In this page, new articles of Academic Topics are displayed. Many other articles are displayed in the Academic Topics pages in the member-limitted page. Faculty members, students, graduates, and ex-faculty members introduce various academic research topics that have been or are currently being conducted in the schools and departments of SOKENDAI.
大隅先生のノーベル賞は、Discoveries of mechanisms for autophagy(オートファジーの機構の発見)が受賞理由となっています。受賞理由となっている最初の論文では、出芽酵母のオートファジーのプロセスを光学顕微鏡観察する手法が報告されました1。この発見を基盤に、光学顕微鏡を用いてオートファジー変異体のスクリーニングが行われ、15種類のオートファジー変異体が同定されました2。
1.Takeshige K, Baba M, Tsuboi S, Noda T, Ohsumi Y. Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. J Cell Biol. 1992;119(2):301-11.
2.Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993;333(1-2):169-74.
3.Suzuki K, Kirisako T, Kamada Y, Mizushima N, Noda T, Ohsumi Y. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J. 2001;20(21):5971-81.
4.Suzuki K, Akioka M, Kondo-Kakuta C, Yamamoto H, Ohsumi Y. Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae. J Cell Sci. 2013;126(Pt 11):2534-44.
Nishimura T, Sato T, Yamamoto Y, Watakabe I, Ohkawa Y, Suyama M, et al: foxl3 is agerm cell-intrinsic factor involved in sperm-egg fate decision in medaka. Science 349:328–331 (2015).
2017/03/14
Unexpected Reunion of Gravity
and Non-equilibrium Physics
Shin Nakamura Professor, Dept.of Physics, Chuo University (加速器科学専攻修了(2001.03)、第6回長倉賞(2000.12)、第1回総研大科学者賞(2015.04)) 受理:2015.09.10
Albert Einstein was one of the most talented physicists in history. He invented important theories in physics, including theories of special relativity, photoelectric effect, and Brownian motion. Amazingly, these three theories were made in the same year, 1905, that is called Einstein’s miracle year.
Special relativity has been improved to general relativity, a theory of gravity, ten years later. Now, general relativity is established as a standard theory of gravity that is necessary not only for cosmology but also for construction of the GPS system that is important to our modern life. The theory of Brownian motion ignited non-equilibrium physics, the physics of systems out of equilibrium. The theory of photoelectric effect brought him a Nobel Prize.
Once century after the miracle year, physicists found a surprising unexpected “reunion” of the Einstein’s theories. The key idea is the AdS/CFT correspondence that is a correspondence between a theory of particles (gauge theory) and a theory of general relativity. This correspondence says, a system of gauge particles is equivalent to a system of gravity. If we consider a many-body system at thermal equilibrium, a mathematically equivalent description of the system is given by using a black hole physics in the gravity side.
Currently, I am working on theoretical physics mainly focusing to application of the AdS/CFT correspondence to non-equilibrium physics. Non-equilibrium physics deals with systems of many particles that are out of equilibrium. Although most of the phenomena we find in our daily life are non-equilibrium processes, their theoretical description is still a challenge. By using the AdS/CFT correspondence, we have a chance to describe the non-equilibrium systems in the language of general relativity. Interestingly, it is often the case that the gravitational description is much easier than the original description of non-equilibrium systems. For example, I have theoretically discovered a new type of phase transition of conductors where the nature of conduction, such as conductivity, suddenly jumps under out-of-equilibrium conditions (Fig. 1). I am trying to make a collaboration with experimental physicists to verify the transition in real materials.
Fig. 1 An example of “jump” of the conductivity. Conductivity is given by the current density (J) divided by the electric field (E). Hence the jump of the electric field indicates the jump of the conductivity of the material. (The figure was taken from [S. Nakamura, Phys. Rev. Lett. 109 (2012) 120602] and was edited.)
2017/03/14
Toward Practical Use:
Numerical Algorithms Based on Linear Algebra for Applications
Keiichi Morikuni Ass.Professor, Dept. of Computer Science, University of Tsukuba (情報学専攻修了、第18回長倉賞受賞、2013.03) 受理:2015.09.16
In the 5-year Ph.D. program, I studied computational methods called preconditioners for solving large-scale least squares problems. The problems are fundamental in industry, engineering, and social sciences and are, for example, to fit models to observations. For the solutions, I focused on using modern iterative methods whose convergence can be accelerated by using preconditioning. Typical preconditioners are based on incomplete matrix factorizations, although additional memory is required to store the factors whose size is competitive with the size of a given problem (Figure 1). I designed efficient numerical algorithms to precondition the modern iterative methods by using classical iterative methods. The proposed methods were applied to practical problems such as image reconstruction problems in biology and adaptive optics in astronomy. I showed with numerical experiments that the proposed methods outperform state-of-the-art methods (Figure 2). For this study, I was awarded the Nagakura Research Incentive Award.
After the graduation, I further investigated the convergence of those methods and characterize the solution that the methods give. In addition, I generalized the methods and broaden the scopes of the problems. On the other hand, making use of the Ph.D. work on numerical linear algebra, my research field is extending. In these days, I am focusing on eigenvalue computations using a contour integral-based numerical method. Eigenvalues are characteristic quantities of a matrix (array of numbers). The study has applications such as structural analysis and data science. In particular, in order to obtain more accurate or realistic solutions, I am studying techniques to employ prior knowledge of the property of the solution (Figure 3).
Figure 1. Required memory.
Figure 2. Convergence history for Maragal_6. Joint work with Ken Hayami of the National Institute of Informatics. The test matrix is from the University of Florida Sparse Matrix Collection.
Image segmentation. Identifying the hat and face as one object, the person is well segmented. Joint work with Shunya Ueta and Tetsuya Sakurai of the University of Tsukuba. The original image is from the Berkeley Segmentation Dataset and Benchmark.
2017/03/14
Between the Past and the Present:
Archaeological Heritage in Modern Peru
Daniel Dante SAUCEDO SEGAMI
Visiting Researcher, National Museum of Ethnology-Japan (比較文化学専攻修了(2014.09)、第20回総研大研究賞受賞(2015.03)) 受理:2015.09.15
As a result of globalization, archaeological heritage has become an important element of tourism. Recent discoveries can be followed on Internet, attracting the attention of people from all over the world to remote areas, driving interest to visit them. The affluence of tourists and the economic boost for acquiring local services have become important reasons for regional and local governments to support tourism. Because of this situation, the idea that archaeological heritage can be protected and used to improve local economies by its revalorization through tourism has become very popular in Peru.
However, there are several issues that arise when tourism is chosen as the main purpose for archaeological heritage. Are all archaeological sites prepared to receive tourists and give them the services they need? Are all archaeological sites interesting enough for people to travel to these remote places, maintaining a steady number in order to boost local economies? Do all stakeholders involved (governments, local people, archaeologists, among others) agree on what should be considered heritage and how to use it? What is the definition of heritage that every stakeholder carries?
My research aims to answer these questions by positioning archaeological remains as the center of different relationships established by stakeholders, identifying the different values given to these remains. To achieve this objective, I use the perspective of Public Archaeology, a field of archaeology that studies how archaeology is immersed in contemporary society. My fieldwork includes identifying and interviewing stakeholders, carrying out participant observation of their relationship between them and archaeological remains.
Figure 1: Archaeological pottery used as decoration at La Zaranda town
(Photo by Daniel Saucedo-Segami, 20/10/2011)
Figure 2: Shamanist ritual of baño de florecimiento at Huaca Loro during excavations of SAP
(Photo by Daniel Saucedo-Segami, 05/08/2008)
Figure 3: Local representations of Sicán artifacts at Ferreñafe city