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Systems dynamics model

Zhixiang Lu, Yongping Wei, Qi Feng, Jiali Xie, Honglang Xiao, Guodong Cheng
There is limited quantitative understanding of interactions between human and environmental systems over the millennial scale. We aim to reveal the co-evolutionary dynamics of the human-environment system in a river basin by simulating the water use and net primary production (NPP) allocation for human and environmental systems over the last 2000years in Heihe River basin (HRB) in northwest China. We partition the catchment total evapotranspiration (ET) into ET for human and environmental systems with a social-hydrological framework and estimate the NPP for human and environmental systems using the Box-Lieth model, then classify the co-evolutionary processes of the human-environment system into distinct phases using the rate of changes of NPP over time, and discover the trade-offs or synergies relationships between them based on the elasticity of change of the NPP for humans to the change of NPP for environment...
April 17, 2018: Science of the Total Environment
Patrick Campbell, Yang Zhang, Fang Yan, Zifeng Lu, David Streets
Emissions from the transportation sector are rapidly changing worldwide; however, the interplay of such emission changes in the face of climate change are not as well understood. This two-part study examines the impact of projected emissions from the U.S. transportation sector (Part I) on ambient air quality in the face of climate change (Part II). In Part I of this study, we describe the methodology and results of a novel Technology Driver Model (see graphical abstract) that includes 1) transportation emission projections (including on-road vehicles, non-road engines, aircraft, rail, and ship) derived from a dynamic technology model that accounts for various technology and policy options under an IPCC emission scenario, and 2) the configuration/evaluation of a dynamically downscaled Weather Research and Forecasting/Community Multiscale Air Quality modeling system...
April 17, 2018: Environmental Pollution
Bianca K Stöcker, Johannes Köster, Eli Zamir, Sven Rahmann
Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of these systems emerge not only from the protein interactions themselves but also from the dependencies between these interactions, as generated by allosteric effects or mutual exclusion due to steric hindrance. Therefore, formal models for integrating and utilizing information about interaction dependencies are of high interest. Here, we describe an approach for endowing protein networks with interaction dependencies using propositional logic, thereby obtaining constrained protein interaction networks ("constrained networks")...
April 20, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
M Azari, A V Le, M Lübken, M Denecke
A mathematical model for a granular biofilm reactor for leachate treatment was validated by long-term measured data to investigate the mechanisms and drivers influencing biological nitrogen removal and microbial consortia dynamics. The proposed model, based on Activated Sludge Model (ASM1), included anaerobic ammonium oxidation (anammox), nitrifying and heterotrophic denitrifying bacteria which can attach and grow on granular activated carbon (GAC) particles. Two kinetic descriptions for the model were proposed: with and without soluble microbial products (SMP) and extracellular polymeric substance (EPS)...
April 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Güçlü Insel, Ahmet Karagunduz, Murat Aksel, Emine Cokgor, Gokce Kor-Bicakci, Goksin Ozyildiz, Ismail Toroz, Bulent Keskinler
In this study, an integrated aerobic membrane bioreactor (MBR)-nanofiltration (NF) system has been applied for advanced treatment of Opium processing wastewaters to comply with strict discharge limits. Aerobic MBR treatment was successfully applied to high strength industrial wastewater. In aerobic MBR treatment, a non-fouling unique slot aeration system was designed using computational fluid dynamics techniques. The MBR was used to separate treated effluent from dispersed and non-settleable biomass. Respirometric modeling using MBR sludge indicated that the biomass exhibited similar kinetic parameters to that of municipal activated sludge systems...
April 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Bercem Dutagaci, Lim Heo, Michael Feig
A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtained refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins...
April 20, 2018: Proteins
Lida I Michalaki, Dimitris A Goussis
The multi-scale dynamics of a two-compartment with first order absorption Target-Mediated Drug Disposition (TMDD) pharmacokinetics model is analysed, using the Computational Singular Perturbation (CSP) algorithm. It is shown that the process evolves along two Slow Invariant Manifolds (SIMs), on which the most intense components of the model are equilibrated, so that the less intensive are the driving ones. The CSP tools allow for the identification of the components of the TMDD model that (i) constrain the evolution of the process on the SIMs, (ii) drive the system along the SIMs and (iii) generate the fast time scales...
