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Sharp bending and wrapping of DNA around proteins and nanoparticles (NPs) has been of extensive research interest. Here, we present the potential of mean force (PMF) for wrapping a DNA double helix around a cationic NP using coarse-grained models of a double-stranded DNA and a cationic NP. Starting from a NP wrapped around by DNA, the PMF was calculated along the distance between the center of the NP and one end of the DNA molecule. A relationship between the distance and the extent of DNA wrapping is used to calculate the PMF as a function of DNA wrapping around a NP. In particular, the PMF was compared for two DNA sequences of (AT)25/(AT)25 and (AC)25/(GT)25, for which the persistence lengths are different by ∼10 nm. The simulation results provide solid evidence of the thermodynamic preference for complex formation of a cationic NP with more flexible DNA over the less flexible DNA. Furthermore, we estimated the elastic energy of DNA bending, which was in good order-of-magnitude agreement with the theoretical prediction of elastic rods. This work suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnologies, in which the position and dynamics of NPs are regulated on large-scale DNA structures, or the structural transformation of DNA is triggered by the sequence-dependent binding of NPs.

PURPOSE: Leukocyte telomere length (LTL) is a potential indicator of cellular senescence. However, its relationship with the type and volume of regular exercise is unclear. Therefore, we investigated the effects of the type and volume of long-term regular exercise on the LTL in middle-aged men (N=109, mean age=44.7±4.1 years [range: 40-56 years]).METHODS: For all participants, the volume of physical activity (PA) was evaluated using a self-report questionnaire, and blood samples were collected simultaneously. We cross-sectionally examined the associations among the type and volume of PA, LTL, telomerase activity (TA), mitochondrial DNA copy number (mtDNA), and body composition in three groups: 1) bodybuilders (BBs) with at least 5 years of athletic experience (n=36, mean age: 42.3±3.3 years [40-51 years]), 2) cyclists (CCs) with an athletic career similar to that of the BBs (n=37, mean age: 45.4±4.4 years [range: 40-53 years]), and 3) healthy ordinary people (CON; n=36, mean age: 46.3±3.3 years [range: 40-56 years]).RESULTS: The LTL showed a significant positive correlation with the volume of PA (r=.285, p=.003), regardless of the type of PA. Furthermore, the LTLs were longer in the BB (p=.007) and CC (p=.003) groups (who performed moderate-to-vigorous PA for 150 minutes or more per week) than in the CON group. Conversely, the TA was significantly higher in the BB group (p=.009) than in the CON group; however, it only tended to be high in the CC group (p=.115). There were no intergroup differences in both the mtDNA (p=.127) and 8-hydroxydeoxyguanosine (p=.289) levels.CONCLUSIONS: The TA was found to increase, and thus prevent telomere loss, in middle-aged men who performed PA of moderateto-vigorous intensity, regardless of the PA type.

PURPOSE: This study aimed to investigate the effect of turmeric intake alone or in combination with resistance training on liver enzymes in adult men who regularly consumed alcohol at least twice a week.METHODS: Twelve men (age: 36.0±5.26 years, weight: 99.9±17.9 kg, and height: 184.0±6.5 cm) were randomly assigned to the turmeric intake (2-3 g/day) alone (TI, n=6) group or the TI plus resistance training (60 minutes of RT 3 times a week) (TI+RT, n=6) group for 8 weeks. Blood was collected before and after 8 weeks of treatment. The analyzed variables included glutamic oxaloacetic transaminase (GOT), glutamic pyruvic transaminase (GPT), γ-glutamyl transferase (γ-GTP), and GOT/GPT ratio.RESULTS:There was no significant interaction effect in all variables, but the main effect was found in all variables only in TI+RT group. The Cohen’s d effect size on the main effects of the TI+RT group on GOT (d=0.548), GPT (d=0.835), γ-GTP (d=0.623), and GOT/GPT ratio (d=0.800) ranged from 0.548-0.835, respectively. However, body composition such as percent body fat (%, p>.05) and muscle mass (kg, p>.05) did not show the main effect on time points as well as the interaction effect (p>.05).CONCLUSIONS:Although the 8-week TI treatment did not show any statistically significant change, TI treatment showed a tendency to decrease in GOT, GPT, and γ-GTP, and the GOT/GPT ratio tends to increase. Therefore, there was a synergic effect of the TI plus RT treatment or the sum of the two treatments for 8 weeks.

