Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study

The computational result reveals the distinction between absorption and emission phenomena of nucleobases tagged with fluorophore on h-BN and aluminium doped h-BN nanosheets, which can be used as biosensing platforms for nucleic acids.

FAIRSCAPE: a Framework for FAIR and Reproducible Biomedical Analytics

Results of computational analyses require transparent disclosure of their supporting resources, while the analyses themselves often can be very large scale and involve multiple processing steps separated in time. Evidence for the correctness of any analysis should include not only a textual description, but also a formal record of the computations which produced the result, including accessible data and software with runtime parameters, environment, and personnel involved. This article describes FAIRSCAPE, a reusable computational framework, enabling simplified access to modern scalable cloud-based components. FAIRSCAPE fully implements the FAIR data principles and extends them to provide fully FAIR Evidence, including machine-interpretable provenance of datasets, software and computations, as metadata for all computed results. The FAIRSCAPE microservices framework creates a complete Evidence Graph for every computational result, including persistent identifiers with metadata, resolvable to the software, computations, and datasets used in the computation; and stores a URI to the root of the graph in the result’s metadata. An ontology for Evidence Graphs, EVI (https://w3id.org/EVI), supports inferential reasoning over the evidence. FAIRSCAPE can run nested or disjoint workflows and preserves provenance across them. It can run Apache Spark jobs, scripts, workflows, or user-supplied containers. All objects are assigned persistent IDs, including software. All results are annotated with FAIR metadata using the evidence graph model for access, validation, reproducibility, and re-use of archived data and software.

A modified proximal point algorithm involving nearly asymptotically quasi-nonexpansive mappings

In this paper, we propose a modified proximal point algorithm based on the Thakur iteration process to approximate the common element of the set of solutions of convex minimization problems and the fixed points of two nearly asymptotically quasi-nonexpansive mappings in the framework of $\operatorname{CAT}(0)$ CAT ( 0 ) spaces. We also prove the Δ-convergence of the proposed algorithm. We also provide an application and numerical result based on our proposed algorithm as well as the computational result by comparing our modified iteration with previously known Sahu’s modified iteration.

Theoretical Studies of Au3+/0/- Clusters Using Density Funtional Theory

In this study, the PW91PW91 method with LANL2DZ level was carried out to settle the dispute about the most stable structure of Au3+/0/-. Molecular orbital analyses and Walsh diagram were adopted to rationalize our computational result about the ground state geometry of Au3+/0/-. Our results show that the most stable geometry of Au3 is bent structure (C2v) with bond angle 146.0°. The less stable structure is equilateral triangle structure (D3h) with relative energies of 1.74 eV. The D3h structure possesses multiplicity 4 while the C2v structure 2. In addition, the most stable geometry of Au3+ and Au3- are equilateral triangle structure (D3h) and linear structure (D∞h), respectively. The preference of geometric change can be rationalized simply by using Walsh diagram. Besides, the linear structure of Au3 is found to be transition states (TS) of inversion of B-Au3. The inversion barrier is estimated to be 0.04 eV.

Development of Ex-Vessel Phenomena Analysis Model for Multi-Scenario Simulation System, SPECTRA

The simulation system named SPECTRA for a severe accident in sodium-cooled fast reactors has been developed. The SPECTRA computes in- and ex-vessel phenomena and evaluates various scenarios during the severe accident. This paper provides a newly developed computational models for the ex-vessel phenomena including gas and aerosol transport, sodium-concrete interaction, and sodium fire as a part of the SPECTRA. The base module computing thermal hydraulics behavior by a lumped mass model was verified through the analysis of a 2-cells ventilation problem. The computational result of the SPECTRA agreed with the theoretical solutions both in the case with and without temperature change. The sodium-concrete interaction model was verified through code to code comparison. The computational result showed that ablation of a concrete surface started after surface temperature reached to a certain value. The computed ablation depth almost completely agreed with the result by the CONTAIN-LMR code. The ex-vessel module was applied to the computation assuming sodium leak from a reactor vessel and a primary cooling loop. This computation demonstrated increase of temperature and pressure due to sodium-concrete interaction and sodium fire.

