arXiv subjects

Eli Eisenberg

Publications and source records attributed to Eli Eisenberg.

At least 19 recordsLinked to original sources

arXiv2014

Topological phase transition in a discrete quasicrystal

We investigate a two-dimensional tiling model. Even though the degrees of freedom in this model are discrete, it has a hidden continuous global symmetry in the infinite lattice limit, whose corresponding Goldstone modes are the quasicrystalline phasonic degrees of freedom. We show that due to this continuous symmetry, and despite the apparent discrete nature of the model, a topological phase transition from a quasi-long-range ordered to a disordered phase occurs at a finite temperature, driven by vortex proliferation. We argue that some of the results are universal properties of two-dimensional systems whose ground state is a quasicrystalline state.

cond-mat.stat-mech↗

arXiv2013

Phonon-mediated damping of mechanical vibrations in a finite atomic chain coupled to an outer environment

We study phonon-mediated damping of mechanical vibrations in a finite quantum-mechanical atomic-chain model. Our study is motivated by the quest to understand the quality factors (Q) of nanomechanical resonators and nanoelectromechanical systems (NEMS), as well as actual experiments with suspended atomic chains and molecular junctions. We consider a finite atomic chain which is coupled to a zero-temperature outer environment, modeled as two additional semi-infinite chains, thus inducing "clamping-losses". Weak coupling to the outer environment ensures that the clamping losses are small, and that the initially discrete nature of the phonon spectrum is approximately maintained. We then consider a phonon damping process known as "Landau-Rumer damping", where phonons in the excited mode of vibration decay into other modes through anharmonic phonon-phonon interaction. The approximately discrete nature of the phonon spectrum leads to sharp nonmonotonic changes in Q as parameters are varied, and to the appearance of resonances in the damping. The latter correspond to the existence of decay processes where the participating phonons approximately conserve energy. We explore means to control the damping by changing either the number of atoms in the chains or the ratio between the longitudinal and transverse speeds of sound, thereby suggesting future experiments to observe this resonance-like behavior.

cond-mat.mes-hall↗

arXiv2011

Possibility of Electron Pairing in Small Metallic Nanoparticles

We investigate the possibility of electron pairing in small metallic nanoparticles at zero temperature. In these particles both electrons and phonons are mesoscopic, i.e. modified by the nanoparticle's finite size. The electrons, the phonons, and their interaction are described within the framework of a simplified model. The effective electron-electron interaction is derived from the underlying electron-phonon interaction. The effect of both effective interaction and Coulomb interaction on the electronic spectrum is evaluated. Results are presented for aluminum, zinc and potassium nanoparticles containing a few hundred atoms. We find that a large portion of the aluminum and zinc particles exhibit modifications in their electronic spectrum due to pairing correlations, while pairing correlations are not present in the potassium particles.

cond-mat.supr-con↗

arXiv2010

A finite-temperature liquid-quasicrystal transition in a lattice model

We consider a tiling model of the two-dimensional square-lattice, where each site is tiled with one of the sixteen Wang tiles. The ground states of this model are all quasi-periodic. The systems undergoes a disorder to quasi-periodicity phase transition at finite temperature. Introducing a proper order-parameter, we study the system at criticality, and extract the critical exponents characterizing the transition. The exponents obtained are consistent with hyper-scaling.

cond-mat.stat-mech↗

arXiv2010

Direct measurements of the dynamical correlation length indicate its divergence at an athermal glass transition

The super-cooled $N3$ model exhibits an increasingly slow dynamics as density approaches the model's random closest packing density. Here, we present a direct measurement of the dynamical correlation function $G_4(r,t)$, showing the emergence of a growing length scale $ξ_4$ across which the dynamics is correlated. The correlation length measured, up to 120 lattice sites, power-law diverges as the density approaches $ρ_t$, the density at which the fluid phase of the model is predicted to terminate. It is shown that the four-point susceptibility, often used as an agent to estimate $ξ_4$, does not depend simply on the latter. Rather, it depends strongly on the short-range behavior of $G_4(r,t)$. Consequently, $χ_4$ peaks before $ξ_4$ reaches its maximal value. The two quantities should therefore be studied independently.

