Monte Carlo simulation of the neutron detection wall at RIBLL II in HIRFL-CSR

With the construction of the new Radioactive Ion Beam Line in Lanzhou (RIBLL II) which connects the CSRm and the CSRe, an experimental setup for physics research is highly required. A large area neutron detection wall is the main part of the setup. This paper introduced the detection principle of the neutron detection wall and the Monte-Carlo simulation of its design under the environment of the Geant4 toolkit. We presented the final design with the optimized parameters and the performance of the wall.

基于GEANT4的CsI(Tl)闪烁体探测器的Monte Carlo模拟；Monte Carlo Simulation of CsI(Tl) Scintillator Detector with GEANT4 ToolKit

对闪烁光在晶体内的传输以及光电子倍增过程进行了建模,基于GEANT4软件包对CsI(T1)闪烁体探测器进行了蒙特卡罗模拟,得到了不同形状、尺寸和包装的CsI(Tl)晶体测量γ射线的能谱。对比模拟和测试结果,两者得到了很好的符合,从而验证了模拟参数的合理性和可靠性。该模拟程序的建立为闪烁体探测器的设计提供了更精确的开发工具。

Effect of polydispersity on the self-assembly structure of diblock copolymers under various confined states: A Monte Carlo study

We studied the self-assembly of polydisperse diblock copolymers under various confined states by Monte Carlo simulation. When the copolymers were confined within two parallel walls, it was found that the ordered strip structures appeared alternately with the increase in wall width. Moreover, the wall width at which the ordered structure appeared tended to increase with an increase in the polydispersity index (PDI). On the other hand, the simulation results showed that the copolymers were likely to form ordered concentric strip structures when they were confined within a circle wall.

Self-assembly of diblock copolymer mixtures in confined states: A Monte Carlo study

The self-assembly of diblock copolymer mixtures (A-b-B/A-b-C or A-b-B/B-b-C mixtures) subjected to cylindrical confinement (two-dimensional confinement) was investigated using a Monte Carlo method. In this study, the boundary surfaces were configured to attract blocks A but repel blocks B and C. Relative to the structures of the individual components, the self-assembled structures of mixtures of the diblock copolymers were more complex and interesting. Under cylindrical confinement, with varying cylinder diameters and interaction energies between the boundary surfaces and the blocks, we observed a variety of interesting morphologies. Upon decreasing the cylinder's diameter, the self-assembled structures of the A(15)B(15)/A(15)C(15) mixtures changed from double-helix/cylinder structures (blocks B and C formed double helices, whereas blocks A formed the outer barrel and inner core) to stacked disk/cylinder structures (blocks B and C formed the stacked disk core, blocks A formed the outer cylindrical barrel), whereas the self-assembled structures of the A(15)B(7)/B7C15 mixtures changed from concentric cylindrical barrel structures to screw/cylinder structures (blocks C formed an inside core winding with helical stripes, whereas blocks A and B formed the outer cylindrical barrels) and then finally to the stacked disk/cylinder structures.

A Monte Carlo simulation of morphology and structure for thin films of symmetric triblock copolymer after quenching and annealing

Self-assembly thin films of symmetric triblock copolymer after annealing and quenching were examined by an effective Monte Carlo simulation method. The defects in the ordered lamellae of the thin films after quenching, which were dependent on the initialization of copolymer melts, are removed in the thin films after annealing. The mean-square gyration radius and end-to-end distance of copolymer chains in the thin films after annealing are smaller than those in the thin films after quenching because of the complete relaxation of polymer during annealing. We also find that the density of A block in the region near to the surface is higher than that in the interior of the thin films. As a result, it is different from the thin films of symmetric A(n)B(n) diblock copolymer, in which surface ordering forms before the interior, that ordering phenomena occurs first in the interior region in the thin films of symmetric A(n)B(m)A(n). triblocl copolymer.

Investigation of sol-gel transition in Pluronic F127/D2O solutions using a combination of small-angle neutron scattering and Monte Carlo simulation

Physical gelation in the concentrated Pluronic F127/D2O solution has been studied by a combination of small-angle neutron scattering (SANS) and Monte Carlo simulation. A 15% F127/D2O solution exhibits a sol-gel transition at low temperature and a gel-sol transition at the higher temperature, as evidenced by SANS and Monte Carlo simulation studies. Our SANS and simulation results also suggest that the sol-gel transition is dominated by the formation of a percolated polymer network, while the gel-sol transition is determined by the loss of bound solvent. Furthermore, different diffusion behaviors of different bound solvents and free solvent are observed. We expect that this approach can be further extended to study phase behaviors of other systems with similar sol-gel phase diagrams.

Monte Carlo simulation of the aggregation of rod-flexible triblock copolymers in a thin film

The aggregation of rod-flexible ABA and BAB triblock (A was rod block and repulsive with block B) copolymers in a thin film was studied as a function of varying the rigidity (eta) and the length of the rod block by Monte Carlo simulation. The rigidity of block A was defined as eta = R-c/R-max in this study. R-c, was the end-to-end distance below which the conformation of the block was not allowed, whereas R-max, was the longest end-to-end distance that the block could be. If eta = 0 the block was flexible, whereas if eta = 1 the block was a straight rod. The simulation results showed that the ABA triblock copolymer film were likely to form lamella structure with increasing the rigidity (eta) of block A. The lamellas were parallel each other and perpendicular to the film surface. However, the aggregation of BAB triblock copolymers tended to change from lamella to cylinder structure with increasing the rigidity (eta) of block A. Typical lamella and cylinder co-exist structure was obtained at eta = 0.504 for the BAB copolymer film. On the other hand, the simulation results indicated that the film changed from disorder to order, then to disorder structure with increasing the relative length of B block for both ABA and BAB copolymer films.

Monte Carlo simulation of phase separation of A/B/A-B ternary mixtures

Monte Carlo simulations were used to model A/B/A-B ternary mixtures with different AB diblock copolymer volume fractions for which both the dispersed and continuous phase volume fractions were kept constant. For concentrations of the diblock copolymer below a critical value, the domain size increment of the dispersed phase decreases linearly with the copolymer concentration. This is in agreement with the predictions of Noolandi and Hong. The dependence of the domain size as a function of the copolymer volume fraction can also be fitted by the equation of Tang and Huang. Our simulations indicate, for the first time, that the micelles form before saturation of the interface occurs. This means that the formation of the micelles is not a result of the saturation of the interface.

Fault identification through the combination of symbolic conflict recognition and Markov Chain-aided belief revision

F. Smith and Q. Shen. Fault identification through the combination of symbolic conflict recognition and Markov Chain-aided belief revision. IEEE Transactions on Systems, Man and Cybernetics, Part A: Systems and Humans, 34(5):649-663, 2004.

Ukryty punkt krytyczny w mieszaninach binarnych – badania metodami symulacji Monte – Carlo

Wydział Fizyki

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of the interface side chains. The method, called semi-definite programming-based underestimation (SDU), employs a general quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its application to docking in the rotational and translational space SE(3) is not straightforward due to the geometry of that space. We introduce a strategy that uses separate independent variables for side-chain optimization, center-to-center distance of the two proteins, and five angular descriptors of the relative orientations of the molecules. The removal of the center-to-center distance turns out to vastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to local free energy minima and shows similarity to the model of macromolecular association that proceeds through a series of collisions. Results for standard protein docking benchmarks establish that in this space the free energy landscape is a funnel in a reasonably broad neighborhood of the native state and that the SDU strategy can generate docking predictions with less than 5 � ligand interface Ca root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared to Monte Carlo methods.