International Symposium on Computational Science2019
February 21, 2019
Kanazawa University, Japan
Date February 21, 2019
Venue Natural Science and Technology Hall 5, building C4• Oral presentations: Lecture room 6• Poster presentations: Lecture room 2
Kanazawa University, Japan (Kakuma campus)
Kakuma-machi, Kanazawa 920-1192
URL http://polaris.s.kanazawa-u.ac.jp/iscs2019/14:00 – 14:05

Opening (room 6)

Invited lectures (25min + 5min Q&A)
14:05 – 14:35

Reza Rendian Septiawan (Bandung Institute of Technology)
An ODE control system of a rigid body on an ocean wave for a surfer
simulation in the SPH method

14:35 – 15:05

Dam Hieu Chi (JAIST)
Mining Materials Data

15:05 – 15:20

Break

15:20 – 16:40

Short presentations (25 x 3min)

16:45 – 18:00

Poster session (room 2)

1

List of short presentations
1. Muhamad Nasruddin Manaf (Kanazawa University)
Origin of a Negative Fermi Contact Term of Anomalous Muonium in Silicon: FirstPrinciples Study
2. Fathiyya Izzatun Az Zahra (Kanazawa University)
Investigation Spherical Complex Desgin of Finite Unitary Reflection Group
3. Phansphitcha Gugaew (Kanazawa University)
Numerical Study of Stem Cell Growth Model
4. Afrioni Roma Rio (Kanazawa University)
Effect of External Magnetic Field to the Perpendicular Magnetic Thin Films fromFirst-Principles Approach
5. Uswatun Hasanah (Bandung Institute of Technology, Kanazawa University)
Solving matrix-valued convection problems using the generalized Lie derivative
6. Imam Wijaya (Kanazawa University)
Stability estimates and a Lagrange-Galerkin scheme for a Navier-Stokes type model offlow in non-homogeneous porous media
7. Radhinka Bagaskara (Kanazawa University)
Accelerating Molecular Dynamics Simulation with Parallel Computation
8. Arwansyah Muhammad Saleh (Kanazawa University)
Theoretical Study on Stability of RA-VII for Anti-Cancer Agent by Molecular Docking
and Molecular Dynamics Simulation
9. Thomas Aquino Ariasoca (Kanazawa University)
First-principles calculation of hydrogen adsorption on graphene and silicene
10. Marleni Wirmas (Kanazawa University)
First-principles study on electronic and optical properties of Titanium Dioxide: DFTand QSGW method
11. Afifah Maya Iknaningrum (Kanazawa University)
3D simulation of Navier-Stokes flows in straight and curved cylindrical domain
12. Rifky Syariati (Kanazawa University)
Large Anomalous Nernst Effect in The Ferromagnetic 1-T MnSe2
13. Yuto Aizawa (Kanazawa University)
Mathematical formulation of neural network and deep learning algorithm
14. Monika Nur (Kanazawa University)
Structural Study of Surface Alloys on Ag(111) Surface Through Density Functional
Theory2

15. Tharana Yosprakob (Kanazawa University and Chulalongkorn University)
Cahn-Hilliard Equation with Pattern Control
16. Ahmad Fauzan Fibriansyah (Kanazawa University)
Ring of the weight enumerator of triply even codes
17. Henokh Lugo Hariyanto (Kanazawa University)
Numerical study of vortex interactions in hyperbolic Ginzburg-Landau-type equation
18. Yuto Tanaka (Kanazawa University)
First-principles calculation on thermoelectric properties of group-V two-dimensional
materials
19. Ramadhan Paninggalih (Bandung Institute Of Technology / Kanazawa University)
Numerical Level Set Method For Heat Equation With A Codimension One Source
20. Hana Pratiwi Kadarisman (Kanazawa University)
First-principles calculation of gallium monovacancy in gallium nitride
21. Nuntanut Foosarmpok (Chulalongkorn University, Kanazawa University)
A Comparison of Methods for the European Option Pricing
22. Md. Masum Murshed (Kanazawa University, University of Rajshahi)
A study on the stability of the shallow water equations with a transmission boundary
condition in terms of energy estimates
23. Mutiara Dewi Lestari (Kanazawa University)
Theoritical Study on Dynamics of Vesicle by a Coarse-grained Model
24. Achmad Maulana Gani (Kanazawa University)
Investigation of magnetic field effects in solid α-oxygen using van der Waals density
functional approach
25. Habibi Azka Nasution (Kanazawa University)
Theoretical Study of Bubble Dynamics by Coarse-Grained Model

3

An ODE control system of a rigid body on an ocean wave for asurfer simulation in the SPH method
Reza Rendian Septiawan
Institut Teknologi Bandung (za22061991@gmail.com, reza@cphys.fi.itb.ac.id)

In this work we use a smoothed particle hydrodynamics (SPH) method coupled with arigid body simulation to simulate a surfing board on top of an ocean wave. External forces areapplied to the board to represent a surfer trying to control a surfing board. An ordinary
differential equation (ODE) control is used to manipulate the external forces based on a
position, velocity, and an inclination angle of the surfing board. The control system
successfully helps the surfing board to move to and maintain its desired position.
Keywords: ODE, rigid body simulation, smoothed particle hydrodynamics, surfing board
simulation.