cond-mat.stat-mech↗

arXiv2007

Super-Poissonian Shot Noise as a Measure of Dephasing in Closed Quantum Dots

Electron-electron interactions play a major role in determining the low-temperature rate of phase loss of electrons in mesoscopic systems. The study of the dephasing rate is expected to contribute to the understanding of the many-body nature of such systems. Closed quantum dots are of special interest in this respect, due to theoretical predictions suggesting a possible transition temperature below which the dephasing rate vanishes. This prediction has attracted much attention, since closed quantum dots are prime candidates for storage units in quantum computers, and thus their phase coherence properties are of great importance. However, an effective method for measuring the dephasing rate within a closed quantum dot is still lacking. Here we study two-level systems and show that the Fano factor has a sharp peak as a function of the chemical potential, the location of which can be simply related to the dephasing rate. We thus suggest to use the properties of the Fano factor peak in the super-Poissonian regime as a probe for the dephasing rate.

cond-mat.mes-hall↗

arXiv2007

Estimation of critical exponents from the cluster coefficients: Application to hard spheres

For a large class of repulsive interaction models, the Mayer cluster integrals can be transformed into a tridiagonal symmetric matrix, whose elements converge to a constant with a 1/n^2 correction. We find exact expressions, in terms of these correction terms, for the two critical exponents describing the density near the two singular termination points of the fluid phase. We apply the method to the hard-spheres model and find that the metastable fluid phase terminates at rho_t=0.751(5). The density near the transition is given by (rho_t-rho)~(z_t-z)^sigma', where the critical exponent is predicted to be sigma'=0.0877(25). The termination density is close to the observed glass transition, and thus the above critical behavior is expected to characterize the onset of glassy behavior in hard spheres.

cond-mat.stat-mech↗

arXiv2006

Connectivity and expression in protein networks: Proteins in a complex are uniformly expressed

We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is largely due to interacting pairs which are part of protein complexes. We solve a generic model of complex formation and show explicitly that complexes form most efficiently when their members have roughly the same concentrations. Therefore, the observed similarity in interacting protein concentrations could be attributed to optimization for efficiency of complex formation.

q-bio.MN↗

arXiv2005

Analysis of the ordering transition of hard disks through the Mayer cluster expansion

The available virial coefficients for the 2D hard disks model are transformed into a matrix representation of the thermodynamic potentials, which allows for an accurate description of the whole fluid phase, up to the phase transition. We find that the fluid phase terminates at the transition point, supporting the Kosterlitz-Thouless-Halperin-Nelson-Young picture of a second order phase transition into a Hexatic phase. The density and pressure at the transition are calculated from the available first ten virial coefficients, and are found to be in excellent agreement with recent Monte-Carlo calculations. Finally, we calculate the equation of state in the critical region.

cond-mat.stat-mech↗

arXiv2005

Is there any sense in antisense editing?

A number of recent studies have hypothesized that sense-antisense RNA transcript pairs create dsRNA duplexes that undergo extensive A-to-I RNA editing. Here we studied human and mouse genomic antisense regions, and found that the editing level in these areas is negligible. This observation puts in question the scope of sense-antisense duplexes formation in-vivo, which is the basis for a number of proposed regulatory mechanisms.

q-bio.GN↗

arXiv2005

Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome

Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae. Results: Taking into account the absence of a significantly large yeast EST database, we use microarray expression data collected for genomic regions erroneously believed to be coding to study the expression pattern of non-coding regions in the Saccharomyces cerevisiae genome. We find that at least 164 out of 589 (28%) such regions are expressed under specific biological conditions. In particular, looking at the probes that are located opposing other known genes at the same genomic locus, we find that 88 out of 341 (26%) of these genes support antisense transcription. The expression patterns of these antisense genes are positively correlated. We validate these results using RT-PCR on a sample of 6 non-coding transcripts. Conclusions: 1. The yeast genome is transcribed on a scale larger than previously assumed. 2. Correlated transcription of antisense genes is abundant in the yeast genome. 3. Antisense genes in yeast are non-coding.