April 19, 2018: Journal of Mathematical Biology
Cris R Hasan, Bernd Krauskopf, Hinke M Osinga
Many physiological phenomena have the property that some variables evolve much faster than others. For example, neuron models typically involve observable differences in time scales. The Hodgkin-Huxley model is well known for explaining the ionic mechanism that generates the action potential in the squid giant axon. Rubin and Wechselberger (Biol. Cybern. 97:5-32, 2007) nondimensionalized this model and obtained a singularly perturbed system with two fast, two slow variables, and an explicit time-scale ratio ε...
April 19, 2018: Journal of Mathematical Neuroscience
Yuli Wang, Raehyun Kim, Samuel S Hinman, Bailey Zwarycz, Scott T Magness, Nancy L Allbritton
The relationship between intestinal stem cells (ISCs) and the surrounding niche environment is complex and dynamic. Key factors localized at the base of the crypt are necessary to promote ISC self-renewal and proliferation, to ultimately provide a constant stream of differentiated cells to maintain the epithelial barrier. These factors diminish as epithelial cells divide, migrate away from the crypt base, differentiate into the postmitotic lineages, and end their life span in approximately 7 days when they are sloughed into the intestinal lumen...
March 2018: Cellular and Molecular Gastroenterology and Hepatology
Francesca Uberti, Vera Morsanuto, Sabrina Ghirlanda, Sara Ruga, Nausicaa Clemente, Cristina Boieri, Renzo Boldorini, Claudio Molinari
Objective: Wound healing is a dynamic, interactive, and complex process that involves a series of events, including inflammation, migration, proliferation, granulation tissue formation, and matrix remodeling. Despite the high frequency of serious slow-healing wounds, there is still no adequate therapy. The aim of this study is to evaluate a new highly diluted acetylcholine (Ach) formulation obtained through a sequential kinetic activation (SKA) method applied to a wound healing in vivo model to verify the hypothesis that a low dose of Ach could be a more physiological stimulus for healing, by stimulating muscarinic and nicotinic receptors and their related intracellular pathways...
April 1, 2018: Advances in Wound Care
Martin Hoffmann, Jörg Galle
Kinetic models are at the heart of system identification. A priori chosen rate functions may, however, be unfitting or too restrictive for complex or previously unanticipated regulation. We applied general purpose piecewise linear functions for stochastic system identification in one dimension using published flow cytometry data on E.coli and report on identification results for equilibrium state and dynamic time series. In metabolic labelling experiments during yeast osmotic stress response, we find mRNA production and degradation to be strongly co-regulated...
2018: NPJ Systems Biology and Applications
Luis Ruiz Pestana, Natalie Minnetian, Laura Nielsen Lammers, Teresa Head-Gordon
When driven out of equilibrium, many diverse systems can form complex spatial and dynamical patterns, even in the absence of attractive interactions. Using kinetic Monte Carlo simulations, we investigate the phase behavior of a binary system of particles of dissimilar size confined between semiflexible planar surfaces, in which the nanoconfinement introduces a non-local coupling between particles, which we model as an activation energy barrier to diffusion that decreases with the local fraction of the larger particle...
February 14, 2018: Chemical Science
Piero Colli Franzone, Luca F Pavarino, Simone Scacchi
We introduce and study some scalable domain decomposition preconditioners for cardiac electro-mechanical 3D simulations on parallel HPC (High Performance Computing) architectures. The electro-mechanical model of the cardiac tissue is composed of four coupled sub-models: (1) the static finite elasticity equations for the transversely isotropic deformation of the cardiac tissue; (2) the active tension model describing the dynamics of the intracellular calcium, cross-bridge binding and myofilament tension; (3) the anisotropic Bidomain model describing the evolution of the intra- and extra-cellular potentials in the deforming cardiac tissue; and (4) the ionic membrane model describing the dynamics of ionic currents, gating variables, ionic concentrations and stretch-activated channels...