Mining materials data
Hieu-Chi Dam
Japan Advanced Institute of Science and Technology
1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan
Phone:+81-761-51-1731; E-mail: dam@jaist.ac.jp

Data mining is a broad discipline that aims to develop and use methods for extracting
meaningful information and knowledge from large data sets. Recently, data mining methods
have successfully been employed to the field of computational materials science. In this work,through examples, we demonstrate that data mining techniques can be used to automaticallyextract practical knowledge of chemical physics from materials systems. A predictive data
mining approach can be applied to first-principles calculation data to computationally model
the chemical and physical properties of materials with high accuracy and low computational
cost [1,2]. A descriptive data mining approach can be used to obtain interpretable insights into
the actuating mechanisms of physical phenomena from experimental and first-principles
calculation data [3]. Further, combinations of the two approaches can be used to support thematerials design process [4]. We also discuss the foundation and future of this research
direction from both mathematical and physical/chemical perspectives.
References
1) T. L. Pham and H. C. Dam et al., J. Chem. Phys., 145, 15, 154103 (2016).
2) T. L. Pham and H. C. Dam et al., STAM, 18, 1, 756-765 (2017).
3) D. N. Nguyen and H. C. Dam et al., IUCrJ, 5, 830–840 (2018).
4) H. C. Dam et al., J. Chem. Phys., 140, 4, 044101 (2014).

Origin of a Negative Fermi Contact Term of Anomalous Muonium
in Silicon: First-Principles Study
Muhamad Nasruddin Manaf 1∗, Susumu Minami 1, Fumiyuki Ishii 2 and Mineo Saito 3
1

Graduate School of Natural Sciences and Technology, Kanazawa University, Kanazawa 9201192, Japan
2
Nanomaterials Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
3
Faculty of Mathematics and Physics, Kanazawa University, Kanazawa 920-1192, Japan*E-mail : muhamad.nasruddin.manaf@mail.ugm.ac.id
The study of defects in materials has been attracting scientific interest during the last
three decades [1]. The study significantly contributes to the development of electronic devices.
Hydrogen is one of the essential impurities in materials, especially in semiconductors [2].
Hydrogen can induce an unfavorable effect such as passivation of the shallow acceptor anddonor, which reduces the performance of semiconductor devices [2,3]. On the other hand,hydrogen is in some cases a shallow impurity, which gives a favorable effect [4]. Muon spinresonance (µSR) is a useful tool to study hydrogen in materials [5]. The muon is an elementary
particle whose mass is 1/9 of that of proton. The muon in a semiconductor captures the electron
and forms muonium. The muonium has similarities with hydrogen. Therefore, the µSR can
predict the dynamics of hydrogen in materials. Muonium in silicon is one of the mostintensively studied systems [6,7]. Anomalous muonium in silicon was found to be located at
the center of the bond and it has a negative value of the Fermi contact interaction (FCI).
Previous theoretical studies presented large deviation from the experimental data and has notwell explained the origin of the negative value of the FCI [3,8]. In this paper, we well reproduce
the experimental value of FCI; the deviation from the experimental data is about 0.2 MHz [9].
We investigate the origin of negative value of FCI by considering a linear tri-hydrogenmolecule, which is a simplified model of the present system.

References
1. H.J. Queisser and E.E. Haller, Science 281, 945 (1998).
2. Hydrogen in Semiconductors, edited by J. Pankove and N.M. Johnson (Academic, New
York, 1991).
3. C.G. Van de Walle and Blӧchl, Phys.Rev.B 47, 4244 (1993).
4. K. Shimomura et.al., Phys.Rev.Lett. 92, 135505 (2004).
5. R.L. Lichti, Protons and Muons in Materials Science, edited by E.A. Davies and S.F.J. Cox(Taylor and Francis, London, 1996).
6. B.D. Patterson et.al., Phys.Rev.Lett. 40, 1347 (1978).
7. R.F. Kiefl, et.al., Phys.Rev.Lett. 60, 224 (1988).
8. R.H. Luchsinger, Y. Zhou and P. Meier, Phys.Rev.B 55, 6927 (1997).
9. M.N. Manaf, S. Minami, F. Ishii and M. Saito (in preparation)

Investigation Complex Spherical Designs ofFinite Unitary Reflection Groups
Fathiyya Izzatun Az Zahra1 , Manabu Oura2
Faculty of Natural Science and Technology Kanazawa University
fathiyyaazzahra@gmail.com1

Unitary group generated by reflectiom ( u.g.g.r.) G is considered as a groupwhich can construct a complex spherical design if Harm(k, l)G = {0}. One way
to check Harm(k, l)G = {0} is by using dimension argument. In this research, thedimension of Harm(k, l)G for u.g.g.r G4 − G37 is calculated by using a generating
function for harmonic polynomials.

1

Numerical Study of Stem Cell Growth Models
Phansphitcha Gugaew1 ,Hirofumi Notsu2 ,Makoto Sato3 and Nakamura Ken-ichi4
1

Faculty of Science, Chulalongkorn University
Faculty of Mathematics and Physics, Kanazawa University
3
Institute for Frontier Science Initiative, Kanazawa University

1,2,3

3

(1 poohdd28@hotmail.com,2 notsu@se.kanazawa-u.ac.jp,
makotos@staff.kanazawa-u.ac.jp,4 k-nakamura@se.kanazawa-u.ac.jp)
Abstract

Stem cells are the body’s master cells. All other cells arise from stem cells, including blood
cells, nerve cells and others. Many researchers and doctors hope stem cell studies can help many
problems in the medical areas. In this study, we are interested in a stem cell growth which may
be useful in various stem cell systems. We study the stem cell growth model by using numericalmethod to see its behaviour. Moreover, focusing on a specific effect of the shape of intermediatestem cells’ region, we consider a reduced model. After that, we apply a special numerical techniqueto solve this reduced model. Then we present numerical examples which clearly illustrate the effectof the shape of region.

