arXiv subjects

Eleni Katifori

Publications and source records attributed to Eleni Katifori.

47 records · Page 3Linked to original sources

arXiv2015

Topological phenotypes constitute a new dimension in the phenotypic space of leaf venation networks

The leaves of angiosperms contain highly complex venation networks consisting of recursively nested, hierarchically organized loops. We describe a new phenotypic trait of reticulate vascular networks based on the topology of the nested loops. This phenotypic trait encodes information orthogonal to widely used geometric phenotypic traits, and thus constitutes a new dimension in the leaf venation phenotypic space. We apply our metric to a database of 186 leaves and leaflets representing 137 species, predominantly from the Burseraceae family, revealing diverse topological network traits even within this single family. We show that topological information significantly improves identification of leaves from fragments by calculating a "leaf venation fingerprint" from topology and geometry. Further, we present a phenomenological model suggesting that the topological traits can be explained by noise effects unique to specimen during development of each leaf which leave their imprint on the final network. This work opens the path to new quantitative identification techniques for leaves which go beyond simple geometric traits such as vein density and is directly applicable to other planar or sub-planar networks such as blood vessels in the brain.

q-bio.QM↗

arXiv2014

Scaling of phloem structure and optimality of photoassimilate transport in conifer needles

The phloem vascular system facilitates transport of energy-rich sugar and signaling molecules in plants, thus permitting long range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated by differences in sugar concentration between distal parts of the plant. The phloem is an intricate distribution system, and many questions about its regulation and structural diversity remain unanswered. Here, we investigate the phloem structure in the simplest possible geometry: a linear leaf, found, for example, in the needles of conifer trees. We measure the phloem structure in four tree species representing a diverse set of habitats and needle sizes, from 1 cm (\textit{Picea omorika}) to 35 cm (\textit{Pinus palustris}). We show that the phloem shares common traits across these four species and find that the size of its conductive elements obeys a power law. We present a minimal model that accounts for these common traits and takes into account the transport strategy and natural constraints. This minimal model predicts a power law phloem distribution consistent with transport energy minimization, suggesting that energetics are more important than translocation speed at the leaf level.

physics.bio-ph↗

arXiv2014

Extracting Hidden Hierarchies in 3D Distribution Networks

Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function. Yet, the set of tools that can characterize such a weighted cycle-rich architecture in a physically relevant, mathematically compact way is sparse. In order to fill this void, we have developed a new algorithm that rests on an abstraction of the physical `tiling' in the case of a two dimensional network to an effective tiling of an abstract surface in space that the network may be thought to sit in. Generically these abstract surfaces are richer than the flat plane and as a result there are now two families of fundamental units that may aggregate upon cutting weakest links -- the plaquettes of the tiling and the longer `topological' cycles associated with the abstract surface itself. Upon sequential removal of the weakest links, as determined by the edge weight, neighboring plaquettes merge and a tree characterizing this merging process results. The properties of this characteristic tree can provide the physical and topological data required to describe the architecture of the network and to build physical models. The new algorithm can be used for automated phenotypic characterization of any weighted network whose structure is dominated by cycles, such as mammalian vasculature in the organs, the root networks of clonal colonies like quaking aspen, or the force networks in jammed granular matter.

q-bio.QM↗

arXiv2014

Structural Self-Assembly and Glassy Dynamics in Locally Adaptive Networks

Transport networks play a key role across four realms of eukaryotic life: slime molds, fungi, plants, and animals. In addition to the developmental algorithms that build them, many also employ adaptive strategies to respond to stimuli, damage, and other environmental changes. We model these adapting network architectures using a generic dynamical system on weighted graphs and find in simulation that these networks ultimately develop a hierarchical organization of the final weighted architecture accompanied by the formation of a system-spanning backbone. In addition, we find that the long term equilibration dynamics exhibit glassy behavior characterized by long periods of slow changes punctuated by bursts of reorganization events.

