arXiv subjects

E. Almaas

Publications and source records attributed to E. Almaas.

17 recordsLinked to original sources

arXiv2008

Genetic noise control via protein oligomerization

Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamic role of protein-protein interactions. Here we have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its random switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise.

q-bio.MN↗

arXiv2006

The Activity Reaction Core and Plasticity of Metabolic Networks

Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses (FBA) have proved highly successful in analyzing the capabilities of cellular metabolism, including its capacity to predict deletion phenotypes, the ability to calculate the relative flux values of metabolic reactions and the properties of alternate optimal growth states. Here, we use FBA to thoroughly assess the activity of the Escherichia coli, Helicobacter pylori, and Saccharomyces cerevisiae metabolism in 30,000 diverse simulated environments. We identify a set of metabolic reactions forming a connected metabolic core that carry non-zero fluxes under all growth conditions, and whose flux variations are highly correlated. Furthermore, we find that the enzymes catalyzing the core reactions display a considerably higher fraction of phenotypic essentiality and evolutionary conservation than those catalyzing non-core reactions. Cellular metabolism is characterized by a large number of species-specific conditionally-active reactions organized around an evolutionary conserved always active metabolic core. Finally, we find that most current antibiotics interfering with the bacterial metabolism target the core enzymes, indicating that our findings may have important implications for antimicrobial drug target discovery.

q-bio.MN↗

arXiv2005

Fifteen Minutes of Fame: The Dynamics of Information Access on the Web

While current studies on complex networks focus on systems that change relatively slowly in time, the structure of the most visited regions of the Web is altered at the timescale from hours to days. Here we investigate the dynamics of visitation of a major news portal, representing the prototype for such a rapidly evolving network. The nodes of the network can be classified into stable nodes, that form the time independent skeleton of the portal, and news documents. The visitation of the two node classes are markedly different, the skeleton acquiring visits at a constant rate, while a news document's visitation peaking after a few hours. We find that the visitation pattern of a news document decays as a power law, in contrast with the exponential prediction provided by simple models of site visitation. This is rooted in the inhomogeneous nature of the browsing pattern characterizing individual users: the time interval between consecutive visits by the same user to the site follows a power law distribution, in contrast with the exponential expected for Poisson processes. We show that the exponent characterizing the individual user's browsing patterns determines the power-law decay in a document's visitation. Finally, our results document the fleeting quality of news and events: while fifteen minutes of fame is still an exaggeration in the online media, we find that access to most news items significantly decays after 36 hours of posting.

physics.soc-ph↗

arXiv2004

Statistics of Weighted Networks

We study the statistics of growing networks in which each link carries a weight (k_i k_j)^theta, where k_i and k_j are the node degrees at the endpoints of link ij. Network growth is governed by preferential attachment in which a newly-added node attaches to a node of degree k with rate A_k=k+lambda. For general values of theta and lambda, we compute the total weight of a network as a function of the number of nodes N and the distribution of link weights. Generically, the total weight grows as N for lambda>theta-1, and super-linearly otherwise. The link weight distribution is predicted to have a power law form that is modified by a logarithmic correction for the case lambda=0. We also determine the node strength, defined as the sum of the weights of the links that attach to the node, as function of k. Using known results for degree correlations, we deduce the scaling of the node strength on k and N.

cond-mat.stat-mech↗

arXiv2004

Minimum spanning trees on weighted scale-free networks

A complete understanding of real networks requires us to understand the consequences of the uneven interaction strengths between a system's components. Here we use the minimum spanning tree (MST) to explore the effect of weight assignment and network topology on the organization of complex networks. We find that if the weight distribution is correlated with the network topology, the MSTs are either scale-free or exponential. In contrast, when the correlations between weights and topology are absent, the MST degree distribution is a power-law and independent of the weight distribution. These results offer a systematic way to explore the impact of weak links on the structure and integrity of complex networks.

cond-mat.dis-nn↗

arXiv2004

Global organization of metabolic fluxes in the bacterium, Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions. We implement a flux balance analysis of the E. coli MG1655 metabolism, finding that the network utilization is highly uneven: while most metabolic reactions have small fluxes, the metabolism's activity is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high flux backbone. The identified behavior likely represents a universal feature of metabolic activity in all cells, with potential implications to metabolic engineering.

