アブストラクト
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Molecular Dynamics Study on Cluster Damaged DNA Containing Apurinic/Apyrimidinic Sites on the Same Strand
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Kazushi Terakawa, Susumu Fujiwara, Tomoko Mizuguchi, Yoshiteru Yonetani, Naoya Shikazono, Ken Akamatsu, Hiroaki Nakamura
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DNA has susceptibility to alkylation, oxidation, and irradiation, which can lead damage to the molecular structures such as base damage, apurinic/apyrimidinic site (AP site), and strand breaks. These damages are usually repaired by enzymes in the cell. However, when the damages are locally crowded and clustered, the enzymatic repair cannot work adequately, which can lead to cell death and cancer. In this work, we carried out MD simulations of DNA with AP sites; we particularly focused on a situation in which two AP sites are positioned at the same strand. The results found that the presence of AP sites in DNA significantly changes the structure of DNA, which possibly make a significant effect on the enzymatic repair.
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Proceedings of the AROB-ISBC-SWARM 2023 (The 28th International Symposium on Artificial Life and Robotics, the 8th International Symposium on BioComplexity, the 6th International Symposium on Swarm Behavior and Bio-Inspired Robotics), (Online, January 25-27, 2023) pp.1341-1342.
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Molecular Dynamics Simulation of Cluster Damaged DNA Composed of Apurinic/Apyrimidinic Sites
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Kazushi Terakawa, Susumu Fujiwara, Tomoko Mizuguchi, Yoshiteru Yonetani, Hiroaki Nakamura
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DNA has susceptibility to alkylation, oxidation, and irradiation, which can produce damage to the molecular structures such as 8-oxoguanine, apurinic/apyrimidinic site (AP site), and strand breaks. These damages are usually repaired by enzymes in the cell. However, when the damages are locally crowded and clustered, the enzymatic repair cannot work adequately, which can lead to cell death and cancer. In this work, we carried out MD simulations of DNA with AP sites, and here we particularly focused on a situation in which two AP sites are positioned at the same strand. From the analysis of the DNA structural changes, we will clarify why effect of the AP sites is different between the same and complementary strands.
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Proceedings of the AROB-ISBC-SWARM 2022 (The 27th International Symposium on Artificial Life and Robotics, the 7th International Symposium on BioComplexity, the 5th International Symposium on Swarm Behavior and Bio-Inspired Robotics), (Online, January 25-27, 2022) pp.1855-1856.
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The role of DNA sequence in the stability of double-stranded structure
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Tomoko Mizuguchi, Takashi Aoki, Susumu Fujiwara
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The separation process of double-stranded DNA was examined for three different base sequences using molecular dynamics simulations. We applied an external force to an atom on the DNA backbone and calculated the work required to pull the double strands away. A DNA fragment consisting of guanine-cytosine pairs shows a sharper change in work than DNA fragments consisting of adenine-thymine pairs. This fact is attributed to the difference in the number of hydrogen bonds between base pairs. Meanwhile, even between the same base pairs, the ease of breaking hydrogen bonds differs depending on the surrounding sequence.
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Proceedings of the AROB-ISBC-SWARM 2022 (The 27th International Symposium on Artificial Life and Robotics, the 7th International Symposium on BioComplexity, the 5th International Symposium on Swarm Behavior and Bio-Inspired Robotics), (Online, January 25-27, 2022) pp.1555-1556.
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Molecular Dynamics Study of Polymer-Water Interaction in Zwitterionic Polymer Brush-Water Interface
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Yuya Fujinaga, Susumu Fujiwara, and Tomoko Mizuguchi
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In the medical fields, zwitterionic polymer brushes have received considerable attention owing to their highly
antifouling effect. The structure of hydrated polymer brushes and the dynamics of hydrated water have been recognized as
important factors for antifouling in recent studies. Molecular dynamics simulations of the all-atom models composed of
zwitterionic polymer brushes and water are performed to clarify the effect of polymer brush tacticity on the dynamics of
interfacial water. Our simulations show that shape of polymer brushes and dynamics of water differ between syndiotactic
zwitterionic polymer brushes and isotactic ones. It is also found that the lifetime for hydrogen bond of syndiotactic model is
longer than that of isotactic model. It is concluded that there is certainly difference in the dynamics of interfacial water
depending on the tacticity of polymer brushes.
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Proceedings of the AROB-ISBC-SWARM 2022 (The 27th International Symposium on Artificial Life and Robotics, the 7th International Symposium on BioComplexity, the 5th International Symposium on Swarm Behavior and Bio-Inspired Robotics), (Online, January 25-27, 2022) pp.1490-1491.
