The amount and value of information in biology

The notion of the value of information is discussed. The value one attributes to information is determined by the result of its reception by an open nonequilibrium system. Qualitative reasoning shows that the concept of value of information makes sense only in nonequilibrium situations, and is directly connected with the nonredundancy of information. In biology it is the value and not the amount of information that is important. The value of information is especially high if there are instabilities in the system; these are connected with the notions of purpose and of freedom of will. The notion of selective value, introduced by Eigen in the theory of the prebiological evolution of macromolecules, is discussed. The amount of information in various codons is calculated and the conventional definition of its value is given based on the determination of the danger of the replacement of one amino acid by another with a different value of hydrophobicity. It is shown that the relative probability of transversion is considerably lower than that of transition. As most nonsense mutations are transversions, the genetic code provides decreased probability for the most dangerous mutations. It is shown that the information of the codonUGG(Trp) is highest in both amount and value.     

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.     

Stability-transport modeling of the SINP tokamak discharges

A one-dimensional stability transport code has been developed to simulate the evolution of tokamak plasma discharges. Explicit finite-difference methods have been used to follow the temporal evolution of the electron temperature equation. The poloidal field diffusion equation has been solved at every time step. The effects of MHD instabilities have been incorporated by solving equations for MHD mixing and tearing modes as and when required. The code has been applied to follow the evolution of tokamak plasma discharges obtained in the Saha Institute of Nuclear Physics (SINP) tokamak. From these simulations, we have been able to identify the possible models of thermal conductivity, diffusion and impurity contents in these discharges. Effects of different MHD modes have been estimated. It has been found that in low q ₀ discharge m=1, n=1 and m=2, n=1 modes play major role in discharge evolution. These modes are found to result in the positive jump in the loop voltage which was also observed in the experiments. Hollow current density profile j _φ and negative shear in the q profile have also been found in the rising phase of a discharge.     

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”.     

Probing Yukawian gravitational potential by numerical simulations. II. Elliptical galaxies

Since the Newtonian gravitation is largely used to model with success the structures of the universe, such as galaxies and clusters of galaxies, for example, a way to probe and constrain alternative theories, in the weak field limit, is to apply them to model the structures of the universe. We then modified the well known Gadget-2 code to probe alternative theories of gravitation through galactic dynamics. In particular, we modified the Gadget-2 code to probe alternatives theories whose weak field limits have a Yukawa-like gravitational potential. As a first application of this modified Gadget-2 code we simulate the evolution of elliptical galaxies. These simulations show that galactic dynamics can be used to constrain the parameters associated with alternative theories of gravitation.     

Information-theoretic stability and evolution criteria in irreversible thermodynamics

Generalized information gains are used to derive stability conditions, for steady states, periodic orbits and invariant sets, and general evolution criteria, both global and local with respect to the time variable, in irreversible thermodynamics. Meixner's passivity condition and the Glansdorff-Prigogine stability and evolution criteria are found to be special cases thereof. The information gain quantities include Kullback's three kinds of divergences, the first two of which are dual to each other and yield criteria which are symmetric in the average densities of the system's extensive variables and the conjugate parameters, but which are nonsymmetric in the irreversible fluxes and forces, while the third one does not involve the entropy function of the system. Furthermore, Renyi's information gain of order and Csiszar'sf-divergence are treated. The latter is used to construct a most general information gain quantity as a Liapunov function and evolution criterion, which, however, for local stability and evolution conditions is still equivalent to the use of the second-order variation of the entropy.Supported by the Deutsche Forschungsgemeinschaft.     

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.     

Evolution with time of the dielectric properties of dispersed ice microcrystals

Summary The evolution with time of the characteristics of the dielectric relaxation of water molecules in dispersions of ice microcrystals has been studied by means of the thermally stimulated depolarization current (TSDC) method. With advancing stage of evolution,i.e. with increasing preservation time at constant preservation temperature and with increasing preservation temperature at constant preservation time, the mean values of relaxation time and activation energy have been found to decrease. The extent and the rate of the evolution have been compared to those in other forms of ice: ice samples with high content of disturbance, polycrystalline ice samples and single ice crystals. The observed similarities and differences in the behaviour of the different ice forms have been discussed in terms of the influence of extrinsic physical and chemical defects on the generation and motion of orientational Bjerrum defects.     

