环形装置中三维MHD平衡与稳定性的计算机模拟

一、引 言 在聚变研究中,环形等离子体的磁约束起着重要作用。目前托卡马克研究的进展令人鼓舞,其理论与实验比较符合,定标关系清楚。但是无论从聚变的最终目标来看,还是从实验的安排考虑,完全轴对称的几何形状给各方面部带来许多不便。人们希望知道如果把环形几何中加进直线段,或者把圆环改成不具有对称性的环形,会对等离子体约束产生何种影响?     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides

The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model -sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.     

Study on δ‐form complex in syndiotactic polystyrene–organic molecules systems. IV. Formation of complexes with a mixture of solvents and structural changes during the sorption of solvents by syndiotactic polystyrene mesophase membranes

The syndiotactic polystyrene (sPS) δ form was crystallized from mixtures with different compositions of p‐chlorotoluene–chlorobenzene (p‐CT–CB) and p‐chlorotoluene–1,1,2‐trichloroethane (p‐CT–TCE). The presence of the δ form and TTGG helical conformation was confirmed by Fourier transform infrared and wide‐angle X‐ray diffraction (WAXD) analyses. In sPS/p‐CT–CB and sPS/p‐CT–TCE δ‐form membranes, the relative absorbance (RA) of the p‐chlorotoluene (p‐CT) solvent peak was very high even at very low concentrations of p‐CT in comparison with the RA of higher concentrations of chlorobenzene (CB) or 1,1,2‐trichloroethane (TCE) in the mixtures. However, the RAs of both CB and TCE solvent peaks decreased with decreasing concentrations of CB and TCE in the mixtures. A negligible decrease in the RA of the TTGG helical content was observed with a decreasing concentration of CB or TCE. The WAXD results showed that the 2θ peak positions of the [010] and [ 10] planes of the sPS/p‐CT–CB and sPS/p‐CT–TCE δ‐form membranes appeared in the same position and were almost equal to those of the sPS–p‐CT δ‐form membrane. The mesophases of the sPS–p‐CT [p‐CT (A‐M)] and sPS–TCE [TCE (A‐M)] membranes were used for the sorption studies with different concentrations of various solvents. The sorption amount of aromatic solvents by both p‐CT (A‐M) and TCE (A‐M) mesophase membranes was higher than that of aliphatic solvents, regardless of the size, shape, and nature of the molecular cavity. The 2θ peak of the [010] plane of the sPS membranes slowly approached the original δ‐form value when the sPS mesophase membranes were immersed in various solvents of different concentrations for 48 h. The shifting of the 2θ peak of the [010] plane to the original δ form depended on the nature and concentration of the immersion solvents. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2380–2387, 2005     

Influence of the variable wall thickness of the sample tubes and a quartz Dewar on the EPR signal intensity in a single TE102 and double TE104 rectangular cavity

The response of a single TE₁₀₂ and double TE₁₀₄ rectangular cavity to the insertion of samples contained in tubes with variable wall thickness and a quartz Dewar into the cavity has been analyzed. A direct, indirect, and concurrent (positive or negative) “lens effect” inside the double TE₁₀₄ rectangular cavity is discussed. The experimental dependence of the EPR signal intensity on the wall thickness of the sample tube, δ, for the line-like samples with identical length of the sample material column, L=30 mm, recorded in the microwave cavity showed a directly proportional increase of the relative “lens effect” with the increase of the wall thickness of the tube in the interval, δ∈<0.1 mm, >0.5 mm. The insertion of the variable-temperature double-wall quartz Dewar (home-built, resonant frequency shift, ca. −300 MHz) into the single TE₁₀₂ rectangular cavity showed the same relative “lens effect”, with ca. 1.5-time increase of the EPR signal intensity, for a point-like sample and the line-like samples with material columns of diameter of 1 and 1.3 mm, and wall thickness of the sample tubes, δ∈<0.1 mm, >0.5 mm. The increased effect of the Dewar arises because the active volume of the quartz Dewar tube walls is always much more larger than the active volume of the sample tube wall. In the case of the double TE₁₀₄ rectangular cavity, the insertion of the quartz Dewar: (i) into the same cavity, in which the sample is present, caused a direct “lens effect”, with ca. 1.8-fold increase of the EPR signal intensity; however, (ii) into the complementary cavity, in which the sample is absent, caused an indirect “lens effect”, with ca. 0.6-fold decrease of the EPR signal intensity. With the Dewar and sample in one cavity and a large empty sample tube in the complementary cavity, a concurrent (positive or negative) “lens effect” can be observed. Thus, the possible increase/decrease of the EPR signal intensity depends on the volume ratio of the quartz Dewar tube walls and large sample tube wall inserted into the double TE₁₀₄ rectangular cavity. Each of the above phenomena may be a significant source error in quantitative EPR spectrometry unless the samples to be compared in the quantitative EPR analysis are contained in sample tubes having the same wall thickness and each EPR spectra should be recorded inside an identical quartz Dewar.     

