对乙基苯酚的单色共振双光子电离光谱

对乙基苯酚是构成酪氨酸分子的重要基团,根据其光谱特性可以洞察酪氨酸的光学特性。我们采用超声分子束技术获得了对乙基苯酚的单色共振双光子电离光谱,首次报道了800~1 500cm-1范围的高分辨率激发态振动谱。配合量子化学理论计算分析了各谱对应的振动模式。结果表明取代基越长,分子的激发能越低;取代基的方向对激发能有明显影响;取代基会使苯环平面内的振动能量降低,但取代链的长短对振动能量没有明确影响。研究结果为分子的里德堡态、动力学和零动能光谱的相关研究提供了重要的参考数据。     

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.     

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.     

Rate-distortion scenario for the emergence and evolution of noisy molecular codes

We discuss, in terms of rate-distortion theory, the fitness of molecular codes as the problem of designing an optimal information channel. The fitness is governed by an interplay between the cost and quality of the channel, which induces smoothness in the code. By incorporating this code fitness into population dynamics models, we suggest that the emergence and evolution of molecular codes may be explained by simple channel design considerations.     

Physics of evolution: Selection without fitness

Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish. Survival probabilities and proliferation rates are typically associated with the ‘fitness’ of particular variations. In this paper we argue that the notion of fitness is an a posteriori concept, in the sense that one can assign higher fitness to species that survive but one can generally not derive or predict fitness per se. Proliferation rates can be measured, whereas fitness landscapes, i.e. the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. In this spirit, here we propose a random matrix model of evolution where selection mechanisms are encoded in interaction matrices of species, thereby extending the previous work of ours by a control parameter describing suppressors in the system. We are able to recover some key facts of evolution dynamics endogenously, such as punctuated equilibrium, i.e. the existence of intrinsic large extinction events, and, at the same time, periods of dramatic diversification, as known e.g. from the fossil record. Further, we comment on two fundamental technical problems of a ‘physics of evolution’, the non-closedness of its phase space and the problem of co-evolving boundary conditions, apparent in all systems subject to evolution.     

Integral and differential form of the protein folding problem

The availability of the complete genomic sequences of many species, including human, has raised enormous expectations in medicine, pharmacology, ecology, biotechnology and forensic sciences. However, knowledge is only a first step toward understanding, and we are only at the early stage of a scientific process that might lead us to satisfy all the expectations raised by the genomic projects. In this review I will discuss the present status of computational methods that attempt to infer the unique three-dimensional structure of proteins from their amino acid sequences. Although this problem has been defined as the “holy grail” of biology, it represents only one of the many hurdles in our path towards the understanding of life at a molecular level.     

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”.     

Origin and evolution of metabolic pathways

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less-dependent on exogenous sources of organic compounds.Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria and Eukarya revealed that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the arisal of new metabolic abilities. Among these gene elongations, gene and operon duplications undoubtedly played a major role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence giving rise to new genes coding for new metabolic abilities. Gene duplication has been invoked in the different schemes proposed to explain why and how the extant metabolic pathways have arisen and shaped. Both the analysis of completely sequenced genomes and directed evolution experiments strongly support one of them, i.e. the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis and nitrogen fixation, suggested that other different hypothesis, i.e. the retrograde hypothesis or the semi-enzymatic theory, may account for the arisal of some metabolic routes.     

Space-time evolution of hadronization

Beside its intrinsic interest for the insights it can give into color confinement, knowledge of the space-time evolution of hadronization is very important for correctly interpreting jet-quenching data in heavy-ion collisions and extracting the properties of the produced medium. On the experimental side, the cleanest environment to study the space-time evolution of hadronization is semi-inclusive deeply inelastic scattering on nuclear targets. On the theoretical side, two frameworks are presently competing to explain the observed attenuation of hadron production: quark energy loss (with hadron formation outside the nucleus) and nuclear absorption (with hadronization starting inside the nucleus). I will discuss recent observables and ideas which will help to distinguish these two mechanisms and to measure the time scales of the hadronization process. PACS 25.30.-c; 25.75.-q; 24.85.+p; 13.87.Fh     

Early evolution of transversally thermalized partons

The idea that the parton system created in relativistic heavy-ion collisions (i) emerges in a state with transverse momenta close to thermodynamic equilibrium and (ii) its evolution at early times is dominated by the 2-dimensional (transverse) hydrodynamics of the ideal fluid is investigated. It is argued that this mechanism may help to solve the problem of early equilibration.     

Emergent properties of gene evolution: Species as attractors in phenotypic space

The question how the observed discrete character of the phenotype emerges from a continuous genetic distance metrics is the core argument of two contrasted evolutionary theories: punctuated equilibrium (stable evolution scattered with saltations in the phenotype) and phyletic gradualism (smooth and linear evolution of the phenotype). Identifying phenotypic saltation on the molecular levels is critical to support the first model of evolution. We have used DNA sequences of ∼1300 genes from 6 isolated populations of the budding yeast Saccharomyces cerevisiae. We demonstrate that while the equivalent measure of the genetic distance show a continuum between lineage distance with no evidence of discrete states, the phenotypic space illustrates only two (discrete) possible states that can be associated with a saltation of the species phenotype. The fact that such saltation spans large fraction of the genome and follows by continuous genetic distance is a proof of the concept that the genotype-phenotype relation is not univocal and may have severe implication when looking for disease related genes and mutations. We used this finding with analogy to attractor-like dynamics and show that punctuated equilibrium could be explained in the framework of non-linear dynamics systems.     

