Combination Of Simulation Methods Research Articles

ENERGY Pro: Spatially explicit agent-based model on achieving positive energy districts

This article describes the ENERGY Pro agent-based model using the Overview, Design Concept, and Details + Human Decision-making (ODD+D protocol). The model is empirically explicit and aims to investigate the adoption decisions of homeowners in Amsterdam on different energy-efficient retrofitting (EER) measures. Following the ODD+D protocol, this study uncovers the conceptual framework used for model construction, the spatial microsimulation process of expanding the data, and the model implementation details. The article also describes sensitivity analysis, validation results, and how to use and adapt the model. With this article, the authors aim to make the model replicable and accessible to other researchers and inspire them using the combination of social simulation and spatial microsimulation in studying the energy transition.•The agent-based model is described using the ODD+D protocol.•The combination of simulation methods is used for constructing an empirical model.•The model on energy transition can be adapted for other cities.

Using Simulation as Project-Based Learning to Improve Students’ Speaking Skill on Business English Course

The aim of this study is to know the increasing students’ speaking ability by using simulation as project-based learning on business English course. This research used classroom action research with a combination of simulation method as project-based learning on the Business English course. The use of simulation has been implemented on the Business English course at Faculty of Economics, management study program at Kadiri Islamic University. Sixth-semester students performed presentations as simulations and practiced speaking in groups. This research was conducted in two research cycles which the average score of students' speaking performance increased significantly significant from 58.23 to 67.65. Students also have a positive perception to this method which most of students agree that simulation can provide motivation, simulation is a fun way of learning, and simulations provide learning experiences and provide more value from learning self-study. Students’ perception of project-based learning indicate that this method can improve their speaking performance. By the combination of simulation methods as project-based learning, students' speaking ability can increase.

The Carboxylate Ligand as an Oxide Relay in Catalytic Water Oxidation.

Carboxylate groups have diverse functionalities in ligands of transition metal catalysts. Here we present a conceptually different function of the carboxylates: the oxide relay. It functions by providing an intramolecular nucleophilic oxygen close to the oxo group to facilitate O-O bond formation and at a later stage a remote electrophilic center to facilitate OH- nucleophilic attack. Empirical valence bond-molecular dynamics (EVB-MD) models were generated for key bond forming steps, diffusion coefficients and binding free energies from potential of mean force estimations were calculated from molecular dynamics (MD) simulations, activation free energies of chemical steps were calculated using density functional theory (DFT). The catalyst studied is the extremely active Ru(tda)(py)2 water oxidation catalyst. The combination of simulation methods allowed for estimation of the turnover frequencies, which were within 1 order of magnitude from the experimental results at different pH values. From the calculated reaction rates we find that at low pH the OH- anion nucleophilic attack is the rate-limiting step, which changes at high pH to the O-O bond formation step. Both steps are extremely rapid, and key to the efficiency is the oxide relay functionality of a pendant carboxylate group. We cannot exclude all alternative mechanisms and suggest isotope experiments using 18O-labeled water to support or invalidate the oxide relay mechanism. The functionality was discovered for a ruthenium catalyst, but since there is nothing in the mechanism restricting it to this metal, the oxide relay functionality could open new ways to design the next-generation water oxidation catalysts with improved activity.

Atomistic Molecular-Dynamics Simulations Enable Prediction of the Arginine Permeation Pathway through OccD1/OprD from Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine.