Steered Molecular Dynamics

Izrailev, Sergei; Stepaniants, S.; Isralewitz, Barry; Kosztin, Dorina; Lü, Hui; Molnár, F.; Wriggers, Willy; Schulten, Klaus

doi:10.1007/978-3-642-58360-5_2

Cited by 390 publications

(362 citation statements)

References 75 publications

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“…42 The SMD simulations (see Supplementary Methods) determined activation energies of the coalescence reactions as a function of relative rod configuration. For a given configuration of two deposited rods, the activation energy was determined by analyzing the integrated force acting on one rod as it was steered towards the other, stationary rod:…”

Section: Modeling Of Nanoparticle Attachmentmentioning

confidence: 99%

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Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

Welch¹,

Woehl²,

Park

et al. 2015

ACS Nano

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Optimization of colloidal nanoparticle synthesis techniques requires an understanding of underlying particle growth mechanisms. Non-classical growth mechanisms are particularly important as they affect nanoparticle size and shape distributions which in turn influence functional properties. For example, preferential attachment of nanoparticles is known to lead to the formation of mesocrystals, although the formation mechanism is currently not well understood. Here we employ in situ liquid cell scanning transmission electron microscopy (STEM) and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally observed preference for end-to-end attachment of silver nanorods is a result of weaker solvation forces occurring at rod ends. SMD reveals that when the side of a nanorod approaches another rod, perturbation in the surface bound water at the nanorod surface creates significant energy barriers to attachment. Additionally, rod morphology (i.e. facet shape) effects can explain the majority of the side attachment effects that are observed experimentally.

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Section: Modeling Of Nanoparticle Attachmentmentioning

confidence: 99%

“…42 Pairs of pentagonal silver nanorods, having specified relative configurations, were placed inside a model in situ STEM holder.…”

Section: Smdmentioning

confidence: 99%

Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

Welch¹,

Woehl²,

Park

et al. 2015

ACS Nano

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“…Steered molecular dynamics (SMD) [10,28] calculations were carried out to simulate the average force required to detach the herbicide diclofop from the ACC active site cavity. As shown in Fig.…”

Section: Steered Molecular Dynamicsmentioning

confidence: 99%

Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors

Amarante

Oliveira

Bueno

et al. 2014

Journal of Molecular Graphics and Modelling

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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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Steered Molecular Dynamics

Cited by 390 publications

References 75 publications

Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors

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

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