A Graph-Based Framework for Multiscale Modeling of Physiological Transport

Trillions of chemical reactions occur in the human body every second, where the generated products are not only consumed locally but also transported to various locations in a systematic manner to sustain homeostasis. Current solutions to model these biological phenomena are restricted in computability and scalability due to the use of continuum approaches in which it is practically impossible to encapsulate the complexity of the physiological processes occurring at diverse scales. Here, we present a discrete modeling framework defined on an interacting graph that offers the flexibility to model multiscale systems by translating the physical space into a metamodel. We discretize the graph-based metamodel into functional units composed of well-mixed volumes with vascular and cellular subdomains; the operators defined over these volumes define the transport dynamics. We predict glucose drift governed by advective–dispersive transport in the vascular subdomains of an islet vasculature and cross-validate the flow and concentration fields with finite-element–based COMSOL simulations. Vascular and cellular subdomains are coupled to model the nutrient exchange occurring in response to the gradient arising out of reaction and perfusion dynamics. The application of our framework for modeling biologically relevant test systems shows how our approach can assimilate both multi-omics data from in vitro–in vivo studies and vascular topology from imaging studies for examining the structure–function relationship of complex vasculatures. The framework can advance simulation of whole-body networks at user-defined levels and is expected to find major use in personalized medicine and drug discovery.

Processing–Structure–Performance Relationship in Organic Transistors: Experiments and Model

In this paper, organic thin film transistors with different configurations are fabricated, and the effect on their performance when tailoring the semiconductor/insulator and semiconductor/contact interfaces through suitable treatments is analyzed. It is shown that the admittance spectroscopy used together with a properly developed electrical model turns out to be a particularly appropriate technique for correlating the performance of devices based on new materials in the manufacturing methods. The model proposed here to describe the equivalent metal–insulator–semiconductor (MIS) capacitor enables the extraction of a wide range of parameters and the study of the physical phenomena occurring in the transistors: diffusion of mobile ions through the insulator, charge trapping at the interfaces, dispersive transport in the semiconductor, and charge injection at the metal contacts. This is necessary to improve performance and stability in the case, like this one, of a novel organic semiconductor being employed. Atomic force microscopy images are also exploited to support the relationship between the semiconductor morphology and the electrical parameters.

A graph-based framework for multi-scale modeling of physiological transport

Trillions of chemical reactions occur in the human body every second, where the generated products are not only consumed locally but also transported to various locations in a systematic manner to sustain homeostasis. Current solutions to model these biological phenomena are restricted in computability and scalability due to the use of continuum approaches where it is practically impossible to encapsulate the complexity of the physiological processes occurring at diverse scales. Here we present a discrete modeling framework defined on an interacting graph that offers the flexibility to model multiscale systems by translating the physical space into a metamodel. We discretize the graph-based metamodel into functional units composed of well-mixed volumes with vascular and cellular subdomains; the operators defined over these volumes define the transport dynamics. We predict glucose drift governed by advective-dispersive transport in the vascular subdomains of an islet vasculature and cross-validate the flow and concentration fields with finite-element based COMSOL simulations. Vascular and cellular subdomains are coupled to model the nutrient exchange occurring in response to the gradient arising out of reaction and perfusion dynamics. The application of our framework for modeling biologically relevant test systems shows how our approach can assimilate both multi-omics data from in vitro - in vivo studies and vascular topology from imaging studies for examining the structure-function relationship of complex vasculatures. The framework can advance simulation of whole-body networks at user-defined levels and is expected to find major use in personalized medicine and drug discovery.

Application of divided convective-dispersive transport model to simulate variability of conservative transport processes inside a planted horizontal subsurface flow constructed wetland

This paper offers a novel application of our model worked out in Maple environment to help understand the very complex transport processes in horizontal subsurface flow constructed wetland with coarse gravel (HSFCW-C). We made tracer measurements: Inside a constructed wetland, we had 9 sample points, and samples were taken from each point at two depths. Our model is a divided convective-dispersive transport (D-CDT) model which makes a fitted response curve from the sum of two separate CDT curves showing the contributions of the main and side streams. Analytical solutions of CDT curves are inverse Gaussian distribution functions. This model was fitted onto inner points of the measurements to demonstrate that the model gives better fitting to the inner points than the commonly used convective-dispersive transport model. The importance of this new application of the model is that it can resemble transport processes in these constructed wetlands more precisely than the regularly used convective-dispersive transport (CDT) model. The model allows for calculations of velocity and dispersion coefficients. The results showed that this model gave differences of 4–99% (of velocity) and 2–474% (of dispersion coefficient) compared with the CDT model and values were closer to actual hydraulic behavior. The results also demonstrated the main flow path in the system.

