Non-coding RNAs and complex distributed genetic networks

In eukaryotic cells, the mRNA-protein interplay can be dramatically influenced by non-coding RNAs (ncRNAs). Although this new paradigm is now widely accepted, an understanding of the effect of ncRNAs on complex genetic networks is lacking. To clarify what may happen in this case, we propose a mean-field kinetic model describing the influence of ncRNA on a complex genetic network with a distributed architecture including mutual protein-mediated regulation of many genes transcribed into mRNAs. ncRNA is considered to associate with mRNAs and inhibit their translation and/or facilitate degradation. Our results are indicative of the richness of the kinetics under consideration. The main complex features are found to be bistability and oscillations. One could expect to find kinetic chaos as well. The latter feature has however not been observed in our calculations. In addition, we illustrate the difference in the regulation of distributed networks by mRNA and ncRNA.     

Non-coding RNAs and a layered architecture of genetic networks

In eukaryotic cells, protein-coding sequences constitute a relatively small part of the genome. The rest of the genome is transcribed to non-coding RNAs (ncRNAs). Such RNAs form the cornerstone of a regulatory network that operates in parallel with the protein network. Their biological functions are based primarily on the ability to pair with and deactivate target messenger RNAs (mRNAs). To clarify the likely role of ncRNAs in complex genetic networks, we present and comprehensively analyze a kinetic model of one of the key counterparts of the network architectures. Specifically, the genes transcribed to ncRNAs are considered to interplay with a hierarchical two-layer set of genes transcribed to mRNAs. The genes forming the bottom layer are regulated from the top and negatively self-regulated. If the former regulation is positive, the dependence of the RNA populations on the governing parameters is found to be often non-monotonous. Specifically, the model predicts bistability. If the regulation is negative, the dependence of the RNA populations on the governing parameters is monotonous. In particular, the population of the mRNAs, corresponding to the genes forming the bottom layer, is nearly constant.     

Electronic structure and optical gain of InAsPN/GaP(N) quantum dots

The electronic structure and optical gain of InAsPN/GaP(N) quantum dots (QDs) are investigated in the framework of the effective-mass envelope function theory. The strain distribution is calculated using the valence force field (VFF) method. With GaP barrier, for smaller InAsPN QDs, the minimum transition energy may occur at a lower phosphorous (P) composition, but for larger QDs, the transition energy increases as P composition increases due to the increased bandgap of alloy QDs. When the nitrogen (N) composition increases, the transition energy decreases due to the stronger repulsion between the conduction band (CB) and the N resonant band, and the transition matrix element (TME) is more affected by the transition energy rather than N–CB mixing. To obtain laser materials with a lattice constant comparable to Si, we incorporated 2% of N into the GaP barrier. With this GaP_0.98N_0.02 barrier, the conduction band offset is reduced, so the quantum confinement is lower, resulting in a smaller transition energy and longer wavelength. At the same time, the TME is reduced and the optical gain is less than those without N in the barrier at a low carrier density, but the peak gain increases faster when the carrier density increases. Finally it can surpass and reach a greater saturation optical gain than those without N in the barrier. This shows that incorporating N into GaP barriers is an effective way to achieve desirable wavelength and optical gain.     

Interplay of noncoding RNAs,mRNAs, and proteins during the growth of eukaryotic cells

Numerous biological functions of noncoding RNAs (ncRNAs) in eukaryotic cells are based primarily on their ability to pair with target mRNAs and then either to prevent translation or to result in rapid degradation of the mRNA-ncRNA complex. Using a general model describing this scenario, we show that ncRNAs may help to maintain constant mRNA and protein concentrations during the growth of cells. The possibility of observation of this effect on the global scale is briefly discussed.     

