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Tsunaka Y.,Japan Science and Technology Agency | Tsunaka Y.,Kyoto University | Tsunaka Y.,International Institute for Advanced Studies | Fujiwara Y.,Kyoto University | And 4 more authors.
Genes and Development | Year: 2016

Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling duringDNAtranscription, replication, and repair. Our structural and biochemical studies of human FACT–histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3–H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid–H2A steric collision on the H2A-docking surface of the H3–H4 tetramer within the nucleosome induces H2A–H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone. © 2016 Tsunaka et al.


Zhou B.,Nanjing University | Zhou B.,Osaka University | Zhou B.,Accelerator Centre | Funaki Y.,Accelerator Centre | And 10 more authors.
Physical Review Letters | Year: 2013

We investigate the α+O16 cluster structure in the inversion-doublet band (Kπ=01±) states of Ne20 with an angular-momentum-projected version of the Tohsaki-Horiuchi-Schuck-Röpke (THSR) wave function, which was successful "in its original form" for the description of, e.g., the famous Hoyle state. In contrast with the traditional view on clusters as localized objects, especially in inversion doublets, we find that these single THSR wave functions, which are based on the concept of nonlocalized clustering, can well describe the Kπ=01- band and the Kπ=01+ band. For instance, they have 99.98% and 99.87% squared overlaps for 1- and 3- states (99.29%, 98.79%, and 97.75% for 0+, 2+, and 4 + states), respectively, with the corresponding exact solution of the α+O16 resonating group method. These astounding results shed a completely new light on the physics of low energy nuclear cluster states in nuclei: The clusters are nonlocalized and move around in the whole nuclear volume, only avoiding mutual overlap due to the Pauli blocking effect. © 2013 American Physical Society.


Sato K.,RIKEN | Kuramoto Y.,International Institute for Advanced Studies | Ohtaki M.,Waseda University | Shimamoto Y.,Rockefeller University | And 2 more authors.
Physical Review Letters | Year: 2013

At an intermediate activation level, striated muscle exhibits autonomous oscillations called SPOC, in which the basic contractile units, sarcomeres, oscillate in length, and various oscillatory patterns such as traveling waves and their disrupted forms appear in a myofibril. Here we show that these patterns are reproduced by mechanically connecting in series the unit model that explains characteristics of SPOC at the single-sarcomere level. We further reduce the connected model to phase equations, revealing that the combination of local and global couplings is crucial to the emergence of these patterns. © 2013 American Physical Society.


Funaki Y.,Accelerator Centre | Horiuchi H.,Osaka University | Horiuchi H.,International Institute for Advanced Studies | Tohsaki A.,Osaka University
Progress in Particle and Nuclear Physics | Year: 2015

The purpose of this article is firstly to review the study of the cluster-gas-like structure, especially the α-cluster-condensate-like structure, which is a novel type of nuclear structure. The second purpose is to explain the recent proposal of the container model of general cluster dynamics which is a novel powerful cluster model that may be adopted in place of the traditional cluster models of resonating group method (RGM) and generator coordinate method (GCM) of Brink wave functions. The container model has been proposed based on the Tohsaki-Horiuchi-Schuck-Röpke (THSR) wave function which was introduced to investigate the α-cluster-condensate-like states. The main reason for the introduction of the container model was the striking fact that the RGM/GCM wave functions of various cluster states which include both gas-like and non-gas-like states are almost 100% equivalent to single THSR wave functions. For the sake of historical evolution, we give a concise review of various cluster models before the introduction of the THSR wave function. In particular, because the idea of the cluster-gas-like structure was proposed in the 1970s for explaining the properties of the Hoyle state, this review of traditional cluster models is indispensable. In view of the importance of the THSR wave function, various characteristic properties of the THSR wave function are explained. Since, at least until now, most calculations of matrix elements with the THSR wave functions have been done only analytically in order to get sufficient numerical accuracy, some analytical manipulations of the THSR wave function will be explained. © 2015 Elsevier B.V. All rights reserved.


Kori H.,Ochanomizu University | Kori H.,Japan Science and Technology Agency | Kuramoto Y.,International Institute for Advanced Studies | Jain S.,University of Virginia | And 2 more authors.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2014

A theoretical analysis is presented to show the general occurrence of phase clusters in weakly, globally coupled oscillators close to a Hopf bifurcation. Through a reductive perturbation method, we derive the amplitude equation with a higher-order correction term valid near a Hopf bifurcation point. This amplitude equation allows us to calculate analytically the phase coupling function from given limit-cycle oscillator models. Moreover, using the phase coupling function, the stability of phase clusters can be analyzed. We demonstrate our theory with the Brusselator model. Experiments are carried out to confirm the presence of phase clusters close to Hopf bifurcations with electrochemical oscillators. © 2014 American Physical Society.


Suzuki K.W.,Laval University | Ueda H.,Kochi University | Nakayama K.,Kyoto University | Tanaka M.,International Institute for Advanced Studies
Journal of Plankton Research | Year: 2012

Stage-specific horizontal distribution was compared between two sympatric oligohaline copepods to elucidate their life-history strategies related to reproduction: free-spawning Sinocalanus sinensis and egg-carrying Pseudodiaptomus inopinus. Copepods were sampled by vertical hauls of a 100-μm mesh plankton net along the macrotidal Chikugo River estuary in southwestern Japan from 2005 to 2006. Sinocalanus sinensis dominated throughout the year except for the warm season, when P. inopinus outnumbered S. sinensis. The spatiotemporal correspondence of peak densities with the estuarine turbidity maximum was evident for S. sinensis but ambiguous for P. inopinus. Nauplii of S. sinensis were always distributed on average downstream from copepodids and adults, whereas P. inopinus usually showed the opposite pattern of stage-specific horizontal distribution. During large freshwater discharges, S. sinensis was more subject to washout from the estuary. In addition, the potential vulnerability of S. sinensis to droughts was suggested by low tolerance for high salinities. Consequently, egg-carrying P. inopinus has higher flexibility to live under varying estuarine conditions especially during the warm season. In contrast, ecological specializations, such as tidal vertical migration and detritivorous feeding, are considered to underlie the dominance of the free-spawning S. sinensis under the conditions prevailing in the macrotidal environment. © 2012 The Author.


