Nonlinear Dispersive Model of Electroporation for Irregular Nucleated Cells.

In this work, the electroporation phenomenon induced by pulsed electric field on different nucleated biological cells is studied. A nonlinear, non-local, dispersive, and space-time multiphysics model based on Maxwell's and asymptotic Smoluchowski's equations has been developed to calculate the transmembrane voltage and pore density on both plasma and nuclear membrane perimeters. The irregular cell shape has been modeled by incorporating in the numerical algorithm the analytical functions pertaining to Gielis curves. The dielectric dispersion of the cell media has been modeled considering the multi-relaxation Debye-based relationship. Two different irregular nucleated cells have been investigated and their response has been studied applying both the dispersive and non-dispersive models. By a comparison of the obtained results, differences can be highlighted confirming the need to make use of the dispersive model to effectively investigate the cell response in terms of transmembrane voltages, pore densities, and electroporation opening angle, especially when irregular cell shapes and short electric pulses are considered. Bioelectromagnetics. 2019;40:331-342. © 2019 Wiley Periodicals, Inc.

Scaling Relationships among the Mass of Eggshell, Albumen, and Yolk in Six Precocial Birds.

The proportions in the size of the avian egg albumen, yolk, and shell are crucial for understanding bird survival and reproductive success because their relationships with volume and surface area can affect ecological and life history strategies. Prior studies have focused on the relationship between the albumen and the yolk, but little is known about the scaling relationship between eggshell mass and shape and the mass of the albumen and the yolk. Toward this end, 691 eggs of six precocial species were examined, and their 2-D egg profiles were photographed and digitized. The explicit Preston equation, which assumes bilateral symmetrical geometry, was used to fit the 2-D egg profiles and to calculate surface areas and volumes based on the hypothesis that eggs can be treated as solids of profile revolution. The scaling relationships of eggshell mass (Ms), albumen mass (Ma), and yolk mass (My), as well as the surface area (S), volume (V), and total mass (Mt) were determined. The explicit Preston equation was validated in describing the 2-D egg profiles. The scaling exponents of Ma vs. Ms, My vs. Ms, and My vs. Ma were smaller than unity, indicating that increases in Ma and My fail to keep pace with increases in Ms, and that increases in My fail to keep pace with increases in Ma. Therefore, increases in unit nutrient contents (i.e., the yolk) involve disproportionately larger increases in eggshell mass and disproportionately larger increases in albumen mass. The data also revealed a 2/3-power scaling relationship between S and V for each species, that is, the simple Euclidean geometry is obeyed. These findings help to inform our understanding of avian egg construction and reveal evolutionary interspecific trends in the scaling of egg shape, volume, mass, and mass allocation.

Scaling relationships between the total number of leaves and the total leaf area per culm of two dwarf bamboo species.

Total leaf area per plant is an important measure of the photosynthetic capacity of an individual plant that together with plant density drives the canopy leaf area index, that is, the total leaf area per unit ground area. Because the total number of leaves per plant (or per shoot) varies among conspecifics and among mixed species communities, this variation can affect the total leaf area per plant and per canopy but has been little studied. Previous studies have shown a strong linear relationship between the total leaf area per plant (or per shoot) (A T) and the total number of leaves per plant (or per shoot) (N T) on a log-log scale for several growth forms. However, little is known whether such a scaling relationship also holds true for bamboos, which are a group of Poaceae plants with great ecological and economic importance in tropical, subtropical, and warm temperate regions. To test whether the scaling relationship holds true in bamboos, two dwarf bamboo species (Shibataea chinensis Nakai and Sasaella kongosanensis 'Aureostriatus') with a limited but large number of leaves per culm were examined. For the two species, the leaves from 480 and 500 culms, respectively, were sampled and A T was calculated by summing the areas of individual leaves per culm. Linear regression and correlation analyses reconfirmed that there was a significant log-log linear relationship between A T and N T for each species. For S. chinensis, the exponent of the A T versus N T scaling relationship was greater than unity, whereas that of S. kongosanensis 'Aureostriatus' was smaller than unity. The coefficient of variation in individual leaf area increased with increasing N T for each species. The data reconfirm that there is a strong positive power-law relationship between A T and N T for each of the two species, which may reflect adaptations of plants in response to intra- and inter-specific competition for light.

