What do we want from computer simulation of SIMS using clusters?

Webb, R.P.

doi:10.1016/j.apsusc.2008.05.138

Cited by 6 publications

(2 citation statements)

References 33 publications

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“…Therefore, while recombination cannot be entirely discounted, there exists reasonable evidence to support that the Si containing fragments acquired in these experiments do reflect chemical interactions between the porous silicon substrate and organic material loaded therein. Molecular dynamic simulations could be used to investigate this phenomenon more rigorously [27] and could be addressed in the future with greater computational power [28].…”

Section: Resultsmentioning

confidence: 99%

Use of TOF-SIMS to study adsorption and loading behavior of methylene blue and papain in a nano-porous silicon layer

Kempson

Barnes

Prestidge

2010

J. Am. Soc. Mass Spectrom.

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TOF-SIMS was applied to study the cross-sectional distribution of methylene blue and papain in porous silicon layers. Elemental and molecular information were used to study their distributions in the porous region and the chemistry of their adsorption. Methylene blue (MW ϭ 284 Da) [4], and the delivery of active pharmaceutical ingredients [5,6]. The ongoing interest in pSi for use as a therapeutic delivery system is due to the large internal surface area available, the readily modified surface chemistry [7] and, in particular, the excellent in vivo biodegradation and biocompatibility (low toxicity) of the silicon substrate, hydrolysing to form orthosilicic acid, which is readily excreted [8]. The loading dynamics of molecules into a pSi matrix is dependent on wetting and the size of the pores. Likewise, the interaction between a loaded molecule and the pSi substrate is of interest, particularly in the case of protein based therapeutics, whose bioactivity is dependent on remaining in a specific 3D conformation.TOF-SIMS analysis provides information regarding elemental and molecular species present in a sample surface (i.e., within 1-1.5 nm) with high mass resolution (up to ϳ10,000 m/⌬m) and spatial resolution for imaging (ϳ1 micron). Molecular and elemental information is obtained for organic and inorganic materials providing a powerful technique to image organic compounds associated with inorganic substrates or vice versa [9,10]. This has been demonstrated by imaging solid-state pharmaceutical formulations [11][12][13][14], however, to date this has not been extended to porous silicon substrates.In this study, TOF-SIMS was used to map the distribution of methylene blue and papain across porous silicon layers after loading from aqueous solution. Methylene blue (C 16 H 18 N 3 S ϩ , MW ϭ 284.12 g/mol) is a relatively small organic dye molecule commonly used in adsorption studies and can be considered analogous to therapeutic molecules. A molecular mass of 284 g/mol is within a reasonable mass range for a TOF-SIMS' Ga ϩ primary ion beam and can be easily and uniquely identified without interference or confusion from spectral peaks originating from the silicon substrate or in the instance of organic contamination. This molecule was chosen for its convenience, and to assess the ability to use smaller organic fragments to reflect the distribution of the molecule of interest. This is important to be able to extend this work to studying larger molecules, such as proteins and enzymes of pharmaceutical interest, which will not provide a molecular ion in TOF-SIMS. In contrast to methylene blue, papain is a much larger molecule, detailed elsewhere [15], comprising 212 residue units in two domains, giving a molecular weight of 23,406 g/mol. Papain is a cysteine protease hydrolase enzyme present in papaya. This molecular weight is far greater than can be detected with TOF-SIMS, however, fragmentation products can be detected. Smaller organic fragments can be compared with the distribution of methylene blue to investigate si...

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Section: Resultsmentioning

confidence: 99%

Use of TOF-SIMS to study adsorption and loading behavior of methylene blue and papain in a nano-porous silicon layer

Kempson

Barnes

Prestidge

2010

J. Am. Soc. Mass Spectrom.

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“…Material ejection can be observed in the HVI simulation with the SPH method . Webb pointed out that there is a need for a quick physical model in cluster simulations that will aid experiment design and interpretation.…”

Section: Introductionmentioning

confidence: 99%

New approach for simulation of large cluster impact using smoothed particle hydrodynamics method

Lee

2014

Surface & Interface Analysis

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Using large-scale atomistic simulations, it has been shown that the macroscopic cratering behavior emerges for projectile impacts on Au at projectile sizes between 1000 and 10 000 Au atoms at impact velocities comparable to typical meteoroid velocities. This indicates that the continuum model-like fluid can be a possible candidate for the physical model of large cluster sputtering. Smoothed particle hydrodynamics (SPH) is a mesh-free particle method for obtaining approximate numerical solutions of the equations of fluid dynamics by replacing the fluid with a set of particles. In this work, SPH has been introduced for the first time as an alternative but macroscopic thus quick method for the computer simulation of large cluster impact. It has been demonstrated that cratering process can be observed at the impact simulation of water cluster on water target. The SPH simulation can be applied after improvements in physical models and algorithms to investigate the sputtering effect on solid target using water cluster primary ion beams.

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Modeling the interaction of keV clusters with molecular solids

Mody¹,

Webb²

2011

Surface & Interface Analysis

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The use of polyatomic (cluster) ion beams for SIMS has proven to be an efficient method for the characterization of solids. Computer simulation programs such as Molecular Dynamics (MD) are often run to gain an insight into the ion-solid interactions that take place under these circumstances; however, for simulations to be able to make accurate predictions, a massive amount of computational resources are required to be at hand. These include several months in simulation time and the use of very large targets, not to mention that a single simulation run is a representation of only a single ion trajectory. Thus, MD simulations are invaluable for gaining insight into ion-solid interactions but are less so for being able to provide information when time constraints are put in place. The work here aims to achieve a prediction model that, when completely functional, will be able to deal with the pressures of the clock. This, we believe, is achievable by employing simpler modeling criteria that are dependant upon aspects of an initial energy deposition profile within the target under irradiation. Copyright © 2010 John Wiley & Sons, Ltd

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What do we want from computer simulation of SIMS using clusters?

Cited by 6 publications

References 33 publications

Use of TOF-SIMS to study adsorption and loading behavior of methylene blue and papain in a nano-porous silicon layer

Use of TOF-SIMS to study adsorption and loading behavior of methylene blue and papain in a nano-porous silicon layer

New approach for simulation of large cluster impact using smoothed particle hydrodynamics method

Modeling the interaction of keV clusters with molecular solids

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