q-bio.GN↗

arXiv2005

Evolutionarily conserved human targets of adenosine to inosine RNA editing

A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding the proteomic repertoire. Genetic recoding by editing was so far observed for only a few mammalian RNAs that are predominantly expressed in nervous tissues. However, as these editing targets fail to explain the broad and severe phenotypes of ADAR1 knockout mice, additional targets for editing by ADARs were always expected. Using comparative genomics and expressed sequence analysis, we identified and experimentally verified four additional candidate human substrates for ADAR-mediated editing: FLNA, BLCAP, CYFIP2 and IGFBP7. Additionally, editing of three of these substrates was verified in the mouse while two of them were validated in chicken. Interestingly, none of these substrates encodes a receptor protein but two of them are strongly expressed in the CNS and seem important for proper nervous system function. The editing pattern observed suggests that some of the affected proteins might have altered physiological properties leaving the possibility that they can be related to the phenotypes of ADAR1 knockout mice.

q-bio.GN↗

arXiv2004

Is abundant A-to-I RNA editing primate-specific?

A-To-I RNA editing is common to all eukaryotes, associated with various neurological functions. Recently, A-to-I editing was found to occur abundantly in the human transcriptome. Here we show that the frequency of A-to-I editing in humans is at least an order of magnitude higher as that of mouse, rat, chicken or fly. The extraordinary frequency of RNA editing in human is explained by the dominance of the primate-specific Alu element in the human transcriptome, which increases the number of double-stranded RNA substrates.

q-bio.GN↗

arXiv2004

Systematic identification of abundant A-to-I editing sites in the human transcriptome

RNA editing by members of the double-stranded RNA-specific ADAR family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential for mammalian development. Currently, only a limited number of human ADAR substrates are known, while indirect evidence suggests a substantial fraction of all pre-mRNAs being affected. Here we describe a computational search for ADAR editing sites in the human transcriptome, using millions of available expressed sequences. 12,723 A-to-I editing sites were mapped in 1,637 different genes, with an estimated accuracy of 95%, raising the number of known editing sites by two orders of magnitude. We experimentally validated our method by verifying the occurrence of editing in 26 novel substrates. A-to-I editing in humans primarily occurs in non-coding regions of the RNA, typically in Alu repeats. Analysis of the large set of editing sites indicates the role of editing in controlling dsRNA stability.

q-bio.GN↗

arXiv2003

Human housekeeping genes are compact

We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in "housekeeping" genes, showing constitutive expression in all tissues. We compare selected aspects of their genomic structure with a set of background genes. We find that the introns, untranslated regions and coding sequences of the housekeeping genes are shorter, indicating a selection for compactness in these genes.

q-bio.GN↗

arXiv2003

Preferential attachment in the protein network evolution

The Saccharomyces cerevisiae protein-protein interaction map, as well as many natural and man-made networks, shares the scale-free topology. The preferential attachment model was suggested as a generic network evolution model that yields this universal topology. However, it is not clear that the model assumptions hold for the protein interaction network. Using a cross genome comparison we show that (a) the older a protein, the better connected it is, and (b) The number of interactions a protein gains during its evolution is proportional to its connectivity. Therefore, preferential attachment governs the protein network evolution. The evolutionary mechanism leading to such preference and some implications are discussed.

cond-mat.stat-mech↗

arXiv2002

Polarization of interacting bosons with spin

We demonstrate rigorously that in the absence of explicit spin-dependent forces one of the ground states of interacting bosons with spin is always fully polarized -- however complicated the many-body interaction potential might be. Depending on the particle spin, the polarized ground state will generally be degenerate with other states, but one can specify the exact degeneracy. For T>0 the magnetization and susceptibility necessarily exceed that of a pure paramagnet. These results are relevant to recent experiments exploring the relation between triplet superconductivity and ferromagnetism, and the Bose-Einstein condensation of atoms with spin. They eliminate the possibility, raised in some theoretical speculations, that the ground state or positive temperature state might be antiferromagnetic.

cond-mat.stat-mech↗

arXiv2001

Calculation of dephasing times in closed quantum dots

Dephasing of one-particle states in closed quantum dots is analyzed within the framework of random matrix theory and Master equation. Combination of this analysis with recent experiments on the magnetoconductance allows for the first time to evaluate the dephasing times of closed quantum dots. These dephasing times turn out to depend on the mean level spacing and to be significantly enhanced as compared with the case of open dots. Moreover, the experimental data available are consistent with the prediction that the dephasing of one-particle states in finite closed systems disappears at low enough energies and temperatures.

cond-mat.mes-hall↗