Complex dynamics of life at different scales: from genomic to global environmental issues

This introduction to the Theme Issue, Complex dynamics of life at different scales: from genomic to global environmental issues, gives a short overview on why the ideas and concepts in complexity and nonlinearity are relevant to the understanding of life in its different manifestations. Also, it discusses how life phenomena can be thought of as composing different scales of organization. Finally, the articles in this thematic publication are briefly commented on in terms of their relevance in helping to understand the complexity of life systems.     

Aquatic suction feeding dynamics: insights from computational modelling

Aquatic suction feeding in vertebrates involves extremely unsteady flow, externally as well as internally of the expanding mouth cavity. Consequently, studying the hydrodynamics involved in this process is a challenging research area, where experimental studies and mathematical models gradually aid our understanding of how suction feeding works mechanically. Especially for flow patterns inside the mouth cavity, our current knowledge is almost entirely based on modelling studies. In the present paper, we critically discuss some of the assumptions and limitations of previous analytical models of suction feeding using computational fluid dynamics.     

Streamlining science with structured data archives: insights from stroke rehabilitation

Recent advances in bibliometrics have focused on text-mining to organize scientific disciplines based on author networks, keywords, and citations. These approaches provide insights, but fail to capture important experimental data that exist in many scientific disciplines. The objective of our paper is to show how such data can be used to organize the literature within a discipline, and identify knowledge gaps. Our approach is especially important for disciplines relying on randomized control trials. Using stroke rehabilitation as an informative example, we construct an interactive graphing platform to address domain general scientific questions relating to bias, common data elements, and relationships between key constructs in a field. Our platform allows researchers to ask their own questions and systematically search the literature from the data up.     

Service life analysis from field data on age distributions

In survey investigations of building stocks for example, data on age distributions of construction details are often collected. What interests the material scientist, though, is not the age distribution but rather the service life distribution. Presented herein will be a renewal process model describing the relationship between such an age distribution found and the corresponding service life distribution being sought. The model comprises a phenomenological parameter to accommodate correlations between objects and the service life’s determining factors. However, it is shown that, because of numerical ambiguity, the correlation parameter cannot be uniquely determined from an age distribution. Therefore, some additional information and data processing are required before the full advantage of this model can be realized. This somewhat difficult part has yet to be completed. Nevertheless, in its present form, the model does point out possible ranges of service life distribution parameters in terms of the correlation strength, thus providing uncertainties in the distribution parameters, which up until now have normally been overlooked when estimating the service lives of building materials. For wide service life distributions, it is shown that the possible parameter ranges will also the rather wide.     

How are completely desolvated ions produced in electrospray ionization: insights from molecular dynamics simulations

We apply molecular dynamics (MD) simulations to study the final phase of electrospray ionization (ESI), where an ion loses all of its associated solvent molecules. By applying an electric field to a cluster of H(2)O molecules solvating an ion and including a surrounding gas of varying pressure, we demonstrate that collisions with the gas play a major role in removing this final layer of solvent. We make quantitative predictions of the critical velocity required for the cluster to start losing molecules via collisions with gas and propose that this should be important in real ESI experiments. Such collisions have heretofore not been explicitly considered in discussions of the ESI process.     

The route from order to chaos of soil moisture dynamics at large spatial scales

Abstract

This study analyzes the relationship between soil moisture and lagged soil moisture according to the nonlinear soil moisture balance equation. The phase plane diagram and chaotic analysis show that the phenomena of the nonlinear dynamics equation, such as fixed point, limit cycle, and chaotic type of behavior, will become quite complex. At given parameters and lagged time, the limit evolution of soil moisture whose time delay is equal to 21 days is a strange attractor and the fractal dimension is 1.56. The ultimate soil moisture evolution is through a period doubling route from order to chaos.     

Reliability estimations of components from masked system life data

This paper introduces estimations of reliability values for the individual components in a series system using masked system life data. In particular, we compute the maximum likelihood and Bayes estimates of component reliabilities when the system components have constant failure rates. In obtaining Bayes estimates, it is assumed that the component reliabilities are independent random variables having piecewise linear prior distributions. The model is illustrated for a two-component series. A numerical simulation study is presented to show how one can utilize the present approach to compute estimations of component reliabilities for a practical problem. Further, we investigate the comparison between the maximum likelihood and Bayes estimates, based on the respective percentage errors.     

A comparison of damage models formulated on different material scales

This contribution aims at characteristic damage mechanisms of materials at two levels of observation, (a) at the macro-scale in the sense of classical continuum damage mechanics, and (b) at the meso-scale utilizing the so-called microplane concept. The constitutive formulations are embedded in a thermodynamically consistent framework. The microplane formulation is based on a volumetric–deviatoric split (V–D), which is motivated from a macroscopic viewpoint. The main advantage of this formulation is that the material behavior at a material point is characterized by constitutive laws formulated on the individual microplanes, allowing to describe anisotropic material behavior in a very natural and simple way. One particular advantage of the present version of a microplane formulation is also its close relation to macroscopic models which enables the interpretation and identification of the microplane constitutive laws in terms of well-known macroscopic constitutive laws. The appropriate choice of the microplane loading functions is illustrated by a comparison of the microplane damage formulation with a macroscopic two-parameter damage model.     

