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     

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     

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．     

Evolving genetic code

In 1985, we reported that a bacterium, Mycoplasma capricolum, used a deviant genetic code, namely UGA, a "universal" stop codon, was read as tryptophan. This finding, together with the deviant nuclear genetic codes in not a few organisms and a number of mitochondria, shows that the genetic code is not universal, and is in a state of evolution. To account for the changes in codon meanings, we proposed the codon capture theory stating that all the code changes are non-disruptive without accompanied changes of amino acid sequences of proteins. Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed.     

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.     

变分代数能量自洽法研究Li_2分子部分电子态的解析势能

在课题组前期建立的计算双核分子体系解析势能函数的代数能量自洽法(algebraic energy consistent method,AECM)的基础上,引入了经改进得到的精确研究双核分子完全振动能谱的变分代数法(variational algebraic method,VAM),获得了计算双核分子体系精确解析势能函数的变分代数能量自洽法(variational algebraic energy consistent method,VAECM)。基于有限的精确实验振动能谱数据,利用VAECM方法研究了Li_2分子1~3Δ_g,3~3Σ_g~+,1~3Σ_g~-和b~3Π_u等4个电子态的完全振动能谱和解析势能函数。获得了各电子态包含高阶的振动光谱常数、完全振动能谱、振动力常数fn和势能展开系数an,并通过可调变分参数λ最终确定了VAECM解析势能函数的具体表达形式。计算结果与其他方法的研究结果进行了比较,VAECM方法获得的振动能谱数据和势能解析表达形式能更好地描述这些电子态在渐近区和离解区的物理行为,消除了利用前期AECM方法研究这些电子态在离解区出现的非物理势垒现象。     

自旋弛豫时间测定对固体代谢物分子力学性质的研究

自旋弛豫时间测定是研究固体物质分子动力学性质的有效手段,已广泛应用于植物糖、氨基酸、维生素、肾上腺素以及睾丸激素等多类代谢物分子动力学性质的研究中. 近来上述方法也被用于其他代谢物分子动力学性质与其多晶型相变的关系以及对代谢物结构依赖性的研究. 该文将在介绍自旋弛豫时间及其测定方法的基础上,着重对自旋弛豫时间测定研究植物糖、氨基酸及其衍生物分子动力学性质的应用工作进行讨论.     

Towards a Model for Protein Production Rates

In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two “bottlenecks” (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel “edge” effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions. PACS numbers: 05.70.Ln, 64.90.+b, 87.14.Gg     

计算7Li2振动能级煌振动-转动能级的辛格式矩阵法

利用辛格式矩阵法计算了双原子分子⁷Li₂在A¹Σ_u⁺态的振动能级和振动-转动能级,并与Ley-Koo等的计算结果作了比较.结果显示,辛格式矩阵法是收敛的和可靠的,是计算双原子分子的振动能级和振动-转动能级的合理的数值方法.     

Embedding dynamics for round-off errors near a periodic orbit

We study the propagation of round-off errors near the periodic orbits of a linear map conjugate to a planar rotation with rational rotation number. We embed the two-dimensional discrete phase space (a lattice) in a higher-dimensional torus, where points sharing the same round-off error are uniformly distributed within finitely many convex polyhedra. The embedding dynamics is linear and discontinuous, with algebraic integer coefficients. This representation affords efficient algorithms for classifying and computing the orbits and their exact densities, which we apply to the case of rational rotation number with denominator 7, corresponding to certain algebraic integers of degree three. We provide evidence that the hierarchical arrangement of orbits previously detected in quadratic cases [Lowenstein et al., Chaos 7, 49-66 (1997)] disappears, and that the growth of the number of orbits with the period is algebraic.(c) 2000 American Institute of Physics.     

双原子分子离子XY+部分电子态完全振动能谱的精确研究

关于双原子分子离子XY 的完全振动能谱,目前还没有实验和理论的数据报道。本文首次应用代数方法AM(Algebraic Method),获得了BeH -X1Σ 态,CO -X2Σ 态,F2 -X2Πg态,O2 -A2Πu态和Li2 -X2Σg 态的精确振动光谱常数和完全振动能谱,解决了实验方法和精确量子力学理论方法难以获得双原子分子离子XY 的包含最高振动能级在内的所有高阶振动能级的精确数值这一问题。所有研究结果表明:由部分较低的实验精确振动能级,可用AM产生双原子分子离子XY 的精确振动光谱常数和包含全部激发态的完全振动能谱;所得的AM振动能谱比其他理论方法得到的结果更好。     

用代数能量方法研究氢化物双原子分子的完全振动能谱和离解能

本文用研究双原子分子振动能谱的新方法-代数方法(AM),研究了KH-X1Σ+,RbH-X1Σ+,DF-X1Σ+和DCl-X1Σ+等四个氢化物双原子分子的电子基态的振动光谱常数和振动能谱;用代数能量方法(AEM)研究了相应电子态的分子离解能.研究结果表明:使用实验获得的少数精确的振动能级[Eυ],由AM方法得到的振动能谱不仅能够重复这些电子态的已知实验能级,还能够得到用现代实验方法或精确的量子理论方法很难得到的所有高振动激发态的能级.由AEM方法能够得到比用文献发表的振动光谱常数计算获得的离解能值更准确的分子离解能.     

