遗传密码的进化稳定性

本评述了遗传密码的进化有关的物理问题。主要讨论了：1）从进化稳定性的观点研究遗传密码的简并规则,证明了现有密码表中多重态的简并规则是突变危险性极小的;2）从进化稳定性的观点研究了遗传密码表中氨基酸和终止密码子的排布,导出了总体突变危险性极小的表,并证明了标准密码表是在某些约束（这些约束反映了密码形成时期的初始条件）下总体突变危险性极小的表;3）密码表中20种氨基酸和终止密码简并度的分布,以及改变简并度条件下密码反常的出现。     

遗传密码的进化稳定性

本文评述了遗传密码的进化有关的物理问题。主要讨论了 :1 )从进化稳定性的观点研究遗传密码的简并规则 ,证明了现有密码表中多重态的简并规则是突变危险性极小的 ;2 )从进化稳定性的观点研究了遗传密码表中氨基酸和终止密码子的排布 ,导出了总体突变危险性极小的表 ,并证明了标准密码表是在某些约束 (这些约束反映了密码形成时期的初始条件 )下总体突变危险性极小的表 ;3)密码表中 2 0种氨基酸和终止密码简并度的分布 ,以及改变简并度条件下密码反常的出现     

The coevolution theory of the origin of the genetic code

A review of the coevolution theory of the origin of the genetic code is presented. This theory maintains that the origin of the code should be sought in the biosynthetic relationships between amino acids. In particular, some amino acids, the precursors, occupied the structure of the genetic code early on. As the product amino acids developed from these precursors, part or all of the codon domain of the precursor amino acid was ceded to the product amino acids, which resulted in the structuring of the genetic code. This paper therefore reviews the evidence in favour of this theory. The existence of some molecular fossils representing the biosynthetic pathways on which the coevolution theory suggests biosynthetic transformations took place (precursor amino acid → product amino acid) seems to be a strong corroboration of this theory. A generalisation imposed by this theory on the ancestral metabolic state is then discussed and, finally, the main prospects that seem to stem from the coevolution theory are presented.     

遗传密码是怎样破译的

文章具体介绍了遗传密码破译的过程：三联体密码的提出；克里克对遗传密码性质的阐述和实验证明；尼伦伯格关于同聚核苷酸对应的氨基酸的发现；奥乔亚关于异聚核苷酸对应的氨基酸的发现；科拉纳关于密码子系列次序的确定；全部密码子的破译及其特征．     

The Chern‐Simons Current in Systems of DNA‐RNA Transcriptions

A Chern‐Simons current, coming from ghost and anti‐ghost fields of supersymmetry theory, can be used to define a spectrum of gene expression in new time series data where a spinor field, as alternative representation of a gene, is adopted instead of using the standard alphabet sequence of bases . After a general discussion on the use of supersymmetry in biological systems, we give examples of the use of supersymmetry for living organism, discuss the codon and anti‐codon ghost fields and develop an algebraic construction for the trash DNA, the DNA area which does not seem active in biological systems. As a general result, all hidden states of codon can be computed by Chern‐Simons 3 forms. Finally, we plot a time series of genetic variations of viral glycoprotein gene and host T‐cell receptor gene by using a gene tensor correlation network related to the Chern‐Simons current. An empirical analysis of genetic shift, in host cell receptor genes with separated cluster of gene and genetic drift in viral gene, is obtained by using a tensor correlation plot over time series data derived as the empirical mode decomposition of Chern‐Simons current.     

The structural analysis of protein sequences based on the quasi-amino acids code

Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (∑,+,*) is introduced, where ∑ is the set of 64 codons. According to the characteristics of (∑,+,*), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕,○x) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of `the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3).     

Symmetry and codon usage correlations in the genetic code

The ratios of the codon usage in the quartets and sextets for the vertebrate series exhibit a correlated behaviour which fits naturally in the framework of the crystal basis model of the genetic code [1]. Moreover the observed universal behaviour of these suitably normalized ratios can be easily explained.     

