arXiv subjects

A. -L. Barabasi

Publications and source records attributed to A. -L. Barabasi.

36 records · Page 2Linked to original sources

arXiv2002

The topology of the transcription regulatory network in the yeast, S. cerevisiae

MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene activity coupled with the assessment of perturbed transcriptome (i. e., global mRNA expression) patterns represents one approach toward this goal, and may provide a backbone into which other measurements can be later integrated. RESULT: We use microarray data on 287 single gene deletion Saccharomyces cerevisiae mutant strains to elucidate generic relationships among perturbed transcriptomes. Their comparison with a method that preferentially recognizes distinct expression subpatterns allows us to pair those transcriptomes that share localized similarities. Analyses of the resulting transcriptome similarity network identify a continuum hierarchy among the deleted genes, and in the frequency of local similarities that establishes the links among their reorganized transcriptomes. We also find a combinatorial utilization of shared expression subpatterns within individual links, with increasing quantitative similarity among those that connect transcriptome states induced by the deletion of functionally related gene products. This suggests a distinct hierarchical and combinatorial organization of the S. cerevisiae transcriptional activity, and may represent a pattern that is generic to the transcriptional organization of all eukaryotic organisms. AVAILABILITY: Detailed analyses of the comparison method and free software are available from the authors and at http://angel.elte.hu/bioinf

cond-mat.stat-mech↗

arXiv2002

Percolation in Directed Scale-Free Networks

Many complex networks in nature have directed links, a property that affects the network's navigability and large-scale topology. Here we study the percolation properties of such directed scale-free networks with correlated in- and out-degree distributions. We derive a phase diagram that indicates the existence of three regimes, determined by the values of the degree exponents. In the first regime we regain the known directed percolation mean field exponents. In contrast, the second and third regimes are characterized by anomalous exponents, which we calculate analytically. In the third regime the network is resilient to random dilution, i.e., the percolation threshold is p_c->1.

cond-mat.dis-nn↗

arXiv2002

Nanowire formation on sputter eroded surfaces

Rotated ripple structures (RRS) on sputter eroded surfaces are potential candidates for nanoscale wire fabrication. We show that the necessary condition for RRS formation is that the width of the collision cascade in the longitudinal direction has to be larger than that in the transverse direction, which can be achieved by using high energy ion beams. By calculating the structure factor for the RRS we find that they are more regular and their amplitude is more enhanced compared to the much studied ripple structure forming in the linear regime of sputter erosion.

cond-mat.mtrl-sci↗

arXiv2001

Comparable system-level organization of Archaea and Eukaryotes

A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment within the constraints of an organism's innate characteristics. Elucidation of the origin and evolutionary relationship of species has been complemented by nucleotide sequence and gene content analyses, with profound implications for recognizing life's major domains. Understanding of evolutionary relationships may be further expanded by comparing systemic higher-level organization among species. Here we employ multivariate analyses to evaluate the biochemical reaction pathways characterizing 43 species. Comparison of the information transfer pathways of Archaea and Eukaryotes indicates a close relationship between these domains. In addition, whereas eukaryotic metabolic enzymes are primarily of bacterial origin, the pathway-level organization of archaeal and eukaryotic metabolic networks is more closely related. Our analyses therefore suggest that during the symbiotic evolution of eukaryotes, incorporation of bacterial metabolic enzymes into the proto-archaeal proteome was constrained by the host's pre-existing metabolic architecture.

cond-mat.stat-mech↗

arXiv2001

Monte Carlo Simulation of Sinusoidally Modulated Superlattice Growth

The fabrication of ZnSe/ZnTe superlattices grown by the process of rotating the substrate in the presence of an inhomogeneous flux distribution instead of successively closing and opening of source shutters is studied via Monte Carlo simulations. It is found that the concentration of each compound is sinusoidally modulated along the growth direction, caused by the uneven arrival of Se and Te atoms at a given point of the sample, and by the variation of the Te/Se ratio at that point due to the rotation of the substrate. In this way we obtain a ZnSe$_{1-x}$Te$_x$ alloy in which the composition $x$ varies sinusoidally along the growth direction. The period of the modulation is directly controlled by the rate of the substrate rotation. The amplitude of the compositional modulation is monotonous for small angular velocities of the substrate rotation, but is itself modulated for large angular velocities. The average amplitude of the modulation pattern decreases as the angular velocity of substrate rotation increases and the measurement position approaches the center of rotation. The simulation results are in good agreement with previously published experimental measurements on superlattices fabricated in this manner.

cond-mat.mtrl-sci↗

arXiv2001

Granular Drag on a Discrete Object: Shape Effects on Jamming

We study the drag force on discrete objects with circular cross section moving slowly through a spherical granular medium. Variations in the geometry of the dragged object change the drag force only by a small fraction relative to shape effects in fluid drag. The drag force depends quadratically on the object's diameter as expected. We do observe, however, a deviation above the expected linear depth dependence, and the magnitude of the deviation is apparently controlled by geometrical factors.

