Total Simulation System Research Articles

A LA-BTC MOF as a sensor element of an electronic nose for selective adsorption of biomarkers of diseases: Molecular dynamics simulations of adsorption

The advanced non-invasive diagnostic method is an analysis of exhaled volatile organic compounds (VOCs), which are regarded as biomarkers of various diseases. A gravimetric-type electronic nose (e-nose) has shown great promise in exhaled VOC-pattern identification, and its efficiency is determined by the adsorption capacity of the sensing materials towards a specific VOC. The present study employed molecular dynamics (MD) calculations with the OPLS all-atom force field to investigate the adsorption of an isolated molecule of volatile fatty acids, acetone, ethanol, methanol, acetic aldehyde, neopentane, and ethane in a unit cell of the lanthanum-based metal-organic framework (La-BTC MOF), which was proposed as a potential sensing material for the gravimetric-type e-nose. The adsorption potential determined as a change in the potential energy, ΔEp, of the total simulation system upon the penetration of a single molecule into a unit pore of La-BTC MOF was calculated for all the targeted VOCs and water to be 1.56–10.78 kJ·mol−1, following the order: ethane < neopentane < acetic aldehyde < ethanol < methanol < water < acetone < butanoic acid < caproic acid. Therefore, the biomarkers with ΔEp > ΔEp(water) ∼ 7.3 kJ/mol can be captured from the exhaled breath. According to the MD calculations, an oxygen-containing biomarker molecule in the adsorbed state was oriented by its oxygen atom towards the La3+ cation, so that the O---La3+ distance of 0.28–0.32 nm was the shortest among those for other constituent atoms. Thus, the strong electrostatic interactions between the oxygen atoms of the adsorbate molecules and the La3+ cation of the adsorbent were most responsible for the capture of the oxygen-containing biomarkers by the La-BTC MOF. The competing adsorption effect between water and oxygen-containing biomarker molecules was examined in dependence on the water content and the way the water molecules were introduced into the simulation system.

An innovative magnetic state generator using machine learning techniques

We propose a new efficient algorithm to simulate magnetic structures numerically. It contains a generative model using a complex-valued neural network to generate k-space information. The output information is hermitized and transformed into real-space spin configurations through an inverse fast Fourier transform. The Adam version of stochastic gradient descent is used to minimize the magnetic energy, which is the cost of our algorithm. The algorithm provides the proper ground spin configurations with outstanding performance. In model cases, the algorithm was successfully applied to solve the spin configurations of magnetic chiral structures. The results also showed that a magnetic long-range order could be obtained regardless of the total simulation system size.

Simulation on progressive collapse behaviour of whole ship model under extreme waves using idealized structural unit method

To ensure the safety of navigating ship, working loads and structural load-carrying capacity are two important aspects. In the present paper, a total simulation system combing load calculation and structural collapse analysis is applied to simulate progressive collapse behaviour of a single-hull Kamsarmax type bulk carrier. A three dimensional singularity distribution method is adopted to calculate pressure distribution with time history. A mixed structural model, collapse part simulated by ISUM elements and remaining part by elastic FEM elements with relative coarse mesh, is proposed for collapse analysis. Progressive collapse behaviour obtained by ISUM is good agreement with that by nonlinear software package, MARC. However, the calculation time of ISUM analysis is about 1/70 of MARC analysis. The applicability to structure system, high accuracy and sufficient efficiency of ISUM had been demonstrated.

Modeling and Simulation of Sensorless Control of BLDC Motor Based on Submersible Pump

In this paper, modeling selects sensorless control of permanent magnet brushless DC motor in terms of work condition of submersible pump under water. Motor reduced by Hall sensor so that maintenance. Motor was controlled by state space and back EMF zero-crossing in Matlab/Simulink, and constitute total simulation system along with the other modules. Eventually, motor character was estimated in accordance with waveforms of simulation, which offers foundation for the design of actual motor control system.

Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct.

The three-dimensional solution structure of two DNA decamers of sequence d(CCACXGGAAC)-(GTTCCGGTGG) with a modified nucleotide containing a cholesterol derivative (X) in its C1 '(chol)alpha or C1 '(chol)beta diastereoisomer form has been determined by using NMR and restrained molecular dynamics. This DNA derivative is recognized with high efficiency by the UvrB protein, which is part of the bacterial nucleotide excision repair, and the alpha anomer is repaired more efficiently than the beta one. The structures of the two decamers have been determined from accurate distance constraints obtained from a complete relaxation matrix analysis of the NOE intensities and torsion angle constraints derived from J-coupling constants. The structures have been refined with molecular dynamics methods, including explicit solvent and applying the particle mesh Ewald method to properly evaluate the long range electrostatic interactions. These calculations converge to well defined structures whose conformation is intermediate between the A- and B-DNA families as judged by the root mean square deviation but with sugar puckerings and groove shapes corresponding to a distorted B-conformation. Both duplex adducts exhibit intercalation of the cholesterol group from the major groove of the helix and displacement of the guanine base opposite the modified nucleotide. Based on these structures and molecular dynamics calculations, we propose a tentative model for the recognition of damaged DNA substrates by the UvrB protein.