Note: Intro -- Quantum Ising Phases and Transitions in Transverse Ising Models -- Preface -- Contents -- Chapter 1: Introduction -- 1.1 The Transverse Ising Models -- 1.2 A Simple Version of the Model and Mean Field Phase Diagram -- 1.3 Properties of Ising Models in a Transverse Field: A Summary -- Chapter 2: Transverse Ising Chain (Pure System) -- 2.1 Symmetries and the Critical Point -- 2.1.1 Duality Symmetry of the Transverse Ising Model -- 2.1.2 Perturbative Approach -- 2.2 Eigenvalue Spectrum: Fermionic Representation -- 2.2.1 The Ground State Energy, Correlations and Exponents -- 2.3 Diagonalisation Techniques for Finite Transverse Ising Chain -- 2.3.1 Finite-Size Scaling -- 2.3.2 The Diagonalisation Techniques -- 2.3.2.1 Strong Coupling Eigenstate Method -- 2.4 Real-Space Renormalisation -- 2.4.1 Block Renormalisation Group Method -- 2.5 Finite Temperature Behaviour of the Transverse Ising Chain -- 2.6 Experimental Studies of the Transverse Ising Chain -- Appendix 2.A -- 2.A.1 Jordan-Wigner Fermions -- 2.A.2 To Diagonalise a General Hamiltonian Quadratic in Fermions -- 2.A.3 Calculation of Correlation Functions -- Chapter 3: Transverse Ising System in Higher Dimensions (Pure Systems) -- 3.1 Mapping to the Effective Classical Hamiltonian: Suzuki-Trotter Formalism -- 3.2 The Quantum Monte Carlo Method -- 3.2.1 In nite M Method -- 3.3 Discretised Path Integral Technique for a Transverse Ising System -- 3.4 In nite-Range Models -- 3.4.1 Husimi-Temperley-Curie-Weiss Model in a Transverse Field -- 3.4.2 Fully Connected p-Body Model in a Transverse Field -- 3.5 Scaling Properties Close to the Critical Point -- 3.6 Real-Space and Field-Theoretic Renormalisation Group -- 3.6.1 Real-Space Renormalisation Group -- 3.6.2 Field-Theoretic Renormalisation Group -- Appendix 3.A -- 3.A.1 Effective Classical Hamiltonian of the Transverse Ising Model. , 3.A.2 Derivation of the Equivalent Quantum Hamiltonian of a Classical Spin System -- Chapter 4: ANNNI Model in Transverse Field -- 4.1 Introduction -- 4.2 Classical ANNNI Model -- 4.3 ANNNI Chain in a Transverse Field -- 4.3.1 Some Results in the Hamiltonian Limit: The Peschel-Emery Line -- 4.3.2 Interacting Fermion Picture -- 4.3.3 Real-Space Renormalisation Group Calculations -- Critical Ground State Energy -- 4.3.4 Field-Theoretic Renormalisation Group -- 4.3.5 Numerical Methods -- Strong Coupling Eigenstate Method (SCEM) -- 4.3.6 Monte Carlo Study -- 4.3.7 Recent Works -- 4.4 Large S Analysis -- 4.5 Results in Higher Dimensions -- (i) Phase Diagram in the Mean Field Approximation -- (ii) Phase Diagram from Path Integral Approach -- 4.6 Nearest Neighbour Correlations in the Ground State -- Appendix 4.A -- 4.A.1 Hartree-Fock Method: Mathematical Details -- 4.A.2 Large S Analysis: Diagonalisation of the Hamiltonian in Spin Wave Analysis -- 4.A.3 Perturbative Analysis -- Chapter 5: Dilute and Random Transverse Ising Systems -- 5.1 Introduction -- 5.2 Dilute Ising System in a Transverse Field -- 5.2.1 Mapping to the Effective Classical Hamiltonian: Harris Criterion -- 5.2.2 Discontinuous Jump in Gammac(p,T = 0) at the Percolation Threshold -- 5.2.3 Real-Space Renormalisation Group Studies and Scaling -- 5.3 Critical Behaviour of Random Transverse Field Ising Models -- 5.3.1 Analytical Results in One Dimension -- 5.3.2 Mapping to Free Fermions -- 5.3.3 Numerical Results in Two and Higher Dimensions -- Chapter 6: Transverse Ising Spin Glass and Random Field Systems -- 6.1 Classical Ising Spin Glasses: A Summary -- 6.2 Quantum Spin Glasses -- 6.2.1 Experimental Realisations of Quantum Spin Glasses -- 6.3 Sherrington-Kirkpatrick (SK) Model in a Transverse Field -- 6.3.1 Phase Diagram -- 6.3.1.1 Mean Field Estimates -- 6.3.1.2 Monte Carlo Studies. , 6.3.1.3 Exact Diagonalisation Results -- 6.3.2 Susceptibility and Energy Gap Distribution -- 6.3.3 SK Model with Antiferromagnetic Bias -- 6.3.3.1 Mean-Field Theory -- 6.3.3.2 The Condition on Which Antiferromagnet Phase Survives -- 6.4 Edwards-Anderson Model in a Transverse Field -- 6.4.1 Quantum Monte Carlo Results -- 6.5 A General Discussion on Transverse Ising Spin Glasses -- 6.5.1 The Possibility of Replica Symmetric Ground States in Quantum Glasses -- 6.6 Ising Spin Glass with p-Spin Interactions in a Transverse Field -- 6.6.1 p-Body Spin Glass with Ferromagnetic Bias -- 6.7 Random Fields -- 6.7.1 Classical Random Field Ising Models -- 6.7.2 Random Field Transverse Ising Models (RFTIM) -- 6.7.2.1 Mean Field Studies -- 6.7.2.2 Mapping of Random Ising Antiferromagnet in Uniform Longitudinal and Transverse Fields to RFTIM -- 6.7.3 Concluding Remarks on the Random Field Transverse Ising Model -- 6.8 Mattis Model in a Transverse Field -- Appendix 6.A -- 6.A.1 The Vector Spin Glass Model -- 6.A.2 The Effective Classical Hamiltonian of a Transverse Ising Spin Glass -- 6.A.3 Effective Single-Site Hamiltonian for Long-Range Interacting RFTIM -- 6.A.4 Mapping of Random Ising Antiferromagnet in Uniform Longitudinal and Transverse Fields to RFTIM -- 6.A.5 Derivation of Free Energy for the SK Model with Antiferromagnetic Bias in a Transverse Field -- 6.A.5.1 Saddle Point Equations -- 6.A.5.2 At the Ground State -- Chapter 7: Dynamics of Quantum Ising Systems -- 7.1 Tunnelling Dynamics for Hamiltonians Without Explicit Time Dependence -- 7.1.1 Dynamics in Ising Systems: Random Phase Approximation -- 7.1.2 Dynamics in Dilute Ising Spin Systems -- 7.1.3 Dynamics in Quantum Ising Glasses -- 7.2 Non-equilibrium Dynamics in Presence of Time-Dependent Fields -- 7.2.1 Time-Dependent Bogoliubov-de Gennes Formalism -- 7.2.2 Quantum Quenches. , 7.2.2.1 Relaxation Dynamics After Sudden Quantum Quench -- 7.2.2.2 Nearly Adiabatic Dynamics Following a Slow Quench -- Kibble-Zurek Scaling -- 7.2.3 Oscillating Fields: Quantum Hysteresis -- Dynamic Phase Transition -- The AC Susceptibility -- 7.2.3.1 Exact Results for a Transverse Ising Chain -- 7.2.4 Response due to a Pulsed Transverse Field in Absence of a Longitudinal Field -- Appendix 7.A -- 7.A.1 Mean Field Equation of Motion -- 7.A.1.1 Some Analytic Solutions in the Linearised Limit -- 7.A.1.2 Approximate Analytic Form of Dynamic Phase Boundary -- 7.A.2 Landau-Zener Problem and Parabolic Cylinder Functions -- 7.A.3 Microscopic Equation of Motion