SPM

Advanced Algorithm & Systems

201666

[ (IrAu)S. Ogura et al., Phys. Rev. B 73, 125442 (2006); S. Ogura and K. Fukutani, J. Phys.: Condens. Matter 21 (2009) 474210.]

SPM

(1)

SPM

(2)69

SPMDFTB()

69STM, STS, AFM, KPFM

Si(111)(77)DAS

Si(111)(77)DASSTM

3D

F U

stacking-faultedstacking-unfaulted

DFTB

DFTBSi(111)-7x7 DASSTM

SPM

DFTB()

Si(111)-7x7 DAS (dimer-adatom-stacking fault)STM(2009)

69

DFTB preliminary DB

20169

69

DFTB (2015/12/25)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 181 H He2 Li Be B C N O F Ne3 Na Mg Al Si P S Cl Ar4 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr5 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe6 Cs Ba *1 Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn7 Fr Ra *2 Rf Db Sg Bh Hs Mt Ds Rg Cn 113 Fl 115 Lv 117 118

*1 La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu*2 Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr

27 (2015/09/26)12 H, C, N, O, Al, Si, P, Ti, Ru, W, Pt, Au15 Li, B, F, Na, Mg, S, Cl, Cu, Ga, Ge, As, Br, Ag, I, Bi

32 17 Sc, V, Cr, Mn, Fe, Co, Ni, Zn, Y, Zr, Nb, Mo, Tc, Rh, Pd, Re, Ir 8 La, Ce, Gd, Tb, Dy, Ho, Er, Tm 4 Se, In, Sb, Te 3 K, Rb, Cs

1010 Be, Ca, Sr, Ba, Cd, Sn, Hg, Pb, Yb, U

69

AFM

Protein Data Bank

LiqAFM

GeoAFM()

CG()

SPM

:SPM(DFTB)

SPMSPMSPM

XXXXXXSPMDFTB69SPM

AFM(m)

AFM()

STM()

20174STM()

STMSTSKPFM

AFM

AFM

Analyzer

SetModel

DFTB

CG

MDMDCG RISM

LiqAFM

GeoAFM

FemAFM

no

no

no

no

yes

yes

yes

yes

SPM8

Analyzer

SetModel

GeoAFM

FemAFM

LiqAFM

CG

MD

DFTB

AFM

AFM

AFM

AFM

AFM

SPM()

Analyzer()(1)

()

(

)

Analyzer()(2)

()

(Sobel)

GeoAFM(AFM)(1)

ConeGroEL()AFM(140[]140[]200[])

AFM

Tip: Cone shape

Sample:

Myosin V (PDB: 2dfs)

Result of GeoAFM

Analyzer

1

VAFM

ExperimentSimulation

GeoAFM (AFM)(2)

H.Asakawa, K.Ikegami, M.Setou, N.Watanabe, M.Tsukada, T.Fukuma. Biophysical Journal 101(5), 1270-1276 (2011).AFM

GeoAFMAFM

GeoAFM (AFM)(3)

tubulinFM-AFMAFM

FemAFM(AFM)(1)

HOPG(HighlyOriented PyrolyticGraphite)

(CLG(L))AFM

FemAFM(AFM)(2)

DNA(Self-assembled Three-Dimensional DNA)AFM

Tip: double tip

Sample:

1-clg on HOPG

Frequency shift mode

Constant height (static) mode

double-tipHOPG1-clgAFMAFM

FemAFM(AFM)(3)

AFM

LiqAFM(AFM)(1)

:

0.891 x 10-6 m2/s

:997.0 kg/m3

:

1.396 x 10-6 m2/s

:785.0 kg/m3

n-:

4.34 x 10-6 m2/s

:769.99 kg/m3

Head height vs. time Amplitude vs. time

n-

LiqAFM(AFM)(2)

LiqAFM(AFM)(3)

AFM

f < 0

f 0

CG

CG-RISM

L. Gross et al., Science 325, 1110-1114 (2009).

Good agreement

CO

C22H14

CG(AFM)(1)

CG(AFM)(2)

AFM

z2

CG (AFM)(3)

AFM

Tip: capped SWCNT,

diameter = 7.99 ,

length = 12.08 ,

Atomic configuration is fixed.

Sample: SWCNT,

diameter = 15.57 ,

length = 40.95 ,

both edges are fixed in space,

the others can be relaxed. withdrawal

approach

CNT

withdrawal

approach

approach withdrawal

CNT

CG (AFM)(4)

ExperimentS. Decossas et al., Europhys. Lett., 53 (6), pp. 742-748 (2001).

MWCNT()Si3N4CNT1000 nmCNT2000 nm

40% Digital Dimension 3100 AFM0.58 or 0.06 N/m Si3N420-50nmMWCNT25nmnmm

()CNT

MD(AFM)(1)

MD(AFM)(2)

AFMcollagen

Tip: capped SWCNT

Diameter: 7.8

Height: 29.1

Sample: SWCNT

Diameter: 15.6

Height: 62.1

(1)(2)(3)(4)(5)

(1)

(2)

(5)

(3)

(4)

zz

(1)CNTCNT(2)CNTCNT(3)CNTCNT(4)CNTCNT(5)CNTCNT

(2)(4)CNTCNTCNTCNT

MD(AFM)(3)

CNTCNT

DFTB(SPM[])(1)

Si(001)AFM

1.04e+5 nA

0.02e+5 nA

-0.30e+4 nA

-5.70e+4 nA

+1.0V -1.0V

: Si4H9: Si(001)-c(4x2)-: 2.32

STM

Si(001)

K. Hata, S. Yasuda, and H.

Shigekawa, Phys. Rev. B 60,

8164 (1999).

Si(001)-c(4x2)STM

DFTB(SPM[])(2)

KPFM

Si(001)-c(4x2)KPFM

DFTB(SPM[])(3)

KPFM

KPFM

AFM

: H-Si4H10: Si(001)-c(4x2)

-: 6

: H-Si4H10: Si(001)-c(4x2)

Si(001)-c(4x2)(N)KPFM

DFTB(SPM[])(4)

LCPD

: Pt14: TiO2(110)

KPFMTiO2(110)LCPD

TiO2(110)LCPD()

DFTB(SPM[])(5)

H

Si

: Si4H10: Si(001)-: 6.5

: Si4H10: Si(001)-c(4x2)-: 6.0

DFTB(SPM[])(6)

104HSi[001]

[-110]

)11()110(2 TiO

[110]

[-110]

Surface Science Reports,66, (2011),1-27

KPFM

AFM

KPFM -2.5AFM -3.5[001]

[-110]

: Si4H10 : TiO2(110)-(1x1)

TiO2(110)AFM, KPFM

DFTB(SPM[])(7)

Au(111)coroneneSTM

CoroneneNa

DFTBSTM

DFTB(SPM[])(8)

CoroneneNaAu(111)STMHSi

STM

STM

Au(111)CoroneneNaHSiSTM

STM

Coronene

DFTBSTM

CoroneneNaAu(111)STMHSi

CoroneneNa

STM

STM

Au(111)CoroneneNaHSiSTM

CoroneneNa

STM