Recent radiation damage studies and developments of the Marlowe code

Radiation damage in materials relevant to applications evolves over time scales spanning from the femtosecond – the characteristic time for an atomic collision – to decades – the aging time expected for nuclear materials. The relevant kinetic energies of atoms span from thermal motion to the MeV range.The question motivating this contribution is to identify the relationship between elementary atomic displacements triggered by irradiation and the subsequent microstructural evolution of metals in the long term. The Marlowe code, based on the binary collision approximation (BCA) is used to simulate the sequences of atomic displacements generated by energetic primary recoils and the Object Kinetic Monte Carlo code LAKIMOCA, parameterized on a range of ab initio calculations, is used to predict the subsequent long-term evolution of point defect and clusters thereof. In agreement with full Molecular Dynamics, BCA displacement cascades in body-centered cubic (BCC) Fe and a face-centered cubic (FCC) Fe\bond Ni\bond Cr alloy display recursive properties that are found useful for predictions in the long term.The case of defects evolution in W due to external irradiation with energetic H and He is also discussed. To this purpose, it was useful to extend the inelastic energy loss model available in Marlowe up to the Bethe regime. The last version of the Marlowe code (version 15) was delivered before message passing instructions softwares (such as MPI) were available but the structure of the code was designed in such a way to permit parallel executions within a distributed memory environment. This makes possible to obtain N different cascades simultaneously using N independent nodes without any communication between processors. The parallelization of the code using MPI was recently achieved by one author of this report (C.J.O.). Typically, the parallelized version of Marlowe allows simulating millions of displacement cascades using a limited number of processors (<64) within only few hours of CPU time.     

Transient oscillations in Soret-driven convection in a colloidal suspension

We present measurements of the transient stage of Soret-driven convective instability. The sample is a diluted colloidal suspension of silica spheres in water with an unusually large negative Soret coefficient S_T. A large temperature gradient (heating from above) is rapidly applied over the sample, while a shadowgraph imaging technique provides images of the convective flow. From the processing of the variance of the intensity of the images we are able to recover the time evolution of the overall intensity of the convective flow. A typical evolution of such signal exhibits, after a latency time, a peak followed by some damped oscillations leading to a steady-state value. Both the onset time _p (the temporal position of the first peak), and the oscillation period _osc show a power law dependence as a function of the solutal Rayleigh number R_s. The exponents found are compared with predictions from existing models.     

Thermodynamic,transport, and optical properties of dense silver plasma calculated using the GreeKuP code

The transport and optical properties of a dense silver plasma are calculated using our parallel GreeKuP code. The code uses the results of Vienna ab initio simulation package (VASP) as input information and is based upon the Kubo–Greenwood formula. The calculation is performed at the normal density 10.5 g/cm³ and 3 kK ≤ T ≤ 20 kK. Under these conditions, the results are strongly influenced by the presence of the d‐electrons in silver: the real part of dynamic electrical conductivity has a non‐Drude shape, the temperature dependence of thermal conductivity is non‐monotonic, and the Wiedemann–Franz law is violated.     

A fitter code for Deep Virtual Compton Scattering and Generalized Parton Distributions

We have developed a fitting code based on the leading-twist handbag Deep Virtual Compton Scattering (DVCS) amplitude in order to extract Generalized Parton Distribution (GPD) information from DVCS observables in the valence region. In a first stage, with simulations and pseudo-data, we show that the full GPD information can be recovered from experimental data if enough observables are measured. If only some of these observables are measured, valuable information can still be extracted, with certain observables being particularly sensitive to certain GPDs. In a second stage, we make a practical application of this code to the recent DVCS Jefferson Lab Hall-A data from which we can extract numerical constraints for the two H GPD Compton form factors. An erratum to this article can be found at     

Evolution from BCS superconductivity to Bose condensation: analytic results for the crossover in three dimensions

We provide an analytic solution for the mean-field equations and for the relevant physical quantities at the Gaussian level, in terms of the complete elliptic integrals of the first and second kinds, for the crossover problem from BCS superconductivity to Bose-Einstein condensation of a three-dimensional system of free fermions interacting via an attractive contact potential at zero temperature. This analytic solution enables us to follow the evolution between the two limits in a particularly simple and transparent way, as well as to verify the absence of singularities during the evolution. Received: 9 May 1997 / Revised: 4 August 1997 / Accepted: 6 November 1997     

Transverse-momentum dependence of <Emphasis Type="Italic">J</Emphasis>/<Emphasis Type="Italic">ψ</Emphasis> shadowing effects

We present a new approach to estimate the effect of gluon shadowing in nucleus + nucleus collisions and its consequences on the J/ψ production yield. Using kinematical information available from the measured J/ψ production in proton + proton collisions at  GeV, we build a Glauber Monte Carlo code which takes into account shadowing in two alternative ways: multiple-scattering corrections or Q ² evolution of parton densities. We exploit the dependence of these different parameterizations to the J/ψ transverse momentum and we give the first predictions on the resulting p _T dependence of the nuclear modification factor in deuteron + gold collisions at the same energy.     