Quantification of structural and material failure mechanisms across different length scales: from instability to brittle-ductile transitions

Structures may fail due to a myriad of different causes. Often, distinction is made between structural and material failure, that means a structure can fail, while the material is still intact (this is the case in so-called stability loss), or the material fails, which, as consequence, may lead to structural failure. The material behavior may turn out difficult to be mathematically guessed at the macro-level. On the other hand, a lot may be known about the chemistry or the microstructure of the material of interest. Herein, we aim at categorizing different scenarios which in the end provoke structural failure, discussing various cases investigated during the last five years, at the Institute for Mechanics of Materials and Structures of Vienna University of Technology: A well-chosen eigenvalue problem shows considerable potential for categorizing stability loss. We then turn to complex composite materials with a hierarchical organization, where a single constituent dominates the overall quasi-brittle failure of the material, such as lignin in wood and wood products, or the cement–water reaction products (shortly called hydrates) in cement-based materials. The picture changes if the first inelastically behaving constituent is related to ductile load carrying, then the loads within the microstructure are re-distributed before the overall material fails: this turns out to be the case in bone. Finally, due to highly confined multiaxial stress states, the elastic portion of the overall energy invested into the material may become negligible—and then yield design analysis employed on material volumes gives an idea of the highly ductile behavior of complex confined materials, such as asphalt. What integrates all the reported cases is the high capacity of mature mathematical and mechanical formulations to reveal the intricate, yet decipherable nature of the (continuum) mechanics of materials and structures.     

Derivation of crack closure and crack growth rate data from effective-strain fatigue life data for fracture mechanics fatigue life predictions

This study deals with the behavior of short cracks growing out of notches. Three types of load histories are used: (a) a fully-reversed constant amplitude history; (b) a periodic compressive overload history consisting of repeated load blocks containing one fully-reversed constant amplitude yield–stress magnitude cycle (the overload) followed by a group of smaller constant amplitude cycles having the same maximum stress as the overload cycle; (c) and a service strain history. Procedures are presented for deriving crack closure data and crack growth rate vs effective stress intensity factor range data from data obtained by subjecting a small number of smooth laboratory specimens to simple periodic compressive overload tests to obtain closure-free strain-life data. These procedures are illustrated in an example in which fatigue life predictions are made for a service strain history applied to notched plate specimens. The fatigue life predictions based on the measured and the derived crack closure and crack growth rate data are in good agreement with the experimentally determined fatigue lives.     

Networks originating from the multiple cracking of different scales in rocks and swelling soils

The objective of this work is not a fracture prediction or prevention. We are interested in modeling the crack network geometry in rocks and swelling soils and in the application of the model to rock volume fragmentation or preferential flow in swelling soils. Natural and explosion-induced rock fragmentation is important in geophysics and mining. Preferential flow in swelling soils is important in agricultural and environmental engineering. The presentation gives a brief review of the authors' work in this area. A concentration criterion of crack connection and effective independency of cracks in the case of multiple cracking are a basis for the modeling of a crack network. This basis enables one to introduce a condition of fragment formation at crack connection and a number of relevant concepts (an average cracking – an average crack number of x dimension in volume; crack connection probability of x dimension; fragment formation probability; average and maximum fragment dimensions; crack connectedness – a ratio connected to the total number of cracks; and crack network tortuosity), as well as to suggest quantitative relations between the concepts. In the frame of an application, the average fragment dimension and crack connectedness (or the maximum fragment dimension and fragment formation probability) can depend on the spatial coordinates and parameters specific for the application. The simplest application relates to the block-dimension distribution of a rock mass for statistically homogeneous conditions. The second application relates to the granulometric composition of a blasted rock mass in quarries. In this case the specific parameters are the preliminary rock disturbance (including natural cracking), charge construction, blasting scheme and others. The third application relates to the shrinkage crack network geometry in swelling clay soils, the spatial coordinate being the soil depth. The specific parameters are an upper layer thickness (of a few tens of centimeters) of intensive cracking and the maximum crack depth (its boundary being the depth of the water table level). Crack width, depth, spacing, volume, and tortuosity of the crack network are estimated by using the shrinkage curve of the soil and a water content profile. The fourth application relates to the hydraulic properties of capillary crack networks in swelling soils as compared to those of the soil matrix. For all the applications considered, comparison between the model prediction and available data shows good agreement.     

