Binding conformation prediction between human acetylcholinesterase and cytochrome c using molecular modeling methods

The acetylcholinesterase (AChE) is important to terminate acetylcholine-mediated neurotransmission at cholinergic synapses. The pivotal role of AChE in apoptosome formation through the interactions with cytochrome c (Cyt c) was demonstrated in recent study. In order to investigate the proper binding conformation between the human AChE (hAChE) and human Cyt c (hCyt c), macro-molecular docking simulation was performed using DOT 2.0 program. The hCyt c was bound to peripheral anionic site (PAS) on hAChE and binding mode of the docked conformation was very similar to the reported crystal structure of the AChE and fasciculin-II (Fas-II) complex. Two 10ns molecular dynamics (MD) simulations were carried out to refine the binding mode of docked structure and to observe the differences of the binding conformations between the absent (Apo) and presence (Holo) of heme group. The key hydrogen bonding residues between hAChE and hCyt c proteins were found in Apo and Holo systems, as well as each Tyr341 and Trp286 residue of hAChE was participated in cation-pi (π) interactions with Lys79 of hCyt c in Apo and Holo systems, respectively. From the present study, although the final structures of the Apo and Holo systems have similar binding pattern, several differences were investigated in flexibilities, interface interactions, and interface accessible surface areas. Based on these results, we were able to predict the reasonable binding conformation which is indispensable for apoptosome formation.     

Simulation-based workforce assignment in a multi-organizational social network for alliance-based software development

The development of alliance-based software requires the collaboration of many stakeholders. These different stakeholders across multiple organizations form a complex social network. The goal of this paper is to develop a novel modeling framework, which will help task managers devise optimal workforce assignments considering both short-term and long-term aspects of the software development process. The proposed framework is composed of an assignment module and a prediction module. For a given task, the assignment module first selects a candidate workforce mix. Based on the candidate workforce mix, the prediction module then predicts the short-term performance (productivity) as well as the long-term performance (workforce training and robustness of the organization) of the organization. Then, the assignment module selects another candidate mix, and this iteration continues until an optimal workforce mix is found. The prediction module and the assignment module are based on an agent-based simulation method and a multi-objective optimization model, respectively. The proposed modeling framework is illustrated with a software enhancement request process in Kuali, an alliance-based open source software development project involving 12 organizations. The constructed framework is executed with varying parameters to demonstrate its use and benefit in the software enhancement process.     

Hybrid simulation and optimization-based design and operation of integrated photovoltaic generation,storage units,and grid

Unlike fossil-fueled generation, solar energy resources are geographically distributed and highly intermittent, which makes their direct control extremely difficult and requires storage units as an additional concern. The goal of this research is to design and develop a flexible tool, which will allow us to obtain (1) an optimal capacity of an integrated photovoltaic (PV) system and storage units and (2) an optimal operational decision policy considering the current and future market prices of the electricity. The proposed tool is based on hybrid (system dynamics model and agent-based model) simulation and meta-heuristic optimization. In particular, this tool has been developed for three different scenarios (involving different geographical scales), where PV-based solar generators, storage units (compressed-air-energy-storage (CAES) and super-capacitors), and grid are used in an integrated manner to supply energy demands. Required data has been gathered from various sources, including NASA and TEP (utility company), US Energy Information Administration, National Renewable Energy Laboratory, commercial PV panel manufacturers, and publicly available reports. The constructed tool has been demonstrated to (1) test impacts of several factors (e.g. demand growth, efficiencies in PV panel and CAES system) on the total cost of the integrated generation and storage system and an optimal mixture of PV generation and storage capacity, and to (2) demonstrate an optimal operational policy.     

Concurrent consideration of evacuation safety and productivity in manufacturing facility planning using multi-paradigm simulations

Manufacturing facilities are expected to maintain a high level of production and at the same time, employ strict safety standards to ensure the safe evacuation of the people in the event of emergencies (fire is considered in this paper). These two goals are often conflicting. This paper presents a methodology to evaluate evacuation safety versus productivity concurrently for various, widely known manufacturing layouts. While the safety performance indicators such as evacuation times are inferred from the crowd (agent based) simulation, the productivity performance indicators (e.g. throughput) are analyzed using the discrete event simulation. To this end, this research focuses on creating innovative techniques for developing accurate crowd simulations, where Belief-Desire-Intention (BDI) agent framework is employed to build each person’s individual actions and the interactions between them. The data model and rule based action algorithms for each agent are reverse-engineered from the human-in-the-loop experiments in the immersive virtual reality environments. Finally, experiments are conducted using the constructed simulations to compare safety and productivity for different layouts. To demonstrate the proposed methodology, an automotive power-train (engine and transmission) manufacturing plant was used. Initial results look quite promising.     

