KEYWORDS: Nanopores, Particles, Monte Carlo methods, Molecules, Temperature metrology, Computer simulations, Temperature distribution, Atmospheric particles, Quantum numbers, Thin films
A deep understanding of the spatiotemporal distribution characteristics of material molecules, emitted from nanopores, near the top surface of nanoporous thin films has practical application value for the preparing biomedical optical sensing films and nano-photonic sensors, delivering and screening of drug molecules, and so on. In this study, the direct simulation Monte Carlo method as employed to investigate the velocity and amount distribution pattern of particles emitted from a nanopore (multi-nanopores) with 80 nm diameter and 1 μm depth at various initial temperatures (T=300 K, 400 K, and 500 K) near the top surface of a nanoporous structure film. Especially, the variation of particle number, temperature, and pressure over time in the regions of 500 nm and 1000 nm were analyzed, as well as the variation of temperature and pressure along the nanopore axis with the variation of Knudsen number. Additionally, the impact of more pores on particle number and temperature distribution over space and time was analyzed. The simulation results show a symmetric distribution of particle numbers, with lower temperatures in the axial region compared to the initial temperature, significant temperature changes on both sides, and a continuous decrease in pressure. The along-travel temperature reaches its maximum value at a distance of 4 μm from the center of the nanopore, with a subsequent decrease in temperature as the Knudsen number increases. These research results have new inspirations for gas sensing and enhancing optical sensing with nanoporous thin films, as well as designing functional optic material with micro-/nano- structures.
Bendamustine (BENDA) has both alkylating and purinergic antitumor activities and remains effective in some cancers that have developed drug resistance, and there are few studies on the interaction mechanism of BENDA with DNA. In this paper, the interaction mechanism between BENDA and calf thymus DNA (ctDNA) was systematically investigated at the single molecular level, mainly by using ultraviolet-visible spectroscopy (UV-vis), Confocal Raman spectroscopy, and molecular docking. In UV-vis absorption spectroscopy experiments, the effects of ctDNA solution concentration, temperature, time and Na+ ions on the spectral production were investigated, respectively, and the experimental results showed that the interaction mode between BENDA and ctDNA was external bonding, i.e., groove binding and electrostatic binding. In addition, the disappearance and shift of the corresponding characteristic peaks in the Raman peaks indicate that BENDA interacts mainly with the phosphate backbone and base G of the ctDNA molecule, and causes some shifts in other bases and deoxyribose. Molecular docking simulations show that BENDA binds in the minor groove region of DNA and that the N and O atoms in the BENDA structure form intermolecular hydrogen bonds with base G, respectively. The results of this paper help to understand the mechanism of action of anti-cancer drugs and provide some reference for the development of new drugs with less toxic side effects.
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