Networks originating from the multiple cracking of different scales in rocks and swelling soils

The objective of this work is not a fracture prediction or prevention. We are interested in modeling the crack network geometry in rocks and swelling soils and in the application of the model to rock volume fragmentation or preferential flow in swelling soils. Natural and explosion-induced rock fragmentation is important in geophysics and mining. Preferential flow in swelling soils is important in agricultural and environmental engineering. The presentation gives a brief review of the authors' work in this area. A concentration criterion of crack connection and effective independency of cracks in the case of multiple cracking are a basis for the modeling of a crack network. This basis enables one to introduce a condition of fragment formation at crack connection and a number of relevant concepts (an average cracking – an average crack number of x dimension in volume; crack connection probability of x dimension; fragment formation probability; average and maximum fragment dimensions; crack connectedness – a ratio connected to the total number of cracks; and crack network tortuosity), as well as to suggest quantitative relations between the concepts. In the frame of an application, the average fragment dimension and crack connectedness (or the maximum fragment dimension and fragment formation probability) can depend on the spatial coordinates and parameters specific for the application. The simplest application relates to the block-dimension distribution of a rock mass for statistically homogeneous conditions. The second application relates to the granulometric composition of a blasted rock mass in quarries. In this case the specific parameters are the preliminary rock disturbance (including natural cracking), charge construction, blasting scheme and others. The third application relates to the shrinkage crack network geometry in swelling clay soils, the spatial coordinate being the soil depth. The specific parameters are an upper layer thickness (of a few tens of centimeters) of intensive cracking and the maximum crack depth (its boundary being the depth of the water table level). Crack width, depth, spacing, volume, and tortuosity of the crack network are estimated by using the shrinkage curve of the soil and a water content profile. The fourth application relates to the hydraulic properties of capillary crack networks in swelling soils as compared to those of the soil matrix. For all the applications considered, comparison between the model prediction and available data shows good agreement.     

Discovery of extra-terrestrial life: assessment by scales of its importance and associated risks

The Rio Scale accepted by the SETI Committee of the International Academy of Astronautics in 2002 is intended for use in evaluating the impact on society of any announcement regarding the discovery of evidence of extra-terrestrial (ET) intelligence. The Rio Scale is mathematically defined using three parameters (class of phenomenon, type of discovery and distance) and a δ factor, the assumed credibility of a claim. This paper proposes a new scale applicable to announcements alleging evidence of ET life within or outside our Solar System. The London Scale for astrobiology has mathematical structure and logic similar to the Rio Scale, and uses four parameters (life form, nature of phenomenon, type of discovery and distance) as well as a credibility factor δ to calculate a London Scale index (LSI) with values ranging from 0 to 10. The level of risk or biohazard associated with a purported discovery is evaluated independently of the LSI value and may be ranked in four categories. The combined information is intended to provide a scalar assessment of the scientific importance, validity and potential risks associated with putative evidence of ET life discovered on Earth, on nearby bodies in the Solar System or in our Galaxy.     

Estimation of metabolic pathway systems from different data sources

Parameter estimation is the main bottleneck of metabolic pathway modelling. It may be addressed from the bottom up, using information on metabolites, enzymes and modulators, or from the top down, using metabolic time series data, which have become more prevalent in recent years. The authors propose here that it is useful to combine the two strategies and to complement time-series analysis with kinetic information. In particular, the authors investigate how the recent method of dynamic flux estimation (DFE) may be supplemented with other types of estimation. Using the glycolytic pathway in Lactococcus lactis as an illustration example, the authors demonstrate some strategies of such supplementation.     

Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.     

Multi-scale modelling of the dynamics of cell colonies: insights into cell-adhesion forces and cancer invasion from in silico simulations

Studying the biophysical interactions between cells is crucial to understanding how normal tissue develops, how it is structured and also when malfunctions occur. Traditional experiments try to infer events at the tissue level after observing the behaviour of and interactions between individual cells. This approach assumes that cells behave in the same biophysical manner in isolated experiments as they do within colonies and tissues. In this paper, we develop a multi-scale multi-compartment mathematical model that accounts for the principal biophysical interactions and adhesion pathways not only at a cell–cell level but also at the level of cell colonies (in contrast to the traditional approach). Our results suggest that adhesion/separation forces between cells may be lower in cell colonies than traditional isolated single-cell experiments infer. As a consequence, isolated single-cell experiments may be insufficient to deduce important biological processes such as single-cell invasion after detachment from a solid tumour. The simulations further show that kinetic rates and cell biophysical characteristics such as pressure-related cell-cycle arrest have a major influence on cell colony patterns and can allow for the development of protrusive cellular structures as seen in invasive cancer cell lines independent of expression levels of pro-invasion molecules.     

In search of representativeness: evolving the environmental data quality model.

Environmental regulatory policy states a goal of "sound science." The practice of good science is founded on the systematic identification and management of uncertainties; i.e., knowledge gaps that compromise our ability to make accurate predictions. Predicting the consequences of decisions about risk and risk reduction at contaminated sites requires an accurate model of the nature and extent of site contamination, which in turn requires measuring contaminant concentrations in complex environmental matrices. Perfecting analytical tests to perform those measurements has consumed tremendous regulatory attention for the past 20-30 years. Yet, despite great improvements in environmental analytical capability, complaints about inadequate data quality still abound. This paper argues that the first generation data quality model that equated environmental data quality with analytical quality was a useful starting point, but it is insufficient because it is blind to the repercussions of multifaceted issues collectively termed "representativeness." To achieve policy goals of "sound science" in environmental restoration projects, the environmental data quality model must be updated to recognize and manage the uncertainties involved in generating representative data from heterogeneous environmental matrices.