cond-mat.dis-nn↗

arXiv2001

Measuring preferential attachment for evolving networks

A key ingredient of current models proposed to capture the topological evolution of complex networks is the hypothesis that highly connected nodes increase their connectivity faster than their less connected peers, a phenomenon called preferential attachment. Measurements on four networks, namely the science citation network, Internet, actor collaboration and science coauthorship network indicate that the rate at which nodes acquire links depends on the node's degree, offering direct quantitative support for the presence of preferential attachment. We find that for the first two systems the attachment rate depends linearly on the node degree, while for the latter two the dependence follows a sublinear power law.

cond-mat.stat-mech↗

arXiv2001

Stick-Slip Fluctuations in Granular Drag

We study fluctuations in the drag force experienced by an object moving through a granular medium. The successive formation and collapse of jammed states give a stick-slip nature to the fluctuations which are periodic at small depths but become "stepped" at large depths, a transition which we interpret as a consequence of the long-range nature of the force chains and the finite size of our experiment. Another important finding is that the mean force and the fluctuations appear to be independent of the properties of the contact surface between the grains and the dragged object. These results imply that the drag force originates in the bulk properties of the granular sample.

cond-mat.dis-nn↗

arXiv2001

Weighted Evolving Networks

Many biological, ecological and economic systems are best described by weighted networks, as the nodes interact with each other with varying strength. However, most network models studied so far are binary, the link strength being either 0 or 1. In this paper we introduce and investigate the scaling properties of a class of models which assign weights to the links as the network evolves. The combined numerical and analytical approach indicates that asymptotically the total weight distribution converges to the scaling behavior of the connectivity distribution, but this convergence is hampered by strong logarithmic corrections.

cond-mat.dis-nn↗

arXiv2000

Modeling relaxation and jamming in granular media

We introduce a stochastic microscopic model to investigate the jamming and reorganization of grains induced by an object moving through a granular medium. The model reproduces the experimentally observed periodic sawtooth fluctuations in the jamming force and predicts the period and the power spectrum in terms of the controllable physical parameters. It also predicts that the avalanche sizes, defined as the number of displaced grains during a single advance of the object, follow a power-law, $P(s)\sim s^{-τ}$, where the exponent is independent of the physical parameters.

cond-mat.soft↗

arXiv2000

The large-scale organization of metabolic networks

In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the key role these networks play in sustaining various cellular functions, their large-scale structure is essentially unknown. Here we present the first systematic comparative mathematical analysis of the metabolic networks of 43 organisms representing all three domains of life. We show that, despite significant variances in their individual constituents and pathways, these metabolic networks display the same topologic scaling properties demonstrating striking similarities to the inherent organization of complex non-biological systems. This suggests that the metabolic organization is not only identical for all living organisms, but complies with the design principles of robust and error-tolerant scale-free networks, and may represent a common blueprint for the large-scale organization of interactions among all cellular constituents.

cond-mat.stat-mech↗

arXiv2000

Quantum Dot and Hole Formation in Sputter Erosion

Recently it was experimentally demonstrated that sputtering under normal incidence leads to the formation of spatially ordered uniform nanoscale islands or holes. Here we show that these nanostructures have inherently nonlinear origin, first appearing when the nonlinear terms start to dominate the surface dynamics. Depending on the sign of the nonlinear terms, determined by the shape of the collision cascade, the surface can develop regular islands or holes with identical dynamical features, and while the size of these nanostructures is independent of flux and temperature, it can be modified by tuning the ion energy.

cond-mat↗

arXiv1999

Jamming and Fluctuations in Granular Drag

We investigate the dynamic evolution of jamming in granular media through fluctuations in the granular drag force. The successive collapse and formation of jammed states give a stick-slip nature to the fluctuations which is independent of the contact surface between the grains and the dragged object -- thus implying that the stress-induced collapse is nucleated in the bulk of the granular sample. We also find that while the fluctuations are periodic at small depths, they become "stepped" at large depths, a transition which we interpret as a consequence of the long-range nature of the force chains.

cond-mat.dis-nn↗

arXiv1999

Liquid induced transitions in granular media

We investigate the effect of interstitial liquid on the physical properties of granular media by measuring the angle of repose as a function of the liquid content. The resultant adhesive forces lead to three distinct regimes in the observed behavior as the liquid content is increased: a granular regime in which the grains move individually, a correlated regime in which the grains move in correlated clusters, and a plastic regime in which the grains flow coherently. We discuss these regimes in terms of two proposed theories describing the effects of liquid on the physical properties of granular media.