Measuring principle of vertical target density based on single linear array CCD camera

In consideration of the complexity and the high cost of the dual CCD intersection vertical target when it is used indoor. A novel measuring principle of one linear array CCD camera vertical target is presented. One low-power semiconductor sector-like laser with projection board is used to be the lamp-house of the CCD camera. The detection light screen of the CCD camera and the laser lamp-house are adjusted to same plane. When the projectile through the detection light screen, it blocks the part light of the laser and leaves a shadow of projectile on the board. The shadow and its coordinate are acquired and calculated by the CCD camera and computer, and the projectile coordinate of X and Y can be gotten through image processing and further calculation. The measuring principle and the formulas are given, and the measuring error is analyzed. The result indicates that the coordinate error of X and Y less than 1.5 and 2.2 mm, respectively, when the detection light screens is 1 m × 1 m, The principle presented has the advantages that measurement principle is simple, low cost and easy engineering.     

Faddeev–Jackiw canonical path integral quantization for a general scenario,its proper vertices and generating functionals

We generalize the Faddeev–Jackiw canonical path integral quantization for the scenario of a Jacobian with J=1 to that for the general scenario of non-unit Jacobian, give the representation of the quantum transition amplitude with symplectic variables and obtain the generating functionals of the Green function and connected Green function. We deduce the unified expression of the symplectic field variable functions in terms of the Green function or the connected Green function with external sources. Furthermore, we generally get generating functionals of the general proper vertices of any n-points cases under the conditions of considering and not considering Grassmann variables, respectively; they are regular and are the simplest forms relative to the usual field theory.     

Magnetic and electronic properties of Cr- and Mn-doped SnO2: ab initio calculations

The ab initio calculations, based on the Korringa–Kohn–Rostoker (KKR) approximation method combined with the coherent potential approximation (CPA), indicated as KKR–CPA, have been used to study the stability of ferromagnetic and ferrimagnetic states, for systems that are SnO₂ doped and co-doped with two transition metals, that is, chromium and manganese. Our results indicate that the ferromagnetic state is more stable than the spin-glass state for the (Sn_1−xCr_xO₂; x = 0.07, 0.09, 0.12 and 0.15)-doped system, while the spin-glass state is more stable than the ferromagnetic state for the (Sn_1−xMn_xO₂; x = 0.02 and 0.05)-doped system. However, the ferromagnetic and/or the ferrimagnetic states are stable for the (Sn_0.98−xMn_0.02Cr_xO₂; x = 0.05, 0.09 and 0.13)-doped system depending on the Cr concentration. Moreover, we estimated the Curie temperature (T_c) for the Cr-doped tin dioxide (SnO₂), and we explained the origin of magnetic behaviour through the total density of states for different doped and co-doped SnO₂ systems.     

Spectroscopical splitting of Cu ion energy levels in magnesium lead fluoro silicate glasses

Homogeneous 40.0 MgO-(10-x) PbF₂-50.0 SiO₂: x CuO glasses were prepared using melt-quenching technique under controlled conditions. Spectroscopic studies (UV-vis absorption, ESR, FT-IR) are carried out for these glasses. One broad characteristic visible absorption band is observed around 700-850 nm in these glasses, the optical band gap decreases as the content of the CuO increases in the glass network up to 0.7 mol % then reversal trend is observed. ESR spectra of all these glasses show resonance peaks characteristic of Cu²⁺ ions and hyperfine splitting is resolved with increasing the CuO content in the glass network. From the observed ESR spectra, the spin-Hamiltonian parameters have been evaluated and indicate that Cu²⁺ ions have octahedral coordination with a strong tetragonal distortion in these glasses. By correlating ESR and optical absorption data, the molecular orbital coefficients have been evaluated. FT-IR spectra give important information about the nature of bonds in the glass matrix. The density of the glasses is also measured and is found to decrease with the increase CuO contents in the glass matrix. The physical parameters along with spectroscopic parameters are measured.     

Decompositioning method to compute scattering by complex shaped particles using a multiple scattering T-matrix approach

In a recent paper we proposed a decompositioning method to compute scattering by aggregated cylindrical fibres using a multiple scattering T-matrix approach. In this paper we extend this approach to scatterers lacking rotational symmetry. To investigate the capability of this method a square prism and a cube are decomposed into a number of subscatterers and scattering of the original particle shape is computed using multiple scattering. The results are validated using discrete dipole approximation (DDA).     