𝐾𝐵 𝑇

𝜇B
𝜇B

𝐇𝐱
𝐇𝐱
Δ𝐸

𝐇𝐱

Δ𝐸
𝜇B

Solving matrix-valued convection problems
using the generalized Lie derivative
Uswatun Hasanah1,2 , Hirofumi Notsu2
1
Bandung Institute of Technology, 2 Kanazawa University(1 hassan.uswatunhasanah@gmail.com, 2 notsu@se.kanazawa-u.ac.jp)
In this work we recall the mathematical theory of the generalized Lie derivative
and apply the idea of the generalized Lie derivative to find the approximate solutionof matrix-valued convection problems. It is noted that a matrix-valued convection
equation often appears in a system of viscoelastic flow model. Here, two-dimensional
numerical examples are given to see the convergence order.
Key words: generalized Lie derivative, matrix-valued convection problems

Stability estimates and a Lagrange-Galerkin scheme for a Navier-Stokes
type model of flow in non-homogeneous porous media
Imam Wijaya1, Hirofumi Notsu2
1. Division of Mathematical and Physical Science, Kanazawa University, Kanazawa 920-1192, Japan
2. Faculty of Mathematics and Physics, Kanazawa University, Kanazawa 920-1192, Japan
E-mail: robiah.wijaya239@gmail.com and notsu@se.kanazawa-u.ac.jp

The purposes of this work are to study the L2 -stability of a Navier--Stokes type equation
for non-stationary flow in non-homogeneous porous media proposed by Hsu and Cheng in
1989 and to develop a Lagrange--Galerkin scheme with the Adams--Bashforth method tosolve that model numerically. The stability estimate is obtained thanks to the presence of anonlinear drag force term in the model which corresponds to the Forchheimer term. We
derive the Lagrange--Galerkin scheme by extending the idea of the method of characteristics
to overcome the difficulty which comes from the non-homogeneous porosity. Numericalexperiments are conducted to investigate the experimental order of convergence of thescheme. In both simple and complex designs of porosities, our numerical simulations exhibit
natural flow profiles which well describe the flow in non-homogeneous porous media.

Accelerating Molecular Dynamics Simulation with
Parallel Computation
R. Bagaskara1 , N. Ikhsan1 , M. Obata1,2 , and T. Oda 1,2
1

Graduate School of Natural Sciences and Technology, Kanazawa University, Kanazawa 920-1192, Japan
2

Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japanradhinka@cphys.s.kanazawa-u.ac.jp

Molecular dynamics simulation is a method to simulate statistical and dynamical propertiesof particles in a system. The system allows us to observe the interactions among particles during
a period of time. In order to obtain the best result, the system requires a large number (N )of particles and a smaller time step (∆t) in each iteration. However, this could produce longer
computational time that the simulation is inefficient. To solve this problem, one of methods is
to use parallel algorithms to optimize the computational time. By combining Nvidia’s graphicalprocessing units (GPUs) and CUDA application programming interface (API), we can build amolecular dynamics code with parallel algorithm that can maximize the number of particles
and time step while running the simulation more efficiently.
A classical three dimensional molecular dynamics simulation was used in this research.
To determine the particle’s initial positions, we used the Box-Muller transformation method
in order to randomly generate each set of initial coordinate. The integration algorithm ofvelocity Verlet was used to updates the position and velocity. The velocity Verlet method
is well known as its stability and simplicity. The periodic boundary condition was used forthe cubic simulation cell. The Lennard-Jones was used to describes the potential between
particles. The forces, derivatives with respect to the position, is used to update the positionsand velocities in conjunction with the velocity Verlet method. The computational amount inforce calculation is proportional to N 2 . CUDA is a method developed by Nvidia to write andrun parallel programming. CUDA can be used on Nvidia’s own brand GPUs. It’s mainly used
to parallelizing the force calculation, as it’s the most taxing portion of the whole algorithm.
For the tests, we performed the benchmark between two programs, one running on serial
algorithm while the other one is running on parallel algorithm using CUDA. We benchmark
the overall running time of both programs. Within each test we also increased the numberof atoms with the power of 2 (2n ) starting with 1024 atoms. The ∆t is 0.01 second in 1000
steps. On 4096 atoms, the serial program took about 3,191.215 seconds to finish while the
CUDA program 377.365 seconds to finish, roughly about 8 times faster. This research showsthat by using parallel computation we able to greatly speed up the computation performance.
However, there are still rooms for improvements. In the future, a further research is needed to
add more potential interactions to the algorithms, such as intramolecular interaction, Van der
Waals interaction, and Heisenberg interaction.

Theoretical Study on Stability of RA-VII for Anti-Cancer Agent by Molecular Docking
and Molecular Dynamics Simulation
1*

M.S. Arwansyah, 2Y. Noguchi, 2T. Miyakawa, 1K. Kawaguchi,
Y. Hitotsuyanagi, 3S. Yokojima, 2R. Morikawa, 2M. Takasu, 1H. Nagao
1Div. of Math and Phys. Sci, Kanazawa University, 2Sch. of Life Sci, Tokyo University of Pharmacy
and Life Sciences, 3Sch. of Pharm, Tokyo University of Pharmacy and Life Sciences*Email: arwan@wriron1.s.kanazawa-u.ac.jp
3

