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GPU implementation of atomic fluid MD simulation

Dawid Aleksander

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2022

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Vol. 26, No 1

25--37

EN

A computer simulation of an atomic fluid on a GPU was implemented using the CUDA architecture. It was shown that the programming model for efficient numerical computing applications was changing with the development of the CUDA architecture. The introduction of the L2 cache decreased the latency between the global GPU memory and the registers. The performed MD simulation using the global memory and registers showed that the average acceleration relative to the CPU reached 80 times for single-precision calculations. Usually, the shared block memory gives much be4er results for this kind of calculation. We have found that using the shared memory gives acceleration over 116 times in comparison to the CPU. It is about 49% faster than using the global memory and registers. It is shown here that the performance of generally available graphics cards for double-precision calculations is significantly lower than for single-precision calculations. The recorded double-precision acceleration relative to the CPU in our experiment averaged 6 and 7 times for the global and shared memory, respectively. We performed these calculations on two different CUDA enable device systems.

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Multiscale water drop contact angles at selected silica surfaces

Zhang Chen, Wang Xuming, Li Lixia, Jin Jiaqi, Polson Randy, Miller Jan D.

Physicochemical Problems of Mineral Processing

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2022

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Vol. 58, iss. 5

art. no. 152154

EN

In this study, multiscale advancing contact angles for glycerol/water drops at silica surfaces are reported for millidrops, submicron-drops, and nanodrops. Selected silica surfaces were muscovite, silicon, and talc. The contact angles for millidrops (1–2 mm) were determined by the traditional sessile drop technique. For submicron-drops (0.1–1.0 μm), a hollow tip Atomic Force Microscope (AFM) procedure was used. The contact angles for nanodrops (~7 nm) were examined from Molecular Dynamics (MD) simulation. The results were compared to evaluate the effect of drop size on the contact angle. In the case of the hydrophobic talc surface, the 75° advancing contact angle did not vary significantly with drop size. For the hydrophilic muscovite surface, the water drop wet the surface and an advancing contact angle of about 10° was found for the millidrops and submicron-drops. However, for the MD simulated nanodrops, attachment and spreading of the ~7 nm drop created a 2D film of molecular dimensions, the contact angle of which was difficult to define and varied from 0° to 17°. Perhaps of equal interest from the MD simulation results was that the spreading of the glycerol/water nanodrop at the muscovite surface resulted in crystallographic directional transport of water molecules to the extremities of the 2D film. Such separation and segregation left the center of the film with an increased concentration of glycerol. Based on these results, the line tension, which has been found in other investigations to account for contact angle decrease with a decrease in drop size, does not seem to be a significant factor in this study.

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How to stimulate polymeric surfaces biocompatibility and hydroxyapatite formation: experiments supported by MD simulations

Gołda-Cępa Monika, Chytrosz Paulina, Riedlova Kamila, Kulig Waldemar, Ćwiklik Łukasz, Kotarba Andrzej

Engineering of Biomaterials

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2020

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Vol. 23, no. 158 spec. iss.

40

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Molecular dynamics of cholesterol in a thin film surrounding a carbon nanotube

Raczynski P., Dawid A., Sokół M., Grubski Z.

Materials Science Poland

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2005

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Vol. 23, No. 2

429--439

EN

Molecular dynamics ( MD) simulations of the system composed of a single walled carbon nanotube (SWNT) surrounded by a thin film of: a) cholesterol - water mixture and b) pure cholesterol have been carried out. The translational and rotational correlation functions and their Fourier transforms of both cholesterol and water molecules have been calculated for several temperatures and concentrations. The interpretation of translational and rotational dynamics of both cholesterol and water molecules in the specific environment is presented.