arXiv subjects

J. C. Nacher

Publications and source records attributed to J. C. Nacher.

At least 19 recordsLinked to original sources

arXiv2012

Carpet cloaking and Laplace transformation

Recently, researchers have proposed several carpet cloaking designs that are able to hide a real object under a bump in a way that it is perceived as a flat ground plane. Here, we present a method to design two-dimensional isotropic carpet cloaking devices using Laplace transformation. We show that each functional form of a Laplace transformation corresponds to a different carpet cloaking design. Therefore, our approach allows us to systematically design a rich variety of cloaking devices. Our analysis includes several examples containing different bump geometries that illustrate the proposed methodology.

physics.optics↗

arXiv2010

Reflection-less device allows electromagnetic warp drive

One of the striking properties of artificially structured materials is the negative refraction, an optical feature that known natural materials do not exhibit. Here, we propose a simple design, composed of two parallel layers of materials with different refraction indices $n_1=-n_2$, that constructs perfect reflection-less devices. The electromagnetic waves can tunnel from one layer to the other, a feature that resembles a truncation of the physical space leading to an electromagnetic warp drive. Since the refractive indices do not require any large values, this method demonstrates for the first time the practical feasibility of guiding electromagnetic fields in complete absence of reflection phenomena and without degradation of transmission efficiency at all.

physics.optics↗

arXiv2010

Plus-minus construction leads to perfect invisibility

Recent theoretical advances applied to metamaterials have opened new avenues to design a coating that hides objects from electromagnetic radiation and even the sight. Here, we propose a new design of cloaking devices that creates perfect invisibility in isotropic media. A combination of positive and negative refractive indices, called plus-minus construction, is essential to achieve perfect invisibility (i.e., no time delay and total absence of reflection). Contrary to the common understanding that between two isotropic materials having different refractive indices the electromagnetic reflection is unavoidable, our method shows that surprisingly the reflection phenomena can be completely eliminated. The invented method, different from the classical impedance matching, may also find electromagnetic applications outside of cloaking devices, wherever distortions are present arising from reflections.

physics.optics↗

arXiv2008

A Novel Design of Dielectric Perfect Invisibility Devices

The aim of an invisibility device is to guide light around any object put inside, being able to hide objects from sight. In this work, we propose a novel design of dielectric invisibility media based on negative refraction and optical conformal mapping that seems to create perfect invisibility. This design has some advantages and more relaxed constraints compared with already proposed schemes. In particular, it represents an example where the time delay in a dielectric invisibility device is zero. Furthermore, due to impedance matching of negatively refracting materials, the reflection should be close to zero. These findings strongly indicate that perfect invisibility with optically isotropic materials is possible. Finally, the area of the invisible space is also discussed.

physics.optics↗

arXiv2007

Transcription and noise in negative feedback loops

Recently, several studies have investigated the transcription process associated to specific genetic regulatory networks. In this work, we present a stochastic approach for analyzing the dynamics and effect of negative feedback loops (FBL) on the transcriptional noise. First, our analysis allows us to identify a bimodal activity depending of the strength of self-repression coupling D. In the strong coupling region D>>1, the variance of the transcriptional noise is found to be reduced a 28 % more than described earlier. Secondly, the contribution of the noise effect to the abundance of regulating protein becomes manifest when the coefficient of variation is computed. In the strong coupling region, this coefficient is found to be independent of all parameters and in fair agreement with the experimentally observed values. Finally, our analysis reveals that the regulating protein is significantly induced by the intrinsic and external noise in the strong coupling region. In short, it indicates that the existence of inherent noise in FBL makes it possible to produce a basal amount of proteins even though the repression level D is very strong.

q-bio.MN↗

arXiv2005

Two complementary representations of a scale-free network

Several studies on real complex networks from different fields as biology, economy, or sociology have shown that the degree of nodes (number of edges connected to each node) follows a scale-free power-law distribution like $P(k)\approx k^{-γ}$, where $P(k)$ denotes the frequency of the nodes that are connected to $k$ other nodes. Here we have carried out a study on scale-free networks, where a line graph transformation (i.e., edges in an initial network are transformed into nodes) is applied to a power-law distribution. Our results indicate that a power-law distribution as $P(k)\approx k^{-γ+1}$ is found for the transformed network together with a peak for low-degree nodes. In the present work we show a parametrization of this behaviour and discuss its application to real networks as metabolic networks, protein-protein interaction network and World Wide Web.

physics.bio-ph↗

arXiv2005

Symmetry and Dynamics in living organisms: The self-similarity principle governs gene expression dynamics