1. Introduction
RA-VII is a bicyclic hexapeptide isolated from Rubia cordifolia and R. akane (Rubiaceae) [1,2]. This peptide has ananti-tumor activity by inhibiting the protein synthesis in the ribosome [3]. The 60S ribosome catalyzes the peptide
bond formation and contains the polypeptide exit tunnel which is involved in the protein synthesis in cells [4].
Therefore, it become a potential target for tumor therapy by inhibiting its activity in protein translation
mechanism. In this research, we performed molecular docking and molecular dynamics studies to accurately
predict the cytotoxic mechanism of RA-VII as a promising drug for anti-cancer agent.
2. Methods
Molecular docking simulation was performed by using the AutoDock Vina packages with the Lamarckian genetic
algorithm. Then, we performed molecular dynamics simulation to check the conformation of RA-VII in complex
with the partial 60S ribosomal subunit. The energy representation (ER) method developed by Matubayashi group
was used to estimate the solvation free energy (∆" #$ ) between the partial 60S ribosome and RA-VII [5].
3. Results and Discussion
The structure of RA-VII was optimized to a structure with each constituent atom being a good relative spatial
arrangement [6]. The docking simulation showed that binding models of RA-VII bound to 60S ribosomal
subunitat different locations and had different structure each other.We found that the mode 1 had the lowest
docking energy score as -16 kcal/mol. We performed molecular dynamics simulations to validate theconformation of RA-VII in the partial 60S ribosomal subunit during the simulations. Table 1 shows the average ofthe solvation free energy between the partial 60S ribosome and the RA-VII molecule. From our calculation, we
obtained that RA-VII molecule corresponding to model 1, model 2, and model 5 are stable in binding with thepartial 60S ribosome because the solvation free energy of each of those complexes become larger than the valuesof the standard deviations. Meanwhile, model 2 shows the highest value of the solvation free energy between
the complex. It means that the RA-VII molecules of model 2 is not easy to leave from the binding pocket of thepartial 60S ribosome by comparing other models.
Table 1. The average of ∆%&' of the partial 60S ribosome in complex with RA-VII molecule
Calculated %&' (kcal/mol)
Model
∆%&'
Partial 60S Rib/RA-VII
Partial 60S Rib
RA- VII
Model 1-3057.22 (37.28)-3090.48 (35.97)
51.52 (3.99)-18.26 (2.67)
Model 2-7387.87 (129.57)-7387.88 (137.16)
56.50 (4.51)-56.49 (12.11)
Model 5-2727.95 (84.83)-2751.59 (83.16)
52.11 (4.68)-28.47 (3.01)
Keywords: RA-VII molecule, 60S ribosome, molecular docking, MD simulations, solvation free energy

References[1] Itokawa, H. et al. Chem. Pharm. Bull. 1983, 31:1424-1427.
[2] Itokawa, H. et al. Chem. Pharm. Bull. 1992, 40:2928-2989.
[3] Sirdeshpande BV and Toogood PL. Bioorg. Chem. 1995, 23:460-470.
[4] Hansen, JL. et al. J. Mol. Biol. 2003, 330:1061-1075.
[5] Matubayashi, N. et al. J. Chem. Phys. 2008, 128.
[6] Noguchi, Y. et al. Mol. Simul. 2017, 7022:1-12.

First-principles calculation of hydrogen adsorption on graphene andsilicene
Thomas Aquino Ariasoca1,2* and Mineo Saito1
1

Division of Mathematical and Physical Science, Graduate School of Natural Science andTechnology, Kanazawa University, Kanazawa 920-1192, Japan2
Department of Physics, Faculty of Mathematics and Natural Sciences, Universitas GadjahMada, Sekip Utara BLS 21, Yogyakarta 55281, Indonesia* thomasariasoca@cphys.s.kanazawa-u.ac.jp
It has been known that partially hydrogenated graphene and silicene induce ferromagnetism,
whereas fully hydrogenated system will not induce any magnetism. In this regard, we use firstprinciples calculations to investigate the stability and magnetic properties of graphene and silicene
by considering various hydrogen adsorption configuration. First, we consider hydrogen monomer
system to vary the supercell size. In this work, we use 3 × 3 × 1,4 × 4 × 1, and 5 × 5 × 1
supercells. In monohydrogen in silicene, we consider two hydrogen adatom positions: T position(on top of upper Si atom) and V position (on top of lower Si atom). Based on adsorption energy
calculation, it is found that T-position is the most stable for hydrogen monomer. We found that for
the hydrogen monomer in graphene and silicene, the magnetic moments are 1 𝜇𝐵 . Next, we studyhydrogen dimers. For both graphene and silicene, when two hydrogen atoms adsorb the same
sublattices, the magnetic moment is 2 𝜇𝐵 . On the other hand, when two hydrogen atoms adsorb
different sublattices, any magnetism is not induced.
Keywords: DFT, graphene, silicene, hydrogen adsorption

First-Principles Study on Electronic and Optical Properties ofTitanium Dioxide: DFT and QSGW methods
Marleni Wirmas1 , Hasan Al Rasyid1 , Masao Obata1,2 , Tatsuki Oda1,2
1

Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan
2
Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan

Titanium Oxide (TiO2 ) is recognized for its wide-range of practical use as photovoltaic
solar cells, conventional catalyst support, photocatalytic substrate, and photoelectrochemical materials. It is considered as wide-gap semiconductor with long-term stability, non-toxic
environmental and low-cost availability. Among the polymorphous TiO2 structures, anataseand rutile structure are the most stable and synthesizable crystalline that are found in nature[1]. As the part of photovoltaic solar cell, electrons from valence band could be excited
to conduction band form the process of photovoltaic effect. Therefore, band gap is one of
the significant properties of this material. One of its application is Dye-sensitized solar cell
(DSSC), where porous layer of TiO2 is used as anode in the device. The sunlight can passthrough this dye-layered TiO2 where it can excite electron, transported in electrolyte, andproduce some electrical current.
First-Principles calculation were carried out using density functional theory (DFT) on
both structures. However, the band-gap results were found to be underestimated comparedto the experimental result. Previous studies of DFT method also found this same specific problem[2]. To overcome these difficulties, we used a post-DFT method, called QSGW
(Quasi-particle Self-consistent GW) method, which is a better approach than a usual GW
method. It uses a self-consistent treatment (effective exchange correlation potential) to produce an optimum eigenvalue and eigenfunction of quasi-particle state[3], so that the band
gap would be enhanced.
In this study, we present a combined approach of density functional approach and QSGW
approach on the electronic and optical properties of TiO2 in anatase and rutile structure.
The fully optimized structures, obtained by minimizing the total energy and atomic forces(by varying lattice constants) are in good agreement with experiment. Optimized lattice
constants are a = 3.782 Å and c/a = 2.515 (experiment a = 3.784 Å, c/a = 2.512) for
anatase, and a = 4.623 Å, c/a = 0.646 (experiment a = 4.594 Å, c/a = 0.644) for rutile.
We calculated band dispersions, density of states, and dielectric function of both structures.
As expected, the band gaps from QSGW are much more enhanced compared with those ofusual DFT method, but they are overestimated compared with the experimental result. Thisfeatures are consistent with other cases[4]. This discrepancy between both methods were also
investigated, especially in band dispersion. The better result could be taken into accountwhen calculating the surface properties of TiO2 .
[1]Landmann, et al., J. Phys. Condens. Matter 24 (2012) 195503.
[2]R. Asahi, Y. Taga, W. Mannstadt, and A. J. Freeman, Phys. Rev. B 61 (2000) 7459.
[3]T. Kotani, et al., Phys. Rev. B 76 (2007) 165106.
[4]T. Kotani, et al., J. Phys.: Condens. Matter 19 (2007) 365236.

3D simulation of Navier-Stokes flows in straightand curved cylindrical domains
Afifah Maya Iknaningrum1 , Hirofumi Notsu2 , Pen Yuan Hsu3 ,Tsuyoshi Yoneda4
1) Graduate School of Computational Science, Kanazawa University(afifahmaya35@gmail.com)
2) Department of Computational Science, Kanazawa Universty(notsu@se.kanazawa-u.ac.jp)
3) Graduate School of Mathematical Sciences, University of Tokyo(pyhsu@ms.u-tokyo.ac.jp)
4) Department of Mathematics, University of Tokyo(yoneda@ms.u-tokyo.ac.jp)

Research about natural violent flow phenomena like tornado has been doneby researchers using numerical simulations, where Finite Element Method (FEM)
was used to perform numerical computation of axisymmetric Navier-Stokes flows
with no-slip flat boundary in a straight cylindrical domain which correspond toan ideal shaped tornado [1]. But in natural phenomena, the central axis of
tornado might have curvature. Using similar numerical approach, we make 3Dsimulations in curved cylindrical domain to simulate the tornado with curvature. From the result, it is observed that for several pairs of straight and curved
cylindrical domain shape and initial condition, the effect of the domain shapeis larger compared to the effect of the initial condition. It is also found that for
the larger curvature, the distance from the position of maximum magnitude of
the velocity to the central axis is getting larger.

[1] T. P.-Y.Hsu, H. Notsu, “A local analysis of the axisymmetric navier-stokes
flow near a saddle point and no-slip flat boundary,” J. Fluid Mech., vol. 794,
pp. 444–459, 2016.

Large Anomalous Nernst Effect in The Ferromagnetic 1-T MnSe2
Rifky Syariati1 and Fumiyuki Ishii2,3
Graduate School of Natural Science and Technology, Kanazawa University, Kakuma,
Kanazawa 920-1192, Japan (rifky@cphys.s.kanazawa-u.ac.jp)
2
Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa
University, Kakuma, Kanazawa 920-1192, Japan (fishii@mail.kanazawa-u.ac.jp)
3
Nanomaterials Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
1

Abstract
The two-dimensional 1-T MnSe2 has been discovered experimentally by using molecularbeam epitaxy (MBE) in 2018 [1]. This material has essential properties, and it answers thechallenge about the room temperature two-dimensional ferromagnetic material [1,2]. It has
not only high Curie temperature, but also it has perpendicular magnetic anisotropy whichfavorable for thermoelectric based on the anomalous Nernst effect (ANE). By using the firstprinciples calculation, we found that the ANE coefficient is -3.74 µV/K on the Fermi level at
300 K. This result shows that the 1-T MnSe2 has large ANE coefficient which can be a candidate
for new generation of thermoelectric devices.
References[1] O’Hara, D.J., Zhu, T., Trout, A.H., Ahmed, A.S., Luo, Y.K., Lee, C.H., Brenner, M.R., Rajan, S.,
Gupta, J.A., McComb, D.W. and Kawakami, R.K., 2018. Room temperature intrinsic
ferromagnetism in epitaxial manganese selenide films in the monolayer limit. Nano
letters, 18(5), pp.3125-3131.
[2] Kan, M., Adhikari, S. and Sun, Q., 2014. Ferromagnetism in MnX2 (X= S, Se)monolayers. Physical Chemistry Chemical Physics, 16(10), pp.4990-4994.

Matheamtical formulation of neural network and deep learning algorithm
Yuto Aizawa
School of Mathematics and Physics, Kanazawa University
Email:ay.futsal.univ@gmail.com

The machine learning, especially so called the deep learning, is recently widelyused in industry and sciences. However, its mathematical formulation is often
omitted in many application-oriented literatures. We give a brief review on themathematical formulations for tne neural network and deep learning algorithm, andcompare the diﬀerence in the number of nodes numerically.