Small vessels operating in coastal waters are susceptible to propeller failure because of the entanglement of marine debris. Secondary accidents such as the injury of divers may also occur when removing entangling material. Rope cutters are devices used to prevent marine litter from entangling the propeller of small ships. However, installing rope cutters on propeller shafts might affect the working of the propeller. In this study, three-dimensional simulations were performed to investigate the effect of a rope cutter on flow characteristics behind the propeller. The Computational fluid dynamics (CFD) models were validated by particle image velocimetry (PIV) experiments performed in a rope cutter performance testing tank. The study results showed that the installation of a rope cutter on the propeller shaft led to an insignificant reduction in water flow velocity magnitude behind the propeller. Additionally, the effects of the rope cutter on the reductions of thrust (0.87%) and torque (0.76%) of the propeller were also negligible. However, it is very interesting to note that rope cutter installation resulted in a lower vortex formation, leading to a significant reduction in the turbulence intensity behind the propeller by 27.12%, 37.50%, and 47.29% at 100, 150, and 200 rpm propeller speed, respectively. Based on the study results, it can be concluded that rope cutters help to reduce propeller entanglements without significantly affecting the propeller’s working.

Brownian motion subject to a periodic and asymmetric potential can be biased by external, nonequilibrium fluctuations, leading to directional movement of Brownian particles. Sequence-dependent flexibility variation along double-stranded DNA has been proposed as a tool to develop periodic and asymmetric potentials for DNA binding of cationic nanoparticles with sizes below tens of nanometers. Here, we propose that repetitive stretching and relaxation of a long, double-stranded DNA molecule with periodic flexibility gradient can induce nonequilibrium fluctuations that tune the amplitude of asymmetric potentials for DNA-nanoparticle binding to result in directional transport of nanometer-sized particles along DNA. Realization of the proposed Brownian ratchet was proven by Brownian dynamics simulations of coarse-grained models of a single, long DNA molecule with flexibility variation and a cationic nanoparticle.

In this study, a new method has been applied to monitor the low energy phosphorus ion implantation process in dynamic random access memory production line using spectroscopic ellipsometry (SE). The dose sensing ability of SE is similar level to that of wavelength dispersive x-ray fluorescence (XRF) and the energy sensing ability is almost twice stronger than that of XRF. The coefficients of determination of SE have been confirmed that they are higher than 95% both for the implantation dose and implantation energy as variables. In the case of XRF measurement, the photoresist (PR) should be removed by ashing and strip processes before measuring the phosphorus concentration to avoid chamber contamination in high vacuum. However, there is free of contamination issue for SE in the presence of PR, so the phosphorus concentration can be monitored by SE immediately after the ion implantation. Consequently, the qualification time can be reduced at least as much as waiting and running time of the ashing and the strip processes. It is worth to note that the measuring speed of SE is 33 times faster than that of XRF. Considering the advantage of fast SE measurement speed, the number of measurement points was increased from 5 to 21 including 8 points of wafer edge to enhance monitoring of product quality. In this work, the qualification time has been reduced effectively by 39.2% in average in production lines by using SE technology.

Looping of double-stranded DNA molecules with 100-200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a minicircle with a diameter of several to ten nanometers occurs with alterations in the DNA helical structure and may lead to defective kink formation that hampers the use of DNA minicircles, catenanes, and rotaxanes in nanoscale DNA applications. Here, we investigated local variations of a helical twist in sharply bent DNA using microsecond-long all-atom molecular dynamics simulations of six different DNA minicircles, focusing on the sequence dependence of the coupling between DNA bending and its helical twist. Twist angles between consecutive base pairs were analyzed at different locations relative to the direction of DNA bending and, among 10 unique dinucleotide steps, we identified four dinucleotide steps with strong twist-bend coupling, the pyrimidine-purine dinucleotide steps of TA/TA, CG/CG, and CA/TG and the purine-purine dinucleotide step of GA/TC. This work suggests the sequence-dependent structural responses of DNA to strong mechanical deformation, providing new molecular-level insights into the structure and stability of sharply bent DNA minicircles for nanoscale applications.