2018: Frontiers in Physiology
Muhammad Arba, Andry Nur-Hidayat, Ruslin, Muhammad Yusuf, Sumarlin, Rukman Hertadi, Setyanto Tri Wahyudi, Slamet Ibrahim Surantaadmaja, Daryono H Tjahjono
The ubiquitin-proteasome system plays an important role in protein quality control. Currently, inhibition of the proteasome has been validated as a promising approach in anticancer therapy. The 20S core particle of the proteasome harbors β5 subunit which is a crucial active site in proteolysis. Targeting proteasome β5 subunit which is responsible for the chymotrypsin-like activity of small molecules has been regarded as an important way for achieving therapeutics target. In the present study, a series of porphyrin derivatives bearing either pyridine or pyrazole rings as meso-substituents were designed and evaluated as an inhibitor for the β5 subunit of the proteasome by employing molecular docking and dynamics simulations...
April 16, 2018: Computational Biology and Chemistry
Fuxiang Mao, Jihai Lei, Obeng Enoch, Ming Wei, Cui Zhao, Yanping Quan, Wei Yu
The domesticated silkworm is an ideal and economic insect model that plays crucial roles in sericulture and bioreactor. Bombyx mori nucleopolyhedrovirus (BmNPV) is not only an infectious pathogen to B. mori, but also an efficient vector expressing recombinant proteins. Although, the proteomics of silkworm and BmN cell membrane lipid raft towards BmNPV infection had been investigated, proteome results of BmN cells upon BmNPV challenge currently remain ambiguous. In order to explore the interaction between silkworm and BmNPV, we analyzed several pivotal processes of BmNPV infected BmN cell by quantitative mass spectrometry...
April 16, 2018: Journal of Proteomics
Andrew L Krause, Lawrence Kurowski, Kamran Yawar, Robert A Van Gorder
While deterministic metapopulation models for the spread of epidemics between populations have been well-studied in the literature, variability in disease transmission rates and interaction rates between individual agents or populations suggests the need to consider stochastic fluctuations in model parameters in order to more fully represent realistic epidemics. In the present paper, we have extended a stochastic SIS epidemic model - which introduces stochastic perturbations in the form of white noise to the force of infection (the rate of disease transmission from classes of infected to susceptible populations) - to spatial networks, thereby obtaining a stochastic epidemic metapopulation model...
April 16, 2018: Journal of Theoretical Biology
Basel Arafat, Nidal Qinna, Milena Cieszynska, Robert T Forbes, Mohamed A Alhnan
Coumarin therapy has been associated with high levels of inter- and intra-individual variation in the required dose to reach a therapeutic anticoagulation outcome. Therefore, a dynamic system that is able to achieve accurate delivery of a warfarin dose is of significant importance. Here we assess, the ability of 3D printing to fabricate and deliver tailored individualised precision dosing using an in-vitro model. Sodium warfarin loaded filaments were compounded using hot melt extrusion (HME) and further fabricated via fused deposition modelling (FDM) 3D printing to produce capsular-ovoid-shaped dosage forms loaded at 200 and 400 µg dose...
April 16, 2018: European Journal of Pharmaceutics and Biopharmaceutics
Itziar Irurzun-Arana, Alvaro Janda, Sergio Ardanza-Trevijano, Iñaki F Trocóniz
Numerous problems encountered in computational biology can be formulated as optimization problems. In this context, optimization of drug release characteristics or dosing schedules for anticancer agents has become a prominent area not only for the development of new drugs, but also for established drugs. However, in complex systems, optimization of drug exposure is not a trivial task and cannot be efficiently addressed through trial-error simulation exercises. Finding a solution to those problems is a challenging task which requires more advanced strategies like optimal control theory...
April 19, 2018: PLoS Computational Biology
Siming Ma, Andrei S Avanesov, Emily Porter, Byung Cheon Lee, Marco Mariotti, Nadezhda Zemskaya, Roderic Guigo, Alexey A Moskalev, Vadim N Gladyshev
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life-history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer-lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing...
April 19, 2018: Aging Cell
Bobby Ranjan, Ket Hing Chong, Jie Zheng
BACKGROUND: Alzheimer's disease (AD) is a progressive neurological disorder, recognized as the most common cause of dementia affecting people aged 65 and above. AD is characterized by an increase in amyloid metabolism, and by the misfolding and deposition of β-amyloid oligomers in and around neurons in the brain. These processes remodel the calcium signaling mechanism in neurons, leading to cell death via apoptosis. Despite accumulating knowledge about the biological processes underlying AD, mathematical models to date are restricted to depicting only a small portion of the pathology...
April 11, 2018: BMC Systems Biology
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