Molecular solutions to the binary integer programming problem based on DNA computation

Binary optimization is a widely investigated topic in integer linear programming. This study proposes a DNA-based computing algorithm for solving the significantly large binary integer programming (BIP) problem. The proposed approach is based upon Adleman and Lipton's DNA operations to solve the BIP problem. The potential of DNA computation for the BIP problem is promising given the operational time complexity of O(nxk).     

基于血流多普勒原理的血压测量系统设计

血流信号的采集可基于超声多普勒技术。利用多普勒超声探头在肢体主动脉脉搏处采集到血流多普勒频移信号,对信号电压进行放大,一方面直接输入扬声器转变为音频信号,得到多普勒音;同时用频率/电压变换器LM331变换多普勒频移信号,得到脉搏波信号。基于此原理,设计了使用无创、直观的方法获得肢体血流参数,并经PC机处理,最终在显示器上显示脉搏波形和血压数值的方法。     

0-1整数规划问题的半自动化DNA计算模型

对一般的0—1整数规划问题提出了一种半自动化的DNA计算模型。首先产生所给定的0—1整数规划问题的所有可能解,然后设置对应于0—1整数规划问题的约束不等式的探针,利用这些探针设计半自动化装置对所有可能解进行自动分离,最终找出0—1整数规划问题的解。该模型的最大优点在于具有自动化的特点;同时,从理论上来讲,该模型适合含有任意变量的任意0—1整数规划问题的求解。     

分子信标DNA计算模型的研究进展与展望

由于分子信标具有结构简单,灵敏度高及反应迅速等优点,因此,利用分子信标进行数学问题的求解将成为可能.通过对分子信标的计算模型进行详细的介绍,并对分子信标的计算模型的研究思路进行了展望,据此思路,可以建立多种组合优化问题及逻辑门的分子信标计算模型.     

Effects of transmural electrical heterogeneities and electrotonic interactions on the dispersion of cardiac repolarization and action potential duration: A simulation study

It has been shown in the literature that myocytes isolated from the ventricular walls at various intramural depths have different action potential durations (APDs). When these myocytes are embedded in the ventricular wall, their inhomogeneous properties affect the sequence of repolarization and the actual distribution of the APDs in the entire wall. In this article, we implement a mathematical model to simulate the combined effect of (a) the non-homogeneous intrinsic membrane properties (in particular the non-homogeneous APDs) and (b) the electrotonic currents that modulate the APDs when the myocytes are embedded in the ventricular myocardium. In particular, we study the effect of (a) and (b) on the excitation and repolarization sequences and on the distribution of APDs in the ventricles. We implement a Monodomain tissue representation that includes orthotropic anisotropy, transmural fiber rotation and homogeneous or heterogeneous transmural intrinsic membrane properties, modeled according to the phase I Luo-Rudy membrane ionic model. Three-dimensional simulations are performed in a cartesian slab with a parallel finite element solver employing structured isoparametric trilinear finite elements in space and a semi-implicit adaptive method in time. Simulations of excitation and repolarization sequences elicited by epicardial or endocardial pacing show that in a homogeneous slab the repolarization pathways approximately follow the activation sequence. Conversely, in the heterogeneous cases considered in this study, we observed two repolarization wavefronts that started from the epi and the endocardial faces respectively and collided in the thickness of the wall and in one case an additional repolarization wave starting from an intramural site. Introducing the heterogeneities along the transmural epi-endocardial direction affected both the repolarization sequence and the APD dispersion, but these effects were clearly discernible only in transmural planes. By contrast, in planes parallel to epi- and endocardium the APD distribution remained remarkably similar to that observed in the homogeneous model. Therefore, the patterns of the repolarization sequence and APD dispersion on the epicardial surface (or any other intramural surface parallel to it) do not reveal the uniform transmural heterogeneity.     

Real-Time and Remote MCMC Trace Inspection with Beastiary

Bayesian phylogenetics has gained substantial popularity in the last decade, with most implementations relying on Markov chain Monte Carlo (MCMC). The computational demands of MCMC mean that remote servers are increasingly used. We present Beastiary, a package for real-time and remote inspection of log files generated by MCMC analyses. Beastiary is an easily deployed web-app that can be used to summarize and visualize the output of many popular software packages including BEAST, BEAST2, RevBayes, and MrBayes via a web browser. We describe the design and implementation of Beastiary and some typical use-cases, with a focus on real-time remote monitoring.     

甘肃鼠兔贮草越冬及其生物学意义

对采自草甸、灌丛和弃耕地3 种类型栖息地共27 个甘肃鼠兔草堆的研究结果表明, 每个草堆干重在23.8～984.2 g 之间, 平均184.2 g , 总计含有26 种双子叶植物和一些禾本科单子叶植物。分析显示, 草堆大小(食物重量) 与栖息地植被类型无关。在贮存干草堆时, 甘肃鼠兔对不同植物成分具有强烈的选择性, 其中, 单子叶植物和双子叶植物分别占总重量的8.06 %和84.61 % , 与它们各自在栖息地中的生物量百分比51.76 %和39.57 %形成鲜明对照。甘肃鼠兔对植物种类的选择性在一定程度上受栖息地植被类型的影响, 但最喜食的几种植物却基本不变, 它们是美丽风毛菊、棘豆、麻花艽、禾草、线叶龙胆。人工去除栖息地中的干草堆后, 甘肃鼠兔种群越冬存活率从对照样地的51.84 %下降到21.33 % , 表明草堆食物对其成功越冬有一定正效应。野外观察证实, 甘肃鼠兔的鸣声不及同域分布的高原鼠兔发达, 但前者具有贮存食物越冬的习性, 而后者却不贮存越冬食物, 此结果不支持“鼠兔类动物建立草堆的行为与鸣声行为平行发育”的观点。     

微生物连续发酵酶催化动力系统的鲁棒性与并行计算

依据甘油连续发酵生产1,3-丙二醇的非线性酶催化动力系统.针对1,3-丙二醇可能存在的跨膜运输方式建立相应的动力学模型,提出了酶催化动力系统的定量鲁棒性定义,并建立了以鲁棒性为性能指标、非线性动力系统为主要约束的参数辨识模型.由于求解该辨识问题的数值计算量大,在普通的PC机上难以完成,因此本文构建了相应的并行算法.根据数值结果推断出1,3-丙二醇最有可能的跨膜运输方式,这对于进一步研究甘油连续发酵的机理具有重要的参考价值.     

Towards molecular computing: co-development of microfluidic devices and chemical reaction media

Microfluidics provides a powerful technology for both the production of molecular computing components and for the implementation of molecular computing architectures. The potential commercial applications of microfluidics drive rapid progress in this field-but at the same time focus interest on materials that are compatible with physiological aqueous conditions. For engineering applications that consider a broader range of physico-chemical conditions the narrow set of established materials for microfluidics can be a challenge. As a consequence of the large surface to volume ratio inherent in microfluidic technology the material of the device can greatly affect the chemistry in the channels of the device. In practice it is necessary to co-develop the chemical medium to be used in the device together with the microfluidic devices. We describe this process for a molecular computing architecture that makes use of excitable lipid-coated droplets of Belousov-Zhabotinsky reaction medium as its active processing components. We identify fluoropolymers with low melting temperature as a suitable substrate for microfluidics to be used in conjunction with Belousov-Zhabotinsky droplets in decane.