630 research outputs found
Supporting data for the paper "Asymmetric periodic boundary conditions for all-atom molecular dynamics and coarse-grained simulations of nucleic acids"
No full textThe attached files contain the supporting data for the paper: "Asymmetric periodic boundary conditions for all-atom molecular dynamics and coarse-grained simulations of nucleic acids" by Radek Erban and Yuichi Togashi, Journal of Physical Chemistry B, doi.org/10.1021/acs.jpcb.3c03887 (2023
KONFLIK BATIN TOKOH YUICHI TANABE PADA NOVEL 'KITCHEN' KARYA BANANA YOSHIMOTO
No full textManusia akan berusaha memutuskan pilihan terbaik dalam hidupnya. Namun pada kenyatannya manusia kerap kali menghadapi kebimbangan dalam menentukan mana keputusan yang baik atau buruk yang pada akhirnya memicu konflik batin dalam dirinya. Konflik batin sering terjadi pada diri tiap orang, contoh paling sederhana adalah ketika seseorang ingin melanjutkan tidurnya di pagi hari namun ia sadar ia harus bangun dan berangkat bekerja. Jika ia memilih tidur ia akan terlambat bekerja, jika ia memilih bangun ia akan bekerja dalam keadaan masih mengantuk. Dalam hal ini tidur disebut dengan gagasan menyenangkan sedangkan bangun untuk bekerja disebut dengan gagasan tidak menyenangkan. Gagasan mana yang akan dipilih ini tentunya memiliki konsekuensinya masing-masing. Penulis mengambil contoh konflik batin yang digambarkan secara mendetail melalui karya sastra berupa novel berjudul Kitchen karya Banana Yoshimoto. Penulis menemukan penggambaran konflik yang dialami oleh tokoh bernama Yuichi Tanabe pada novel ini. Metode yang digunakan dalam pengambilan data adalah studi literatur. Tujuan penulisan makalah ini adalah menemukan bentuk dari konflik batin yang dialami Yuichi lalu pilihan mana yang akhirnya diputuskan Yuichi ketika mengalami konflik tersebut. Ditemukan 19 data berisi konflik batin yang dialami Yuichi, dan 14 di antaranya merupakan pilihan dengan sifat tidak menyenangkan. Hal ini disebabkan Yuichi punya pengalaman traumatik karena meninggalnya Eriko, ayah kandung Yuichi yang mengubah dirinya menjadi wanita. Pada akhirnya konflik batin yang dialami Yuichi sirna karena Yuichi membuka dirinya terhadap tokoh utama novel ini yaitu gadis bernama Mikage Sakurai.
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Humans will try to decide the best choice in life. But in reality, humans often face indecision in determining which decision is good or bad, which in turn triggers inner conflict within themselves. Inner conflict often occurs in everyone, the simplest example is when someone wants to continue sleeping in the morning but he realizes he has to get up and go to work. If he chooses to sleep he will be late for work, if he chooses to wake up he will work while still sleepy. In this case sleeping is called a pleasant idea while getting up for work is called an unpleasant idea. Which idea to choose has its own consequences. The author takes an example of inner conflict that is described in detail through a literary work in the form of a novel entitled Kitchen by Banana Yoshimoto. The author finds the depiction of conflict experienced by a character named Yuichi Tanabe in this novel. The method used in data collection is literature study. The purpose of writing this paper is to find the form of inner conflict experienced by Yuichi and then which choice Yuichi finally decided when experiencing the conflict. Found 19 data containing inner conflict experienced by Yuichi, and 14 of them are choices with unpleasant properties. This is because Yuichi had a traumatic experience due to the death of Eriko, Yuichi's biological father who turned into a woman. In the end, the inner conflict experienced by Yuichi disappeared because Yuichi opened himself to the main character of this novel, a girl named Mikage Sakurai
Analysis of Amae's Behavior Reflected in the Characters of Mikage and Yuichi in the Novel "Kitchen" Works Yoshimoto Banana
No full textJapan has a unique culture called "Amae" which describes the behavior of a person's dependence on others for attention and affection. This concept is explored in the novel "Kitchen" by Yoshimoto Banana. The research theory used is the moral approach and sociological aspects in the novel. In this research, the author specializes in describing amae behavior as reflected in the characters Mikage and Yuichi in the novel Kitchen and describes the lives of Mikage and Yuichi with the concept of amae. The results of the research show that amae's behavior is reflected in the characters Mikage and Yuichi and explains the lives of the characters Mikage and Yuichi with the concept of amae used by the author in the novel "Kitchen" through three sub-concepts, namely kuyami (feeling regret), toriiru (attracting attention), and tanomu (relying on oneself). These concepts show that good relationships can provide motivation and survival for the characters Mikage and Yuichi. In the novel, the concept of amae is a real example of how Japanese society interacts, influences and relates to its social environment.48 pagesSkripsi Sarjan