基于拟氨基酸编码方法的同义密码子的偏好性与结合强度的相关性研究

计算了基于拟氨基酸编码方法下的同义密码子的相对使用度,分析了78个人类基因（19967个密码子）中基于拟氨基酸编码方法下的同义密码子的偏好使用情况.石秀凡等的研究结果显示了人类基因中基于基因组基因编码方法下,对同义密码子的选择在所有密码子家族中仍都呈现明显一致的偏好.即偏好使用密码子-反密码子结合作用强的密码子,恰好是以 c结尾的密码子;且避免使用结合作用中度的密码子.依据结果和数据分析, 推测人类基因对密码子的选择除了受基因组结构中 isochore和基因签名的影响外,还和密码子-反密码子结合强度密切相 关键词： 拟氨基酸编码方法 同义密码子 偏好 人类基因     

P53基因三周期性与密码子偏好性的相关性

为了进一步研究分析P53抑癌基因的性质,对P53基因的蛋白质编码区以及对应的mRNA的三周期性进行比较分析.通过同义密码子相对使用度和拟同义密码子相对使用度方法对其分别进行计算,分析了蛋白质编码区密码子的偏好性以及mRNA密码子的偏好性.结果表明:P53蛋白质编码区具有很强的三周期性,而对应的mRNA不具有三周期性;P53蛋白质编码区的密码子偏好G或C结尾的密码子程度强于对应的mRNA.说明P53基因密码子的偏好性与三周期性紧密相关,密码子的偏好程度影响着三周期性.进一步从生物角度诠释了P53蛋白质编码区和对应mRNA三周期性的异同.结合P53基因这一特性,有助于提高其基因识别的正确率,对P53基因的深入研究具有重要的意义.     

OCDMA系统中2-D码和3-D码

光码分多址(OCDMA)技术主要应用在接入网中。设计大容量的地址码是该技术实用化的前提。本文在构造2 D素数码的基础上提出了一种用于OCDMA系统的空域/频域/时域3 D地址码。这种码基于素数序列运算。理论分析和数学计算结果表明，3 D码比2 D码的容量更大，系统带宽效率更高，误码率(BER)更低，表现出的性能更好。     

Genetic code: Lucky chance or fundamental law of nature?

The amount of publications devoted to the rise and structure of the genetic code is ever-increasing, which include semantic and structural analyses of the code as well as the problem of the origin of the code among others. The genetic code consisting of its triplet structure and canonical sets of nucleotides and amino acids was previously suggested to be a frozen accident or the result of accidental selection in the process of the evolution of a prebiotic system. These ideas are reviewed in this paper. It becomes clear that the information code is intrinsically related to the physical laws of the universe, and thus life may be an inevitable outcome of our universe. The lack of success in explaining the origin of the code and life itself in the last several decades suggest that we miss something very fundamental about life, possibly something fundamental about matter and the universe itself. Certainly, the advent of the genetic code was no “play of chance”.     

短波自由电子激光放大器数值模拟

介绍在理论上研究自由电子激光(FEL)的MICFEL程序。MICEFL是以单粒子理论为基础的二维放大器程序。利用MICFEL计算的Paladin实验结果与FRED程序计算结果以及25米Paladin实验结果相比均基本符合。理论计算的结果显示了FEL增益光导的特性。     

Information value and information content in the evolutionary strategy of the genetic code

Summary In previous papers we defined the information value of a genetic code as a measure of its efficiency in the utilization of the information stored in the DNA molecule. Here the genetic codes which have been proposed to be intermediate steps in evolution are analysed in terms of information theory. The results show that evolution follows an optimization strategy between increasing the information content and decreasing the information value,i.e. in each evolutionary step the average information value per unitary information content decreases and at the same time the probability of nonsense mutations goes down as the code evolves. To speed up publication, the authors of this paper have agreed to not recive the proofs for correction.     