Spatial evolution of the generation and relaxation of excited carriers near the breakdown of the quantum Hall effect

We have measured the generation and relaxation of excited carriers along their drift direction near the breakdown of the quantum Hall effect (QHE). The dissipative resistivity ρ_xx(x) at current densities close to the critical value for the QHE breakdown was measured as a function of the distance x from the electron injection at x=0. By injecting “cold” electrons into constrictions at supercritical current levels, the evolution of the breakdown along the drift direction was monitored. After a smooth increase of the resistivity with the drifting distance, an avalanche-like rise towards a saturation value occurs. Drastic changes of the resistivity profiles with the applied current were found in a narrow range around the critical current. The observed behavior is attributed to impurity-assisted tunneling between Landau levels. By injecting hot electrons (excited in a periodic set of constrictions) into a region with subcritical current density, the relaxation process was analyzed. Inelastic relaxation lengths with typical values in the range from 0.3 to 4 μm were found, which agree within 10% with the elastic mean free path determined from the Hall mobility at zero magnetic field. We conclude that the energy relaxation process is triggered by scattering at impurity potentials.     

Determining the gamma-ray parameters for BaO–ZnO–B2O3 glasses using MCNP5 code: a comparison study

Rapid technological advancement has multiplied people’s exposure to ionizing radiations greatly. Widespread applications of radiation in different fields (such as agriculture, radiation therapy and scientific research fields) require that humans be protected against unnecessary exposure. In this study, mass attenuation coefficient (μ_m), half-value layer, mean-free path, effective atomic number (Z_eff) and exposure buildup factor have been calculated for xBaO–20ZnO–(80???x)B₂O₃ (x?=?5, 10, 15, 20 and 25?mol%) glass systems. The mass attenuation coefficients of the selected glasses were calculated using simulation method of MCNP5 code. The simulation results have been compared with the experimental data and Xcom at the energies 223.02, 252.98, 287.28, 340.83, 398.97, 481.59, 562.68 and 662.00?keV. The agreement amounts of the mass attenuation coefficient values are from 0.2% to 2.8% and from 0.2% to 6.98% for MCNP5 and Xcom relative to experimental results, while the Monte Carlo program values are higher than that obtained by experimental data, using Xcom and MCNP5 code. The glass sample having the highest value of BaO content show high radiation shielding properties. It indicates that the MCNP5 code can be used for estimation of radiation interaction parameters where experimental results are not available.     

Diffusion on the torus for Hamiltonian maps

For a mapping of the torusT ² we propose a definition of the diffusion coefficientD suggested by the solution of the diffusion equation ofT ². The definition ofD, based on the limit of moments of the invariant measure, depends on the set where an initial uniform distribution is assigned. For the algebraic automorphism of the torus the limit is proved to exist and to have the same value for almost all initial sets in the subfamily of parallelograms. Numerical results show that it has the same value for arbitrary polygons and for arbitrary moments.     

A study of morphological and compositional evolution of nanoprecipitates in the Zr–Nb system and their transformational behavior

The metastable transformational behavior (both martensitic and omega) along with compositional and morphological evolution of bcc β precipitates, dispersed in the hcp α matrix of a Zr–1 wt% Nb alloy, were studied as a function of temperature and time. The evolution of the chemical composition of the β phase suggested preference towards metastable compositions having Nb content higher than the equilibrium value. Thermodynamic analysis showed that the metastable chemical compositions are the driving force for the nucleation of such β precipitates. The β to martensite transformation was observed to be possible only if β precipitate size exceeded a critical value of 160?nm. Micromechanical modeling was performed to estimate the critical size of β precipitate required to induce martensite transformation and the model predictions were in close agreement with the experimental observations. The omega transformation, on the other hand, showed less size dependence.     

Asymptotic behavior of the density for two-particle annihilating exclusion

We consider a stochastic process which presents an evolution of particles of two types,A andB, onZ ^d with annihilations between particles of opposite types. Initially, at each site ofZ ^d, independently of the other sites, we put a particle with probability 2<1 and assign to it one of two types with equal chances. Each particle evolves onZ ^d in the following manner: independently from the others, it waits an exponential time with mean 1, chooses one of its neighboring sites on the latticeZ ^d with equal probabilities, and jumps to the site chosen. If the site to which a particle attempts to move is occupied by another particle of the same type, the jump is suppressed; if it is occupied by a particle of the opposite type, then both are annihilated and disappear from the system. The considered process may serve as a model for the chemical reactionA+Binert. Let (t) denote the density of particles in this process at timet. We prove that there exist absolute finite constantsc(d) andC(d) such that for all sufficiently larget,c(d)t ^–d/4 (t)C(d)t ^–d/4 in the dimensionsd4 andc(d)t ^–1 (t)C(d)t ^–1 in all higher dimensions. This completes and makes more precise the results obtained by us earlier and shows that asymptotically the density behaves like that in a similar process called two-particle annihilating random walks which was studied by Bramson and Lebowitz. Our proofs are based on the approach developed in their and our works. We use the basic properties of random walk and various tools which have been designed to study simple symmetric exclusion processes.