Automated estimation of rare event probabilities in biochemical systems

In biochemical systems, the occurrence of a rare event can be accompanied by catastrophic consequences. Precise characterization of these events using Monte Carlo simulation methods is often intractable, as the number of realizations needed to witness even a single rare event can be very large. The weighted stochastic simulation algorithm (wSSA) [J. Chem. Phys. 129, 165101 (2008)] and its subsequent extension [J. Chem. Phys. 130, 174103 (2009)] alleviate this difficulty with importance sampling, which effectively biases the system toward the desired rare event. However, extensive computation coupled with substantial insight into a given system is required, as there is currently no automatic approach for choosing wSSA parameters. We present a novel modification of the wSSA--the doubly weighted SSA (dwSSA)--that makes possible a fully automated parameter selection method. Our approach uses the information-theoretic concept of cross entropy to identify parameter values yielding minimum variance rare event probability estimates. We apply the method to four examples: a pure birth process, a birth-death process, an enzymatic futile cycle, and a yeast polarization model. Our results demonstrate that the proposed method (1) enables probability estimation for a class of rare events that cannot be interrogated with the wSSA, and (2) for all examples tested, reduces the number of runs needed to achieve comparable accuracy by multiple orders of magnitude. For a particular rare event in the yeast polarization model, our method transforms a projected simulation time of 600 years to three hours. Furthermore, by incorporating information-theoretic principles, our approach provides a framework for the development of more sophisticated influencing schemes that should further improve estimation accuracy.     

RgBF2(+) complexes (Rg = Ar, Kr, and Xe): the cations with large stabilities

Rare gas containing cations with general formula [Rg, B, 2F](+) have been investigated theoretically by second-order Mo?ller-Plesset perturbation, coupled cluster, and complete active space self-consistent field levels of theory with correlation-consistent basis sets. Totally two types of minima, i.e., boron centered C(2) (v) symmetried RgBF(2) (+) (Rg = Ar, Kr, and Xe) which can be viewed as loss of F(-) from FRgBF(2) and linear FRgBF(+) (Rg = Kr and Xe) are obtained at the CCSD(T)∕aug-cc-pVTZ∕SDD and CASSCF(10,8)∕aug-cc-pVTZ∕SDD levels, respectively. It is shown that the RgBF(2) (+) are global minima followed by FRgBF(+) at 170.9 and 142.2 kcal∕mol on the singlet potential-energy surfaces of [Rg, B, 2F](+) (Rg = Kr and Xe) at the CASPT2(10,8) ∕aug-cc-pVTZ∕SDD∕∕CASSCF(10,8)∕aug-cc-pVTZ∕SDD, respectively. The interconversion barrier heights between RgBF(2) (+) and FRgBF(+) (Rg = Kr and Xe) are at least 39 kcal∕mol. In addition, no dissociation transition state associated with RgBF(2) (+) and FRgBF(+) can be found. This suggests that RgBF(2) (+) (Rg = Ar, Kr, and Xe) can exist as both thermodynamically and kinetically stable species, while linear FRgBF(+) (Rg = Kr and Xe) can exist as metastable species compared with the lowest dissociation limit energies just like isoelectronic linear FRgBO and FRgBN(-). From natural bond orbital and atoms-in-molecules calculations, it is found that the positive charge is mainly located on Rg and boron atoms for both types of minima, the Rg-B bonds of ArBF(2) (+), KrBF(2) (+), and XeBF(2) (+) are mostly electrostatic, thus can be viewed as ion-induced dipole interaction; while that of linear FKrBF(+) and FXeBF(+) are covalent in nature. The previous experimental observation of ArBF(2) (+) by Pepi et al. [J. Phys. Chem. B. 110, 4492 (2006)] should correspond to C(2) (v) minimum. The presently predicted spectroscopies of KrBF(2) (+), XeBF(2) (+), FKrBF(+), and FXeBF(+) should be helpful for their experimental identification in the future.     

Non‐Geminate Recombination as the Primary Determinant of Open‐Circuit Voltage in Polythiophene:Fullerene Blend Solar Cells: an Analysis of the Influence of Device Processing Conditions

The physical origin of the open‐circuit voltage in bulk heterojunction solar cells is still not well understood. While significant evidence exists to indicate that the open‐circuit voltage is limited by the molecular orbital energies of the heterojunction components, it is clear that this picture is not sufficient to explain the significant variations which often occur between cells fabricated from the same heterojunction components. We present here an analysis of the variation in open‐circuit voltage between 0.4–0.65 V observed for a range of P3HT/PCBM solar cells where device deposition conditions, electrode structure, active‐layer thickness and device polarity are varied. The analysis quantifies non‐geminate recombination losses of dissociated carriers in these cells, measured under device operating conditions. It is found that at open‐circuit, losses due to non‐geminate recombination are sufficiently large that other loss pathways may effectively be neglected. Variations in open‐circuit voltage between different devices are shown to arise from differences in the rate coefficient for non‐geminate recombination, and from differences in the charge densities in the photoactive layer of the device. The origin of these differences is discussed, particularly with regard to variations in film microstructure. By separately quantifying these differences in rate coefficient and charge density, and by application of a simple physical model based upon the assumption that open‐circuit is reached when the flux of charge photogeneration is matched by the flux of non‐geminate recombination, we are able to calculate correctly the open‐circuit voltage for all the cells studied to within an accuracy of ±5 mV.     