A numerical study was carried out to investigate the effects of methane (CH4), ethane (C2H6), propane (C3H8), butane (C4H10), and dimethyl ether (DME) on the combustion and emission characteristics of a four-stroke gas-diesel dual-fuel (DF) marine engine at full load. Three-dimensional simulations of the combustion process and emission formation inside the engine cylinder in the diesel and DF modes were performed using the AVL FIRE R2018a simulation software to analyze the in-cylinder pressure, temperature, and emission characteristics. The simulation results agreed well with the measured values reported in the engine shop test technical data. The simulation results showed reductions in the in-cylinder peak pressure and temperatures, as well as the emission formations, in the DF modes in comparison to the diesel mode. The DF mode could significantly reduce nitric oxide (NO) emissions (up to 96.225%) of DME compared to the diesel mode. Meanwhile, C3H8 and CH4 fuels effectively reduced the soot (up to 82.78%) and carbon dioxide (CO2) emissions (by 21.33%), respectively, compared to the diesel mode. However, the results also showed longer ignition delay times of the combustion processes when the engine operated in the DF mode, particularly in the DME-diesel mode. The combustion and emission characteristics of the engine were also analyzed when varying the injection timing, the results showed that applying the injection timing adjustment method could further address NO emission problems but led to a decrease in the engine power. Therefore, it is necessary to consider the benefits and disadvantages of adopting the injection timing adjustment strategy to address certain engine emission problems. This study successfully analyzed the benefits of using various gas fuels as alternative fuels and the injection timing adjustment method in DF marine engines to meet the International Maritime Organization (IMO) emission regulations without the use of any emission after-treatment devices.

The remarkable electronic and mechanical properties of nanowires have great potential for fascinating applications; however, the difficulties of assembling ordered arrays of aligned nanowires over large areas prevent their integration into many practical devices. In this paper, we show that aligned VO2 nanowires form spontaneously after heating a thin V2O5 film on a grooved SiO2 surface. Nanowires grow after complete dewetting of the film, after which there is the formation of supercooled nanodroplets and subsequent Ostwald ripening and coalescence. We investigate the growth mechanism using molecular dynamics simulations of spherical Lennard-Jones particles, and the simulations help explain how the grooved surface produces aligned nanowires. Using this simple synthesis approach, we produce self-aligned, millimeter-long nanowire arrays with uniform metal-insulator transition properties; after their transfer to a polymer substrate, the nanowires act as a highly sensitive array of strain sensors with a very fast response time of several tens of milliseconds.

This experimental study was aimed at identifying the near-flammable limit and the unstretched flame speed of outwardly propagating spherical flames according to changes in the mole fraction of oxygen in the oxidizer ( R O ) and mole fraction of R245fa in the fuel ( R R ) for R245fa/CH4/O2/N2 mixtures in a constant volume combustion chamber. The flames observed according to changes in R O and R R of the R245fa mixtures could be divided into three regimes, with typical, transition, and buoyancy-induced behaviors. These representative flame behaviors were similar to those observed in previously reported experiments on R134a mixtures. The R245fa mixtures particularly showed a more expanded near-flammable limit than R134a. The rising velocity U r and the rising length L r in the buoyancy-induced regime with the near-flammable limit were used to identify the buoyancy effect on the flame that rose and propagated outward under normal gravity conditions. In addition, as the slope of the linear relationship between the stretch rates ( k ) and stretched flame speeds ( S d ), the Markstein length ( L b ) of the R245fa mixture tended to be positive in the typical regime and negative in the transition and buoyancy-induced regimes. Such characteristics are similar to those of R134a. However, in the typical regime, the results from a regression analysis on the unstretched flame speeds ( S u ) derived from the same linear relationship showed that the flame inhibition effect from mixing R245fa was smaller than that of R134a.

To reduce the stochastic defect caused by insufficient photon numbers of extreme ultraviolet lithography, a simple additional process has been designed and experimented. The additional process consists of one coating and washing process after pattern formation by lithography. The coating material was named stochastic defect removal coating and was carefully designed to reduce the stochastic defects without harming the lithographic margin. The defect reduction up to 48% was accomplished by failure-free latitude measurement and defect inspection.

We present extensive molecular dynamics simulations of a cationic nanoparticle and a double-stranded DNA molecule to discuss the effect of DNA flexibility on the complex formation of a cationic nanoparticle with double-stranded DNA. Martini coarse-grained models were employed to describe double-stranded DNA molecules with two different flexibilities and cationic nanoparticles with three different electric charges. As the electric charge of a cationic nanoparticle increases, the degree of DNA bending increases, eventually leading to the wrapping of DNA around the nanoparticle at high electric charges. However, a small increase in the persistence length of DNA by 10 nm requires a cationic nanoparticle with a markedly increased electric charge to bend and wrap DNA around. Thus, a more flexible DNA molecule bends and wraps around a cationic nanoparticle with an intermediate electric charge, whereas a less flexible DNA molecule binds to a nanoparticle with the same electric charge without notable bending. This work provides solid evidence that a small difference in DNA flexibility (as small as 10 nm in persistence length) has a substantial influence on the complex formation of DNA with proteins from a biological perspective and suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnology as a new tool to manipulate the structure of DNA molecules mediated by nanoparticle binding.