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．     

Geometric scaling from Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution

We show that the geometric scaling of the total virtual photon-proton cross section data can be explained using standard linear Dokshitzer-Gribov-Altarelli-Parisi perturbative evolution with generic boundary conditions in a wide kinematic region. This allows us to single out the region where geometric scaling may provide evidence for parton saturation.     

Space and time resolved discharge evolution of a large volume X-ray triggered XeCl laser system

The spatial distribution and the temporal development of the net gain have been measured in a ten liter active volume switchless discharge XeCl laser. The experimental results are compared with both zero-dimensional and two-dimensional kinetic code predictions. The comparison between the results of the kinetic codes and of some measurements relevant to the time-dependent discharge homogeneity allows a deeper insight into the influence of the streamer evolution on the discharge characteristics.ENEA StudentENEA Guest     

Molecular evolution under fitness fluctuations

Molecular evolution is a stochastic process governed by fitness, mutations, and reproductive fluctuations in a population. Here, we study evolution where fitness itself is stochastic, with random switches in the direction of selection at individual genomic loci. As the correlation time of these fluctuations becomes larger than the diffusion time of mutations within the population, fitness changes from an annealed to a quenched random variable. We show that the rate of evolution has its maximum in the crossover regime, where both time scales are comparable. Adaptive evolution emerges in the quenched fitness regime (evidence for such fitness fluctuations has recently been found in genomic data). The joint statistical theory of reproductive and fitness fluctuations establishes a conceptual connection between evolutionary genetics and statistical physics of disordered systems.     

Why Perform Code‐to‐Code Comparisons: A Vacuum Arc Discharge Simulation Case Study

Numerical modeling is increasingly becoming an indispensable tool for investigations in many fields of physics. Such modeling is especially useful in today's big science projects as a tool that can provide predictions and design parameters. The reliability of simulation results is thus essential. Code‐to‐code comparisons can help increase our confidence in simulation results, especially when other verification methods – such as comparison to theoretical models or experimental results – are limited or unavailable. In this paper, we describe a code‐to‐code comparison exercise wherein we compare one‐dimensional vacuum arc discharge simulation results from two independent particle‐in‐cell (PIC) codes. As part of our case study, we define a vacuum arc discharge test problem that can be used by other research groups for further comparison. Early disagreement between the two sets of our results motivated us to re‐examine the underlying methods in our codes. After remedying discrepancies, we observe good agreement in vacuum arc discharge time‐to‐breakdown, as well as in the time evolution of particle and current densities. This exercise demonstrates the usefulness of code‐to‐code comparisons and provides an example case study for the benefit of other research groups who may wish to carry out similar code‐to‐code comparisons (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Kinetics of methane and tar evolution during coal pyrolysis

The first objective of this work was to compare the pyrolysis behavior of coals coming from different geographic locations (South Africa, South America, Europe, Australia, and North America). This preliminary study was limited to the kinetics of methane and tar evolution, with data on additional species to be reported in a separate publication. The second objective was to examine the possible relationship between tar and methane evolution during pyrolysis. This study was done by employing a thermogravimetric analyzer coupled with a Fourier-transform infrared spectrometer (TG-FTIR). The evolution curves for 35 coals of different elemental compositions were measured at three different heating rates (10, 30, and 100 K/min). Pyrolysis kinetics were described using a simple first-order reaction model. The technique, first proposed by Kissinger, is based on the variation of the temperature at which a volatile species evolution rate is a maximum (T_max) as a function of the heating rate. The TG-FTIR data for tar evolution reveal a generally consistent behavior for coals from different parts of the world, showing increasing activation energies with increasing coal rank. The same correlation is also true for methane, although the slope of the activation energy versus carbon content curve is rather flat, at least up to about 90% carbon content. The values of activation energies for methane evolution were found to be lower in the case of the Argonne coals, as compared with the non-US coals. A study of the temperatures at which the evolution of methane and tar begins (T_ini), and the temperatures at which the evolution rates reach a maximum (T_max), reveals a correlation between the T_ini for methane and T_max for tar. This may be due to the fact that both tar and methane evolve as a result of similar reactions involved in the breakup and recombination of the coal macromolecular network.     

Ab initio electron theory for hard-magnetic rare-earth-transition-metal intermetallics

For the development of new hard-magnetic materials a better understanding of the physical mechanisms which determine the intrinsic magnetic material parameters are of invaluable importance. In this review it is demonstrated that the modern ab initio electron theory yields a considerable help in this direction and may provide data on quantities which are hard to determine reliably by experiments. As an example, theoretical results are reported for the intrinsic magnetic material parameters (local magnetic moments, local magnetic hyperfine fields, crystal-field parameters and effective exchange interactions) of the series R₂Fe₁₄B (R = rare earth).     

Exp-function method for N-soliton solutions of nonlinear evolution equations in mathematical physics

In this Letter, the Exp-function method is generalized to construct N-soliton solutions of a KdV equation with variable coefficients. As a result, 1-soliton, 2-soliton and 3-soliton solutions are obtained, from which the uniform formula of N-soliton solutions is derived. It is shown that the Exp-function method may provide us with a straightforward and effective mathematical tool for generating N-soliton solutions of nonlinear evolution equations in mathematical physics.     

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs

Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.