我国科普动漫发展现状浅析

在21世纪的新媒体格局下,利用科普动漫进行科技传播已经成为科学技术普及的一种必不可少的手段和方式。但目前我国的科普动漫的发展与很多发达国家相比都较为落后。很多方面都存在着问题。要解决这些问题,需要国家要提出相应政策;建立科普动漫资源共建共享平台;搭建科普创作人才与动漫创作人才的交流与共同创作的平台。     

基于C~*Core的动态内存分配方案与实现

为了解决基于C*Core系列芯片嵌入式开发过程中,C*Core系统在某些情况下由于受操作系统、数据格式差异等因素影响,不能动态分配C*Core系列芯片内存的问题,采用数组与标志位相结合的方法,提出一种C*Core系列芯片在所有情况下都通用的动态内存分配方案。该方案利用C*Core C语言编写实现,程序在苏州国芯公司CS32XDV10开发板上运行后,成功实现了动态分配CCM3118芯片内存功能。     

分数像素快速块匹配运动估计方法综述

介绍了视频压缩中分数像素快速块匹配运动估计的基础原理,由于全搜索算法计算量很大,需要发展快速算法。对现有快速算法进行了研究总结,介绍了所应用的数学模型、向量预测、搜索优化、提前终止4个关键技术及代表算法。最后对分数像素快速块匹配运动估计方法进行了总结和展望。     

判奇电路实现方法探讨

以三输入判奇电路设计为例,通过对其输出函数表达式的形式变换,分别采用多种门电路及译码器、数据选择器等74系列器件进行电路设计,给出了7种电路实现形式,并分析了各种电路实现的优缺点。此例说明了组合逻辑电路设计的灵活性及电路实现的多样性。所采用的设计方法对其他组合逻辑电路设计具有一定的启发与指导意义。     

退火温度对高介电常数Ta2O5薄膜电学性能的影响

利用磁控溅射法在硅(Si)衬底上沉积了Ta2O5薄膜,对薄膜进行了不同温度的退火处理,并利用X射线衍射仪对薄膜的微观结构进行了分析.然后在Si的背面和介电薄膜的上面沉积Pt电极,组成了金属—氧化物—半导体( MOS)电容器,对不同温度下退火得到的薄膜制备的MOS电容器的电学性能进行了研究.结果表明,薄膜在700℃开始结...     

基于LDPC码的无线光通信副载波误码性能分析

为了研究信道编码技术对无线光通信副载波系统差错性能的影响,基于无线光通信链路噪声特性,建立了大气信道等效数学模型。采用低密度奇偶校验(LDPC)码作为信道编码方式引入无线光通信,在不同光强闪烁指数下对基于副载波相移键控调制无线光通信系统进行了差错性能仿真,比较分析了LDPC编码前后副载波调制系统的误比特率,并对二相相移键控及四相相移键控两种系统进行了对比。结果表明,副载波二相相移键控调制系统的差错性能优于四相相移键控系统,同时LDPC码在弱湍流信道具有优越的纠错能力,可以获得比未编码系统较高的编码增益,在无线光通信领域具有一定的应用价值。     

Infrared-induced reactivity of N2O on small gas-phase rhodium clusters

Far- and mid-infrared multiple photon dissociation spectroscopy has been employed to study both the structure and surface reactivity of isolated cationic rhodium clusters with surface-adsorbed nitrous oxide, Rh(n)N(2)O(+) (n = 4-8). Comparison of experimental spectra recorded using the argon atom tagging method with those calculated using density functional theory (DFT) reveals that the nitrous oxide is molecularly bound on the rhodium cluster via the terminal N-atom. Binding is thought to occur exclusively on atop sites with the rhodium clusters adopting close-packed structures. In related, but conceptually different experiments, infrared pumping of the vibrational modes corresponding with the normal modes of the adsorbed N(2)O has been observed to result in the decomposition of the N(2)O moiety and the production of oxide clusters. This cluster surface chemistry is observed for all cluster sizes studied except for n = 5. Plausible N(2)O decomposition mechanisms are given based on DFT calculations using exchange-correlation functionals. Similar experiments pumping the Rh-O stretch in Rh(n)ON(2)O(+) complexes, on which the same chemistry is observed, confirm the thermal nature of this reaction.