Analysis of the magnetic losses in iron-based soft magnetic composites with MgO insulation produced by sol-gel method

This work investigated the magnetic losses of heat treated iron-based soft magnetic composites with a thin MgO insulating layer produced by sol-gel method. The samples were characterized by energy dispersive X-ray spectroscopy, X-ray analysis and Fourier transform infrared spectroscopy. The results show that the surface of the powders contains a thin layer of MgO insulation. The loss results indicate that the hysteresis part for both the core loss and total loss factor was approximately the same for the MgO-insulated compacts and conventional SOMALOY^TM samples with phosphate insulation after annealing at 600 °C. But the MgO-insulated compacts exhibited significantly lower eddy current contribution of both core loss and total loss factor with respect to SOMALOY^TM samples after annealing. Also the contribution of eddy current in the iron particles for MgO insulated compacts (k_p=0.91) was noticeably higher than this contribution for SOMALOY^TM samples (k_p=0.18) after annealing due to the higher electrical resistivity of the MgO-insulated compacts.     

Superluminal energy transmission in the Goos-Hanchen shift of total reflection

The dispersion relation ω² = β²c² − τ²c² of surface electromagnetic waves is corresponding to that E² = p²c² − m₀²c⁴ of a tachyon where the coefficient of proportionality is the squared Planck constant ?². Then we prove the energy flow velocity of the Goos-Hanchen shift in vacuum is cn sin θ_i > c as well according to electrodynamics. These two different ways lead to a same conclusion that energy transport in the Goos-Hanchen effect of total reflection is faster than light.     

Long transients dynamics in biochemical networks

Summary  A Coupled Map Lattice, which simulates gene expression dynamics inside cells and cellular interactions on a regular lattice, shows a complex pattern of temporal behaviour. The model is represented as a network of genes interacting through their products in space and time in a lattice of genetically identical cells. Despite the fact that the system is described through a step function that imposes a simple repertoire of constant or oscillatory steady states, the dynamics over the lattice are extremely complex. One of the main feature of the asymptotic dynamics is the appearance of long transients in certain regions of parameter space, before the attainment of the final stable attractor. These dynamics, that can grow linearly or exponentially with lattice size, can become the only dynamics computationally observable. The study of the global dynamics-i.e. the average value of the variable over the lattice-shows a qualitative different behaviour depending on the region of the parameter space observed. In the case of the linear transient-growth region the system shows an average that falls quickly on a periodic attractor. In the exponential region values of the average quantities show a behaviour that has stochastic properties. At the boundary of these two regimes the system has an average that shows a complex behaviour before attainment of the final attractor. The possible implications of these results for the study of the dynamical aspects of gene regulation, biochemical pathways and in signal transduction in experimental systems are discussed. This work has been partially supported by CNR grant No. 95.01751.CT14 “Studio analitico della dinamica della regolazione genica e della morfogenesi#x201C;, and by funds from the National Ministry of Public Health. FB and RL would like to thank I.S.I., Torino, for the kind hospitality during the workshop of the EEC Network “Complexity and Chaos#x201D;, contract No. ERBCHRX-CT940546, in 1995 and 1996, during which part of this research has been done.     

Chaos synchronization in networks of coupled maps with time-varying topologies

Complexity of dynamical networks can arise not only from the complexity of the topological structure but also from the time evolution of the topology. In this paper, we study the synchronous motion of coupled maps in time-varying complex networks both analytically and numerically. The temporal variation is rather general and formalized as being driven by a metric dynamical system. Four network models are discussed in detail in which the interconnections between vertices vary through time randomly. These models are: 1) i.i.d. sequences of random graphs with fixed wiring probability, 2) groups of graphs with random switches between the individual graphs, 3) graphs with temporary random failures of nodes, and 4) the meet-for-dinner model where the vertices are randomly grouped. We show that the temporal variation and randomness of the connection topology can enhance synchronizability in many cases; however, there are also instances where they reduce synchronizability. In analytical terms, the Hajnal diameter of the coupling matrix sequence is presented as a measure for the synchronizability of the graph topology. In topological terms, the decisive criterion for synchronization of coupled chaotic maps is that the union of the time-varying graphs contains a spanning tree.     