Unique features of animal mitochondrial translation systems: – The non-universal genetic code,unusual features of the translational apparatus and their relevance to human mitochondrial diseases –

In animal mitochondria, several codons are non-universal and their meanings differ depending on the species. In addition, the tRNA structures that decipher codons are sometimes unusually truncated. These features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. These organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. It is plausible that these events brought about the various characteristic features of animal mt translation systems, such as genetic code variations, unusually truncated tRNA and rRNA structures, unilateral tRNA recognition mechanisms by aminoacyl-tRNA synthetases, elongation factors and ribosomes, and compensation for RNA deficits by enlarged proteins. In this article, we discuss molecular mechanisms for these phenomena. Finally, we describe human mt diseases that are caused by modification defects in mt tRNAs.     

高能γ探测系统中的光耦合部件参数优化

建立了Geant4软件粒子输运模拟平台,完成了核聚变高能射线能量-时间联合谱探测系统的探测效率计算数值建模;提出了遗传算法调用Geant4软件的射线探测系统参数优化方法。以自聚焦透镜前端与塑料闪烁体后端面的距离、自聚焦透镜后端面的长度及自聚焦透镜与通信光纤前端的距离为自变量,以耦合效率为适应度函数,实现了高能探测系统中由塑料闪烁体-自聚焦透镜-通信光纤组成的光耦合部件参数的优化算法。优化结果表明,该算法可以提高塑料闪烁体发出的荧光由自聚焦透镜耦合到通信光纤中的效率,最大可达4.77%。     

临界-燃耗耦合计算方法

基于蒙特卡罗模拟方法,采用MCNP的多群计算程序模拟中子输运方程,并与栅元均匀化程序WIMS耦合,实现了临界-燃耗耦合计算。具体过程是:首先扩展MCNP的多群功能,将其能群扩展为69群;然后,由接口程序将WIMS程序产生69群共振、自屏宏观中子截面转化为ACE格式的多群截面;其次,将新产生的多群截面提供给MCNP,完成临界-燃耗计算;最后,利用此耦合程序进行了基准题校核计算以及实验对比。计算结果表明,此耦合程序是可靠和正确的。     

Trade-offs between Error Exponents and Excess-Rate Exponents of Typical Slepian–Wolf Codes

Typical random codes (TRCs) in a communication scenario of source coding with side information in the decoder is the main subject of this work. We study the semi-deterministic code ensemble, which is a certain variant of the ordinary random binning code ensemble. In this code ensemble, the relatively small type classes of the source are deterministically partitioned into the available bins in a one-to-one manner. As a consequence, the error probability decreases dramatically. The random binning error exponent and the error exponent of the TRCs are derived and proved to be equal to one another in a few important special cases. We show that the performance under optimal decoding can be attained also by certain universal decoders, e.g., the stochastic likelihood decoder with an empirical entropy metric. Moreover, we discuss the trade-offs between the error exponent and the excess-rate exponent for the typical random semi-deterministic code and characterize its optimal rate function. We show that for any pair of correlated information sources, both error and excess-rate probabilities exponential vanish when the blocklength tends to infinity.     

Public-Key Cryptosystems and Bounded Distance Decoding of Linear Codes

Error-correcting codes form an important topic in information theory. They are used to correct errors that occur during transmission on a noisy channel. An important method for correcting errors is bounded distance decoding. The public-key cryptosystem is a cryptographic protocol that has two different keys. One of them is a public-key that can be known by everyone, and the other is the private-key only known to the user of the system. The data encrypted with the public-key of a given user can only be decrypted by this user with his or her private-key. In this paper, we propose a public-key cryptosystem based on the error-correcting codes. The decryption is performed by using the bounded distance decoding of the code. For a given code length, dimension, and error-correcting capacity, the new system allows dealing with larger plaintext than other code based public-key cryptosystems.     

用遗传算法构造光正交码

提出了一种利用遗传算法构造任意码长、码重、自相关限、互相关限光正交码(GA-OOC)的方法,设计了新的码字矩阵;分析了基于GA-OOC的光CDMA系统的误码率性能。仿真结果表明:该算法具有构造算法简单、易于编程实现的特点;与基于PC,EPC,QC和BIBD-OOC的光码分多址系统相比,GA-OOC的光码分多址系统具有更好的误码率性能。GA-OOC有望用于构造二维光地址码。