Scattering functions of knotted ring polymers

We discuss the scattering function of a Gaussian random polygon with N nodes under a given topological constraint through simulation. We obtain the Kratky plot of a Gaussian polygon of N=200 having a fixed knot for some different knots such as the trivial, trefoil and figure-eight knots. We find that some characteristic properties of the different Kratky plots are consistent with the distinct values of the mean square radius of gyration for Gaussian polygons with the different knots.Comment: 4pages, 3figures, 3table

On the Dominance of Trivial Knots among SAPs on a Cubic Lattice

The knotting probability is defined by the probability with which an $N$-step self-avoiding polygon (SAP) with a fixed type of knot appears in the configuration space. We evaluate these probabilities for some knot types on a simple cubic lattice. For the trivial knot, we find that the knotting probability decays much slower for the SAP on the cubic lattice than for continuum models of the SAP as a function of $N$. In particular the characteristic length of the trivial knot that corresponds to a `half-life' of the knotting probability is estimated to be $2.5 \times 10^5$ on the cubic lattice.Comment: LaTeX2e, 21 pages, 8 figur

Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis

Jun Ueda, Akihito Harada, Takashi Urahama, Shinichi Machida, Kazumitsu Maehara, Masashi Hada, Yoshinori Makino, Jumpei Nogami, Naoki Horikoshi, Akihisa Osakabe, Hiroyuki Taguchi, Hiroki Tanaka, Hiroaki Tachiwana, Tatsuma Yao, Minami Yamada, Takashi Iwamoto, Ayako Isotani, Masahito Ikawa, Taro Tachibana, Yuki Okada, Hiroshi Kimura, Yasuyuki Ohkawa, Hitoshi Kurumizaka, Kazuo Yamagata, Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis, Cell Reports, Volume 18, Issue 3, 2017, Pages 593-600, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2016.12.065

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

44. Two-point distance distribution of knotted ring polymers at the theta temperature and a topological correction(poster presentation,Soft Matter as Structured Materials)

この論文は国立情報学研究所の電子図書館事業により電子化されました。線状高分子鎖の末端間距離分布に相当する環状高分子鎖の2点間分布が、結び目の制限からどのような影響を受けるかを議論する。また、この分布に対する近似式もシミュレーション結果から考察する

On the criticality of random knots at the θ temperature : A preliminary report(Knots and soft-matter physics: Topology of polymers and related topics in physics, mathematics and biology)

この論文は国立情報学研究所の電子図書館事業により電子化されました。結び目不変量を用いた数値シミュレーションに基づいて、一定の結び目型を持つランダムポリゴン(ランダム結び目)の頂点数Nに関する漸近的な振る舞いは、新しく顕著な臨界現象に対応するという予想を提案する。これまでに多くの研究者によって、ランダム結び目の慣性半径はNに関して排除体積鎖と同じ指数v_=0.588のべき的振る舞いが指摘されている。一方、ランダム結び目に対して分布関数を求めるとガウス的な振る舞いを示す。予備的段階ではあるが、現在、頂点数N=1000の場合でも同様な結果が示された。この結果は指数v_=0.588と矛盾する。Through simulation using knot invariants we suggest that random polygons under a topological constraint (i.e. random knots) should have novel critical behavior. We recall that the mean-square radius of gyration of random knots with N nodes increases with respect to N almost as that of the self-avoiding polygons, as was pointed out by many authors previously. We find that the two-point correlation function is well approximated by a function close to the Gaussian one. Furthermore, our preliminary data analysis for N=1000 also suggest the simialr result. However, the Gaussian behavior is not consistent with the criticality of the self-avoiding walk. We thus suggest that random knots should have nontrivial and new crtical behavior