Computational Science Center• Brief History of CSC
Aug. 2001 – Computational Materials Science Group Launched.
Nov. 2003– 1024 cpu Linux cluster system (2.85 Tflops) set-up
2005 and 2006– The best research group awards in KIST
Jan. 2007– Computational Science Center Launched.
Cu doped GaN– Nano Letters, 7, 3366 (IF=9.960) – Appl. Phys. Lett. 90, 032504 (IF=3.977)
Me-C bonds – Carbon, 46, 185 (IF=4.260)
Thin film interface – Acta Mater. 56, 1011 (IF=3.549)
Protein structure calculation– J. Comp. Chem, 28, 2552 (IF=4.893)
Nanostructured surface – Adv. Mater. 20, 1903 (IF=7.896)
• Highlight Publications (2007~2008)
• Organizational Chart
Head of CSCKwang-Ryeol Lee
HPC & Bio Simulation Nano-materials Simulation
Kwang-Ryeol LeeKyu-Hwan Lee Hwanwon ChungJung Soo Oh Jung-Hae Choi Seung-Cheol LeeMyoung-Woon Moon
Interface & Surface
• Nano and Bio Tecchnology
(sub)atomic scale understandingsof structure, kinetics and properties
HPC & Bio Application
KIST Linux cluster (1024 CPU)
Protein folding by optimization
Simuloscope
Visualization & Analysis
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25 72 20 4052 38 5996 12
14 6757 477110 95 78 4858 2
298 87 3554 61 105 9 93 109 103 31 15
36 100 84 10443 28 62 60 81 3 17 8526 91 71
44 22 65 550 106
7916747671071889
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25 72 20 4052 38 5996 12
14 6757 477110 95 78 4858 2
298 87 3554 61 105 9 93 109 103 31 15
36 100 84 10443 28 62 60 81 3 17 8526 91 71
44 22 65 550 106
7916747671071889
11192498299693346
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Optimization algorithmGenetic algorithm
Ab-Inito Calculation
SiGe
Si50Ge50 1-Dimensional Nanowire
Strain effects on Ge thin films
109.5o
C/Me
90o~130o
Bond characteristics In DLC containing metals
Synth. & Appl.of Nanostructure Surface
Bio-medical Applications of Nanostructure
Fuel cell nano-fiber : Energy
Fundamental Understanding of Surface Nanostructures
Asymmetric surface intermixing during thin-film growth in the Co–Al
Molecular Dynamics
[001]
[100] [110]
θ=2o
[110]
θ=2o
[010]
[001]
[100]
[010]θθ
Structure of Si (001) vicinal surface
[010]θ
-30 -20 -10 0 10 20 30-30
-20
-10
0
10
20
30
Distance from Impact Point [A]
Dis
tanc
e fr
om Im
pact
Poi
nt [A
]
Surface nanostructure evolution by ion bombardment
CNT buckling by sonication(in collaboration with Brown Univ.)
Stable Phase of Ni Nanocluster
• Simulation Scope
Researchers & Developers
Researchers & Developers
Potential DB
Virtual Reality User I/F
MultiscaleSimul. Codes
MassiveComputation
PotentialDevelopment
Computation
Theory Experiment
Traditional
Computational science can- reduce time and cost for R&D- increase research efficiency
Computation
Theory Experiment
Computational science can- reduce time and cost for R&D-
High Performance Computing & Bio Simulation
• Hardware/Software Infrastructure • Bio Simulation
All-Atom De novo Protein Folding with a Scalable Evolutionary Algorithm
(a) : Starting conformation(b), (c) : Overlay of the experimental (red)
and the folded structure (blue). Backbone RMS deviation = 3.43 A ˚
(d) : Schematic illustration of the different routes of the evolutionary algorithm
Simulation Softwares
LAMMPS
EAM/MEAM
SiON FFBrenner Polymers FF
Tersoff
SIESTA TB Calculation
Kinetic MC
Ab initio MD & MC
KIST-MD
Ab-initio Calc. CodesVASP, WIEN2K, SIC-LSDA, DMOL3
Simuloscope
Electron Transport Theory
KIST Suite forComputational
Nanoscience(KIST-SCN)
Residual Stress
Bond Coord.
RDF & P-RDF
Density
Ring Statistics
Action Driven MD
Reactive FF
GROMACS
Crystal Builder
EAM converter
XMD
EAM Brenner
Visualizer
Bond Angle DF
Me-O FF
KIST Linux Cluster 1,024 CPUs
Opening, 2003.12.24
Certificate, 2003.11
512 Computing Nodes
Myrinet
Public Network(KOREN)
Head Node
NFS server
Storage
Partnership & Leadership for nation-wide Supercomputing Infrastructure
PLSI Project
Linux Cluster for ab-initio CalculationOS : CentOS 5.2CPU type : Quad-core Intel Xeon E5450, 3.0GHzNumber of Nodes : 16Number of Cores per node : 8 Memory per node : 32 GBInterconnection Network : Myrinet 10G NIC & SwitchFile Server : 25 TB (GFS, GPFS client)
OptimizationGenetic Algorithm, Simulated Annealing, etc.