1Structural Study of Surface Alloys on Ag(111) Surface ThroughDensity Functional Theory
Monika Nur1, Naoya Yamaguchi1, and Fumiyuki Ishii2
email: monika@cphys.s.kanazawa-u.ac.jp
1. Division of Mathematical and Physical Sciences, Graduate School Natural Science andTechnology, Kanazawa University, Kanazawa 920-1192, Japan
2. Nanomaterials Research Institute, Kanazawa University, Kanazawa 920-1192, Japan

Surface alloys are synthesized by depositing atoms into surfaces, and has attracted
much attention recently due to application, for example, spintronics [1]. Metalsemiconductor interface is of great importance in industry, and, for instance, an Si/Ag
interface is a promising candidate for solar cells [2]. Many kinds of surface alloys has beenstudied: for example, Ge/Ag(111) [3], Ag/Si(111) [4], Pb/Ag(111) [5], Bi/Ag(111) [6],Sn/Ag(111) [7]. Such structural studies of surface alloys may provide important information
to forming metal-semiconductor and metal-metal interfaces.
In this study, we have investigated M/Ag(111) surface alloys systematically, where M isgroup III, IV, and V atoms, B, Al, Ga, In, Tl, C, Si, Ge, Sn, Pb, N, P, As, Sb, and Bi. We focusedon the corrugation parameter defined by the height of M atoms from the Ag atoms in the
top atomic plane. We used OpenMX code [8] and performed first-principles calculation for
M/Ag(111) surface alloys. We will discuss M-atom dependence of corrugation parameters.

Reference[1] C. R. Ast, et al., Phys. Rev. Lett. 98, 186807 (2007).
[2] K. T. Butler, et al., Phys. Rev. B 83, 235307 (2011).
[3] S. Sayawa, J. Goniakowski, and G. Treglia. Phys. Rev. B 61, 8469 (2000).
[4] Y. G. Ding, C. T. Chan, and K. M. Ho, Phys. Rev. Lett. 67, 1454 (1991).
[5] D. Pacile, et al., Phys. Rev. B 73, 245429 (2006).
[6] I. M. Mcleod, et al., Surf. Sci. 604, 1395 (2010).
[7] J. R. Osiecki, and R. I. G. Uhrberg. Phys. Rev. B 87, 075441 (2013).
[8] http://www.openmx-square.org

Cahn-Hilliard Equation with Pattern Control
Tharana Yosprakob1,2 Masato Kimura2
1Chulalongkorn University, THAILAND
2Kanazawa University, JAPAN(t.yosprakob@gmail.com)
In this work, we are interested in pattern control of phase separation described by the
Cahn-Hilliard equation. The volume preservation, energy decay property, and a stability
estimate are presented. Then, we establish the time semi-discrete scheme. Consequently, tocompare the discrete scheme with the Cahn-Hilliard equation, we show error estimates andour convergence theorem. Moreover, we construct different patterns of phase separation in
two-dimension in the numerical results.

Ring of the weight enumerators of triply evencodes
Ahmad Fauzan Fibriansyah and Manabu Oura

Kanazawa University, Institut Teknologi Bandung
Kanazawa University
Abstract. We determine the ring of the weight enumerators of triply evencodes which contain all one vector for small genus.

1

Numerical study of vortex interactions in
hyperbolic Ginzburg-Landau-type equation
Henokh Lugo Hariyanto
Division of Mathematical and Physical Science,
Graduate School of Natural Science and Technology
Kanazawa University (henokh.lugo.h@mail.ugm.ac.id)
The interaction of several vortices for 2D and 3D cases in hyperbolic Ginzburg-Landau-type
equation (HGLE) are investigated numerically. By using explicit scheme, it provides stable
scheme for solving HGLE in a rectangular domain with a specific initial data and Dirichletboundary condition. Several initial data of vortex point(s), vortex line(s), and vortex ring(s) areused to study the behaviour of vortex interactions. We find that the initial data of two vortex
points with winding number w = ±1 behaves like point charge particles. Similar situation
happens in 3d cases when we consider two vortex lines and two vortex rings. There are alsointeresting behaviour when we generate randomly the position of vortices with their winding
number +1 or −1. The remaining number of vortices after time T depend on the total winding
number. Further works are focused on the building of mathematical framework for the vortex
interaction above.

First-principles calculation on thermoelectric properties of group-V
two-dimensional materials
Y. Tanaka1 , M. Saito2 , and F. Ishii2
1
2

Graduate School of Natural Science and Technology, Kanazawa University

Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University

Thermoelectric materials, which can convert heat energy to electric energy, have attracted muchinterests owing to energy issues. To achieve high-performance thermoelectric conversion, we need highelectric conductivities, large Seebeck coeﬃcients and low thermal conductivities. Low-dimensionaland nanostructured materials could be new candidates for eﬃcient thermoelectric conversion [1-3].
The nonequilibrium Green’s function (NEGF) method [4] is suitable for investigating the transport
properties of such nanostructured systems. We focus on group-V two-dimensional (2D) materials.
We perform first-principles calculations by using NEGF method to investigate the spin-orbit coupling (SOC) eﬀect on the thermoelectric properties in α-bismuthene[5], which is the (110) bilayer ofbismuth, and clarify the origin of the anisotropic thermoelectric preterites.
Figure 1 shows the phonon transmittance ζp (ω) and the electron transmittance ζe (E) of αbismuthene. We find anisotropic behaviors in electron and phonon transmittance. Both ζp (ω)
and ζe (E) in the zigzag (ZZ) direction are larger than those in the armchair (AM) direction. The
anisotropy is explained on the basis of the number of transport channels in each direction. The
anisotropy in the thermoelectric properties originates from the anisotropic transmittance. We include the SOC eﬀect in the transmittance calculations and find that ζp (ω) and ζe (E) are aﬀected by
the SOC. Then, we calculate the thermoelectric properties by using the transmittance and estimate
the figure of merit ZT for thermoelectric performance. As shown in Fig. 2, the peak values of ZT in
α-bismuthene are enhanced by the SOC. The peak values of ZT are 0.49 and 1.63 in the non-SOC
calculation and the SOC calculation, respectively.
In conclusion, we found that the anisotropy in the thermoelectric properties of α-bismuthene originates from the anisotropic transmittance explained on the basis of the diﬀerence of the number oftransport channels. We include the SOC eﬀect in our calculations and clarify that the SOC has asubstantial eﬀect on ZT of α-bismuthene.