An extreme change in structural and optical properties of indium oxynitride deposited by reactive gas-timing RF magnetron sputtering

The indium oxynitride (InON) films were achieved by reactive RF magnetron sputtering indium target which has the purity of 99.999% with a novel reactive gas-timing technique. The structural, optical and electrical properties in a series of polycrystalline InON films affected by gas-timing of reactive N₂ and O₂ gases introduced to the chamber were observed. The X-ray photoelectron spectroscopy revealed that the oxygen content in thin films that compounded to indium and nitrogen, which increased from 10% in indium nitride (InN) to 66% in indium oxide (In₂O₃) films. The X-ray diffraction peaks show that the phase of deposited films changes from InN to InON and to In₂O₃ with an increasing oxygen timing. The hexagonal structure of InN films with predominant (0 0 2) and (0 0 4) orientation was observed when pure nitrogen is only used as sputtering gas, while InON and In₂O₃ seem to demonstrate body-center cubic polycrystalline structures depending on gas-timing. The surface morphologies investigated from atomic force microscope of deposited films with varying gas-timing of O₂:N₂ show indifferent. The numerical algorithm method was used to define the optical bandgap of films from transmittance results. The increasing oxygen gas-timing affects extremely to the change of crystallinity phase from InN to InON and to In₂O₃, the increase of optical bandgap from 1.4 to 3.4 eV and the rise of sheet resistance from 15 Ω/□ to insulator.     

Shape effects on the electronic structure and the optical gain of InAsN/GaAs nanostructures: From a quantum lens to a quantum ring

The electronic structures of self-assembled InAs_1−xN_x/GaAs nanostructures from quantum lens to quantum rings (QRs) are calculated using the 10-band k.p method and the valence force field (VFF) method. With the variation of shape of the nanostructure and nitrogen (N) content, it shows that the N and the strains can significantly affect the energy levels especially the conduction band because the N resonant state has repulsion interaction with the conduction band due to the band anticrossing (BAC). The structures with N and greater height have smaller transition energy, and the structures with N have greater optical gain due to its overwhelming greater value of factor _fc+_fv−1$f_{\text{c}}+f_{\text{v}}-1$. After analyzing the shape effect, we suggested that the nanostructures with volcano shape are preferred because the maximum optical gain occurs for quantum volcano. With our simulation result, researchers could select quantum dots (QDs) structures to design laser with better performance.     

Analytical results for a non-Markovian process of gene expression with positive and negative feedbacks

Gene expression is a very complex process and involves many small biochemical reaction steps, resulting in a non-Markovian discrete stochastic process due to molecular memory between individual reactions. At present, this process is successfully investigated by generalized chemical master equation models. However, these models do not consider the role of feedback networks in gene expression. How the interaction between feedbacks and molecular memory affects gene expression still remains not well understood. Here, we establish generalized chemical master equation models of gene expression with positive and negative feedbacks. Assuming that the process of producing proteins follows an Erlang probability distribution, we obtain the analytical expression for this model in a steady state, as well as the measure of the noise of protein numbers. We further find that molecular memory competes with the positive feedback in suppressing the noise of the protein number. For our model with a negative feedback, molecular memory can strengthen the intensity of suppressing this noise. These interesting results imply that molecular memory are as important as the feedbacks to affect gene expression.     

Dynamics of multipionp¯ p annihilation

We construct a dynamical model to study the pion correlations in the 5 annihilation ofp¯ p at rest. For the resonant channels, the simplest Lorentz-invariant couplings have been used. It is found that, in addition to the Bose-Einstein correlations caused by the finite size of the source, the dynamical correlations from the channels with intermediate resonances are important for explaining the experimental two-pion correlation function. The reliability of two standard methods for pion interferometry is tested in our model.On leave from Institute of Nuclear Research, Academia Sinica, P.O. Box 800204, Shanghai 201800, China