Damage to inorganic materials illuminated by focused beam of X-ray free-electron laser radiation
No full textTakahisa Koyama, Hirokatsu Yumoto, Kensuke Tono, Tadashi Togashi, Yuichi Inubushi, Tetsuo Katayama, Jangwoo Kim, Satoshi Matsuyama, Makina Yabashi, Kazuto Yamauchi, and Haruhiko Ohashi "Damage to inorganic materials illuminated by focused beam of x-ray free-electron laser radiation", Proc. SPIE 9511, Damage to VUV, EUV, and X-ray Optics V, 951107 (12 May 2015); https://doi.org/10.1117/12.2182778X-ray free-electron lasers (XFELs) that utilize intense and ultra-short pulse X-rays may damage optical elements. We investigated the damage fluence thresholds of optical materials by using an XFEL focusing beam that had a power density sufficient to induce ablation phenomena. The 1 μ4m focusing beams with 5.5 keV and/or 10 keV photon energies were produced at the XFEL facility SACLA (SPring-8 Angstrom Compact free electron LAser). Test samples were irradiated with the focusing beams under normal and/or grazing incidence conditions. The samples were uncoated Si, synthetic silica glass (SiO2), and metal (Rh, Pt)-coated substrates, which are often used as X-ray mirror materials
Damage threshold of coating materials on x-ray mirror for x-ray free electron laser
No full textTakahisa Koyama, Hirokatsu Yumoto, Takanori Miura, Kensuke Tono, Tadashi Togashi, Yuichi Inubushi, Tetsuo Katayama, Jangwoo Kim, Satoshi Matsuyama, Makina Yabashi, Kazuto Yamauchi, and Haruhiko Ohashi, "Damage threshold of coating materials on x-ray mirror for x-ray free electron laser", Review of Scientific Instruments 87, 051801 (2016) https://doi.org/10.1063/1.4950723.We evaluated the damage threshold of coating materials such as Mo, Ru, Rh, W, and Pt on Si substrates, and that of uncoated Si substrate, for mirror optics of X-ray free electron lasers (XFELs). Focused 1 μm (full width at half maximum) XFEL pulses with the energies of 5.5 and 10 keV, generated by the SPring-8 angstrom compact free electron laser (SACLA), were irradiated under the grazing incidence condition. The damage thresholds were evaluated by in situ measurements of X-ray reflectivity degradation during irradiation by multiple pulses. The measured damage fluences below the critical angles were sufficiently high compared with the unfocused SACLA beam fluence. Rh coating was adopted for two mirror systems of SACLA. One system was a beamline transport mirror system that was partially coated with Rh for optional utilization of a pink beam in the photon energy range of more than 20 keV. The other was an improved version of the 1 μm focusing mirror system, and no damage was observed after one year of operation
Modeling of Nanomachine/Micromachine Crowds: Interplay between the Internal State and Surroundings
No full textThe
activity of biological cells is primarily based on chemical
reactions and typically modeled as a reaction-diffusion system. Cells
are, however, highly crowded with macromolecules, including a variety
of molecular machines such as enzymes. The working cycles of these
machines are often coupled with their internal motion (conformational
changes). In the crowded environment of a cell, motion interference
between neighboring molecules is not negligible, and this interference
can affect the reaction dynamics through machine operation. To simulate
such a situation, we propose a reaction-diffusion model consisting
of particles whose shape depends on an internal state variable, for
crowds of nano- to micromachines. The interference between nearby
particles is naturally introduced through excluded volume repulsion.
In the simulations, we observed segregation and flow-like patterns
enhanced by crowding out of relevant molecules, as well as molecular
synchronization waves and phase transitions. The presented model is
simple and extensible for diverse molecular machinery and may serve
as a framework to study the interplay between the mechanical stress/strain
network and the chemical reaction network in the cell. Applications
to more macroscopic systems, e.g., crowds of cells, are also discussed
Bridging the dynamics and organization of chromatin domains by mathematical modeling
No full textAbstractThe genome is three-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.Extra View toShinkai S, Nozaki T, Maeshima K, Togashi Y. Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells. PLoS Comput Biol. 2016;12(10):e1005136. doi: 10.1371/journal.pcbi.1005136. PubMed PMID: 27764097; PubMed Central PMCID: PMCPMC5072619.FundingThis work was supported by Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Dynamic Approaches to Living System) from MEXT and AMED; KAKENHI under Grant JP16H01408, JP23115007, JP23115005, JP16H04746; CREST grant (JPMJCR15G2) from JST; and Research Fellowship for Young Scientists under Grant JP13J04821, JP16J07205.DisclosureNo potential conflicts of interest were disclosed.AcknowledgementsWe would like to thank Dr. Takashi Toda for comments regarding the manuscript.</jats:sec
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