Publications

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2015
Ronellenfitsch, H, Lasser J, Daly D, Katifori E.  2015.  Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks. Plos Comp Biol. 11(12):e1004680.journal.pcbi_.1004680.pdf
Ronellenfitsch, H, Liesche J, Jensen KH, Holbrook MN, Schulz A, Katifori E.  2015.  Scaling of phloem structure and optimality of photoassimilate transport in conifer needles. Proc. R. Soc. B. 282:20141863. Abstract
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Gräwer, J, Modes CD, Magnasco MO, Katifori E.  2015.  Structural Self-Assembly and Avalanche-Line Dynamics in Locally Adaptive Networks. to appear in PRE. Abstract

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.

2014
Manik, D, Witthaut D, Schäfer B, Matthiae M, Sorge A, Rohden M, Katifori E, Timme M.  2014.  Supply networks: Instabilities without overload. The European Physical Journal Special Topics. 223:2527–2547. AbstractManik_Supply Networks_2014.pdf

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2013
Couturier, E, Dumais J, Cerda E, Katifori E.  2013.  Folding of an opened spherical shell. Soft Matter. 9:8359–8367. AbstractCouturier_Folding_2013.pdf

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Jordan, D, Kuehn S, Katifori E, Leibler S.  2013.  Behavioral diversity in microbes and low-dimensional phenotypic spaces.. PNAS. 110:14018–23. Abstract

Systematic studies of phenotypic diversity–required for understanding evolution–lag behind investigations of genetic diversity. Here we develop a quantitative approach to studying behavioral diversity, which we apply to swimming of the ciliate Tetrahymena. We measure the full-lifetime behavior of hundreds of individual organisms at high temporal resolution, over several generations and in diverse nutrient conditions. To characterize population diversity and temporal variability we introduce a unique statistical framework grounded in the notion of a phenotypic space of behaviors. We show that this space is effectively low dimensional with dimensions that correlate with a two-state "roaming and dwelling" model of swimming behavior. Temporal variability over the lifetime of an individual is correlated with the fraction of time spent roaming whereas diversity between individuals is correlated with the speed of roaming. Quantifying the dynamics of behavioral variation shows that behavior over the lifetime of an individual is strongly nonstationary. Analysis of behavioral dynamics between generations reveals complex patterns of behavioral heritability that point to the importance of considering correlations beyond mothers and daughters. Our description of a low-dimensional behavioral space should enable the systematic study of the evolutionary and ecological bases of phenotypic constraints. Future experimental and theoretical studies of behavioral diversity will have to account for the possibility of nonstationary and environmentally dependent behavioral dynamics that we observe.

2012
Katifori, E, Magnasco MO.  2012.  Quantifying Loopy Network Architectures. PLoS ONE. 7:e37994. Abstract

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 approaches 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.

Papachristou, PK, Katifori E, Diakonos FK, Constantoudis V, Mavrommatis E.  2012.  Quantum versus Classical Dynamics in a driven barrier: the role of kinematic effects. PRE. Abstract

We study the dynamics of the classical and quantum mechanical scattering of a wave packet from an oscillating barrier. Our main focus is on the dependence of the transmission coefficient on the initial energy of the wave packet for a wide range of oscillation frequencies. The behavior of the quantum transmission coefficient is affected by tunneling phenomena, resonances and kinematic effects emanating from the time dependence of the potential. We show that when kinematic effects dominate (mainly in intermediate frequencies), classical mechanics provides very good approximation of quantum results. Moreover, in the frequency region of optimal agreement between classical and quantum transmission coefficient, the transmission threshold, i.e. the energy above which the transmission coefficient becomes larger than a specific small threshold value, is found to exhibit a minimum. We also consider the form of the transmitted wave packet and we find that for low values of the frequency the incoming classical and quantum wave packet can be split into a train of well separated coherent pulses, a phenomenon which can admit purely classical kinematic interpretation.

2011
Schroll, RD, Katifori E, Davidovitch B.  2011.  Elastic building blocks for confined sheets.. PRL. 106:074301. Abstract

We study the behavior of thin elastic sheets that are bent and strained under a weak, smooth confinement. We show that the emerging shapes exhibit the coexistence of two types of domains. 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 under various types of forcing.

2010
Katifori, E, Szöllosi GJ, Magnasco MO.  2010.  Damage and fluctuations induce loops in optimal transport networks.. Physical Review Letters. 104:048704., Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10065 USA Abstract

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.

Katifori, E, Alben S, Cerda E, Nelson DR, Dumais J.  2010.  Foldable structures and the natural design of pollen grains.. PNAS. 107:7635–7639. Abstract

Upon release from the anther, pollen grains of angiosperm flowers are exposed to a dry environment and dehydrate. To survive this process, pollen grains possess a variety of physiological and structural adaptations. Perhaps the most striking of these adaptations is the ability of the pollen wall to fold onto itself to prevent further desiccation. Roger P. Wodehouse coined the term harmomegathy for this folding process in recognition of the critical role it plays in the survival of the pollen grain. There is still, however, no quantitative theory that explains how the structure of the pollen wall contributes to harmomegathy. Here we demonstrate that simple geometrical and mechanical principles explain how wall structure guides pollen grains toward distinct folding pathways. We found that the presence of axially elongated apertures of high compliance is critical for achieving a predictable and reversible folding pattern. Moreover, the intricate sculpturing of the wall assists pollen closure by preventing mirror buckling of the surface. These results constitute quantitative structure-function relationships for pollen harmomegathy and provide a framework to elucidate the functional significance of the very diverse pollen morphologies observed in angiosperms.

2009
Katifori, E, Alben S, Nelson DR.  2009.  Collapse and folding of pressurized rings in two dimensions. Physical Review E. 79:056604. AbstractKatifori_Collapse and folding_2009.pdf

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 arclength-dependent bending moduli and determine how weakened bending modulus segments affect the buckling critical pressure. Rings with a fourfold symmetric modulation are particularly susceptible to collapse. In addition we study the initial postbuckling stages of the pressurized rings to determine possible ring folding patterns.

2007
Katifori, E, Nelson DR.  2007.  Effects of kinked linear defects on planar flux line arrays. EPJB. 59:319-327.
2006
Katifori, E, Nelson DR.  2006.  Vortex pinning by meandering line defects in planar superconductors. Physical Review B. 73:9. Abstract

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.