for Oscillatory Transverse Field -- Chapter 8: Quantum Annealing -- 8.1 Introduction -- 8.2 Combinatorial Optimisation Problems -- 8.3 Optimisation by a Quantum Adiabatic Evolution -- 8.3.1 Non-crossing Rule -- 8.3.2 Quantum Adiabatic Theorem -- 8.4 Implementation of Quantum Annealing -- 8.4.1 Numerical Experiments -- 8.4.2 Experiments -- 8.5 Size Scaling of Energy Gaps -- 8.5.1 Simple Case -- 8.5.2 Annealing over an In nite Randomness Fixed Point -- 8.5.3 Annealing over a First Order Quantum Phase Transition -- 8.5.3.1 Fully Connected p-Body Ising Ferromagnet in a Transverse Field -- 8.5.3.2 Quantum Random Energy Model -- 8.5.3.3 Numerical Studies -- 8.5.4 Anderson Localisation -- 8.6 Scaling of Errors -- 8.7 Convergence Theorems -- 8.7.1 Suf cient Condition of the Schedule -- 8.7.1.1 Complexity -- 8.7.2 Convergence Condition of Quantum Annealing with Quantum Monte Carlo Dynamics -- 8.8 Conclusion -- Appendix 8.A -- 8.A.1 Hopf's Theorem -- 8.A.2 Perron-Frobenius Theorem -- 8.A.3 Theory of the Markov Chain -- 8.A.3.1 Chapman-Kolmogorov Equation -- 8.A.3.2 Time-Independent Transition Probability -- 8.A.3.3 Time-Dependent Transition Probability -- Chapter 9: Applications. , 9.1 Hop eld Model in a Transverse Field -- 9.1.1 Statics and Phase Diagrams -- 9.1.2 Pattern-Recalling Processes -- 9.1.2.1 The Classical System -- 9.1.2.2 The Quantum System -- 9.1.2.3 Quantum Monte Carlo Method -- 9.1.2.4 The Suzuki-Trotter Decomposition -- 9.1.2.5 Derivation of the Deterministic Flows -- 9.1.2.6 The Master Equation -- 9.1.2.7 Static Approximation -- 9.1.2.8 The Classical and Zero-Temperature Limits -- 9.1.2.9 Limit Cycle Solution for Asymmetric Connections -- 9.1.2.10 Result for Two-Patterns -- 9.2 Statistical Mechanics of Information -- 9.2.1 Bayesian Statistics and Information Processing -- 9.2.1.1 General De nition of the Model System -- 9.2.1.2 MAP Estimation and Simulated Annealing -- 9.2.1.3 MPM Estimation and a Link to Statistical Mechanics -- 9.2.2 The Priors and Corresponding Spin Systems -- 9.2.2.1 Image Restoration and Random Field Ising Model -- 9.2.2.2 Error-Correcting Codes and Spin Glasses with p-Body Interaction -- 9.2.3 Quantum Version of Models -- 9.2.4 Analysis of the In nite Range Model -- 9.2.4.1 Image Restoration -- 9.2.4.2 Image Restoration at Finite Temperature -- 9.2.4.3 Hyperparameter Estimation -- 9.2.4.4 Image Restoration Driven by Pure Quantum Fluctuation -- 9.2.4.5 The Nishimori-Wong Condition on the Effective Transverse Field -- 9.2.4.6 Error-Correcting Codes -- 9.2.4.7 Analysis for Finite p -- 9.2.4.8 Phase Diagrams for p-> -- infty and Replica Symmetry Breaking -- 9.2.4.9 The Shannon's Bound and Phase Boundaries -- 9.2.5 Mean Field Algorithms -- 9.2.5.1 Naive Mean Field Algorithm for Image Restoration -- 9.2.5.2 Mean Field Decoding via the TAP-Like Equation for Sourlas Codes -- 9.2.6 Quantum Monte Carlo Method for Information Processing -- 9.2.6.1 Application of Quantum Monte Carlo Method -- 9.2.6.2 Quantum Annealing and Simulated Annealing -- 9.2.6.3 Application to Image Restoration. , 9.2.6.4 Thermal MPM Estimation Versus Quantum MPM Estimation.

