Advances in Chemical Physics -- Contributors to Volume 155 -- Preface to The Series -- Contents -- Modeling Viral Capsid Assembly -- I. Introduction -- A. Virus Anatomies -- B. Virus Assembly -- 1. Experiments That Characterize Capsid Assembly -- 2. Motivation for and Scope of Modeling -- II. Thermodynamics of Capsid Assembly -- A. Driving Forces -- B. Law of Mass Action -- 1. Estimating Binding Energies from Experiments -- III. Modeling Self-Assembly Dynamics and Kinetics of Empty Capsids -- A. Timescales for Capsid Assembly -- 1. Scaling Estimates for Assembly Timescales -- 2. Lag Times -- 3. The Slow Approach to Equilibrium -- B. Rate Equation Models for Capsid Assembly -- C. Particle-Based Simulations of Capsid Assembly Dynamics -- D. Conclusions from Assembly Dynamics Models -- E. Differences Among Models -- F. Higher T Numbers -- 1. Structural Stability of Different Capsid Geometries -- 2. Dynamics of Forming Icosahedral Geometries -- IV. Cargo-Containing Capsids -- A. Structures -- B. The Thermodynamics of Core-Controlled Assembly -- C. Single-Stranded RNA Encapsidation -- D. Dynamics of Assembly Around Cores -- V. Outlook -- References -- Charges at Aqueous Interfaces: Development of Computational Approaches in Direct Contact With Experiment -- I. Introduction -- II. Accounting for Polarizability Effects -- A. Models with Explicit Polarization -- B. Implicit Polarization via Charge Scaling -- C. Beyond Conventional Force Fields -- III. Case Studies -- A. Hydroxide at Aqueous Interfaces -- B. Solvated Electron at the Surface of Water -- IV. Outlook -- References -- Solute Precipitate Nucleation: A Review of Theory and Simulation Advances -- I. Introduction -- II. Classical Nucleation Theory -- A. Homogeneous Nucleation -- B. Heterogeneous Nucleation -- C. Nucleation Theorem -- III. Two-Step Nucleation Theory.

A. Metastable Fluid--Fluid Critical Points -- B. Phenomenological Theories -- C. Coupled Flux Theories and Concentration Fluctuation Gating -- IV. Simulation Challenges -- A. Landau Free Energies and Rare Events -- B. Kramers--Langer--Berezhkovskii--Szabo (KLBS) Theory -- C. Nucleus Size in Simulations -- D. Which Nucleus Size Metric? -- E. Open versus Closed Systems -- V. Case Studies -- A. Laser-Induced Nucleation -- B. Nucleation of Methane Hydrates -- C. Nucleation of Calcium Carbonate -- VI. Closing Remarks -- References -- Water in The Liquid State: A Computational Viewpoint -- I. Introduction -- II. Potential Energy Functions for Liquid Water -- A. Heuristic Models -- B. Multisite Models -- 1. Three-Site Models -- 2. Four-Site Models -- 3. Five-Site Models -- 4. Six Sites and Beyond -- C. Molecular Multipole Models -- 1. The Multipole Expansion -- 2. The Approximate Multipole Expansion -- D. Atomic Multipole Models -- E. Summary -- III. Multipoles -- IV. The Water Molecule in the Pure Liquid -- A. Nuclear Geometry -- B. Electron Density -- C. Multipole Moments -- D. Electrostatic Potential -- E. Summary -- V. Liquid Water -- A. Structure -- B. Density -- C. Thermodynamics -- D. Dynamics -- E. Dielectric Properties -- F. Summary -- VI. Aqueous Solutions -- A. Ionic Solvation -- B. Hydrophobic Solvation -- VII. Conclusions -- References -- Construction of Energy Functions for Lattice Heteropolymer Models: Efficient Encodings for Constraint Satisfaction Programming and Quantum Annealing -- I. Introduction -- A. Motivation and Background -- B. Overview of Mapping Procedure -- II. The ''Turn'' Encoding of Self-Avoiding Walks -- A. Embedding Physical Structure -- B. ''Turn Ancilla'' Construction of E(q) -- 1. Construction of Eback (q) -- 2. Construction of Eoverlap (q) with Ancilla Variables -- 3. Construction of Epair (q) with Ancilla Variables.

C. ''Turn Circuit'' Construction of E(q) -- 1. Sum Strings -- 2. Construction of Eoverlap (q) with Circuit -- 3. Construction of Epair (q) with Circuit -- III. The ''Diamond'' Encoding of SAWs -- A. Embedding Physical Structure -- B. Natively 2-Local E(q) -- 1. Construction of Eone (q) -- 2. Construction of Econnect (q) -- 3. Construction of Eoverlap (q) -- 4. Construction of Epair (q) -- IV. Pseudo-Boolean Function to W-SAT -- A. MAX-SAT and W-SAT -- B. Constructing WCNF Clauses -- C. Solving SAT Problems -- V. W-SAT to Integer--Linear Programming -- A. Mapping to ILP -- B. Solving ILP Problems -- VI. Locality Reductions -- VII. Quantum Realization -- A. Previous Experimental Implementation -- B. Six-Unit Miyazawa--Jernigan Protein -- 1.Eback (q) for Six-Unit SAW on 2D Lattice -- 2.Eoverlap(q) for Six-Unit SAW on 2D Lattice -- 3 Epair (q) for MJ Model PSVKMA -- 4. Setting λ Penalty Values -- 5. Reduction to 2-Local -- 6. QUBO Matrix and Solutions -- VIII. Conclusions -- References -- Author Index -- Subject Index.