A combined scheme of edge-based and node-based smoothed finite element methods for Reissner–Mindlin flat shells

In this paper, a combined scheme of edge-based smoothed finite element method (ES-FEM) and node-based smoothed finite element method (NS-FEM) for triangular Reissner–Mindlin flat shells is developed to improve the accuracy of numerical results. The present method, named edge/node-based S-FEM (ENS-FEM), uses a gradient smoothing technique over smoothing domains based on a combination of ES-FEM and NS-FEM. A discrete shear gap technique is incorporated into ENS-FEM to avoid shear-locking phenomenon in Reissner–Mindlin flat shell elements. For all practical purpose, we propose an average combination (aENS-FEM) of ES-FEM and NS-FEM for shell structural problems. We compare numerical results obtained using aENS-FEM with other existing methods in the literature to show the effectiveness of the present method.     

Fuzzy geographically weighted clustering using artificial bee colony: An efficient geo-demographic analysis algorithm and applications to the analysis of crime behavior in population

Geo-demographic analysis is an essential part of a geographical information system (GIS) for predicting people’s behavior based on statistical models and their residential location. Fuzzy Geographically Weighted Clustering (FGWC) serves as one of the most efficient algorithms in geo-demographic analysis. Despite being an effective algorithm, FGWC is sensitive to initialize when the random selection of cluster centers makes the iterative process falling into the local optimal solution easily. Artificial Bee Colony (ABC), one of the most popular meta-heuristic algorithms, can be regarded as the tool to achieve global optimization solutions. This research aims to propose a novel geo-demographic analysis algorithm that integrates FGWC to the optimization scheme of ABC for improving geo-demographic clustering accuracy. Experimental results on various datasets show that the clustering quality of the proposed algorithm called FGWC-ABC is better than those of other relevant methods. The proposed algorithm is also applied to a decision-making application for analyzing crime behavior problem in the population using the US communities and crime dataset. It provides fuzzy rules to determine the violent crime rate in terms of linguistic labels from socioeconomic variables. These results are significant to make predictions of further US violent crime rate and to facilitate appropriate decisions on prevention such the situations in the future.     

Integrating security and real-time requirements using covertchannel capacity

Database systems for real-time applications must satisfy timing constraints associated with transactions in addition to maintaining data consistency. In addition to real-time requirements, security is usually required in many applications. Multi-level security requirements introduce a new dimension to transaction processing in real-time database systems. In this paper, we argue that, due to the conflicting goals of each requirement, tradeoffs need to be made between security and timeliness. We first define mutual information, a measure of the degree to which security is being satisfied by a system. A secure two-phase locking protocol is then described and a scheme is proposed to allow partial violations of security for improved timeliness. Analytical expressions for the mutual information of the resultant covert channel are derived, and a feedback control scheme is proposed that does not allow the mutual information to exceed a specified upper bound. Results showing the efficacy of the scheme obtained through simulation experiments are also discussed     

Effect of NaOH on the decomposition of halogenated hydrocarbon by supercritical water oxidation

To protect alloys from corrosion phenomena in the supercritical water oxidation (SCWO) process, the effects of neutralizer on the conversion and corrosion were investigated. The surface morphologies of all the alloy coupons exposed to 2,4-Dichlorophenol (2,4-DCP) in the SCWO were significantly changed in microscopic images. The theoretical amount of NaOH as a neutralizer was calculated under the assumption of complete oxidation of 2,4-DCP. The pre-dosed NaOH in the range of 100% to 300% stoichiometric amount could not affect significantly the pH value in the SCWO. Moreover, the pH = 7 was not achieved until 700% stoichiometric amount of NaOH was pre-dosed to the reactor. It is noted that the conversion rate recorded over 99% without oxidant when 800% of NaOH was pre-dosed into the reactor. In addition, under the addition of H₂O₂ as an oxidant, the increased amount of NaOH led to the improvement of conversion rate. The pre-dosed NaOH may contribute to the conversion rate of 2,4-DCP in the SCWO. However, due to low solubility of salt in the SCWO, the fouling problem should be solved in the SCWO process.