Note: Intro -- Preface -- Contents -- Part I: Novel Analytical Procedures for Signal Transduction -- Chapter 1: Phosphoproteomics-Based Network Analysis of Cancer Cell Signaling Systems -- 1.1 Introduction -- 1.2 High-Throughput Phosphoproteomics Technology for Large-Scale Identification and Quantification of Cellular Phosphorylated Molecules -- 1.2.1 Shotgun Proteomics -- 1.2.2 Quantitative Proteomics -- 1.2.3 Phosphoproteomics -- 1.2.4 Time-Resolved Description of Phosphorylation-­Dependent Signaling Networks -- 1.3 Computational Analysis of Cancer Signaling Networks Based on Quantitative Phosphoproteome Data -- 1.3.1 Computational Modeling of ErbB-related Cancer Signaling Networks Based on Phosphoproteome Dynamics -- 1.3.2 Systems Analysis of Breast Cancer Signaling Networks Based on Integration of Phosphoproteome and Transcriptome Dynamics -- 1.3.3 Global Annotation of Glioblastoma Signaling Networks Based on Proteome and Phosphoproteome Data -- 1.4 Future Directions -- References -- Chapter 2: Phos-tag-Based Affinity Chromatography Techniques for Enrichment of the Phosphoproteome -- 2.1 Introduction -- 2.2 Separation of Phosphoproteins from Cell Lysates by Using Phos-tag Toyopearl -- 2.3 Pretreatment of Phosphoproteins Using Phos-tag Agarose for Western Blotting -- 2.4 Separation of Phosphopeptides by Using Phos-tag Magnetic Beads -- 2.5 Conclusions -- References -- Chapter 3: Visualization of Intracellular Signaling with Fluorescence Resonance Energy Transfer-Based Biosensors -- 3.1 Introduction -- 3.2 Fluorescence Resonance Energy Transfer (FRET)-Based Biosensors -- 3.2.1 Genetically Encoded FRET Biosensors -- 3.2.2 Intermolecular FRET Versus Intramolecular FRET -- 3.2.3 The Eevee System, an Optimized Design for Intramolecular FRET Biosensors -- 3.2.4 Stable Expression of Intramolecular FRET Biosensors -- 3.3 FRET Imaging. , 3.3.1 Fluorescence Microscopy for Time-Lapse FRET Imaging -- 3.3.2 Stochastic ERK Activation Revealed by FRET Imaging -- 3.4 Future Directions -- References -- Chapter 4: Technology of Wheat Cell-Free-Based Protein Array for Biochemical Analyses of Protein Kinases and Ubiquitin E3 Ligases -- 4.1 Introduction -- 4.2 Construction of Protein Array -- 4.3 Novel Protein-Protein Interaction Analysis Approach That Combines Wheat Cell-Free Protein Array and AlphaScreen Technology -- 4.3.1 Protein Array-Based Substrate Screening of Protein Kinase -- 4.3.2 Phosphorylation Analysis of Protein Kinase and Substrate Protein -- 4.3.3 Detection of Ubiquitination by AlphaScreen -- 4.3.4 Identification of Responsible E3 Ligases -- 4.4 Future Prospects -- References -- Part II: Mathematical Simulation of Signal Transduction -- Chapter 5: Potential Roles of Spatial Parameters in the Regulation of NF-κB Oscillations, as Revealed by Computer Simulations -- 5.1 Introduction -- 5.2 Signal Transduction of NF-κB and the Roles of Organelles -- 5.3 Oscillation of NF-κB and the Corresponding Computer Simulation Studies -- 5.4 Does the Diffusion Coefficient Affect the Oscillation Pattern of NF-κB? -- 5.5 Spatial Parameters Regulate the Oscillation Pattern of Nuclear NF-κB -- 5.6 Does