The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems composed of basic elements as proteins, genes and chemical compounds, a need remains for improving our understanding of dynamical features of the systems (i.e., temporal-dependence). In this article, we analyze the gene expression dynamics (i.e., how the genes expression fluctuates in time) by using a new constructive approach. This approach is based on only two fundamental ingredients: symmetry and the Markov property of dynamics. First, by using experimental data of human and yeast gene expression time series, we found a symmetry in short-time transition probability from time $t$ to time $t+1$. We call it self-similarity symmetry (i.e., surprisingly, the gene expression short-time fluctuations contain a repeating pattern of smaller and smaller parts that are like the whole, but different in size). Secondly, the Markov property of dynamics reflects that the short-time fluctuation governs the full-time behaviour of the system. Here, we succeed in reconstructing naturally the global behavior of the observed distribution of gene expression (i.e., scaling-law) and the local behaviour of the power-law tail of this distribution, by using only these two ingredients: symmetry and the Markov property of dynamics. This approach may represent a step forward toward an integrated image of the basic elements of the whole cell.

q-bio.BM↗

arXiv2005

Universal collective fluctuations in gene expression dynamics from yeast to human

In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average value over time are strongly correlated and obey a scaling law. As this feature is found in yeast and human organisms, it suggests that probably this coupling is a common dynamical organizing property of all living systems. To understand these observations, we propose a stochastic model which can explain these collective fluctuations, and predict the scaling exponent. Interestingly, our results indicate that the observed scaling law emerges from the self-similarity symmetry embedded in gene expression fluctuations.

q-bio.BM↗

arXiv2005

A stochastic approach to multi-gene expression dynamics

In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of the cell functions. In this process, the correlation among genes is crucial to determine the specific functions of genes. Here, we propose a novel multi-dimensional stochastic approach to deal with the gene correlation phenomena. Interestingly, our stochastic framework suggests that the study of the gene correlation requires only one theoretical assumption -Markov property- and the experimental transition probability, which characterizes the gene correlation system. Finally, a gene expression experiment is proposed for future applications of the model.

q-bio.BM↗

arXiv2004

Flexible construction of hierarchical scale-free networks with general exponent

Extensive studies have been done to understand the principles behind architectures of real networks. Recently, evidences for hierarchical organization in many real networks have also been reported. Here, we present a new hierarchical model which reproduces the main experimental properties observed in real networks: scale-free of degree distribution $P(k)$ (frequency of the nodes that are connected to $k$ other nodes decays as a power-law $P(k)\sim k^{-γ}$) and power-law scaling of the clustering coefficient $C(k)\sim k^{-1}$. The major novelties of our model can be summarized as follows: {\it (a)} The model generates networks with scale-free distribution for the degree of nodes with general exponent $γ> 2$, and arbitrarily close to any specified value, being able to reproduce most of the observed hierarchical scale-free topologies. In contrast, previous models can not obtain values of $γ> 2.58$. {\it (b)} Our model has structural flexibility because {\it (i)} it can incorporate various types of basic building blocks (e.g., triangles, tetrahedrons and, in general, fully connected clusters of $n$ nodes) and {\it (ii)} it allows a large variety of configurations (i.e., the model can use more than $n-1$ copies of basic blocks of $n$ nodes). The structural features of our proposed model might lead to a better understanding of architectures of biological and non-biological networks.

cond-mat.other↗

arXiv2004

Clustering under the line graph transformation: Application to reaction network

Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. The second network can be related to the first one by a technique called line graph transformation (i.e., edges in an initial network are transformed into nodes). Recently, the main topological properties of the metabolic networks have been properly described by means of a hierarchical model. In our work, we apply the line graph transformation to a hierarchical network and the clustering coefficient $C(k)$ is calculated for the transformed network, where $k$ is the node degree. While $C(k)$ follows the scaling law $C(k)\sim k^{-1.1}$ for the initial hierarchical network, $C(k)$ scales weakly as $k^{0.08}$ for the transformed network. These results indicate that the reaction network can be identified as a degree-independent clustering network.

q-bio.MN↗

arXiv2004

A Constructive Approach to Gene Expression Dynamics

The advent of new experimental genomic technologies and the massive increase of DNA sequence information is helping researchers better understand how our genes work. Recently, experiments on mRNA abundance (gene expression) have revealed that gene expression shows a stationary organization described by a power-law distribution (scale-free organization) (i.e., gene expression $k$ decays as $k^{-γ}$), which is highly conserved in all the major five kingdoms of life, from Bacteria to Human. An underlying gene expression dynamics "rich-travel-more" was suggested to recover that evolutional conservation of transcriptional organization. Here we propose a constructive approach to gene expression dynamics with larger scope. Our gene expression construction restores the stationary state, predicts the power-law exponent for different organisms with natural explanation for small correction at high and low expression levels, describes the intermediate state dynamics (time finite) and elucidates the gene expression stability. This approach requires only one assumption: Markov property.

q-bio.BM↗

arXiv2002

Magnetic moments of the Lambda(1405) and Lambda(1670) resonances

By using techniques of unitarized chiral perturbation theory, where the $Λ(1405)$ and $Λ(1670)$ resonances are dynamically generated, we evaluate the magnetic moments of these resonances and their transition magnetic moment. The results obtained here differ appreciably from those obtained with existing quark models. The width for the $Λ(1670) \to Λ(1405) γ$ transition is also evaluated leading to a branching ratio of the order of $2 \times 10^{-6}$.

hep-ph↗

arXiv2001

Two pion photoproduction on nucleons and nuclei in the rho and sigma regions

In this talk we report on two physical processes, the photoproduction of $ρ$ mesons in nuclei and the $π^0 π^0$ photoproduction in nuclei at low energies. In the first case the aim is to observe experimentally the theoretically predicted changes on the $ρ$ properties in the nuclear medium. In the second case one wishes to investigate the modifications of the $ππ$ interaction in the nuclear medium in the region of the $σ$ meson. In the first case we observe that it is quite difficult to see large effects due to the $ρ$ modification in the medium because the detection of the $ρ$ is done through the two pions which are produced in the $Δ$ region and are largely distorted in the medium. In the second case, when the I=0 part of the $ππ$ interaction is substituted by the in medium $ππ$ amplitude, we observe a very large shift of strength in the invariant mass distribution to small values of the mass in $^{12}C$ and $^{208}Pb$ with respect to the distribution of the elementary reaction. This spectacular shift appears to be corroborated by recent experiments at Mainz reported in this same Workshop.

nucl-th↗

arXiv2001

Chiral dynamics and pion-nucleon scattering around the N*(1535) resonance

We study the S-wave interaction of mesons with baryons in the strangeness S=0 sector in a coupled channel unitary approach. The basic dynamics is drawn from the lowest order meson baryon chiral Lagrangians. Small modifications inspired by models with explicit vector meson exchange in the t-channel are also considered. In addition the pi pi N channel is included and shown to have an important repercussion in the results, particularly in the isospin 3/2 sector.

hep-ph↗

arXiv2001

Dynamical meson-baryon resonances with chiral Lagrangians

The s-wave meson-baryon interaction is studied using the lowest-order chiral Lagrangian in a unitary coupled-channels Bethe-Salpeter equation. In the strangeness $S=-1$ sector the low-energy $K^- p$ dynamics leads to the dynamical generation of the $Λ(1405)$ as a ${\bar K}N$ state, along with a good description of the $K^- p$ scattering observables. At higher energies, the $Λ(1670)$ is also found to be generated dynamically as a $K Ξ$ quasibound state for the first time. For strangeness S=0, it is the $S_{11}(1535)$ resonance that emerges from the coupled-channels equations, leading to a satisfactory description of meson-baryon scattering observables in the energy region around the $S_{11}(1535)$. We speculate on the possible dynamical generation of $Ξ$ resonances within the chiral $S=-2$ sector as ${\bar K} Λ$ or ${\bar K} Σ$ quasibound states.

nucl-th↗

arXiv2001

Study of polarization observables in double pion photoproduction on the proton

Using a model for two pion photoproduction on the proton previously tested in total cross sections and invariant mass distributions, we evaluate here polarization observables on which recent experiments are providing new information. We evaluate cross sections for spin 1/2 and 3/2, which are measured at Mainz and play an important role in tests of the GHD sum rule. We also evaluate the proton polarization asymmetry $Σ$ which is currently under investigation at GRAAL in Grenoble.

nucl-th↗

arXiv2001

The role of Delta(1700) excitation and rho production in double pion photoproduction

Recent information on invariant mass distributions of the $γp\toπ^+π^0 n$ reaction, where previous theoretical models had shown deficiencies, have made more evident the need for new mechanisms, so far neglected or inaccurately included. We have updated a previous model to include new necessary mechanisms. We find that the production of the $ρ$ meson, and the $Δ(1700)$ excitation, through interference with the dominant terms, are important mechanisms that solve the puzzle of the $γp\toπ^+π^0 n$ reaction without spoiling the early agreement with the $γp\toπ^+π^- p$ and $γp\toπ^0π^0 p$ reactions.

nucl-th↗