Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System

The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in vivo dynamics of MinD and MinE and comparing their simulated localization patterns to the observations in experiments and previous computational work. In both cases, our simulation results are in good agreement

Existence results for impulsive neutral functional differential equations with state-dependent delay

In this article, we study the existence of mild solutions for a class of impulsive abstract partial neutral functional differential equations with state-dependent delay. The results are obtained by using Leray-Schauder Alternative fixed point theorem. Example is provided to illustrate the main result

Reaction-diffusion kinetics on lattice at the microscopic scale

Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal scales but cannot directly account for the microscopic effects in the cell such as volume exclusion and diffusion-influenced reactions. Nonetheless, schemes based on the high-resolution microscopic lattice method (MLM) can directly simulate these effects by representing each finite-sized molecule explicitly as a random walker on fine lattice voxels. The theory and consistency of MLM in simulating diffusion-influenced reactions have not been clarified in detail. Here, we examine MLM in solving diffusion-influenced reactions in 3D space by employing the Spatiocyte simulation scheme. Applying the random walk theory, we construct the general theoretical framework underlying the method and obtain analytical expressions for the total rebinding probability and the effective reaction rate. By matching Collins-Kimball and lattice-based rate constants, we obtained the exact expressions to determine the reaction acceptance probability and voxel size. We found that the size of voxel should be about 2% larger than the molecule. MLM is validated by numerical simulations, showing good agreement with the off-lattice particle-based method, eGFRD. MLM run time is more than an order of magnitude faster than eGFRD when diffusing macromolecules with typical concentrations in the cell. MLM also showed good agreements with eGFRD and mean-field models in case studies of two basic motifs of intracellular signaling, the protein production-degradation process and the dual phosphorylation cycle. Moreover, when a reaction compartment is populated with volume-excluding obstacles, MLM captures the non-classical reaction kinetics caused by anomalous diffusion of reacting molecules

Towards identification of finger flexions using single channel surface electromyography - able bodied and amputee subjects

This research has established a method for using single channel surface electromyogram (sEMG) recorded from the forearm to identify individual finger flexion. The technique uses the volume conduction properties of the tissues and uses the magnitude and density of the singularities in the signal as a measure of strength of the muscle activity. Methods: SEMG was recorded from the flexor digitorum superficialis muscle during four different finger flexions. Based on the volume conduction properties of the tissues, sEMG was decomposed into wavelet maxima and grouped into four groups based on their magnitude. The mean magnitude and the density of each group were the inputs to the twin support vector machines (TSVM). The algorithm was tested on 11 able-bodied and one trans-radial amputated volunteer to determine the accuracy, sensitivity and specificity. The system was also tested to determine inter-experimental variations and variations due to difference in the electrode location. Results: Accuracy and sensitivity of identification of finger actions from single channel sEMG signal was 93% and 94% for able-bodied and 81% and 84% for trans-radial amputated respectively, and there was only a small inter-experimental variation. Conclusions: Volume conduction properties based sEMG analysis provides a suitable basis for identifying finger flexions from single channel sEMG. The reported system requires supervised training and automatic classification

Pioneering Renewable Energy Solutions: Insights from ICARGET 2023

Arjunan et al., Guest Editors, proudly present the selected papers from ICARGET 2023, showcasing cutting-edge advancements and diverse perspectives in this special issue of the Transactions on Energy Systems and Engineering Applications (TESEA). This collection covers a broad array of topics including solar, wind, bioenergy, and energy storage solutions, each offering significant insights, methodologies, and practical applications. The research underscores the critical need for sustainable energy solutions, interdisciplinary collaboration, and the socio-economic and environmental impacts of renewable energy deployment. The editorial team extends sincere gratitude to TESEA, the authors, reviewers, and readers for their invaluable contributions to advancing renewable and green energy technologies

The impact of Bt cotton on poor households in rural India

The impact of genetically modified (GM) crops on the poor in developing countries is still the subject of controversy. While previous studies have examined direct productivity effects of Bacillus thuringiensis (Bt) cotton and other GM crops, little is known about wider socioeconomic outcomes. We use a microeconomic modelling approach and comprehensive survey data from India to analyse welfare and distribution effects in a typical village economy. Bt cotton adoption increases returns to labour, especially for hired female workers. Likewise, aggregate household incomes rise, including for poor and vulnerable farmers. Hence, Bt cotton contributes to poverty reduction and rural development

The effect of prior walking on coronary heart disease risk markers in South Asian and European men.

Purpose: Heart disease risk is elevated in South Asians possibly due to impaired postprandial metabolism. Running has been shown to induce greater reductions in postprandial lipaemia in South Asian than European men but the effect of walking in South Asians is unknown. Methods: Fifteen South Asian and 14 White European men aged 19-30 years completed two, 2-d trials in a randomised crossover design. On day 1, participants rested (control) or walked for 60 min at approximately 50% maximum oxygen uptake (exercise). On day 2, participants rested and consumed two high fat meals over a 9h period during which 14 venous blood samples were collected. Results: South Asians exhibited higher postprandial triacylglycerol (geometric mean (95% confidence interval) 2.29(1.82 to 2.89) vs. 1.54(1.21 to 1.96) mmol·L-1·hr-1), glucose (5.49(5.21 to 5.79) vs. 5.05(4.78 to 5.33) mmol·L-1·hr-1), insulin (32.9(25.7 to 42.1) vs. 18.3(14.2 to 23.7) µU·mL-1·hr-1) and interleukin-6 (2.44(1.61 to 3.67) vs. 1.04(0.68 to 1.59) pg·mL-1·hr-1) than Europeans (all ES ≥ 0.72, P≤0.03). Between-group differences in triacylglycerol, glucose and insulin were not significant after controlling for age and percentage body fat. Walking reduced postprandial triacylglycerol (1.79(1.52 to 2.12) vs. 1.97(1.67 to 2.33) mmol·L-1·hr-1) and insulin (21.0(17.0 to 26.0) vs. 28.7(23.2 to 35.4) µU·mL-1·hr-1) (all ES ≥ 0.23. P≤0.01), but group differences were not significant. Conclusions: Healthy South Asians exhibited impaired postprandial metabolism compared with White Europeans, but these differences were diminished after controlling for potential confounders. The small-moderate reduction in postprandial triacylglycerol and insulin after brisk walking was not different between the ethnicities