Figure 2: Figure of merit ZT of α-bismuthene at 300 K.
Figure 1:

Transmittance of α-bismuthene. (a) and (b) : Phonontransmittance. (c) and (d) : electron transmittance.

References[1] L. D. Hicks and M. S. Dresselhaus, Phys. Rev. B 47, 12727 (1993).
[2] L. D. Hicks and M. S. Dresselhaus, Phys. Rev. B 47, 16631 (1993).
[3] M. S. Dresselhaus, G. Chen, M. Y. Tang, R. Yang, H. Lee, D. Wang, Z. Ren, J.-P. Fleurial, and P. Gogna, Adv. Mater.
19, 1043 (2007).
[4] T. Ozaki, K. Nishio, and H. Kino, Phys. Rev. B 81, 035116 (2010).
[5] T. Nagao, J. T. Sadowski, M. Saito, S. Yaginuma, Y. Fujikawa, T. Kogure, T. Ohno, Y. Hasegawa, S. Hasegawa, and T.
Sakurai, Phys. Rev. Lett. 93, 105501 (2004).

Numerical Level Set Method For theHeat Equation With a Codimension
One Source
Ramadhan Paninggalih
Kanazawa University (ramadhanpaninggalih@gmail.com)
February 18, 2019
Abstract
The research motivation comes from phase transition phenomena, for example crystal growth. The
evolution of heat can be described by the heat equation with a source concentrated on a curve or asurface, where the crystal surface becomes the heat source. The research goal is to introduce a numericalmethod for this problem. We use the Poisson equation with a curve heat source as a test problem andapply the finite element method using the FEniCS library for the implementation. The right-hand sideof the weak form becomes a surface integral and can be expressed in three ways adapted mesh, point
sources and a level set method. Adapted mesh and point sources are supported by FEniCS but the levelset method is not (research contribution). We compare error and time cost of the three methods.

First-principles calculation of gallium monovacancy in gallium nitride
Hana Pratiwi Kadarisman and Mineo Saito
Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa
920-1192, Japan
Email address: hanapratiwik@stu.kanazawa-u.ac.jp (Hana Pratiwi K.)

Gallium nitride is a wide band gap semiconductor (Eg=3.47 eV) [1]. The Ga
monovacancy (VGa) in GaN affects the physical properties of the GaN. In this paper, we
carry out calculations of gallium monovacancy in GaN based on the density functional
theory. We study the spin-polarized state in the gallium monovacancy system. By using
the calculated lattice constant of the bulk, we construct the supercell to simulate the Ga
monovacancy. In the optimized geometry, the four N atoms near the vacancy site aredisplaced outwardly. The calculated magnetic moment is 3µB. By calculating the spin
density distributions in the real space, we find that the majority spin is localized and theminority is delocalized. We also find that the positron lifetime for the majority spin isshorter than that of the minority spin.
Keyword: GaN, monovacancy, spin-polarization, geometry, positron, annihilation,
lifetime.

Reference[1] I. Vurgaftman, J.R. Meyer, and L. R. Ram-Mohan., J. Appl. Phys, 89, 5815 (2001).
[2] P. Dev, Yu Xue, and P. Zhang, Phys. Rev. Lett. 100, 1172014 (2008).

A Comparison of Methods for The European Option Pricing
Nuntanut Foosarmpok
Graduate School of Natural Science and Technology, Kanazawa University
nuntanut-pin-kjn@hotmail.com
Abstract
The derivative securities are important in financial industries as they perform remarkable risk and profit management. One of the derivative securities is
option. In this work, we focus an option in European type and its properties. Additionally, we approximate the European option pricing with two methods, which
are the Black-Scholes formula and the Monte Carlo simulation, by a numericalapproach. We found that both of the results are in agreement.

A study on the stability of the shallow water equations with a transmission
boundary condition in terms of energy estimates
Md. Masum Murshed1,3, Kouta Futai1, Masato Kimura2, Hirofumi Notsu2
1. Division of Mathematical and Physical Science, Kanazawa University, Kanazawa 920-1192, Japan
2. Faculty of Mathematics and Physics, Kanazawa University, Kanazawa 920-1192, Japan
3. Department of Mathematics, University of Rajshahi, Rajshahi 6205, Bangladesh
Email: mmmurshed82@gmail.com , futai.k.1275@stu.kanazawa-u.ac.jp, mkimura@se.kanazawau.ac.jp and notsu@se.kanazawa-u.ac.jp

In this study, the stability of the shallow water equations (SWEs) with a transmission boundary
condition is studied theoretically and numerically. For a suitable energy, some mathematicalresults are derived to confirm the stability of the SWEs with the Dirichlet and the slip boundary
conditions. Based on the mathematical results, the stability of SWEs with the transmission
boundary condition is also confirmed numerically by finite difference method (FDM) in termsof the energy. From the numerical results, it is found that for the transmission boundary
condition the total energy decays with respect to time.