NF-κB Oscillate in B Lymphocytes? -- 5.7 Conclusion -- References -- Chapter 6: Stochastic Simulation of Stress Granules -- 6.1 Introduction -- 6.2 Stress Granules -- 6.3 Methodology of SS -- 6.3.1 Random Walk -- 6.3.2 Collision -- 6.3.3 Reaction Probability -- 6.3.4 Transportation on Microtubules (MTs) -- 6.3.5 Structure of SS Programs -- 6.3.6 Performance -- 6.4 A Model for SG Formation -- 6.5 Simulation Results -- 6.6 Conclusion -- References -- Chapter 7: Temporal Coding of Insulin Signaling -- 7.1 Introduction -- 7.1.1 Temporal Patterns of Insulin -- 7.1.2 Regulation of Metabolites by Insulin. , 7.2 Temporal Coding of Insulin Action Through Multiplexing of the AKT Pathway -- 7.2.1 Insulin Induces Different Temporal Patterns of Signaling Molecules -- 7.2.2 Development of the Computational Model -- 7.2.3 Characteristics Produced by the Network Structure and Kinetics -- 7.2.4 Possible Physiological Roles of Temporal Coding of Insulin Functions -- 7.3 The Selective Control of Metabolites by Temporal Patterns of Insulin -- 7.3.1 Temporal Patterns of Metabolites Induced by Insulin -- 7.3.2 Development of the Computational Model -- 7.3.3 Characteristics Produced by Network Structures and Kinetics -- 7.3.4 Possible Physiological Roles of the Temporal Coding of Metabolites -- 7.4 Discussion -- 7.4.1 Possible Pathological Roles of the Temporal Coding of Insulin -- 7.4.2 Importance of the Study Focusing on Temporal Patterns -- 7.4.3 Toward Understanding of the "Pathogenic Dysregulation of Signaling" -- References -- Part III: Structural Analysis of Signal Transduction -- Chapter 8: Structural Biology of Protein Post-transcriptional Modifications and Cellular Signaling -- 8.1 Structural Basis for DNA-Specific Immune Activation by Cyclic GMP-AMP Synthase -- 8.1.1 Overall Architecture of cGAS -- 8.1.2 dsDNA-Specific Activation of cGAS -- 8.1.3 cGAMP Production and Signal Transduction by cGAS -- 8.2 Specific Recognition of Linear Polyubiquitin by A20 Zinc Finger 7 Regulates NF-κB -- 8.2.1 Crystal Structure of the A20 OTU Domain -- 8.2.2 Crystal Structure of the A20 ZF4 Domain -- 8.2.3 Crystal Structure of the A20 ZF7 Domain -- 8.3 Crystal Structure of the Dominant-Negative Helix-Loop-­Helix Transcriptional Regulator, HHM -- 8.3.1 Overall Structure -- 8.3.2 Structural Comparison with Canonical bHLH Transcription Factors -- 8.3.3 Dynamic Equilibrium of HHM -- 8.3.4 Disruption of the V-Shaped Structure Impairs the Transcription Factor Specificity of HHM. , References -- Chapter 9: Structural Basis for Signal Initiation by TNF and TNFR -- 9.1 Introduction -- 9.2 Structure of TNF -- 9.3 Overall Structure of the TNF-TNFR2 Complex -- 9.4 Comparison of the Structures of TNFR2 and TNFR1 -- 9.5 Structural Implication for the Design of Receptor-­Selective Drugs -- 9.6 Network Model of the TNF-TNFR2 Complexes -- References -- Chapter 10: Regulation of NF-κB Pathway by Linkage-­Specific Ubiquitin-Binding Domains -- 10.1 Polyubiquitin Chains Regulate the Canonical NF-κB Pathway -- 10.2 Structural Basis for the Recognition of K63-Linked Chains by the NZF Domain of TAB2 and TAB3 -- 10.3 Structural Basis