publications
2023
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Counting Distinguishable RNA Secondary StructuresNakajima, Masaru, and Smith, Andrew DJournal of Computational Biology 2023
RNA secondary structures are essential abstractions for understanding spacial folding behaviors of those macromolecules. Many secondary structure algorithms involve a common dynamic programming setup to exploit the property that secondary structures can be decomposed into substructures. Dirks et al. noted that this setup cannot directly address an issue of distinguishability among secondary structures, which arises for classes of sequences that admit nontrivial symmetry. Circular sequences are among these. We examine the problem of counting distinguishable secondary structures. Drawing from elementary results in group theory, we identify useful subsets of secondary structures. We then extend an algorithm due to Hofacker et al. for computing the sizes of these subsets. This yields a cubic-time algorithm to count distinguishable structures compatible with a given circular sequence. Furthermore, this general approach may be used to solve similar problems for which the RNA structures of interest involve symmetries.
2022
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Development of an interactive code for quick data analyses between STOR-M tokamak experimental plasma dischargesNakajima, Masaru, Basu, Debjyoti, Melnikov, Alexander V, McColl, David, and Xiao, ChijinSymmetry 2022
Saskatchewan Torus-Modified (STOR-M) is a small tokamak, well known for various fusion-related basic experimental studies such as edge turbulent heating, different instabilities, Alternating Current (AC) tokamak operation, Ohmic H-mode triggering by the electrode biasing, fueling and momentum injection by Compact Torus (CT) injection, and the effects of Resonance Magnetic Perturbations (RMPs), among others. Some of those experiments require real-time visualization of magnetic surface reconstructions either through EFIT or quick analyses and visualization of experimental data during experiments. Recently, experimental studies of Geodesic Acoustic Mode (GAM) and zonal flows were performed in the STOR-M tokamak. The GAM experiments strongly require the collection of fluctuation data from different Langmuir probes installed at different poloidal locations, but on the same magnetic surfaces. This is requires the adjustment of radial locations between discharges. It is therefore important to analyze and visualize the features of all probe data quickly during discharges. For this purpose, a Python code was developed and used for quick analysis of the data. This article describes the development of the code using Python and its use in detail.
2021
2020
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Application of high frequency biasing and its effect in STOR-M tokamakBasu, Debjyoti, Nakajima, Masaru, Melnikov, AV, Martinell, Julio J, McColl, David, Singh, Raj, Xiao, Chijin, and Hirose, AkiraNuclear Fusion 2020
A pulsed oscillating power amplifier has been developed to apply high frequency biasing voltage to an electrode at the edge of the STOR-M tokamak plasma. The power amplifier can deliver a peak-to-peak oscillating voltage ±60 V and current 30 A within the frequency range 1 kHz–50 kHz. The electrode is located in the equatorial plane at radius ρ= 0.88. The frequency of the applied voltage has been varied between discharges. It is observed that the plasma density and soft x-ray intensity from the plasma core region usually increase at lower frequency regime 1 kHz–5 kHz as well as relatively higher frequency regime 20 kHz–25 kHz but seldom increase in between them. Increment of τhas been observed 40% and 20% for the frequency regimes of 1 kHz–5 kHz and 20 kHz–25 kHz, respectively, and τincrement is 25% for both frequency regimes. Transport simulation has been carried out using the ASTRA simulation code for STOR-M tokamak parameters to understand the physical process behind experimental observations at the higher frequency branch. The model is based on geodesic acoustic mode (GAM) excitement at resonance frequency associated with Ware-pinch due to the oscillating electric field produced by biasing voltage, which can suppress anomalous transport. Simulation results reproduce the experimental trends quite well in terms of the density, particle confinement, as well as energy confinement time evolution. All the results indicate that high frequency biasing is capable of improving confinement efficiently.
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Development of a broad band AC power amplifier for real time turbulence feedback control experiment in the Saskatchewan Torus-modified (STOR-M) tokamakBasu, Debjyoti, Nakajima, Masaru, Melnikov, AV, McColl, David, Xiao, Chijin, and Hirose, AkiraReview of Scientific Instruments 2020
A gated oscillating power amplifier has been developed for high frequency biasing and real time turbulent feedback experiments in the Saskatchewan Torus-modified tokamak. This oscillator is capable of providing a peak to peak oscillating output voltage of around ±60 V with a current around 30 A within the frequency band 1 kHz–50 kHz without any distortions. The overall output power is amplified by a two-stage metal oxide semiconductor field-effect transistor power op-amp as well as nine identical push–pull amplifiers in the final stages. The power amplifier input signal, collected from the plasma floating potential during the tokamak discharge, is optically isolated from the tokamak vessel ground. The filtered floating potential fluctuations with a band width of 5 kHz–40 kHz were amplified and fed to an electrode inserted into the plasma edge to study the response of the plasma turbulence. We observe that magnetic fluctuations are suppressed due to real time feedback of the floating potential.
