum chemical information allows the interactive exploration of chemical reactivity. An approach which utilizes a force‐feedback device as an input and an output device to transmit the quantum mechanical information to the operator is HQC introduced by us in 2009 6, 7. A force‐feedback device as in HQC is also utilized in the interactive molecular dynamics framework,9 which implements a classical treatment of the forces in molecular systems.…”

Section: Principles Of Real‐time Quantum Chemistrymentioning

confidence: 99%

“…After having elaborated on the available and future quantum chemical methods for Real‐time Quantum Chemistry implementations, we shall now discuss their benefits for HQC6, 7 and subsequently discuss their capabilities in an out‐of‐the‐box application presented in the next section.…”

Section: Direct Hqcmentioning

confidence: 99%

“…This overview includes algorithms for parallel implementation and for specialized hardware such as graphical processing units (GPUs). Finally, we discuss the feasibility of a direct approach to haptic quantum chemistry (HQC)6, 7 which implements the ideas of Real‐time Quantum Chemistry. To illustrate what can already be done with currently available quantum chemistry software we present some exploratory calculations.…”

Section: Introductionmentioning

confidence: 99%

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Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

Visweswaran

Lightfoot

Gilchrist

2012

Cathet Cardio Intervent

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Cardiac tamponade represents a medical emergency necessitating emergent pericardiocentesis. Use of two-dimensional echocardiography (ECHO) has improved the safety of pericardiocentesis, but procedural challenges may occur when performed in an emergent manner outside of the catheterization laboratory without availability of fluoroscopy and readily available pressure transducers. The most problematic situation is the initial finding of bloody fluid on aspiration where intrapericardial versus intravascular location of the needle must be determined. We report two cases of cardiac tamponade managed with the use of a novel, disposable lightweight digital pressure transducer to directly measure intrapericardial pressures during an ECHO guided pericardiocentesis. In both cases the fluid initially encountered was grossly bloody and rapid definition of whether this was pericardial fluid versus an inappropriately located needle in the vascular space was critical. This type of novel, disposable self contained manometer has the potential to further minimize complications associated with pericardiocentesis. It offers a cost effective alternative and answers questions about the shifting point of service for pericardiocentesis from the invasive cath lab to less costly locations (Drummond, et al., J Am Soc Echocardiogr 1998;11:433-435).

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Section: Principles Of Real‐time Quantum Chemistrymentioning

confidence: 99%

Section: Direct Hqcmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

Visweswaran

Lightfoot

Gilchrist

2012

Cathet Cardio Intervent

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“…Haptic Quantum Chemistry [7,8], Interactive Quantum Chemistry [9,10] and Real-time Quantum Chemistry [11,12] offer new alternative approaches to study reactivity in large three-dimensional molecular systems by providing an instantaneous response of the system to the structural manipulation.…”

Section: Introductionmentioning

confidence: 99%

Interactive Chemical Reactivity Exploration

et al. 2014

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Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transitionstate structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.

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“…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

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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.

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Generation of Potential Energy Surfaces in High Dimensions and Their Haptic Exploration

Cited by 34 publications

References 47 publications

Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

Interactive Chemical Reactivity Exploration

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

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