for the Specific Recognition of M1-Linked Chains by HOIL-1L-NZF -- 10.4 Structural Basis for the Specific Recognition of M1-Linked Chains by NEMO-UBAN -- 10.5 Concluding Remarks -- References -- Part IV: Regulation of Signal Transduction by Post- translational Modifications and Its Pathogenic Dysregulation -- Chapter 11: NF-κB Signaling and Lymphoid Malignancies -- 11.1 NF-κB Signaling -- 11.2 Lymphoid Malignancies with Activated NF-κB Activity -- 11.3 Hodgkin Lymphoma -- 11.4 Multiple Myeloma -- 11.5 Adult T-Cell Leukemia -- 11.5.1 Tax-Dependent NF-κB Activation -- 11.5.2 Tax-Independent NF-κB Activation -- 11.6 Disruption of Negative Feedback Mechanisms -- 11.7 A20 Blocks Cell Death in HTLV-I-Infected Cells -- 11.8 Conclusions -- References -- Chapter 12: Ubiquitination-Mediated NF-κB Regulation in Inflammatory Response -- 12.1 NF-κB Pathway -- 12.1.1 NF-κB Transcription Factor -- 12.1.2 IκB Kinase (IKK) -- 12.2 Various Ubiquitinations Regulate NF-κB Signaling -- 12.2.1 Ubiquitin Cycle -- 12.2.2 Ubiquitin Ligases in the NF-κB Pathway -- 12.2.2.1 TRAF -- 12.2.2.2 Inhibitor of Apoptosis (IAP) -- 12.2.2.3 SCFβ-TrCP -- 12.2.2.4 LUBAC -- 12.3 NF-κB Activation Pathway in the Inflammatory Response. , 12.3.1 Inflammatory Cytokine-Induced NF-κB Activation -- 12.3.2 Innate Immunity Response and Linear Ubiquitination -- 12.4 Pathophysiological Roles of LUBAC -- 12.4.1 Ablation of LUBAC Subunits Causes Immunodeficiency and Inflammation -- 12.4.2 LUBAC Modulates Adaptive Immunity Through the Regulation of B Cell Function -- 12.5 Downregulation of NF-κB Signaling by DUBs -- 12.5.1 A20 (TNFAIP3) -- 12.5.2 OTULIN (Gumby) -- 12.5.3 CYLD -- 12.6 Concluding Remarks -- References -- Chapter 13: NF-κB Signaling in Osteoclastogenesis -- 13.1 Activation of the Transcription Factor NF-κB -- 13.2 Physiological and Pathological Roles of Osteoclasts -- 13.3 NF-κB Activation Induced by the RANK-TRAF6 Signal Pathway Is Crucial for Osteoclastogenesis -- 13.4 HCR, a Unique Domain in RANK, Plays a Critical Role in Osteoclastogenesis -- 13.5 Peptides Derived from the HCR of the RANK Cytoplasmic Tail Are Anti-Osteoclastogenic -- 13.6 Conclusions -- References -- Chapter 14: Mitogen-Activated Protein Kinase Signaling and Cancer -- 14.1 Introduction -- 14.2 The ERK Cascade and Cancer -- 14.2.1 Regulation of ERK Signaling by Ubiquitin-Like Proteins -- 14.2.1.1 Receptor Tyrosine Kinases (RTKs) -- 14.2.1.2 Ras Family Proteins -- 14.2.1.3 Scaffold Proteins -- 14.2.1.4 ERK -- 14.2.1.5 Transcription Factors -- 14.2.2 Regulation of ERK Signaling by MEK Sumoylation -- 14.3 SAPK Pathways and Cancer -- 14.3.1 Regulation of the MTK1 MAPKKK by a Family of GADD45 Proteins -- 14.3.2 Physiological Roles of GADD45-MTK1 Signaling in Development and Cell Fate Decisions -- 14.3.3 Aberrant Regulation of GADD45-MTK1 Signaling in Cancer -- 14.3.4 Centrosome Integrity Is Maintained Under Stress by a Network of PLK4, p53, and SAPK Pathways -- 14.4 Conclusion and Remarks -- References -- Chapter 15: Critical Roles of the AKT Substrate Girdin in Disease Initiation and Progression. , 15.1 Involvement of AKT in Developing Human Diseases.