Theoritical Study on Dynamics of Vesicle by a
Coarse-grained Model
M.D. Lestari1,a , K. Kawaguchi1,2,b , and H. Nagao1,2,c
1

Graduate School of Natural Sciences and Technology, Kanazawa University, Kanazawa 920-1192, Japan
2
Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japanamutiara@wriron1.s.kanazawa-u.ac.jpbkkawa@wriron1.s.kanazawa-u.ac.jpcnagao@wriron1.s.kanazawa-u.ac.jp

Membranes are ubiquitous in nature, and are essential for cellular life. Many crucial biological functions take place at or near membranes. Vesicles are a model system used to study
the dynamic behaviour of biological cells, similiar in some respects to red blood cells. A vesicle
is a droplet of viscous fluid encapsulated by a phospholipid bilayer membrane suspended in a
fluid of either the same or different viscocity as the inner one. Both the volume and the surface
area of the vesicle is conserved. In this work, motion of membrane particle performs Brownian
motion. The theory of Brownian motion is used to approximate the dynamics of nonequilibrium
systems. The fundamental equation is called the Langevin equation. It contains both frictional
forces and random forces. We have succeeded to perform simulation of vesicle using langevindynamics equation with conserved volume and surface area.

1

Investigation of magnetic field effects in solid α-oxygenusing van der Waals density functional approach
A. M. Gani1,a , I. Pardede1 , M. Obata1,2 , and T. Oda1,2
1

Graduate School of Natural Sciences and Technology, Kanazawa University, Kanazawa 920-1192, Japan
2
Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japanaachmadmgani@cphys.s.kanazawa-u.ac.jp

Oxygen molecule, in the ground electronic state possesses nonzero spin (S =1), which makes
the oxygen molecule a magnetic system. The low-temperature phase of solid α-oxygen isan electron-spin antiferromagnetic insulator consisting of single element. An analysis of thecomprehensive magnetic field-temperature (H -T ) phase diagram in solid oxygen indicates thepossibility that there exist phases induced by a magnetic field. This makes solid oxygen an
extremely interesting object [1,2]. A sudden increase in magnetization and in light transmission
in the visible range is observed when pulsed magnetic fields greater than 90 T were applied.
This findings indicate that the first-order phase transition from α-phase occur in ultrahighmagnetic fields and that there is a new phase θ-oxygen. In this research, we performed firstprinciples calculations on antiferromagnetic solid α-oxygen under external magnetic field andmeasured its magnetic properties.
In this calculation, we used the spin density functional theory (SDFT), fully relativistic
ultra-soft pseudopotential plane-wave basis method, magnetic dipole contribution using spin
density and two-spinols wave function [3]. We included spin-orbit interaction in this calculation
with the exchange-correlation of conventional type (GGA) and spin polarized van der Waals
density functional (vdW). The k point sampling of 8x8x8 mesh was used. Experimental lattice
constant was referred from the neutron-diffraction measurement[4]. We applied the external
magnetic field in the range of 0-100 T.
Our result shows that the magnetization is increased with the non linear behavior as theexternal magnetic field increases. The total spin magnetic momenta at 100 T are 0.307µB and
0.309µB in the x and z directions, respectively, for vdW. The GGA values were 0.368µB and
0.364µB . The magnetization was fitted to the 4th order polynomial function of external field.
The susceptibility component (χαβ ), where α and β = x, y, z, was calculated from the first
derivative of polynomial function. The value of χxx , χyy , χzz at zero field were 2.755 × 10−3 ,0, and 2.777 × 10−3 µB /T, for vdW. χxx , χyy , χzz were 3.094 × 10−3 , 0, and 3.079 × 10−3 µB /T
for GGA values. The uniform susceptibility (χuni ) is obtained by taking the average of the
diagonal components. The obtained values were 1.844 × 10−3 and 2.058 × 10−3 µB /T for vdW
and GGA, respectively. The χuni is slightly larger for the GGA compared to vdW. Those values
are smaller than the experiment [2]. The difference may come from several factors, such as thelack of treatment of Landau diagmanetism, susceptibility contribution from orbital moment
and underestimation in the bandgap. The present results imply that we can combine SDFT
with the external magnetic field in order to calculate magnetic properties such as magnetization
curve and susceptibility.
[1]C. Uyeda, et al., J. Phys. Soc. Jpn. 54, pp. 1107-1115 (1985)[2]T. Nomura, et al., Phys. Rev. 96, 054439 (2017)[3]M. Obata, et al., AIP Advances 8, 101419 (2018)[4]R. J. Meier, R. B. Helmholdt, Phys. Rev. B 29, 1387 (1984)

1

Theoretical Study of Bubble Dynamics by Coarse-Grained Model
Habibi Azka Nasution1,a , Kazutomo Kawaguchi2,b , Hidemi Nagao3,c1
Graduate School of Natural Science and Technology, Kanazawa University, 920-1192,
Japan
2−3
Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japanahabibi@wriron1.s.kanazawa-u.ac.jpbkkawa@wriron1.s.kanazawa-u.ac.jpcnagao@wriron1.s.kanazawa-u.ac.jp
It is interesting to study the biological system. One of them is how to describe a surface of the system. In this work, we simulate on the dynamics of system surface, where thesystem that we propose is a bubble system. In this study, we solve the Langevin equationof motion to approach the bubble system. We have two potential energy function V1 andV2 for our bubble dynamics. Then, we used Taylor’s expansion as an approach to numericalcalculations. First, we simulated the surface of the bubble system with a fixed configuration.
Second, we simulated the surface of the bubble system with a changed configuration. Surface
transition systems such as bubble systems has been proposed. In this study, the Langevinequation which has a potential function as the principle of minimization of surface area andvolume conservation can be implemented.

1