• Polymer(Korea)
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• v.35 no.6
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• pp.513-519
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• 2011

Molecular simulations via the molecular dynamics method have been carried out to investigate the dynamic collision properties of penetrable-sphere model fluids. The collision frequencies, the mean free paths, the angle distributions of the hard-type reflection and the soft-type penetration, and the effective packing fractions are computed over a wide range of the packing fraction ${\phi}$ and the repulsive energy ${\varepsilon}^*$. The soft-type collisions are dominated for lower repulsive energy systems, while the hardtype collisions for higher repulsive energy systems. Very interestingly, the ratio of the soft-type (or, the hard-type) collision frequency to the total collision frequency is directly related with the Boltzmann factor of acceptance (or rejection) probabilities in the canonical ensemble Monte Carlo calculations. Such dynamic collision properties are shown to be restricted for highly repulsive and dense systems of ${\varepsilon}^*{\geqq}3.0 $and ${\phi}{\geqq}0.7$, indicating the cluster forming structures in the penetrable-sphere model.

• Mass Spectrometry Letters
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• v.12 no.4
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• pp.131-136
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• 2021

Collision-induced dissociation of peptides involves a series of proton-transfer reactions in the activated peptide. To describe the kinetics of energy-variable dissociation, we considered the heat capacity of the peptide and the Marcus-theory-type proton-transfer rate. The peptide ion was activated to the high internal energy states by collision with a target gas in the collision cell. The mobile proton in the activated peptide then migrated from the most stable site to the amide oxygen and subsequently to the amide nitrogen (N-protonated) of the peptide bond to be broken. The N-protonated intermediate proceeded to the product-like complex that dissociated to products. Previous studies have suggested that the proton-transfer equilibria in the activated peptide affect the dissociation kinetics. To take the extent of collisional activation into account, we assumed a soft-sphere collision model, where the relative collision energy was fully available to the internal excitation of a collision complex. In addition, we employed a Marcus-theory-type rate equation to account for the proton-transfer equilibria. Herein, we present results from the integrated thermochemical approach using a tryptic peptide of ubiquitin.

• Journal of Information Processing Systems
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• v.8 no.4
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• pp.713-720
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• 2012

Unlike FEM (Finite Element Method), which provides an accurate deformation of soft objects, FFD (Free Form Deformation) based methods have been widely used for a quick and responsive representation of deformable objects in real-time applications such as computer games, animations, or simulations. The FFD-AABB (Free Form Deformation Axis Aligned Bounding Box) algorithm was also suggested to address the collision handling problems between deformable objects at an interactive rate. This paper proposes an enhanced FFD-AABB algorithm to improve the frame rate of simulation by adding the bounding sphere based collision test between 3D deformable objects. We provide a comparative analysis with previous methods and the result of proposed method shows about an 85% performance improvement.