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アブストラクト
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Investigation of phase behavior of bolaamphiphilic solution using
dissipative particle dynamics simulation
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Ryōen Shirasaki, Hu-Jun Qian, Susumu Fujiwara and Hiroaki Nakamura
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We study the phase behavior of bolaamphiphilic solution performing
the dissipative particle dynamics simulations of coarse-grained
bolaamphiphilic molecules with explicit solvent molecules.
The phase structure becomes a micellar phase at a low concentration
of bolaamphiphilic molecules in water, and that it changes to complex
mesophases as the concentration increases.
Our simulations show that there are six kinds of phases: isotropic
micellar, micellar, rod-shaped micellar, hexagonal, network-structure
and lamellar.
The network-structure and the lamellar phases disappear when the
restoring potential against the bending of bolaamphiphilic molecules
in our simulation model is excluded; and the isotropic micellar
and the hexagonal phases disappear when the restoring potential
is included.
This suggests that the strength of the restoring potential against
the bending of bolaamphiphilic molecules has an important role
in the formation of the mesophases.
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Proceedings of the 30th JSST Annual Conference (JSST 2011)
International Conference on Modeling and Simulation Technology
[CD-ROM] (Tokyo, Japan, October 22-23, 2011) pp. 208-214.
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Simulation study of the structural formation in systems with
short-range interaction
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Susumu Fujiwara and Tetsuya Sato
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By carrying out the molecular dynamics simulations of 100 short
polymer chains, each of which consists of 20 CH2 groups,
we show that the orientationally ordered structure
at low temperature is formed from a random structure
at high temperature by a sudden cooling.
The essentially extended chains form a monolayer structure.
The ratio of the lattice constants a/b takes the hexagonal value
31/2 at 400 K and decreases as the temperature decreases.
From detailed analysis of the local orientational order, it is found
that the growth of the local ordered clusters proceeds
in a stepwise fashion.
From the analysis of the molecular mobility, we find that
the longitudinal chain motion increases dramatically with increasing
temperature while the transverse chain motion is not so dependent
on the temperature variation.
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Proceedings of the Second Asian Pacific Plasma Theory Conference
(APPTC '97) ,
Eds. Y. Tomita, Y. Nakamura and T. Hayashi (National Institute for
Fusion Science, NIFS-PROC-38, 1998) pp. 289-294.
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Simulation study of the structural formation in thermodynamically
closed systems
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Susumu Fujiwara, Tetsuya Sato, Takaya Hayashi, Kunihiko Watanabe,
Ritoku Horiuchi, Yasushi Todo, Hisanori Takamaru, Tomo-Hiko Watanabe,
Akira Kageyama, Keisuke Araki and Hideaki Miura
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By carrying out the molecular dynamics simulations of a single polymer
chain with 500 segments, we show that the orientationally ordered structure
at low temperature is formed from a random-coil structure at high temperature
by a stepwise cooling. The radii of gyration and the orientational order
parameters show that the transition temperature region from the random-coil
structure to the orientationally ordered structure is 350<T<550 K.
From detailed analyses of the orientationally ordered structure at T=100 K,
it is found that the lengths of stems and each fold region along the
principal axis with the smallest moment of inertia are around 20 A
and 10 A,
respectively.
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Proceedings of the 1996 International Conference of Plasma
Physics, Eds. H. Sugai and T. Hayashi (The Japan Society of Plasma
Science and Nuclear Fusion Research, 1996) pp. 838-841.
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Simulational and Analytic Studies of Anomalous Relaxation in Disordered
Systems
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Fumiko Yonezawa, Susumu Fujiwara and Sohei Gomi
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Anomalous relaxations observed in various kinds of disordered systems are
discussed. In particular, the structural relaxations in supercooled liquids
are studied by making use of molecular dynamics simulations. On the belief
that the essential aspects of anomalous relaxations are explained in the
framework of one-body pictures, we carry out analytic and simulational studies
both of the fractal time random walk and of random walks in spaces of fractal
and non-fractal dimensions, from which we show that the anomalous relaxations
of the stretched-exponential type as well as of the Cole-Cole type take place
even in these systems.
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Proceedings of the IIAS Workshop on Mathematical Approach to
Fluctuations, Vol. II, Editor: T. Hida (World Scientific
Publishing Co. Pte. Ltd., Singapore, 1995) pp. 340-362.
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Last modified on 03/31/23
Copyright (C) 1996-2024
Susumu Fujiwara