Numerical Research of Fluid Flow and Solute Transport in Rough Fractures under Different Normal Stress

The effects of roughness and normal stress on hydraulic properties of fractures are significant during the coupled shear flow test. Knowing the laws of fluid flow and solute transport in fractures is essential to ensure the nature and safety of geological projects. Although many experiments and numerical simulations of coupled shear flow test have been conducted, there is still a lack of research on using the full Navier-Stokes (N-S) equation to solve the real flow characteristics of fluid in three-dimensional rough fractures. The main purpose of this paper is to study the influence of roughness and normal stress on the fluid flow and solute transport through fractures under the constant normal stiffness boundary condition. Based on the corrected successive random addition (SRA) algorithm, fracture surfaces with different roughness expressed by the Hurst coefficient ( H ) were generated. By applying a shear displacement of 5 mm, the sheared fracture models with normal stresses of 1 MPa, 3 MPa, and 5 MPa were obtained, respectively. The hydraulic characteristics of three-dimensional fractures were analyzed by solving the full N-S equation. The particle tracking method was employed to obtain the breakthrough curves based on the calculated flow field. The numerical method was verified with experimental results. It has been found that, for the same normal stress, the smaller the fracture H value is (i.e., more tough the fracture is), the larger the mechanical aperture is. The ratio of hydraulic aperture to mechanical aperture ( e h / e m ) decreases with the increasing of normal stress. The smaller the H value, the effect of the normal stress on the ratio e h / e m is more significant. The variation of transmissivity of fractures with the flow rate exhibits similar manner with that of e h / e m . With the normal stress and H value increasing, the mean velocity of particles becomes higher and more particles move to the outlet boundary. The dispersive transport behavior becomes obvious when normal stress is larger.

Bacterial density as an unexpected factor regulating decomposition by soil oligotrophs

Bacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the accessibility of bacteria to their substrate. The influence of bacterial metabolic traits on this control has however received little attention in highly heterogeneous spatial conditions under advective-dispersive transport of bacteria and substrates. Here, we develop a biochemical transport model to screen the interactive impacts of dispersion and metabolic traits on mineralization. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the source of substrate induced a significant increase in 2,4-D mineralization, revealing the existence of a control of decomposition by the bacterial density, in addition to the accessibility to the substrate. This regulation of degradation by density becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (i.e. oligotrophs). The model output suggests that the distance between bacteria adapted to oligotrophic environments is a stronger regulator of degradation than the distance between substrate source and these bacteria. Such oligotrophs, commonly found in soils, compete with each other for substrate even under remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, appears more versatile and accurate than the substrate-dependent Monod model. In view of their strong interactions, biochemical and transport processes cannot be handled independently but should be integrated, in particular when biochemical processes of interest are carried out by oligotrophs.Abstract FigureHighlights–Biodegradation in soils results from strong biochemical and transport couplings–Biodegradation depends on bacterial density, in addition to substrate accessibility–Bacterial density regulation counterbalances substrate accessibility regulation–Density regulation is enhanced for oligotrophic bacteria–The ratio-dependent Contois model is relevant to represent this double regulation

Fractal Generalization of the Scher–Montroll Model for Anomalous Transit-Time Dispersion in Disordered Solids

The Scher–Montroll model successfully describes subdiffusive photocurrents in homogeneously disordered semiconductors. The present paper generalizes this model to the case of fractal spatial disorder (self-similar random distribution of localized states) under the conditions of the time-of-flight experiment. Within the fractal model, we calculate charge carrier densities and transient current for different cases, solving the corresponding fractional-order equations of dispersive transport. Photocurrent response after injection of non-equilibrium carriers by the short laser pulse is expressed via fractional stable distributions. For the simplest case of one-sided instantaneous jumps (tunneling) between neighboring localized states, the dispersive transport equation contains fractional Riemann–Liouville derivatives on time and longitudinal coordinate. We discuss the role of back-scattering, spatial correlations induced by quenching of disorder, and spatiotemporal non-locality produced by the fractal trap distribution and the finite velocity of motion between localized states. We derive expressions for the photocurrent and transit time that allow us to determine the fractal dimension of the distribution of traps and the dispersion parameter from the time-of-flight measurements.