Takahiro Kenmotsu

Structural Change of DNA Induced by Nucleoid Proteins: Growth Phase-Specific Fis and Stationary Phase-Specific Dps

The effects of nucleoid proteins Fis and Dps of Escherichia coli on the higher order structure of a giant DNA were studied, in which Fis and Dps are known to be expressed mainly in the exponential growth phase and stationary phase, respectively. Fis causes loose shrinking of the higher order structure of a genome-sized DNA, T4 DNA (166 kbp), in a cooperative manner, that is, the DNA conformational transition proceeds through the appearance of a bimodal size distribution or the coexistence of elongated coil and shrunken globular states. The effective volume of the loosely shrunken state induced by Fis is 30-60 times larger than that of the compact state induced by spermidine, suggesting that cellular enzymes can access for DNA with the shrunken state but cannot for the compact state. Interestingly, Dps tends to inhibit the Fis-induced shrinkage of DNA, but promotes DNA compaction in the presence of spermidine. These characteristic effects of nucleotide proteins on a giant DNA are discussed by adopting a simple theoretical model with a mean-field approximation.

Hybrid simulation between molecular dynamics and binary collision approximation codes for hydrogen injection into carbon materials

Abstract Molecular dynamics (MD) simulation with modified Brenner’s reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, the size of MD simulation box is generally set less than several nm because of the limits of a computer performance. To extend the size of the MD simulation, we develop a hybrid simulation code between MD code using REBO potential and binary collision approximation (BCA) code. Using the BCA code instead of computing all particles with a high kinetic energy for every step in the MD simulation, considerable computation time is saved. By demonstrating a hydrogen atom injection into a graphite by the hybrid simulation code, it is found that the hybrid simulation code works efficiently in a large simulation box.

Modeling of wall recycling effects on the global particle balance in magnetic fusion devices

A zero-dimensional particle balance model has been developed to compute hydrogen inventories in the four major reservoirs; core plasma, scraped-off layer (SOL), gas region, and wall of a magnetic fusion reactor system. This model takes as input separately calculated hydrogen reemission and reflection coefficients. Model applications have successfully reproduced the core plasma transient behavior with and without density decay observed in the large helical device (LHD). Particle balance modeling has also been done for a hypothetical steady-state reactor employing carbon as the plasma-facing material. Results indicate that codeposition-induced wall pumping is quite effective in controlling the core density although, on the other hand, the tritium inventory concerns environmental safety.

Erosion of accel grids of ion engine due to sputtering

The erosion rates of extraction electrodes of ion sources due to ion beam irradiation are largely affected by amount of projectiles retained in the electrodes. A Monte Carlo simulation code ACAT has been used to calculate sputtering yields and reflection coefficients by simulating the accumulation effect of projectiles in a target material. The results for Xe projectiles-C target combination have indicated that both sputtering yields and reflection coefficients are largely enhanced by Xe retention, particularly at larger incident angle for the surface normal with low incident energy.

Effects of roughness and temperature on low-energy hydrogen positive and negative ion reflection from silicon and carbon surfaces

Angle-resolved energy distribution functions of positive and negative hydrogen ions produced from a rough-finished Si surface under 1 keV proton irradiation have been measured. The corresponding distribution from a crystalline surface and a carbon surface are also measured for comparison. Intensities of positive and negative ions from the rough-finished Si are substantially smaller than those from crystalline Si. The angular distributions of these species are broader for rough surface than the crystalline surface. No significant temperature dependence for positive and negative ion intensities is observed for all samples in the temperature range from 300 to 400 K.

Effect of low-frequency ultrasound on double-strand breaks in giant DNA molecules

Double-strand breaks in giant DNA molecules caused by continuous ultrasound at a frequency of 30 kHz were quantified using single-molecule observations. The effect of the sound pressure was investigated by placing a tube containing DNA solution under an anti-node of the acoustic standing wave. Almost no breaks occurred below the threshold sound pressure. Above this threshold, the probability of strand breaks increased linearly with sound pressure. Acoustic cavitation detected with a hydrophone strongly suggests that the main mechanism of the DNA strand break is via cavitation generated by the ultrasound.

Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms

We performed monomolecular observations on linear and circular giant DNAs (208 kbp) in an aqueous solution by the use of fluorescence microscopy. The results showed that the degree of conformational fluctuation in circular DNA was ca. 40% less than that in linear DNA, although the long-axis length of circular DNA was only 10% smaller than that of linear DNA. Additionally, the relaxation time of a circular chain was shorter than that of a linear chain by at least one order of magnitude. The essential features of this marked difference between linear and circular DNAs were reproduced by numerical simulations on a ribbon-like macromolecule as a coarse-grained model of a long semiflexible, double-helical DNA molecule. In addition, we calculated the radius of gyration of an interacting chain in a circular form on the basis of the mean field model, which provides a better understanding of the present experimental trend than a traditional theoretical equation.

Dynamical simulation of surface compositional changes in ni–cu alloys during high-temperature ion sputtering

Abstract Using the ACAT–DIFFUSE code, we tried to follow Lams experimental compositional changes near the surface of Ni-40 at% Cu alloys at various temperatures (25–550°C), where the experiments were performed with a normally incident beam of 3 keV Ne+ ions. The ACAT–DIFFUSE code include both kinetic processes and thermal processes which take place during ion bombardment. If we assume that the segregation energy is a decreasing function of ion-fluence, the experimental ion-fluence dependence of the Cu/Ni ratios at the first layer can be reproduced by the ACAT–DIFFUSE code. The simulated depth profiles at the steady state are in good agreement with the measured depth profiles for T ≤ 300°C. The contribution of atoms at the second layer to the sputtered flux is much less than Lams value even at high temperature.

Divalent cation shrinks DNA but inhibits its compaction with trivalent cation

Our observation reveals the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA 166 kbp) by fluorescence microscopy. It was found that divalent cations, Mg(2+) and Ca(2+), inhibit DNA compaction induced by a trivalent cation, spermidine (SPD(3+)). On the other hand, in the absence of SPD(3+), divalent cations cause the shrinkage of DNA. As the control experiment, we have confirmed the minimum effect of monovalent cation, Na(+) on the DNA higher-order structure. We interpret the competition between 2+ and 3+ cations in terms of the change in the translational entropy of the counterions. For the compaction with SPD(3+), we consider the increase in translational entropy due to the ion-exchange of the intrinsic monovalent cations condensing on a highly charged polyelectrolyte, double-stranded DNA, by the 3+ cations. In contrast, the presence of 2+ cation decreases the gain of entropy contribution by the ion-exchange between monovalent and 3+ ions.

Low-energy particle interaction with plasma-irradiated metal surfaces

In fusion experiments, plasma erodes walls of devices containing various elements including carbon. The eroded carbon penetrates into edge plasma and is transported backwards forming the carbon-adsorbed layers on the surfaces of components like mirrors for optical plasma diagnostics. To characterize the carbon-adsorbed layers by measuring energy distribution of particles reflected from the surface, we have used the experimental setup equipped with a magnetic deflection momentum analyzer and the time-of-flight energy analyzer of neutrals. Ion beams in the energy range 1–2 keV irradiated the samples of Mo and W with carbon deposition on them that were prepared in separate plasma chambers. The beams produced ions and neutrals with characteristic emission angle and energy distribution depending upon conditions of the sample surfaces. Experimental results are compared with the numerical calculation model ACAT (Atomic Collisions in Amorphous Targets) and the evaluations on how the structure of deposition layers may affect the particle reflection on solid surfaces were made.