2019
2018
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Towards understanding the min-sum message passing algorithm for the minimum weighted vertex cover problem: An analytical approachNakajima, Masaru, Xu, Hong, and Kumar, Sven Koenig TK SatishIn the International Symposium on Artificial Intelligence and Mathematics 2018
We constructed an analytical framework to study the min-sum message passing algorithm applied to minimum weighted vertex cover problems. Our framework correctly predicts the asymptotic behavior of the algorithm applied to minimum weighted vertex cover problem with single loop. Step toward analytical understanding of message passing algorithm.
2017
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Geodesic acoustic mode (GAM) like oscillations and RMP effect in the STOR-M tokamakBasu, Debjyoti, Nakajima, Masaru, Melnikov, AV, McColl, David, Rohollahi, Akbar, Elgriw, Sayf, Xiao, Chijin, and Hirose, AkiraNuclear Fusion 2017
A new kind of quasi-coherent mode was observed in ohmic plasma in the STOR-M tokamak. It is featured with a clear solitary peak around 30–35 kHz in the power spectra of the ion saturation current (I_\rm sat) of Langmuir probe as well as poloidal and toroidal mode numbers (m = 1,n = 0) as per the prediction of conventional geodesic acoustic mode (GAM) theory. The dispersion relation of the mode is also similar to GAM and it also shows collisional damping. In contrast to conventional GAM, the floating potential ϕ of the observed GAM-like mode does not show similar symmetric poloidal and toroidal mode numbers (m = 0,n = 0), but has (m = 1,n = 1). The GAM-like mode has also a pronounced magnetic component with mixed poloidal modes (m=3 \rm and m=5; n=1 ), as observed by Mirnov coils. This mode is suppressed by the application of resonance magnetic perturbations.
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Design of rotating resonant magnetic perturbation coil system in the STOR-M tokamakElgriw, Sayf, Adegun, Joseph, Patterson, Michael, Rohollahi, Akbar, Basu, Debjyoti, Nakajima, Masaru, Colville, Kale, Gomez, Daniel, Greenwald, Chelsea, Zhang, Jiping, and others,Fusion Engineering and Design 2017
The interaction between resonant magnetic perturbations (RMP) and plasma is an active topic in fusion energy research. RMP involves the use of radial magnetic fields generated by external coils installed on a tokamak device. The resonant interaction between the plasma and the RMP field has many favorable effects such as suppression of instabilities and, under certain conditions, improvement of discharge parameters in tokamaks. The RMP technique has been successfully implemented in the STOR-M tokamak. A set of (m = 2, n = 1) helical coils carrying a current pulse was used to study the effects of RMP on magnetic islands, plasma rotation, and other edge plasma parameters. A new RMP system is being developed for the STOR-M tokamak. The system consists of a number of external saddle coils distributed in the poloidal and toroidal directions and powered by AC power supplies to generate a rotating RMP field. Numerical simulations have been carried out to calculate several parameters for the new RMP system such as the magnetic field and the dominant modes generated by the coils. The dominant mode generated by the new RMP coil system may be tuned to (2, 1) with significant contributions from (2, 3) and (2, 5) modes.
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Modification of toroidal flow velocity through momentum Injection by compact torus injection into the STOR-M tokamakRohollahi, A, Elgriw, S, Basu, D, Wolfe, S, Hirose, A, and Xiao, CNuclear Fusion 2017
In the Saskatchewan torus-modified (STOR-M) tokamak, tangential compact torus injection (CTI) experiments have been performed with normal (counter-clockwise, CCW, top view) and reversed (clockwise, CW, top view) plasma current directions while the compact torus (CT) injection direction remains in the CCW direction. The intrinsic toroidal flow direction reverses when the discharge current is reversed. However, the change in the toroidal flow direction is always toward the CTI direction (CCW). It has been determined that the momentum in high density and high velocity CT is more than ten times larger than the intrinsic toroidal rotation momentum in the typical STOR-M plasma. Therefore, the modification of the plasma toroidal rotation velocity is attributed to momentum transfer from CT to the tokamak discharge.