A numerical study was carried out to investigate the effects of injector spray angle (SA) and injection position (IP) on the combustion and emission characteristics of a two-stroke ME-GI marine engine at full load. Three-dimensional (3D) simulations of the combustion process and emission formations inside the cylinder of the engine operating in the diesel and DF modes were performed using the ANSYS Fluent simulation software to analyze the in-cylinder pressure, temperature, and emission characteristics. The simulation results were compared and showed good agreement with the experimental results reported in the engine’s shop test technical data. The simulation results showed that the IP of 0.02 m with an SA of 40 degrees helps to enhance the engine performance; however, if the main target is reducing engine exhaust gas emissions, an IP of 0.01 m is highly recommended to be used. At this IP, the specific SA of 40, 45, or 50 degrees that should be used will depend on which emissions (NO, soot, CO2, etc.) need to be reduced. This study successfully investigated the effects of injector SA and IP on the combustion and emission characteristics of the researched engine and would be a good reference for engine design and operating engineers.

We investigate the dopant trap level and equilibrium concentration of Si(110)/a-SiO 2 2 interface with a wide variety of dopants (B, C, N, Br, Cl, F and H). The electronic and atomic properties of intrinsic and extrinsic defects are analyzed using First-principles calculation. It is shown that the average trap levels for hole and electron deepen as the electronegativity of the dopant increases. Also, we applied a simple thermodynamic model to evaluate the equilibrium concentration of active trap as a function of dopant concentration at the interface. From the model it turns out that H and F completely passivate the intrinsic Pb center of Si and reduce the trap concentration, while other elements, especially N, Br and Cl, induces new trap states which amounts to several times more than the pre-existing Pb center.

We report Brownian dynamics simulations of tracer diffusion in regularly crosslinked polymer networks in order to elucidate the transport of a tracer particle in polymer networks. The average mesh size of homogeneous polymer networks is varied by assuming different degrees of crosslinking or swelling, and the size of a tracer particle is comparable to the average mesh size. Simulation results show subdiffusion of a tracer particle at intermediate time scales and normal diffusion at long times. In particular, the duration of subdiffusion is significantly prolonged as the average mesh size decreases with increasing degree of crosslinking, for which long-time diffusion occurs via the hopping processes of a tracer particle after undergoing rattling motions within a cage of the network mesh for an extended period of time. On the other hand, the cage dynamics and hopping process are less pronounced as the mesh size decreases with increasing polymer volume fractions. The interpretation is provided in terms of fluctuations in network mesh size: at higher polymer volume fractions, the network fluctuations are large enough to allow for collective, structural changes of network meshes, so that a tracer particle can escape from the cage, whereas, at lower volume fractions, the fluctuations are so small that a tracer particle remains trapped within the cage for a significant period of time before making infrequent jumps out of the cage. This work suggests that fluctuation in mesh size, as well as average mesh size itself, plays an important role in determining the dynamics of molecules and nanoparticles that are embedded in tightly meshed polymer networks.

Additional file 1: Supplementary Figure S1. The frequency distribution histograms of the diameter class (top) and biomass class (bottom) measured in the tree communities in the Albongbunji Basin over a period of 11 years.

Additional file 2: Plate 1. The survey plot was installed in Albongbunji Basin, Ulleungdo, taken in 2019 (left). This young beech forest (approximately 60 years old) is in the stem exclusion stage of forest development. Broken stems of the canopy species Prunus takesimensis (Ulleungdo cherry, endemic species) and Acer pictum var. mono originated from gap events induced by stochastic disturbances (wind and mechanical damage), which were observed at an earlier stage than in traditional development models. The forest floor of the survey plot is continuously changing in terms of micro-level geomorphology due to soil deposition caused by heavy rains. In part of the survey plot, soil deposition has been taking place since 2016 (right). The red arrow on the picture is the spot where the number tag was attached at the breast height (120 cm) in 2009.

DNA is a very long polymeric molecule that governs the genetic processes in cells, and its structural regulation is critical to their functions. In addition, several uses of DNA as a novel material...