Plant Morphology and Function, Geometric Morphometrics, and Modelling: Decoding the Mathematical Secrets of Plants.

Functional plant traits include a plant's phenotypic morphology, nutrient element characteristics, and physiological and biochemical features, reflecting the survival strategies of plants in response to environmental changes [...].

A simple way to calculate the volume and surface area of avian eggs.

Egg geometry can be described using Preston's equation, which has seldom been used to calculate egg volume (V) and surface area (S) to explore S versus V scaling relationships. Herein, we provide an explicit re-expression of Preston's equation (designated as EPE) to calculate V and S, assuming that an egg is a solid of revolution. The side (longitudinal) profiles of 2221 eggs of six avian species were digitized, and the EPE was used to describe each egg profile. The volumes of 486 eggs from two avian species predicted by the EPE were compared with those obtained using water displacement in graduated cylinders. There was no significant difference in V using the two methods, which verified the utility of the EPE and the hypothesis that eggs are solids of revolution. The data also indicated that V is proportional to the product of egg length (L) and maximum width (W) squared. A 2/3-power scaling relationship between S and V for each species was observed, that is, S is proportional to (LW2 )2/3 . These results can be extended to describe the shapes of the eggs of other species to study the evolution of avian (and perhaps reptilian) eggs.

Inequality Measure of Leaf Area Distribution for a Drought-Tolerant Landscape Plant.

Measuring the inequality of leaf area distribution per plant (ILAD) can provide a useful tool for quantifying the influences of intra- and interspecific competition, foraging behavior of herbivores, and environmental stress on plants' above-ground architectural structures and survival strategies. Despite its importance, there has been limited research on this issue. This paper aims to fill this gap by comparing four inequality indices to measure ILAD, using indices for quantifying household income that are commonly used in economics, including the Gini index (which is based on the Lorenz curve), the coefficient of variation, the Theil index, and the mean log deviation index. We measured the area of all leaves for 240 individual plants of the species Shibataea chinensis Nakai, a drought-tolerant landscape plant found in southern China. A three-parameter performance equation was fitted to observations of the cumulative proportion of leaf area vs. the cumulative proportion of leaves per plant to calculate the Gini index for each individual specimen of S. chinensis. The performance equation was demonstrated to be valid in describing the rotated and right shifted Lorenz curve, given that >96% of root-mean-square error values were smaller than 0.004 for 240 individual plants. By examining the correlation between any of the six possible pairs of indices among the Gini index, the coefficient of variation, the Theil index, and the mean log deviation index, the data show that these indices are closely related and can be used interchangeably to quantify ILAD.

Comparison of a universal (but complex) model for avian egg shape with a simpler model.

Recently, a universal equation by Narushin, Romanov, and Griffin (hereafter, the NRGE) was proposed to describe the shape of avian eggs. While NRGE can simulate the shape of spherical, ellipsoidal, ovoidal, and pyriform eggs, its predictions were not tested against actual data. Here, we tested the validity of the NRGE by fitting actual data of egg shapes and compared this with the predictions of our simpler model for egg shape (hereafter, the SGE). The eggs of nine bird species were sampled for this purpose. NRGE was found to fit the empirical data of egg shape well, but it did not define the egg length axis (i.e., the rotational symmetric axis), which significantly affected the prediction accuracy. The egg length axis under the NRGE is defined as the maximum distance between two points on the scanned perimeter of the egg's shape. In contrast, the SGE fitted the empirical data better, and had a smaller root-mean-square error than the NRGE for each of the nine eggs. Based on its mathematical simplicity and goodness-of-fit, the SGE appears to be a reliable and useful model for describing egg shape.

Quantifying the Variation in the Geometries of the Outer Rims of Corolla Tubes of Vinca major L.

Many geometries of plant organs can be described by the Gielis equation, a polar coordinate equation extended from the superellipse equation, r=a|cosm4φ|n2+|1ksinm4φ|n3-1/n1. Here, r is the polar radius corresponding to the polar angle φ; m is a positive integer that determines the number of angles of the Gielis curve when φ ∈ [0 to 2π); and the rest of the symbols are parameters to be estimated. The pentagonal radial symmetry of calyxes and corolla tubes in top view is a common feature in the flowers of many eudicots. However, prior studies have not tested whether the Gielis equation can depict the shapes of corolla tubes. We sampled randomly 366 flowers of Vinca major L., among which 360 had five petals and pentagonal corolla tubes, and six had four petals and quadrangular corolla tubes. We extracted the planar coordinates of the outer rims of corolla tubes (in top view) (ORCTs), and then fitted the data with two simplified versions of the Gielis equation with k = 1 and m = 5: r=acos54φn2+sin54φn3-1/n1 (Model 1), and r=acos54φn2+sin54φn2-1/n1 (Model 2). The adjusted root mean square error (RMSEadj) was used to evaluate the goodness of fit of each model. In addition, to test whether ORCTs are radially symmetrical, we correlated the estimates of n2 and n3 in Model 1 on a log-log scale. The results validated the two simplified Gielis equations. The RMSEadj values for all corolla tubes were smaller than 0.05 for both models. The numerical values of n2 and n3 were demonstrated to be statistically equal based on the regression analysis, which suggested that the ORCTs of V. major are radially symmetrical. It suggests that Model 1 can be replaced by the simpler Model 2 for fitting the ORCT in this species. This work indicates that the pentagonal or quadrangular corolla tubes (in top view) can both be modeled by the Gielis equation and demonstrates that the pentagonal or quadrangular corolla tubes of plants tend to form radial symmetrical geometries during their development and growth.

Comparison of Two Simplified Versions of the Gielis Equation for Describing the Shape of Bamboo Leaves.

Bamboo is an important component in subtropical and tropical forest communities. The plant has characteristic long lanceolate leaves with parallel venation. Prior studies have shown that the leaf shapes of this plant group can be well described by a simplified version (referred to as SGE-1) of the Gielis equation, a polar coordinate equation extended from the superellipse equation. SGE-1 with only two model parameters is less complex than the original Gielis equation with six parameters. Previous studies have seldom tested whether other simplified versions of the Gielis equation are superior to SGE-1 in fitting empirical leaf shape data. In the present study, we compared a three-parameter Gielis equation (referred to as SGE-2) with the two-parameter SGE-1 using the leaf boundary coordinate data of six bamboo species within the same genus that have representative long lanceolate leaves, with >300 leaves for each species. We sampled 2000 data points at approximately equidistant locations on the boundary of each leaf, and estimated the parameters for the two models. The root−mean−square error (RMSE) between the observed and predicted radii from the polar point to data points on the boundary of each leaf was used as a measure of the model goodness of fit, and the mean percent error between the RMSEs from fitting SGE-1 and SGE-2 was used to examine whether the introduction of an additional parameter in SGE-1 remarkably improves the model's fitting. We found that the RMSE value of SGE-2 was always smaller than that of SGE-1. The mean percent errors among the two models ranged from 7.5% to 20% across the six species. These results indicate that SGE-2 is superior to SGE-1 and should be used in fitting leaf shapes. We argue that the results of the current study can be potentially extended to other lanceolate leaf shapes.

'biogeom': An R package for simulating and fitting natural shapes.

Many natural objects exhibit radial or axial symmetry in a single plane. However, a universal tool for simulating and fitting the shapes of such objects is lacking. Herein, we present an R package called 'biogeom' that simulates and fits many shapes found in nature. The package incorporates novel universal parametric equations that generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings, and three growth-rate equations that generate the profiles of ovate leaves and the ontogenetic growth curves of animals and plants. 'biogeom' includes several empirical datasets comprising the boundary coordinates of bird eggs, fruits, lanceolate and ovate leaves, tree rings, seeds, and sea stars. The package can also be applied to other kinds of natural shapes similar to those in the datasets. In addition, the package includes sigmoid curves derived from the three growth-rate equations, which can be used to model animal and plant growth trajectories and predict the times associated with maximum growth rate. 'biogeom' can quantify the intra- or interspecific similarity of natural outlines, and it provides quantitative information of shape and ontogenetic modification of shape with important ecological and evolutionary implications for the growth and form of the living world.

