Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

---

Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

Correction for the Concentration Polarization for Simultaneous Reduction of Several Reactants: Platinum(II) Aquachloride Complexes

The reaction of electroreduction of platinum(II) aquachloride complexes on a negatively charged dropping mercury electrode is used to determine specific features of interpretation of experimental data in the case of parallel conversion of several forms of a reactant, connected with the manner of introducing a correction for the concentration polarization. The difference in the charges of species undergoing simultaneous reduction gives rise to ambiguity when analyzing kinetic data on the dependence of current on the supporting-electrolyte concentration at constant electrode charge. A new self-consistent technique for deducing model parameters (ratio between reactant discharge rate constants) is proposed.     

Complexation of Ni (II) and Zn(II) ions by 3-(1-naphthyI)-2-mercaptopropenoic acid

The complexation equilibria between Ni(II) and Zn(II) metal ions with 3-(1-naphthyl)-2-mercaptopropenoic acid (H₂NMP) were studied by glass electrode potentiometry, at 25 °C and 1.0 mol·dm^–3 in NaClO₄ as constant ionic medium in 50% (v/v) water-ethanol solutions. Formation constants for the complexes Ni(NMP), Ni(NMP) ₂ ^2– , Zn(NMP) and Zn(NMP) ₂ ^2– , refined by the MINIGLASS program, are reported.     

A Space-Time Polynomial Collocation Method for Solving 3D Burgers Equations北大核心CSCD

Burgers方程是一类应用广泛的非线性偏微分方程,方程中的非线性项难以处理。该文提出一种新的时空多项式配点法——多项式特解法求解三维Burgers方程。求解过程分为两步:第一步,对三维Burgers方程中的线性导数项(包括时间导数项),求出相应的多项式特解。第二步,将求出的多项式特解作为基函数,对三维Burgers方程中剩余的非线性项进行迭代求解。与时空多项式函数作为基函数对三维Burgers方程进行直接求解相比,该算法简单易行,得到的近似解精度非常高,算法极其稳定,对于教学过程中提高学生的编程能力,加深对高维Burgers方程的理解能力以及Burgers方程的实际应用具有重要意义。     

Stability of multistage stochastic programming

In this paper, we study the stability of multistage stochastic programming with recourse in a way that is different from that used in studying stability of two-stage stochastic programs. Here, we transform the multistage programs into mathematical programs in the space ⁿ ×L _p with a simple objective function and multistage stochastic constraints. By investigating the continuity of the multistage multifunction defined by the multistage stochastic constraints and applying epi-convergence theory we obtain stability results for linear and linear-quadratic multistage stochastic programs.Project supported by the National Natural Science Foundation of China.     

Misclassification minimization

The problem of minimizing the number of misclassified points by a plane, attempting to separate two point sets with intersecting convex hulls inn-dimensional real space, is formulated as a linear program with equilibrium constraints (LPEC). This general LPEC can be converted to an exact penalty problem with a quadratic objective and linear constraints. A Frank-Wolfe-type algorithm is proposed for the penalty problem that terminates at a stationary point or a global solution. Novel aspects of the approach include: (i) A linear complementarity formulation of the step function that counts misclassifications, (ii) Exact penalty formulation without boundedness, nondegeneracy or constraint qualification assumptions, (iii) An exact solution extraction from the sequence of minimizers of the penalty function for a finite value of the penalty parameter for the general LPEC and an explicitly exact solution for the LPEC with uncoupled constraints, and (iv) A parametric quadratic programming formulation of the LPEC associated with the misclassification minimization problem.This material is based on research supported by Air Force Office of Scientific Research Grant F49620-94-1-0036 and National Science Foundation Grants CCR-9101801 and CDA-9024618.     

Retrieval and chaos in extremely dilutedQ-Ising neural networks

Using a probabilistic approach, the deterministic and the stochastic parallel dynamics of aQ-Ising neural network are studied at finiteQ and in the limitQ. Exact evolution equations are presented for the first time-step. These formulas constitute recursion relations for the parallel dynamics of the extremely diluted asymmetric versions of these networks. An explicit analysis of the retrieval properties is carried out in terms of the gain parameter, the loading capacity, and the temperature. The results for theQ network are compared with those for theQ=3 andQ=4 models. Possible chaotic microscopic behavior is studied using the time evolution of the distance between two network configurations. For arbitrary finiteQ the retrieval regime is always chaotic. In the limitQ the network exhibits a dynamical transition toward chaos.     

Migration of seismic data

Prospecting for oil and gas resources poses the problem of determining the geological structure of the earth's crust from indirect measurements. Seismic migration is an acoustic image reconstruction technique based on the inversion of the scalar wave equation. Extensive computation is necessary before reliable information can be extracted from large sets of recorded data. In this paper a collection of industrial migration techniques, each giving rise to a data parallel algorithm, is outlined. Computer simulations on synthetic seismic data illustrate the problem and the approach.     

一种利用小波降噪的卫星导航信号并行捕获算法

针对全球定位系统（Global Positioning System,GPS）接收机传统捕获算法计算复杂度高、捕获灵敏度低等缺点,提出了一种可降噪的简化并行码相位捕获（Noise Reduction for Simplified Parallel Code Phase Acquisition,NR-SPCA）算法。该算法通过对信号降采样,利用小波变换对二次采样信号作降噪处理,提高了捕获灵敏度;利用GPS信号和C/A码互相关的稀疏性,并行计算降噪后的信号的相关值,提高了运算效率。仿真结果表明,在90%概率捕获成功的前提下,NR-SPCA算法比传统的PCA算法信噪比低1 dB,运算效率提升了100%。该算法还可应用于航天探测、自动驾驶等领域。     

An Artificial Autonomic Nervous System That Implements Heart and Pupil as Controlled by Artificial Sympathetic and Parasympathetic Nerves

The autonomic nervous system maintains homeostasis in organisms through complex neural pathways and responds adaptively to changes in the external and internal environment. The fabrication of an artificial autonomic nervous system is reported that replicates combined effects of sympathetic and parasympathetic nerves on cardiac activity and pupillary control, to mimic the regulation of autonomic nervous system to external changes. The artificial autonomic nerve-controlled pupil contraction and relaxation, modulating the rate of heartbeats for normal cardiac rhythm and arrhythmia as reflected by blink rates of a signal indicator. These functions are switched by using a parallel-channeled synaptic transistor with a special n-i-p heterostructure that has a 2D h-BN insulator in the middle to provide barrier against ion injection into the 2D MoS₂ bottom n-channel and enable short-term plasticity as induced by acetylcholine, and the electrochemical doping reaction occurred at the P3HT nanowire p-channels on top to enable relatively long-term plasticity as induced by noradrenaline. Low-energy consumption down to femtojoule and an ultrahigh paired-pulse facilitation index up to ≈455% are demonstrated. An artificial neural network based on device characteristics achieves a high recognition accuracy for electrocardiogram patterns. This study extends insights into artificial nerves-inspired biological signal processing and recognition.