Digital-Analog Quantum Simulation of Spin Systems in Trapped Ions

65 p.

Simulation of an apodizer's effect for high-density optical storage

The effect of an apodizer with two parallel taper refractive surfaces is theoretically investigated for high-density optical storage. The apodizer may modulate an incident Gaussian beam into an annular beam. Simulation shows that with the increasing inner radius of the modulated beam, the focal spot shrinks obviously. The depolarization effect gets strong simultaneously, which induces the circular symmetry loss of the focal spot. In this process, pattern density of the orthogonal and longitudinal diffractive fields increases remarkably.

Optical near-field simulation of Sb thin film thermal lens and its application in optical recording

Using the finite-difference-time-domain method, the near-field optical distribution and properties of Sb thin film thermal lens are calculated and simulated. The results show as follows. Within the near-field distance to the output plane of thermal lens, the spot size is approximately 100 nm, and its intensity is greatly enhanced, which is higher than that of incident light. The spot shape gradually changes from ellipse to round at the distance of more than 12 nm to the output plane. The above-simulated results are further demonstrated by the static optical recording experiment. (C) 2005 American Institute of Physics.

Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.