q-bio.MN↗

arXiv2004

Theory of Josephson Arrays in a Resonant Cavity

We review our previous work on the dynamics of one- and two-dimensional arrays of underdamped Josephson junctions placed in a single-mode resonant cavity. Starting from a well-defined model Hamiltonian, which includes the effects of driving current and dissipative coupling to a heat bath, we write down the Heisenberg equations of motion for the variables of the Josephson junction and the cavity mode. In the limit of many photons, these equations reduce to coupled ordinary differential equations, which can be solved numerically. We present a review of some characteristic numerical results, which show many features similar to experiment. These include self-induced resonant steps (SIRS's) at voltages $V = n\hbarΩ/(2e)$, where $Ω$ is the cavity frequency, and $n$ is generally an integer; a threshold number $N_c$ of active rows of junctions above which the array is coherent; and a time-averaged cavity energy which is quadratic in the number of active junctions, when the array is above threshold. When the array is biased on a SIRS, then, for given junction parameters, the power radiated into the array varies as the square of the number of active junctions, consistent with expectations for coherent radiation. For a given step, a two-dimensional array radiates much more energy into the cavity than does a one-dimensional array. Finally, in two dimensions, we find a strong polarization effect: if the cavity mode is polarized perpendicular to the direction of current injection in a square array, then it does not couple to the array and no power is radiated into the cavity.

cond-mat.supr-con↗

arXiv2004

Power laws in biological networks

The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological networks, discussing their scale-free and hierarchical features. We illustrate the major network characteristics using examples from the metabolic network of the bacterium Escherichia coli. We also discuss the principles of network utilization, acknowledging that the interactions in a real network have unequal strengths. We study the interplay between topology and reaction fluxes provided by flux-balance analysis. We find that the cellular utilization of the metabolic network is both globally and locally highly inhomogeneous, dominated by "hot-spots", representing connected high-flux pathways.

q-bio.MN↗

arXiv2003

Scaling Properties of Random Walks on Small-World Networks

Using both numerical simulations and scaling arguments, we study the behavior of a random walker on a one-dimensional small-world network. For the properties we study, we find that the random walk obeys a characteristic scaling form. These properties include the average number of distinct sites visited by the random walker, the mean-square displacement of the walker, and the distribution of first-return times. The scaling form has three characteristic time regimes. At short times, the walker does not see the small-world shortcuts and effectively probes an ordinary Euclidean network in $d$-dimensions. At intermediate times, the properties of the walker shows scaling behavior characteristic of an infinite small-world network. Finally, at long times, the finite size of the network becomes important, and many of the properties of the walker saturate. We propose general analytical forms for the scaling properties in all three regimes, and show that these analytical forms are consistent with our numerical simulations.

cond-mat.dis-nn↗

arXiv2003

Radiation forces on an absorbing micrometer-sized sphere in an evanescent field

The vertical radiation force on an absorbing micrometer-sized dielectric sphere situated in an evanescent field is calculated, using electromagnetic wave theory. The present work is a continuation of an earlier paper [E. Almaas and I. Brevik, J. Opt. Soc. Am. B {\bf 12}, 2429 (1995)], in which both the horizontal and the vertical radiation forces were calculated with the constraint that the sphere was nonabsorbing. Whereas the horizontal force can be well accounted for within this constraint, there is no possibility to describe the {\it repulsiveness} of the vertical force, so distinctly demonstrated in the Kawata-Sugiura experiment [Opt. Lett. {\bf 17}, 772 (1992)], unless a departure from the theory of pure nondispersive dielectrics is made in some way. Introduction of absorption, i.e. a complex refractive index, is one natural way of generalizing the previous theory. We work out general expressions for the vertical force for this case and illustrate the calculations by numerical computations. It turns out that, when applied to the Kawata-Sugiura case, the repulsive radiation force caused by absorption is {\it not} strong enough to account for the actual lifting of the polystyrene latex or glass spheres. The physical reason for the experimental outcome is, in this case, most probably the presence of surfactants making the surface of the spheres partially conducting.

physics.optics↗

arXiv2002

Theory of Two-Dimensional Josephson Arrays in a Resonant Cavity

We consider the dynamics of a two-dimensional array of underdamped Josephson junctions placed in a single-mode resonant cavity. Starting from a well-defined model Hamiltonian, which includes the effects of driving current and dissipative coupling to a heat bath, we write down the Heisenberg equations of motion for the variables of the Josephson junction and the cavity mode, extending our previous one-dimensional model. In the limit of large numbers of photons, these equations can be expressed as coupled differential equations and can be solved numerically. The numerical results show many features similar to experiment. These include (i) self-induced resonant steps (SIRS's) at voltages V = (n hbar Omega)/(2e), where Omega is the cavity frequency, and n is generally an integer; (ii) a threshold number N_c of active rows of junctions above which the array is coherent; and (iii) a time-averaged cavity energy which is quadratic in the number of active junctions, when the array is above threshold. Some differences between the observed and calculated threshold behavior are also observed in the simulations and discussed. In two dimensions, we find a conspicuous polarization effect: if the cavity mode is polarized perpendicular to the direction of current injection in a square array, it does not couple to the array and there is no power radiated into the cavity. We speculate that the perpendicular polarization would couple to the array, in the presence of magnetic-field-induced frustration. Finally, when the array is biased on a SIRS, then, for given junction parameters, the power radiated into the array is found to vary as the square of the number of active junctions, consistent with expectations for a coherent radiation.