用代数方法精确研究HF分子B1Σ的振转能谱

基于代数方法(algebraic method)可以获得双原子分子的包含最高振动能级在内的所有高阶振动能级的精确数值这一事实,又提出了一种新的代数方法(algebraic method 2)来精确研究双原子分子电子态的振转能谱和转动常数. 以HF分子的B¹Σ电子态为例,应用algebraic method 2方法研究了该电子态的振动量子数从ν=0到ν=10的所有振转能谱,获得了与实验值符合得非常好的理论结果. 关键词： 代数方法 双原子分子 振转能级     

非天然氨基酸在蛋白质动态特性核磁共振研究中的应用

核磁共振（NMR）是蛋白质结构解析的主要方法之一.除可获得蛋白质的高分辨结构外,NMR还可用于观测最接近生理条件的蛋白质动态构象,获得蛋白质行使生物学功能的详细机制.非天然氨基酸定点标记方法可显著减少大分子量蛋白质的信号数目,降低数据采集和分析难度,已广泛运用于蛋白质结构和功能研究.本文介绍了常用的在蛋白质中引入非天然氨基酸的实验方法,包括蛋白质化学合成法、蛋白质化学修饰法、氟代芳香族氨基酸插入和基因密码子编辑的位点特异性插入等方法,并介绍了部分应用非天然氨基酸结合NMR研究大分子量蛋白的成功案例.此外,此篇综述讨论了目前非天然氨基酸标记在蛋白质研究中的局限性及发展方向.     

A comparison of finite basis set and finite difference Hartree—Fock calculations for the open-shell (X 2Σ+) molecules BaF and YbF

A comparison is made of the accuracy with which the total electronic energy can be calculated by using the finite basis set approach (the algebraic approximation) and the finite difference method in calculations employing the Hartree—Fock model for the open shell ground (X ²Σ⁺) states of the fluorides BaF and YbF. The convergence of the calculations carried out within the algebraic approximation is monitored by employing systematically constructed basis sets of increasing size. The difference between the finite basis set and finite difference Hartree—Fock energies is 2.6μE _h for BaF and 2.8μE _h for YbF. Dipole moments determined within the algebraic approximation are also compared with the corresponding finite difference expectation values.     

Thermodynamic characteristics of a biological organism: Information value of a gene and of a protein as a measure of the efficiency and as an index of selective pressure

Summary For the treatment of the information exchanged by the biological system and the external world, the concept of information amount is not sufficient because of their remoteness from equilibrium states. Further explanations are, in fact, necessary about the effects of the reception of the message,i.e. its information value that is then necessary to define for each case. We have, therefore, defined the information value of a gene and of a protein and analysed a sample of about hundred genes looking for some significative regularity in the frequency of usage of codons and amino acids allowing us to individualize the salient characteristics of a translated sequence of codons. We have found that the most used amino acids have, on the average, a low information value and, for each amino acid type, the most used codons have a lower information value. Moreover, we can say that the composition in amino acids or in codons of a sequence useful for the biological systems is such that more frequent mutations cause the smaller variation in the phenotype. All that shows that our definitions well describe the system of transmission and reception of the information value in a biological organism and that they can be considered as an index of its efficiency,i.e. of its ability to minimize the effects of the mutation of the genotype on the phenotype. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

灰气体加权和辐射模型综合评估及分析

在O_2/CO_2气氛下,参与性介质的非灰气体辐射特性表现出不同于空气气氛下的特性,因此,非灰气体辐射模型的选择和应用在换热过程中将变得十分重要.基于统计窄谱带模型,本文综合评估近年发展应用较广的灰气体加权和(WSGG)模型.结果表明,几种WSGG模型的预测值总体趋势正确,但仍存在着一定的差别.对于发射率,Dorigon等(2013 Int.J.Heat Mass Transfer 64 863)和Bordbar等(2014 Combust.Flame 161 2435)的WSGG模型与基准模型符合较好,相对误差小于20%.与离散坐标法结合,本文求解了PH_2O/PCO_2=1,2时的一维平行平板间辐射换热问题.结果显示,由Dorigon等和Bordbar等的WSGG模型得到的辐射热源和热流密度分布的相对误差均较小(10%左右).Johansson等(2011 Combust.Flame 158893)和Bordbar等的WSGG模型具有更广的适用范围.     

A comparison of finite basis set and finite difference Hartree-Fock calculations for the open- shell (X2Σ+) molecules BeF,MgF, CaF and SrF

A comparison is made of the accuracy with which the total electronic energy can be calculated by using either the finite basis set approach (the algebraic approximation) or finite difference methods in calculations employing the restricted Hartree-Fock model for the open-shell ground (X²Σ+) states of the Group Ha fluorides BeF, MgF, CaF and SrF. The convergence of the calculations carried out within the algebraic approximation is monitored by employing systematically constructed basis sets of increasing size. By using two different grids, the accuracy of the finite difference calculations has been estimated to be of the order of 10^?2 μE _h. The average difference between the finite basis set and finite difference total Hartree-Fock energies is 2.75 μE_h. Dipole moments determined within the algebraic approximation are also compared with the corresponding finite difference expectation values.     

Classical trajectory study of alignment effects in the capture process: He2+-Li1(2pΣ,2pΠ) collisions

A simulation method (CTMC) has been used to investigate the selectivity and alignment effects on the capture process in He²⁺-Li¹(2pΣ,2pΠ) collisions. The anomalous results of the experiment (∼ 50% error) as well as the AO calculation of Gieler et al. in case of capture into He II (n = 4) from the initial Li¹ (2pΣ) state are not found in the present work. Relative velocity and spatial overlap together mainly control the capture process in ion-atom collisions. The n-distribution of the final capture state is also presented.