腔长失调对光腔衰荡法测量精度的影响

 只考虑腔长失调因素下建立了反射率模拟测量的理论模型。根据高斯光束传输规律分析了腔长失调对衰荡腔模式耦合的影响，推导了腔长失调与谐振腔输出脉冲信号、衰荡信号与反射率之间的关系，模拟了腔长失调在±10mm范围内的光脉冲衰荡现象。结果表明：对于光敏面直径为0.2mm的高速探测器，为了保证10^-6的测量精度，腔长的失调量应控制在±1mm之间。在光路调节中采用具有对数变换功能的示波器和动态范围较大的探测器，可以提高测量精度。     

回旋速调管放大器输出腔的特性研究

 利用变截面波导的耦合模理论，根据输出腔中电场幅值分布函数所满足的微分方程组，编写了具有自动优化功能的计算程序，分析研究了不同渐变角度、考虑腔体损耗前后和输出腔与外电路失配时，谐振频率、腔体品质因数和高频场幅值沿轴分布的变化情况，为进一步研究高频场与电子注的互作用和输出腔奠定了基础。     

宽体液腔Janus-Helmholtz换能器

该文使用有限元方法对宽体液腔Janus-Helmholtz(JH)换能器进行了仿真分析,得出了壳体宽度拓展增量对JH换能器工作性能的影响规律。使用三维建模的方式,分析了连接部分对换能器性能的影响及宽体壳体的模态,证明了三维建模的必要性。依据仿真优化结构设计了一款宽体液腔JH换能器并进行了湖上测试。最终测试结果与仿真结果有很好的一致性,相较直筒JH换能器其谐振频率降低300 Hz,发射电压响应最高可达144 dB。     

Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems

Nonequilibrium work relations and fluctuation theorems permit us to extract equilibrium information from nonequilibrium measurements. They find application in single-molecule pulling experiments where molecular free energies can be determined from irreversible work measurements by using unidirectional (e.g., Jarzynski’s equality) and bidirectional (e.g., Crooks fluctuation theorem and Bennet’s acceptance ratio (BAR)) methods. However, irreversibility and the finite number of pulls limit their applicability: the higher the dissipation, the larger the number of pulls necessary to estimate ΔG within a few kBT. Here, we revisit pulling experiments on an RNA three-way junction (3WJ) that exhibits significant dissipation and work-distribution long tails upon mechanical unfolding. While bidirectional methods are more predictive, unidirectional methods are strongly biased. We also consider a cyclic protocol that combines the forward and reverse work values to increase the statistics of the measurements. For a fixed total experimental time, faster pulling rates permit us to efficiently sample rare events and reduce the bias, compensating for the increased dissipation. This analysis provides a more stringent test of the fluctuation theorem in the large irreversibility regime.     

北京大学DC-SC光阴极注入器的升级设计

 基于直流电子枪-超导加速腔（DC-SC）光阴极注入器样机的初步实验结果,北京大学提出了新的注入器的改进设计。新注入器核心结构包括皮尔斯枪和3+1/2超导腔。文章给出了它们的详细结构参数,然后采用程序,对注入器的束流动力学进行了模拟。结果发现：新注入器可以提供具有高束流品质、高平均流强的电子束,束团的电荷量100 pC,横向发射度低于2 mm·mrad,脉宽5 ps,rms束斑可达0.5 mm,重复频率81.25 MHz;也可以提供电荷量为300 pC低重复频率的高峰值流强的电子束,其横向发射度小于3 mm·mrad,脉宽约为9 ps,以满足北京大学自由电子激光（PKU-FEL）实验平台的要求。