Facile Recoding of Selenocysteine in Nature

Selenocysteine (Sec or U) is encoded by UGA, a stop codon reassigned by a Sec‐specific elongation factor and a distinctive RNA structure. To discover possible code variations in extant organisms we analyzed 6.4 trillion base pairs of metagenomic sequences and 24 903 microbial genomes for tRNA^Sec species. As expected, UGA is the predominant Sec codon in use. We also found tRNA^Sec species that recognize the stop codons UAG and UAA, and ten sense codons. Selenoprotein synthesis programmed by UAG in Geodermatophilus and Blastococcus, and by the Cys codon UGU in Aeromonas salmonicida was confirmed by metabolic labeling with ⁷⁵Se or mass spectrometry. Other tRNA^Sec species with different anticodons enabled E. coli to synthesize active formate dehydrogenase H, a selenoenzyme. This illustrates the ease by which the genetic code may evolve new coding schemes, possibly aiding organisms to adapt to changing environments, and show the genetic code is much more flexible than previously thought.     

Automatic code generation for quantum chemistry applications

A unified, computer algebra system‐based scheme of code‐generation for computational quantum‐chemistry programs is presented. Generation of electron‐repulsion integrals and their derivatives as well as exchange‐correlation potential and its derivatives is discussed. Application to general‐purpose computing on graphics processing units is considered.     

距离边数矢量与分子相似度的计算

化学环境编码算法;分子相似度计算;距离边数矢量与分子相似度的计算     

QSPR Modeling of Gibbs Free Energy of Organic Compounds by Weighting of Nearest Neighboring Codes

We examine the encoding of chemical structure of organic compounds by Labeled Hydrogen-Filled Graphs (LHFGs). Quantitative Structure-Property Relationships (QSPR) for a representative set of 150 organic molecules have been derived by means of the optimization of correlation weights of local invariants of the LHFGs. We have tested as local invariants Morgan extended connectivity of zero- and first order, numbers of path of length 2 (P2) and valence shells of distance of 2 (S2) associated with each atom in the molecular structure, and the Nearest Neighboring Codes (NNC). The best statistical characteristics for the Gibbs free energy has been obtained for the NNC weighting. Statistical parameters corresponding to this model are the following n = 100, r² = 0.9974, s = 5.136 kJ/mol, F = 38319 (training set); n = 50, r² = 0.9990, s = 3.405 kJ/mol, F = 48717 (test set). Some possible further developments are pointed out.     

异种机文件传输转换的一种方法

异种计算机互连是现代计算机网络发展的主要方向,实现网络互连的目标之一是数据文件的共享。本文拟在讨论异种计算机之间实现互连之后,如何快速传送各种文件,并详细论述文件转换传输的实现原理。     

Intersections of q-ary perfect codes

The intersections of q-ary perfect codes are under study. We prove that there exist two q-ary perfect codes C ₁ and C ₂ of length N = qn + 1 such that |C ₁ ? C ₂| = k · |P _i |/p for each k ∈ {0,..., p · K ? 2, p · K}, where q = p ^r , p is prime, r ≥ 1, $n = \tfrac{{q^{m - 1} - 1}}{{q - 1}}$ , m ≥ 2, |P _i | = p ^nr(q?2)+n , and K = p ^{n(2r?1)?r(m?1)}. We show also that there exist two q-ary perfect codes of length N which are intersected by p ^nr(q?3)+n codewords.     

Distance regularity of Kerdock codes

A code is called distance regular, if for every two codewords x, y and integers i, j the number of codewords z such that d(x, z) = i and d(y, z) = j, with d the Hamming distance, does not depend on the choice of x, y and depends only on d(x, y) and i, j. Using some properties of the discrete Fourier transform we give a new combinatorial proof of the distance regularity of an arbitrary Kerdock code. We also calculate the parameters of the distance regularity of a Kerdock code.     

Maximum distance separable poset codes

We derive the Singleton bound for poset codes and define the MDS poset codes as linear codes which attain the Singleton bound. In this paper, we study the basic properties of MDS poset codes. First, we introduce the concept of I-perfect codes and describe the MDS poset codes in terms of I-perfect codes. Next, we study the weight distribution of an MDS poset code and show that the weight distribution of an MDS poset code is completely determined. Finally, we prove the duality theorem which states that a linear code C is an MDS -code if and only if is an MDS -code, where is the dual code of C and is the dual poset of      

Polyboxes,Cube Tilings and Rigidity

A non-empty subset A of X=X ₁×???×X _d is a (proper) box if A=A ₁×???×A _d and A _i ?X _i for each i. Suppose that for each pair of boxes A, B and each i, one can only know which of the three states takes place: A _i =B _i , A _i =X _i ?B _i , A _i ?{B _i ,X _i ?B _i }. Let F and G be two systems of disjoint boxes. Can one decide whether ∪F=∪G? In general, the answer is ‘no’, but as is shown in the paper, it is ‘yes’ if both systems consist of pairwise dichotomous boxes. (Boxes A, B are dichotomous if there is i such that A _i =X _i ?B _i .) Several criteria that enable to compare such systems are collected. The paper includes also rigidity results, which say what assumptions have to be imposed on F to ensure that ∪F=∪G implies F=G. As an application, the rigidity conjecture for 2-extremal cube tilings of Lagarias and Shor is verified.