Flower Pollination Algorithm (FPA) to Solve Quadratic Assignment Problem (QAP)

The purpose of this paper is to solve Quadratic Assignment Problem using Flower Pollination Algorithm. Quadratic Assignment Problem discuss about assignment of facilities to locations in order to minimize the total assignment costs where each facility assigns only to one location and each location is assigned by only one facility. Flower pollination Algorithm is an algorithm inspired by the process of flower pollination. There are two main steps in this algorithm, global pollination and local pollination controlled by switch probability. The program was created using Java programming language and implemented into three cases based on its size: small, medium and large. The computation process obtained the objective function value for each data using various values of parameter. According to the pattern of the computational result, it can be concluded that a high value of maximum iteration of the algorithm can help to gain better solution for this problem.

Validasi Model Turbulensi pada Simulasi Numerik Menggunakan Software Fluent dengan Sayap Onera M6

Numerical simulation using Computational Fluid Dynamics (CFD) method is one way of predicting airflow characteristics on the model. This method is widely used because it is relatively inexpensive and faster in getting desired results compared with performing direct testing. The correctness of a computational simulation output is highly dependent on the input and how it was processed. In this paper, simulation is done on Onera M6 Wing, to investigate the effect of a turbulence model’s application on the accuracy of the computational result. The choice of Onera M6 Wing as a simulation’s model is due to its extensive database of testing results from various wind tunnels in the world. Among Turbulence models used are Spalart-Allmaras, K-Epsilon, K-Omega, and SST.Keywords: CFD, fluent, Model, Turbulence, Onera M6, Spalart-Allmaras, K-Epsilon, K-Omega, SST.AbstraksSimulasi numerik dengan menggunakan metode Computational Fluid Dynamics (CFD) merupakan salah satu cara untuk memprediksi karakteristik suatu aliran udara yang terjadi pada model. Metode ini banyak digunakan karena sifatnya yang relatif murah dan cepat untuk mendapatkan hasil dibandingkan dengan melakukan pengujian langsung. Benar tidak hasil sebuah simulasi komputasi sangat tergantung pada inputan yang diberikan serta cara memproses data inputan tersebut. Pada tulisan ini dilakukan simulasi dengan menggunakan sayap onera M6 dengan tujuan untuk mengetahui pengaruh penggunaan model turbulensi terhadap keakuratan hasil komputasi. Pilihan sayap onera M6 sebagai model simulasi dikarenakan model tersebut sudah memiliki database hasil pengujian yang cukup lengkap dan sudah divalidasi dari berbagai terowongan angin di dunia. Model turbulensi yang digunakan diantaranya Spalart-Allmaras, K-Epsilon, K-Omega dan SST.Kata Kunci : CFD, fluent, Model, Turbulensi, Onera M6, Spalart-Allmaras, K-Epsilon, K-Omega, SST.

An Algorithm to Manage Transportation Logistics That Considers Sabotage Risk

This paper presents an algorithm to solve the multilevel location–allocation problem when sabotage risk is considered (MLLAP-SB). Sabotage risk is the risk that a deliberate act of sabotage will happen in a living area or during the transportation of a vehicle. This can change the way decisions are made about the transportation problem when it is considered. The mathematical model of the MLLAP-SB is first presented and solved to optimality by using Lingo v. 11 optimization software, but it can solve only small numbers of test instances. Second, two heuristics are presented to solve large numbers of test instances that Lingo cannot solve to optimality within a reasonable time. The original differential evolution (DE) algorithm and the extended version of DE—the modified differential evolution (MDE) algorithm—are presented to solve the MLLAP-SB. From the computational result, when solving small numbers of test instances in which Lingo is able to find the optimality, DE and MDE are able to find a 100% optimal solution while requiring much lower computational time. Lingo uses an average 96,156.67 s to solve the problem, while DE and MDE use only 104 and 90 s, respectively. Solving large numbers of test instances where Lingo cannot solve the problem, MDE outperformed DE, as it found a 100% better solution than DE. MDE has an average 0.404% lower cost than DE when using a computational time of 90 min. The difference in cost between MDE and DE changes from 0.08% when using 10 min to 0.54% when using 100 min computational time. The computational result also explicitly shows that when sabotage risk is integrated into the method of solving the problem, it can reduce the average total cost from 32,772,361 baht to 30,652,360 baht, corresponding to a 9.61% reduction.