Modeling of Electroporation Induced by Pulsed Electric Fields in Irregularly Shaped Cells.

During the past decades, the poration of cell membrane induced by pulsed electric fields has been widely investigated. Since the basic mechanisms of this process have not yet been fully clarified, many research activities are focused on the development of suitable theoretical and numerical models. To this end, a nonlinear, nonlocal, dispersive, and space-time numerical algorithm has been developed and adopted to evaluate the transmembrane voltage and pore density along the perimeter of realistic irregularly shaped cells. The presented model is based on the Maxwell's equations and the asymptotic Smoluchowski's equation describing the pore dynamics. The dielectric dispersion of the media forming the cell has been modeled by using a general multirelaxation Debye-based formulation. The irregular shape of the cell is described by using the Gielis' superformula. Different test cases pertaining to red blood cells, muscular cells, cell in mitosis phase, and cancer-like cell have been investigated. For each type of cell, the influence of the relevant shape, the dielectric properties, and the external electric pulse characteristics on the electroporation process has been analyzed. The numerical results demonstrate that the proposed model is an efficient numerical tool to study the electroporation problem in arbitrary-shaped cells.

Why Does Not the Leaf Weight-Area Allometry of Bamboos Follow the 3/2-Power Law?

The principle of similarity (Thompson, 1917) states that the weight of an organism follows the 3/2-power law of its surface area and is proportional to its volume on the condition that the density is constant. However, the allometric relationship between leaf weight and leaf area has been reported to greatly deviate from the 3/2-power law, with the irregularity of leaf density largely ignored for explaining this deviation. Here, we choose 11 bamboo species to explore the allometric relationships among leaf area (A), density (ρ), length (L), thickness (T), and weight (W). Because the edge of a bamboo leaf follows a simplified two-parameter Gielis equation, we could show that A ∝ L2 and that A ∝ T2. This then allowed us to derive the density-thickness allometry ρ ∝ Tb and the weight-area allometry W ∝ A(b+3)/2 ≈ A9/8, where b approximates -3/4. Leaf density is strikingly negatively associated with leaf thickness, and it is this inverse relationship that results in the weight-area allometry to deviate from the 3/2-power law. In conclusion, although plants are prone to invest less dry mass and thus produce thinner leaves when the leaf area is sufficient for photosynthesis, such leaf thinning needs to be accompanied with elevated density to ensure structural stability. The findings provide the insights on the evolutionary clue about the biomass investment and output of photosynthetic organs of plants. Because of the importance of leaves, plants could have enhanced the ratio of dry material per unit area of leaf in order to increase the efficiency of photosynthesis, relative the other parts of plants. Although the conclusion is drawn only based on 11 bamboo species, it should also be applicable to the other plants, especially considering previous works on the exponent of the weight-area relationship being less than 3/2 in plants.

Diatom Frustule Morphogenesis and Function: a Multidisciplinary Survey.

Diatoms represent the major component of phytoplankton and are responsible for about 20-25% of global primary production. Hundreds of millions of years of evolution led to tens of thousands of species differing in dimensions and morphologies. In particular, diatom porous silica cell walls, the frustules, are characterized by an extraordinary, species-specific diversity. It is of great interest, among the marine biologists and geneticists community, to shed light on the origin and evolutionary advantage of this variability of dimensions, geometries and pore distributions. In the present article the main reported data related to frustule morphogenesis and functionalities with contributions from fundamental biology, genetics, mathematics, geometry and physics are reviewed.

A geometrical model for testing bilateral symmetry of bamboo leaf with a simplified Gielis equation.

