A C + + computational environment for biomolecular sequence management

The wide production of biomolecular data of the last 30 years, mainly due to the rapid evolving of technologies as well as to the accomplishment of the Genome Projects, led to the necessity of appropriate computational approaches for data storage, manipulation and analyses, giving place to a fast evolving area of Biology: Computational Biology or Bioinformatics.We propose here a new method for the storage of the sequences and their analyses using the C + + programming language, checking the effectiveness of an object oriented approach for new models, suitable to manage data representation and analyses, to improve the efficiency of computational methodologies to solve problems of general interest in bioinformatics. We developed a framework with the aim to decrease the computational costs for the storage and some basic manipulations of nucleic acid sequences. The remarkable reduction of memory requirements with no loss of efficiency makes this approach a first well promising step in order to get a more efficient environment for the manipulation and the management of nucleic acid data sets, in a field of research with hard challenges for Computer and Life Sciences.Mathematics Subject Classification: 68U99G. Toraldo, via Universita’ 100, 80055 Portici, Napoli, Italy     

非定常的热传导-对流问题的非线性Galerkin混合元法(Ⅲ):时间二阶精度的全离散格式

In this paper, a fully discrete format of nonlinear Galerkin mixed element method with two-step discretization of time for the non stationary conduction-convection problems is presented. The existence and the convergence of the fully discrete mixed element solution are shown. On the basis of [9] and [10], we have proved that the schemes have second-order convergence accuracy for the time discretization.     

二维双曲方程基于POD方法的降阶有限差分外推迭代格式

利用特征投影分解(POD)方法建立二维双曲型方程的一种基于POD方法的含有很少自由度但具有足够高精度的降阶有限差分外推迭代格式,给出其基于POD方法的降阶有限差分解的误差估计及基于POD方法的降阶有限差分外推迭代格式的算法实现.用一个数值例子去说明数值计算结果与理论结果相吻合.进一步说明这种基于POD方法的降阶有限差分外推迭代格式对于求解二维双曲方程是可行和有效的.     

Optimal control of self-organized dynamics in cellular signal transduction

We demonstrate how model-based optimal control can be exploited in biological and biochemical modelling applications in several ways. In the first part, we apply optimal control to a detailed kinetic model of a glycolysis oscillator, which plays a central role in immune cells, in order to analyse potential regulatory mechanisms in the dynamics of associated signalling pathways. We demonstrate that the formulation of inverse problems with the aim to determine specific time-dependent input stimuli can provide important insight into dynamic regulations of self-organized cellular signal transduction. In the second part, we present an optimal control study aimed at target-oriented manipulation of a biological rhythm, an internal clock mechanism related to the circadian oscillator. This oscillator is responsible for the approximate endogenous 24 h (latin: circa dies) day-night rhythm in many organisms. On the basis of a kinetic model for the fruit fly Drosophila, we compute switching light stimuli via mixed-integer optimal control that annihilate the oscillations for a fixed time interval. Insight gained from such model-based specific manipulation may be promising in biomedical applications.     

Automatic Smoothing With Wavelets for a Wide Class of Distributions

Wavelet-based denoising techniques are well suited to estimate spatially inhomogeneous signals. Waveshrink (Donoho and Johnstone) assumes independent Gaussian errors and equispaced sampling of the signal. Various articles have relaxed some of these assumptions, but a systematic generalization to distributions such as Poisson, binomial, or Bernoulli is missing. We consider a unifying l₁-penalized likelihood approach to regularize the maximum likelihood estimation by adding an l₁ penalty of the wavelet coefficients. Our approach works for all types of wavelets and for a range of noise distributions. We develop both an algorithm to solve the estimation problem and rules to select the smoothing parameter automatically. In particular, using results from Poisson processes, we give an explicit formula for the universal smoothing parameter to denoise Poisson measurements. Simulations show that the procedure is an improvement over other methods. An astronomy example is given.     

AMlet,RAMlet, and GAMlet: Automatic Nonlinear Fitting of Additive Models,Robust and Generalized,With Wavelets

A simple and yet powerful method is presented to estimate nonlinearly and nonparametrically the components of additive models using wavelets. The estimator enjoys the good statistical and computational properties of the Waveshrink scatterplot smoother and it can be efficiently computed using the block coordinate relaxation optimization technique. A rule for the automatic selection of the smoothing parameters, suitable for data mining of large datasets, is derived. The wavelet-based method is then extended to estimate generalized additive models. A primal-dual log-barrier interior point algorithm is proposed to solve the corresponding convex programming problem. Based on an asymptotic analysis, a rule for selecting the smoothing parameters is derived, enabling the estimator to be fully automated in practice. We illustrate the finite sample property with a Gaussian and a Poisson simulation.     

新一代运载火箭时序仿真系统信号完整性分析

新一代运载火箭时序仿真系统具有数字电路速度快、集成度高的特点,系统要求发出多路高精度时序、时串信号以满足新一代运载火箭地面测试设备的检查与校准需求,因此信号完整性问题在系统设计中不容忽视。针对仿真系统的典型模块(USB 3.0 Super-speed差分线、FPGA外设数据走线、时钟走线)进行建模分析仿真得出PCB硬件电路设计参数,给出时序仿真系统设计信号完整性问题的抑制和解决方法,优化了板级信号质量,改善系统可靠性、工作连续性和输出精度,可有效提高新一代运载火箭测试效率和测试可靠性。     

Single‐crystal diffraction at the Extreme Conditions beamline P02.2: procedure for collecting and analyzing high‐pressure single‐crystal data

Fast detectors employed at third‐generation synchrotrons have reduced collection times significantly and require the optimization of commercial as well as customized software packages for data reduction and analysis. In this paper a procedure to collect, process and analyze single‐crystal data sets collected at high pressure at the Extreme Conditions beamline (P02.2) at PETRA III, DESY, is presented. A new data image format called `Esperanto' is introduced that is supported by the commercial software package CrysAlis^Pro (Agilent Technologies UK Ltd). The new format acts as a vehicle to transform the most common area‐detector data formats via a translator software. Such a conversion tool has been developed and converts tiff data collected on a Perkin Elmer detector, as well as data collected on a MAR345/555, to be imported into the CrysAlis^Pro software. In order to demonstrate the validity of the new approach, a complete structure refinement of boron‐mullite (Al₅BO₉) collected at a pressure of 19.4 (2) GPa is presented. Details pertaining to the data collections and refinements of B‐mullite are presented.     

EPR-NMR Signal Enhancement with a Small Computer

A Digital Equipment Corporation PDP 8/S Computer is interfaced with an EPR Spectrameter to achieve signal enhancement.

A computer-based system for spectrum accumulation and noise averaging of EPR or NMR signals has been designed and implemented. The computer-based system was chosen over other perhaps more conventional systems because of its greater flexibility in the processing of spectra, especially after the accumulation is complete.(1)     

Application of adaptive time-frequency decomposition in ultrasonic NDE of highly-scattering materials

In the paper, adaptive time-frequency decomposition by basis pursuit (BP) is utilized to improve ultrasonic flaw detection in highly-scattering materials as an alternative to the Wavelet Transform technique. The detection of ultrasonic pulses using the BP is described. Computer simulation was performed to verify the signal detection improvements for an ultrasonic wave embodied in white noise, and numerical results show good detection even for signal-noise ratio (SNR) of -18 dB. The improvement in detection is experimentally verified using cast steel samples with artificial flaws.