cond-mat.dis-nn↗

arXiv1999

Dynamics of ripple formation in sputter erosion: nonlinear phenomena

Many morphological features of sputter eroded surfaces are determined by the balance between ion induced linear instability and surface diffusion. However, the impact of the nonlinear terms on the morphology is less understood. We demonstrate that while at short times ripple formation is described by the linear theory, after a characteristic time the nonlinear terms determine the surface morphology by either destroying the ripples, or generating a new rotated ripple structure. We show that the morphological transitions induced by the nonlinear effects can be detected by monitoring the surface width and the erosion velocity.

cond-mat↗

arXiv1997

Roughening of ion-eroded surfaces

Recent experimental studies focusing on the morphological properties of surfaces eroded by ion-bombardment report the observation of self-affine fractal surfaces, while others provide evidence about the development of a periodic ripple structure. To explain these discrepancies we derive a stochastic growth equation that describes the evolution of surfaces eroded by ion bombardment. The coefficients appearing in the equation can be calculated explicitly in terms of the physical parameters characterizing the sputtering process. Exploring the connection between the ion-sputtering problem and the Kardar-Parisi-Zhang and Kuramoto-Sivashinsky equations, we find that morphological transitions may take place when experimental parameters, such as the angle of incidence of the incoming ions or their average penetration depth, are varied. Furthermore, the discussed methods allow us to calculate analytically the ion-induced surface diffusion coefficient, that can be compared with experiments. Finally, we use numerical simulations of a one dimensional sputtering model to investigate certain aspects of the ripple formation and roughening.

cond-mat.stat-mech↗

arXiv1995

Scaling properties of driven interfaces in disordered media

We perform a systematic study of several models that have been proposed for the purpose of understanding the motion of driven interfaces in disordered media. We identify two distinct universality classes: (i) One of these, referred to as directed percolation depinning (DPD), can be described by a Langevin equation similar to the Kardar-Parisi-Zhang equation, but with quenched disorder. (ii) The other, referred to as quenched Edwards-Wilkinson (QEW), can be described by a Langevin equation similar to the Edwards-Wilkinson equation but with quenched disorder. We find that for the DPD universality class the coefficient $λ$ of the nonlinear term diverges at the depinning transition, while for the QEW universality class either $λ= 0$ or $λ\to 0$ as the depinning transition is approached. The identification of the two universality classes allows us to better understand many of the results previously obtained experimentally and numerically. However, we find that some results cannot be understood in terms of the exponents obtained for the two universality classes {\it at\/} the depinning transition. In order to understand these remaining disagreements, we investigate the scaling properties of models in each of the two universality classes {\it above\/} the depinning transition. For the DPD universality class, we find for the roughness exponent $α_P = 0.63 \pm 0.03$ for the pinned phase, and $α_M = 0.75 \pm 0.05$ for the moving phase. For the growth exponent, we find $β_P = 0.67 \pm 0.05$ for the pinned phase, and $β_M = 0.74 \pm 0.06$ for the moving phase. Furthermore, we find an anomalous scaling of the prefactor of the width on the driving force. A new exponent $φ_M = -0.12 \pm 0.06$, characterizing the scaling of this prefactor, is shown to relate the values of the roughness

cond-mat↗

arXiv1994

Avalanches and the Directed Percolation Depinning Model: Experiments, Simulations and Theory

We study the recently-introduced directed percolation depinning (DPD) model for interface roughening with quenched disorder for which the interface becomes pinned by a directed percolation (DP) cluster for $d = 1$, or a directed surface (DS) for $d > 1$. The mapping to DP enables us to predict some of the critical exponents of the growth process. For the case of $(1+1)$ dimensions, the theory predicts that the roughness exponent $α$ is given by $α= ν_{\perp} / ν_{\parallel}$, where $ν_{\perp}$ and $ν_{\parallel}$ are the exponents governing the divergence of perpendicular and parallel correlation lengths of the DP incipient infinite cluster. The theory also predicts that the dynamical exponent $z$ equals the exponent $d_{\rm min}$ characterizing the scaling of the shortest path on a isotropic percolation cluster. The exponent $α$ decreases monotonically with $d$ but does not seem to approach zero for any dimension calculated ($d \le 6$), suggesting that the DPD model has no upper critical dimension for the static exponents. On the other hand, $z$ appears to approach $2$ as $d \rightarrow 6$, as expected by the result $z = d_{\rm min}$, suggesting that $d_c = 6$ for the dynamics. We also perform a set of imbibition experiments, in both $(1+1)$ and $(2+1)$ dimensions, that can be used to test the DPD model. We find good agreement between experimental, theoretical and numerical approaches. Further, we study the properties of avalanches in the context of the DPD model. We relate the scaling properties of the avalanches in the DPD model to the scaling properties for the self-organized depinning (SOD) model, a variant of the DPD model. We calculate the exponent characterizing the avalanches distribution $τ_{\rm aval}$ for $d = 1$ to $d = 6$, and compare our results with recent theoretical

cond-mat↗