Introduction of local magnetism in a superconductor exhibits exchange coupling interaction with the Cooper pairs of superconductor. This interaction locally perturbs or breaks the Cooper pairs, leading to the formation of localized bound states within the superconducting energy gap, known as Yu-Shiba-Rusinov bound states (Shiba states). In
this thesis, we have investigated this phenomenon by introducing magnetic Mn atoms into the Ni Kagome islands grown on an s-wave superconducting Pb(111) substrate. Based on the growth of Mn atoms on the Ni Kagome islands, we have observed two types of structures called as: monomer and trimer. Each structure exhibits different numbers of bound states with distinct energy positions. Where on one hand, the trimer structure exhibits a high degeneracy feature as determined by the analysis of the bound state number. On another hand, the monomer structure shows partial disruption of electron degeneracy. Furthermore, the decay of conductance mapping intensity with lateral distance for both structures has been measured that the decay rate of the trimer structure is relatively higher than that of the monomer structure. Finally, the energy positions of the bound states for the monomer and trimer structures have obtained by using deconvolution process, which are 0.94 meV, 1.04 meV, 1.22 meV and 0.34 meV, 0.84 meV, respectively.
When magnetic atoms are introduced into a metallic substrate, spins of magnetic atoms are screened out by the spin of conduction electrons near the Fermi level, leading to an exchange coupling interaction. This interaction results in a characteristic zero-bias peak observed at the Fermi level, known as the Kondo effect. We have investigated the Kondo effect by introducing magnetic molecules, specifically Iron(II) Phthalocyanine (FePc) molecules on bismuthene grown on an Ag(111) substrate. Based on the growth behavior of FePc molecules, we have observed that the ground state energy of FePc molecules when absorbed on the bismuthene structure is relatively higher than the buckled bismuthene phase, rectangular phase, the edge of the bismuthene phase, and the defects on the bismuthene phase. Additionally, we observe that when FePc molecules with eight hydrogen atoms absorbed on the bismuthene phase, do not exhibit Kondo effect. However, after dehydrogenation of the FePc molecule, local spins are gradually restored, and a pronounced Kondo effect signal has been observed near the Fermi level.

Abstract I
Acknowledgements III
Contents IV
List of Figures VII
List of Tables XVII
1 Introduction 1
1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Superconductor . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.1 Meissner Effect . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.2 Bardeen-Cooper-Schrieffer (BCS) Theory . . . . . . . . . . . . 4
1.2.3 The Hamiltonian of BCS s-wave Superconductor . . . . . . . . 7
1.3 Yu-Shiba Rusinov Bound State (Shiba state) . . . . . . . . . . 13
1.3.1 The Hamiltonian of Shiba State on the BCS s-wave Superconductor 17
1.4 Relevant Literature on Magnetic Atoms on Superconductors . . . 22
1.5 Kondo Effect . . . . . . . . . . . . . . . . . . . . . . . . . 27
1.5.1 Kondo Model . . . . . . . . . . . . . . . . . . . . . . . . . 28
1.5.2 The Anderson Model . . . . . . . . . . . . . . . . . . . . . 32
1.6 Relevant Literature on Transition Metal Phthalocyanine (TMPc) Molecule on Metallic Substrate . . . . . . . . . . . . . . . . . . 37
1.7 Relevant Literature on Ultraflat Bismuthene on Ag(111) Substrate 38
2 Experimental Methods 42
2.1 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . 42
2.2 Vacuum Chamber . . . . . . . . . . . . . . . . . . . . . . . . 45
2.2.1 Dry Scroll Pump . . . . . . . . . . . . . . . . . . . . . . . 45
2.2.2 Turbo Pump . . . . . . . . . .. . . . . . . . . . . . . . . . 46
2.2.3 Ion Pump and Titanium Sublimation Pump (TSP) . . . . . . . . 47
2.3 Vacuum Gauge . . . . . . . . . . . . . . .. . . . . . . . . . . 48
2.3.1 Pirani Gauge . . . . . . . . . . . . . .. . . . . . . . . . . 49
2.3.2 Ion Gauge . . . . . . . . . . . . . . . . . . . . . . . . . . 50
2.4 Residual Gas Analyzer (RGA) . . . . . . . . . . . . . . . . . . 50
2.4.1 Ionizer . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.4.2 Quadrupole Mass Filter . . . . . . . . . . . . . . . . . . . 53
2.4.3 Ion Detector . . . . . . . . . . . . . . . . . . . . . . . . 53
2.5 Vapor Deposition Method . . . . . . . . . . . . . . . . . . . . 54
2.5.1 Electron-Beam Evaporator . . . . . . .. . . . . . . . . . . . 54
2.5.2 Knudsen Cell (K-Cell) . . . . . . . . . . . . . . . . . . . . 56
2.6 Quantum Tunneling Effect . . . . . . . .. . . . . . . . . . . . 56
2.6.1 One-Dimensional Potential Barrier . . . . . . . . . . . . . 57
2.6.2 Tersoff-Hamann Approximation . . . . . . . . . . . . . . . . 59
2.6.3 Scanning Tunneling Microscope (STM) . . . . . . . . . . . . . 62
2.6.4 Scanning Tunneling Spectroscopy (STS) . . . . . . . . . . . . 63
2.7 Scanning Mode . . . . . . . . . . . . . . . . . . . . . . . . . 65
2.7.1 Constant Height Mode . . . . . . . . . . . . . . . . . . . . 65
2.7.2 Constant Current Mode . . . . . . . . . . . . . . . . . . . . 65
2.8 Cooling System . . . . . . . . . . . . . . . . . . . . . . . . 66
2.9 Sample Preparation . . . . . . .. . . . . . . . . . . . . . . . 68
2.9.1 Substrate Preparation . . . . . . . . . . . . . . . . . . . . 68
2.9.2 Mn Atoms on Ni Kagome Island on Pb(111) . . . . . . . . . . 70
2.9.3 Iron(II) Phthalocyanine (FePc) Molecules on Bismuthene on
Ag(111) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
3 Experimental Results 72
3.1 Mn Atoms Adsorbed on Ni Kagome Islands on Pb(111) . . . . . . . 72
3.1.1 Sample Preparation . . . . . . . . . . . . . . . . . . . . . 72
3.1.2 Ni Kagome Islands on Pb(111) . . . . . . . . . . . . . . . . 73
3.1.3 Mn atoms on Ni Kagome Island on Pb(111) . . . . . . . . . . . 73
3.2 FePc Molecules Adsorbed on Bismuthene on Ag(111) . . . . . . 85
3.2.1 Sample Preparation . . . . . . . . . . . . . . . . . . . . . 85
3.2.2 FePc Molecules on Bismuthene on Ag(111) . . . . . . . . . . . 85
3.2.3 Tip Induced Manipulation of FePc Molecules on Bismuthene on
Ag(111) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
3.2.4 The Kondo Resonance Induced by Removing the Hydrogen
Atoms from FePc Molecules on Bismuthene on Ag(111) . . . . 87
4 Summary 91
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