Suzuki K.W.,Laval University | Kasai A.,Kyoto University | Nakayama K.,Kyoto University | Tanaka M.,International Institute for Advanced Studies
Journal of Oceanography | Year: 2012

The inner part of the Ariake Sea is one of the most productive estuarine systems in Japan. To examine potential food items for estuarine organisms, we conducted monthly observations of the dynamics of particulate organic matter along the macrotidal Chikugo River estuary in 2005 and 2006. In the neighboring macrotidal Midori and Kuma River estuaries, comparative observations were made. High turbidity and strong vertical mixing were observed only at low salinities (<10) in the Chikugo River estuary. In contrast, the Midori and Kuma River estuaries were characterized by less turbid and less mixed waters. Concentrations of particulate organic carbon often exceeded 5 mg l -1 in or close to the estuarine turbidity maximum (ETM) of the Chikugo River estuary. However, such high concentrations were rarely observed in the other two estuaries. The observed differences could be attributable to different hydrodynamic processes related to the different lengths of tidal reaches: 23, 8, and 6 km in the Chikugo, Midori, and Kuma Rivers, respectively. In the Chikugo River estuary, spatiotemporal changes of chlorophyll a suggested that phytoplankton occurred abundantly up- and/or downstream from the ETM especially during the warm season. In contrast, pheophytin (i. e., plant detritus) always accumulated in or close to the ETM. Carbon stable isotope ratios and carbon to nitrogen ratios indicated that the plant detritus was derived from phytoplankton and terrestrial plants. The Chikugo River estuary has a high potential to support the production of estuarine organisms through abundant plant detritus in the well-developed ETM all the year round. © 2012 The Oceanographic Society of Japan and Springer.


Suzuki K.W.,Laval University | Nakayama K.,Kyoto University | Tanaka M.,International Institute for Advanced Studies
Journal of Oceanography | Year: 2013

Copepods are considered to be a vital component connecting the unique macrotidal environment to the high productivity and high biodiversity of the Ariake Sea. To examine the spatiotemporal succession of copepod communities, we conducted monthly sampling (vertical hauls of a 100-μm mesh plankton net) in three neighboring macrotidal estuaries between 2005 and 2006. Irrespective of the season, three copepod communities were recognized in relation to the relatively long gradients of salinity and turbidity along the Chikugo and Midori River estuaries. The oligohaline community (salinity 1-10) was observed at higher turbidities (>100 NTU), whereas the freshwater (salinity <1) and meso/polyhaline (salinity >10) communities were associated with lower turbidities (<100 NTU). The oligohaline calanoid Sinocalanus sinensis occurred only in the Chikugo River estuary, maintaining a large biomass (dry weight >10 mg m-3) in or close to the well-developed estuarine turbidity maximum (ETM) throughout the year. In the Midori River estuary, the oligohaline community lacked S. sinensis and showed a minimum biomass during winter (<10 mg m-3). In both estuaries, the freshwater community always remained at a small biomass (<1 mg m-3), whereas the meso/polyhaline community showed marked seasonal changes in biomass (0.1-657 mg m-3). The prevalence of higher salinities allowed only the meso/polyhaline community to occur in the Kuma River estuary. In summary, S. sinensis characterized the copepod community distinctive of the well-developed ETM, potentially serving as an important link to higher trophic levels during winter when copepods are scarce in other areas. © 2012 The Oceanographic Society of Japan and Springer Japan.


Horiuchi H.,Osaka University | Horiuchi H.,International Institute for Advanced Studies
Lecture Notes in Physics | Year: 2010

In this lecture I first review present knowledge about the actual coexistence features of cluster states and mean-field-type states in nuclei. I then discuss how nuclear structure changes from shell-model-like ground state to cluster states. About the actual coexistence features I review them in two parts. In the first part I discuss 8Be, 12C, 16O, and 20Ne. In the second part I discuss 44Ti and 32S where superdeformed atates are observed. The investigation in 32S suggests strong interrelation of 16O + 16O molecular states and superdeformed states. For the discussions of 20Ne, 44Ti and 32S systems, I utilize the results of the detailed studies with antisymmetrized molecular dynamics (AMD). On the basis of these studies of actual coexistence features, I discuss the mechanism of the structure-change between cluster structure and mean-field-type structure and indicate that it comes from the dual nature of nuclear wave functions which have both characters of cluster wave function and mean-field-type wave function. Observed strong E0 transitions between cluster states and the ground state are explained to be a good verification of dual nature of nuclear wave function. © 2010 Springer-Verlag Berlin Heidelberg.


Horiuchi H.,Osaka University | Horiuchi H.,International Institute for Advanced Studies
Journal of Physics: Conference Series | Year: 2013

The major novelties that have emerged in nuclear cluster theory since the last, 9th, cluster conference is reviewed. Among the marked developments made in many traditional and novel subjects of nuclear cluster physics, four subjects are chosen in this introductory talk. They are 1. neutron-rich nuclei, 2. cluster gas, 3. coexistence of cluster and mean-field dynamics, and 4. ab initio approaches. A representative example of the present status of the field is that it is studied in the framework of ab initio nuclear theory as well. We discuss a recent ab initio calculation of the Hoyle state of 12C, which supports its cluster-gas-like structure.

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