The size and shape of plant leaves change with growth, and an accurate description of leaf shape is crucial for describing plant morphogenesis and development. Bilateral symmetry, which has been widely observed but poorly examined, occurs in both dicot and monocot leaves, including all nominated bamboo species (approximately 1,300 species), of which at least 500 are found in China. Although there are apparent differences in leaf size among bamboo species due to genetic and environmental profiles, bamboo leaves have bilateral symmetry with parallel venation and appear similar across species. Here, we investigate whether the shape of bamboo leaves can be accurately described by a simplified Gielis equation, which consists of only two parameters (leaf length and shape) and produces a perfect bilateral shape. To test the applicability of this equation and the occurrence of bilateral symmetry, we first measured the leaf length of 42 bamboo species, examining >500 leaves per species. We then scanned 30 leaves per species that had approximately the same length as the median leaf length for that species. The leaf-shape data from scanned profiles were fitted to the simplified Gielis equation. Results confirmed that the equation fits the leaf-shape data extremely well, with the coefficients of determination being 0.995 on average. We further demonstrated the bilateral symmetry of bamboo leaves, with a clearly defined leaf-shape parameter of all 42 bamboo species investigated ranging from 0.02 to 0.1. This results in a simple and reliable tool for precise determination of bamboo species, with applications in forestry, ecology, and taxonomy.

Comparison of dwarf bamboos (Indocalamus sp.) leaf parameters to determine relationship between spatial density of plants and total leaf area per plant.

The relationship between spatial density and size of plants is an important topic in plant ecology. The self-thinning rule suggests a -3/2 power between average biomass and density or a -1/2 power between stand yield and density. However, the self-thinning rule based on total leaf area per plant and density of plants has been neglected presumably because of the lack of a method that can accurately estimate the total leaf area per plant. We aimed to find the relationship between spatial density of plants and total leaf area per plant. We also attempted to provide a novel model for accurately describing the leaf shape of bamboos. We proposed a simplified Gielis equation with only two parameters to describe the leaf shape of bamboos one model parameter represented the overall ratio of leaf width to leaf length. Using this method, we compared some leaf parameters (leaf shape, number of leaves per plant, ratio of total leaf weight to aboveground weight per plant, and total leaf area per plant) of four bamboo species of genus Indocalamus Nakai (I. pedalis (Keng) P.C. Keng, I. pumilus Q.H. Dai and C.F. Keng, I. barbatus McClure, and I. victorialis P.C. Keng). We also explored the possible correlation between spatial density and total leaf area per plant using log-linear regression. We found that the simplified Gielis equation fit the leaf shape of four bamboo species very well. Although all these four species belonged to the same genus, there were still significant differences in leaf shape. Significant differences also existed in leaf area per plant, ratio of leaf weight to aboveground weight per plant, and leaf length. In addition, we found that the total leaf area per plant decreased with increased spatial density. Therefore, we directly demonstrated the self-thinning rule to improve light interception.

Universal natural shapes: from unifying shape description to simple methods for shape analysis and boundary value problems.

Gielis curves and surfaces can describe a wide range of natural shapes and they have been used in various studies in biology and physics as descriptive tool. This has stimulated the generalization of widely used computational methods. Here we show that proper normalization of the Levenberg-Marquardt algorithm allows for efficient and robust reconstruction of Gielis curves, including self-intersecting and asymmetric curves, without increasing the overall complexity of the algorithm. Then, we show how complex curves of k-type can be constructed and how solutions to the Dirichlet problem for the Laplace equation on these complex domains can be derived using a semi-Fourier method. In all three methods, descriptive and computational power and efficiency is obtained in a surprisingly simple way.

A generic geometric transformation that unifies a wide range of natural and abstract shapes.

To study forms in plants and other living organisms, several mathematical tools are available, most of which are general tools that do not take into account valuable biological information. In this report I present a new geometrical approach for modeling and understanding various abstract, natural, and man-made shapes. Starting from the concept of the circle, I show that a large variety of shapes can be described by a single and simple geometrical equation, the Superformula. Modification of the parameters permits the generation of various natural polygons. For example, applying the equation to logarithmic or trigonometric functions modifies the metrics of these functions and all associated graphs. As a unifying framework, all these shapes are proven to be circles in their internal metrics, and the Superformula provides the precise mathematical relation between Euclidean measurements and the internal non-Euclidean metrics of shapes. Looking beyond Euclidean circles and Pythagorean measures reveals a novel and powerful way to study natural forms and phenomena.