nlin.AO↗

arXiv2011

Quantifying loopy network architectures

Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of methods have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the Asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes) from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

q-bio.QM↗

arXiv2010

Elastic building blocks for confined sheets

We study the behavior of thin elastic sheets that are bent and strained under the influence of weak, smooth confinement. We show that the emerging shapes exhibit the coexistence of two types of domains that differ in their characteristic stress distributions and energies, and reflect different constraints. A focused-stress patch is subject to a geometric, piecewise-inextensibility constraint, whereas a diffuse-stress region is characterized by a mechanical constraint - the dominance of a single component of the stress tensor. We discuss the implications of our findings for the analysis of elastic sheets that are subject to various types of forcing.

cond-mat.soft↗

arXiv2009

Damage and fluctuations induce loops in optimal transport networks

Leaf venation is a pervasive example of a complex biological network, endowing leaves with a transport system and mechanical resilience. Transport networks optimized for efficiency have been shown to be trees, i.e. loopless. However, dicotyledon leaf venation has a large number of closed loops, which are functional and able to transport fluid in the event of damage to any vein, including the primary veins. Inspired by leaf venation, we study two possible reasons for the existence of a high density of loops in transport networks: resilience to damage and fluctuations in load. In the first case, we seek the optimal transport network in the presence of random damage by averaging over damage to each link. In the second case, we seek the network that optimizes transport when the load is sparsely distributed: at any given time most sinks are closed. We find that both criteria lead to the presence of loops in the optimum state.

physics.bio-ph↗

arXiv2008

Collapse and folding of pressurized rings in two dimensions

Hydrostatically pressurized circular rings confined to two dimensions (or cylinders constrained to have only z-independent deformations) undergo Euler type buckling when the outside pressure exceeds a critical value. We perform a stability analysis of rings with arc-length dependent bending moduli and determine how weakened bending modulus segments affect the buckling critical pressure. Rings with a 4-fold symmetric modulation are particularly susceptible to collapse. In addition we study the initial post-buckling stages of the pressurized rings to determine possible ring folding patterns.

cond-mat.soft↗

arXiv2008

Thermal Evolution of the Non Supersymmetric Metastable Vacua in N=2 SU(2) SYM Softly Broken to N=1

It has been shown that four dimensional N=2 gauge theories, softly broken to N=1 by a superpotential term, can accommodate metastable non-supersymmetric vacua in their moduli space. We study the SU(2) theory at high temperatures in order to determine whether a cooling universe settles in the metastable vacuum at zero temperature. We show that the corrections to the free energy because of the BPS dyons are such that may destroy the existence of the metastable vacuum at high temperatures. Nevertheless we demonstrate the universe can settle in the metastable vacuum, provided that the following two conditions are hold: first the superpotential term is not arbitrarily small in comparison to the strong coupling scale of the gauge theory, and second the metastable vacuum lies in the strongly coupled region of the moduli space.

hep-th↗

arXiv2007

Effects of kinked linear defects on planar flux line arrays

In the hard core limit, interacting vortices in planar type II superconductors can be modeled as non-interacting one dimensional fermions propagating in imaginary time. We use this analogy to derive analytical expressions for the probability density and imaginary current of vortex lines interacting with an isolated bent line defect and to understand the pinning properties of such systems. When there is an abrupt change of the direction of the pinning defect, we find a sinusoidal modulation of the vortex density in directions both parallel and perpendicular to the defect.

cond-mat.supr-con↗

arXiv2006

Vortex pinning by meandering line defects in planar superconductors

To better understand vortex pinning in thin superconducting slabs, we study the interaction of a single fluctuating vortex filament with a curved line defect in (1+1) dimensions. This problem is also relevant to the interaction of scratches with wandering step edges in vicinal surfaces. The equilibrium probability density for a fluctuating line attracted to a particular fixed defect trajectory is derived analytically by mapping the problem to a straight line defect in the presence of a space and time-varying external tilt field. The consequences of both rapid and slow changes in the frozen defect trajectory, as well as finite size effects are discussed. A sudden change in the defect direction leads to a delocalization transition, accompanied by a divergence in the trapping length, near a critical angle.

cond-mat.stat-mech↗