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EXPERIMENTAL STUDY OF GEODESIC ACOUSTIC MODE IN THE STOR-M TOKAMAKNakajima, Masaru2017
In this experimental study, we used a set of Langmuir probes in order to observe geodesic acoustic mode (GAM) in plasmas created in the STOR-M tokamak. At four locations of STOR-M, we measured floating potential and ion saturation current. Around 9 ms into the discharge, the end of ramp-up region and the beginning of the flat-top region, we found a dominant peak around 30 kHz in the power spectral densities of ion saturation current. The ion saturation current signals showed the sine theta dependence of the oscillation amplitude, which is one of the characteristics of GAM. Furthermore, the cross spectral analysis on the ion saturation current signals suggested the poloidal mode number of m = 1. As for the floating potential signals, while 30 kHz peak was present around 9 ms, the cross spectral analysis indicated the poloidal mode number of m = 1, which is not expected for GAM. In comparison to the theoretical calculations of GAM frequency, the frequency predicted by the fluid model matched with the experimental results. Based on the above findings, it is concluded that the plasmas in the STOR-M tokamak have a signature of GAM.
2016
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Control of Toroidal Plasma Flow in the STOR-M Tokamak and Investigation of the Geodesic Acoustic ModeRohollahi, A, Basu, D, Elgriw, S, Dreval, MB, McColl, D, Nakajima, M, Adegun, JA, Patterson, M, Xiao, C, Hirose, A, and others,2016
The Saskatchewan Torus Modified (STOR-M) is an iron core tokamak and the only operating tokamak in Canada which has been in operation since 1987. The major and minor radius of the STOR-M are 46 cm and 12 cm respectively. Different types of experiments such as AC operation, Ohmic H-modes by rapid edge heating and Compact Torus Injection (CTI), plasma flow control by applying Resonant Magnetic Perturbation (RMP) and CTI, and recently detection of Geodesic Acoustic Modes (GAM) have been conducted in this tokamak. Experimental data indicate that toroidal rotational flow of the tokamak plasma is controllable by applying a RMP and a tangential CTI. On the other hand experimental results indicate presence of GAM like oscillation in this machine. Detailed discussions have been done in the following sections.
2015
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Effects of electrode biasing in STOR-M TokamakBasu, Debjyoti, Nakajima, Masaru, Rohollahi, Akbar, McColl, David, Adegun, Joseph, Xiao, Chijin, and Hirose, AkiraIn APS Division of Plasma Physics Meeting Abstracts 2015
STOR-M is an iron-core, limiter based tokamak with major and minor radii of 46cm and 12 cm, respectively. Recently, electrode biasing experiments have been carried to study the improved confinement. For this purpose we have developed a DC power supply which can be gated by a high power SCR. The rectangular SS electrode has a height of 10 cm, a width of 2 cm and a thickness of 0.2 cm. The radial position of the electrode throughout the experiments is kept around 4mm inside the limiter in the plasma edge region. After application of positive bias with voltages between +90 V to +110 V during the plasma discharge current flat top with slightly higher edge-qa (nearly 5 to 6), noticeable increment of average plasma density and soft x-ray intensity along the central chord have been observed. No distinguishable change in H α emission has been measured. These phenomena may be attributed to improved confinement formed at the inner region but not at the edge. In the upcoming experimental campaign, Ion Doppler spectroscopy will be used to measure possible velocity shear inside the inner plasma region. Edge plasma pressure gradient will also be measured using Langmuir probes. Detailed experimental results will be presented.
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Indication of GAM and electrode biasing effect on GAM in STOR-M TokamakNakajima, Masaru, Basu, Debjyoti, Rohollahi, Akbar, McColl, David, Adegun, Joseph, Xiao, Chijin, and Hirose, AkiraIn APS Division of Plasma Physics Meeting Abstracts 2015
STOR-M is a small, iron-core, limiter based tokamak with major and minor radii of 46 cm and 12 cm, respectively. Recent experimental studies have been carried out to detect GAM in this machine. Four Langmuir probe sets have been inserted into the plasma. The first three Langmuir probe sets are located in the same toroidal plane, inserted from top, bottom and outboard of the mid-plane. The fourth set is inserted from the outboard of the mid-plane, but toroidally separated from the others by 90°. Each probe set consists of three Langmuir probe tips for Isat, floating potential and I-V curve measurements. Preliminary experimental results with slightly higher edge-qa (within 5 to 6) clearly indicate a 180° phase difference between the up and down density fluctuation signals near 20 kHz. The floating potential fluctuation signals from the same locations at the same frequency showed no observable phase shift. Preliminary data indicate the presence of conventional GAM in STOR-M. In the near future, magnetic fluctuation properties of GAM oscillations in STOR-M as well as the responses of the GAM properties to electrode biasing will be studied. Detailed experimental results will be presented.