cond-mat.supr-con↗

arXiv2001

Dynamics of a Josephson Array in a Resonant Cavity

We derive dynamical equations for a Josephson array coupled to a resonant cavity by applying the Heisenberg equations of motion to a model Hamiltonian described by us earlier [Phys. Rev. B {\bf 63}, 144522 (2001); Phys. Rev. B {\bf 64}, 179902 (E)]. By means of a canonical transformation, we also show that, in the absence of an applied current and dissipation, our model reduces to one described by Shnirman {\it et al} [Phys. Rev. Lett. {\bf 79}, 2371 (1997)] for coupled qubits, and that it corresponds to a capacitive coupling between the array and the cavity mode. From extensive numerical solutions of the model in one dimension, we find that the array locks into a coherent, periodic state above a critical number of active junctions, that the current-voltage characteristics of the array have self-induced resonant steps (SIRS's), that when $N_a$ active junctions are synchronized on a SIRS, the energy emitted into the resonant cavity is quadratic in $N_a$, and that when a fixed number of junctions is biased on a SIRS, the energy is linear in the input power. All these results are in agreement with recent experiments. By choosing the initial conditions carefully, we can drive the array into any of a variety of different integer SIRS's. We tentatively identify terms in the equations of motion which give rise to both the SIRS's and the coherence threshold. We also find higher-order integer SIRS's and fractional SIRS's in some simulations. We conclude that a resonant cavity can produce threshold behavior and SIRS's even in a one-dimensional array with appropriate experimental parameters, and that the experimental data, including the coherent emission, can be understood from classical equations of motion.

cond-mat.supr-con↗

arXiv2001

Characterizing the structure of small-world networks

We give exact relations which are valid for small-world networks (SWN's) with a general `degree distribution', i.e the distribution of nearest-neighbor connections. For the original SWN model, we illustrate how these exact relations can be used to obtain approximations for the corresponding basic probability distribution. In the limit of large system sizes and small disorder, we use numerical studies to obtain a functional fit for this distribution. Finally, we obtain the scaling properties for the mean-square displacement of a random walker, which are determined by the scaling behavior of the underlying SWN.

cond-mat.dis-nn↗

arXiv2000

Resonant-Cavity-Induced Phase Locking and Voltage Steps in a Josephson Array

We describe a simple dynamical model for an underdamped Josephson junction array coupled to a resonant cavity. From numerical solutions of the model in one dimension, we find that (i) current-voltage characteristics of the array have self-induced resonant steps (SIRS), (ii) at fixed disorder and coupling strength, the array locks into a coherent, periodic state above a critical number of active Josephson junctions, and (iii) when $N_a$ active junctions are synchronized on an SIRS, the energy emitted into the resonant cavity is quadratic with $N_a$. All three features are in agreement with a recent experiment [Barbara {\it et al}, Phys. Rev. Lett. {\bf 82}, 1963 (1999)]}.

cond-mat.supr-con↗

arXiv2000

Fractional vortices in the XY model with $π$ bonds

We define a new set of excitations in the XY model which we call ``fractional vortices''. In the frustrated XY model containing $π$ bonds, we make the ansatz that the ground state configurations can be characterized by pairs of oppositely charged fractional vortices. For a chain of $π$ bonds, the ground state energy and the phase configurations calculated on the basis of this ansatz agree well with the results from direct numerical simulations. Finally, we discuss the possible connection of these results to some recent experiments by Kirtley {\it et al} [Phys. Rev. B {\bf 51}, R12057 (1995)] on high-T$_c$ superconductors where fractional flux trapping was observed along certain grain boundaries.

cond-mat↗

arXiv1999

Exact results and scaling properties of small-world networks

We study the distribution function for minimal paths in small-world networks. Using properties of this distribution function, we derive analytic results which greatly simplify the numerical calculation of the average minimal distance, $\bar{\ell}$, and its variance, $σ^2$. We also discuss the scaling properties of the distribution function. Finally, we study the limit of large system sizes and obtain some analytic results.

cond-mat.stat-mech↗

arXiv1999

Evolutionary dynamics in the Bak-Sneppen model on small-world networks

We study the dynamics of the Bak-Sneppen model on small-world networks. For each site in the network, we define a ``connectance,'' which measures the distance to all other sites. We find radically different patterns of activity for different sites, depending on their connectance and also on the topology of the network. For a given network, the site with the minimal connectance shows long periods of stasis interrupted by much smaller periods of activity. In contrast, the activity pattern for the maximally connected site appears uniform on the same time scale. We discuss the significance of these results for speciation events.

cond-mat↗