• Optimization & Algorithms
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25 72 20 4052 38 5996 12
14 6757 477110 95 78 4858 2
298 87 3554 61 105 9 93 109 103 31 15
36 100 84 10443 28 62 60 81 3 17 8526 91 71
44 22 65 550 106
7916747671071889
11192498299693346
2155 45 53101
66 51 19102 3473
2375 5698
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TozongDock : Application of Stochastic Optimization to Protein-Ligand Docking
Wenzel, Hamacher, Phys. Rev. Lett. 82, 3003 (1999)
Morris et al.
Protein-Ligand Docking
Stochastic Tunneling
+
• Visualization : 3-D Stereo Graphic System
Emitter
Visualization Workstation
Crystall eye glasses X 5
Stereo Projector
First Principles Calculation of Materials• Softwares for Ab-Inito Simulations
Ab-initioAb-initio
*VASP: Planewave pseudopotential
NEB: Nudged Elastic BandUtilitiesUtilities
*WIEN2k: Full potential LAPW
CRYSTAL06 : Atomic orbital
ABINIT, CPMD, SIESTA
Structure Utilities : Actively developing
Cluster Expansion : ATAT
• Search for New Functional Materials
CuCu
-6 -4 -2 0 2 4-0.5
-0.4
-0.3
-0.2
-0.1
0.0
0.1
0.2
0.3
0.4
0.5
DO
S (s
tate
s/eV
cel
l)
Energy (E-EF, eV)
1st NN 2nd NN 3rd NN 4th NN 5th NN
Magnetization Density Density of StatesZinc Blende GaN
Diluted Magnetic Semiconductors: Cu doped GaN
• Search for New Functional Materials:Monte Carlo + Ab-Initio
<110>
<1-10>
<001>
ZB r1 r2 r3 r4 r5 r6 r7 r8 r9 r10 SL
-316.0
-315.8
-315.6
-315.4
-315.2
-315.0
-314.8
Tota
l Ene
rgy
(eV/
cell)
315.78 eV
0.82 eV
0.21 eV
ZB
Random
SL
Si
Ge
Si50Ge50 1-Dimensional Nanowire
• Understanding Bond Nature
109.5o
Me
90o~130o
MeΔEMe-C
CMax;1.05
Z;4
35
d=1.54
AlMax;0.69
d=2.05
MoMax;0.69
d=2.10
AgMax;0.63
d=2.273 4 5 6 7 8 9 10 11 12 13 14 15
-1
0
1
2
Fe
Mn
V
ZnCd AlNi
Pd
CoCuAgAu
MoCrW
Ti
Si
C
ΔE
90o (e
V)
atomic group (# of valence e-)
2nd period 3rd period 4th period 5th period 6th period
Metal Incorporated Carbon
Ge on Biaxial Compressive Strain
graded SiGeGe film
Si substrate
Ge film
Si substrate
Ge
Si2 nm
Strained !
• Strain Effects – Thin Film
[0001]
1st Mn
2nd Mn
Compressive strain
0.316eV
• Strain Effects - NanowireDopant Configuration in GaN-nanowire Unstrained
0.032eV
IPD
OPD
Unstrained-IPD
Mn Mn
N
3.09 Å
DO
S
Partial DOS of Mn
E-EF(eV)
Total DOS of Mn
E-EF(eV)
DO
S
Compressive strain-IPD
Mn Mn
N
2.95 Å
DO
S
Partial DOS of Mn
E-EF(eV)
dx2-y2
dz2
dxy
E-EF(eV)
DO
S
Total DOS of Mn
Schrödinger’s Equation
Cohesive energy, Lattice parameterBulk modulus, Electronic propertiesMagnetic Properties etc …
HΨ=EΨ
Molecular Dynamics Simulation• Thin Film and Surface Phenomena in Atomic Scale
Asymmetic Intermixing of Interface
Co
Al
Al
Al
Co
Co
0.1eV Al at 300K0.1eV Co at 300K
Origin of Stress in Amorphous Carbon Film
Experiment
0 50 100 150 200 250 300
-6
-3
0
3
6
9
12
15
Stre
ss [G
Pa]
Beam Energy [eV]
Simulation
0 -100 -200 -300 -400 -5000
2
4
6
8
10
DC Bias (V)
Stre
ss (G
Pa)
High Stress Configuration
2.0~2.2 Å j80~95 º
i
Low Stress Configuration
~2.5 Åj
~105 º
i
1 2 3 4 50
5
10
15
300 eV
150 eV
100 eV
50 eV
10 eV
1 eV
Pair
Cor
rela
tion
Func
tion ρ(
r)
r [A]
Surface Structure Evolution by Ion Bombardment
10 keV Ar ion impacts on Au(001)
Ion
Sputtered atoms
Rearranged atoms
-30 -20 -10 0 10 20 30-30
-20
-10
0
10
20
30
Distance from Impact Point [A]
Dis
tanc
e fr
om Im
pact
Poi
nt [A
]
Pd
T.C. Kim et al., Phys. Rev. Lett., 92, 246104 (2004)
Atomic scale composition separation in CoCu alloy by Ar bombardment
0 100 200 300 400
35
40
45
50
55
60
Ato
mic
per
cent
of C
u
Number of Ar ion bombardment
1st layer 2nd layer 3rd layer 4th layer
Morphology Evolution of Nanoscale Materials
1 atom 50 atom 100 atom
150 atom 200 atom 264 atomAl deposition behavior on Cu (111)
CNT buckling by sonication(in collaboration with Brown Univ.)Stable phase in nanocluster is governed
by the surface energy.
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