Annual Reports in Computational Chemistry

Contributors Section 1: Bioinformatics Preface Potential Landscape and Flux Framework of Nonequilibrium Biological Networks 1. Introduction 2. Biochemical Oscillation 3. Stem-Cell Differentiation and Development: Arrows of Time Acknowledgments Section 2: Simulation Methodologies Predicting Structural and Functional Properties of Membrane Proteins from Protein Sequence 1. Topologies and 3D Structures of Integral Membrane Proteins 2. Predicting TM Helices from Sequence 3. Predicting Structural Features of Helical TM Proteins 4. Predicting the Exposure Status of TM Residues 5. Topology and Exposure Status Prediction of TMB 6. Functional Classification of GPCRs and Membrane Transporters 7. Outlook A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations 1. Introduction 2. Energy-Based Approach to Coarse-Graining 3. Force-Matching Approach to Coarse-Graining 4. Mixed Resolution Dynamics 5. Prospective Utilization 6. Outlook and Summary An Overview of String-Based Path Sampling Methods 1. Introduction 2. Elastic Band Derived Methods 3. Applications 4. Conclusions and Outlook Constructing and Evaluating Predictive Models for Protein Biophysical Characteristics 1. Introduction 2. Characterizing the Error Distribution 3. Outliers 4. Accurate Model Parameters 5. Conclusion Supplementary Data Section 3: Biological Modeling Extracting Experimental Measurables from Molecular Dynamics Simulations of Membranes 1. Introduction 2. Bilayer Structure 3. Bilayer Dynamics 4. Future Direction: Escaping the Timescale Limits of All-Atom MD Acknowledgment Advances in Scalable Computational Chemistry 1. Introduction 2. Software Design 3. Hartree-Fock and Density Functional Theory 4. Gaussian Basis Set HF and DFT 5. Plane-Wave Basis Set DFT 6. CC Methods 7. Perturbation Methods 8. Electron Transfer Methods 9. Relativistic Methods 10. Classical MD Simulation 11. Combined QM/MM 12. Conclusions Acknowledgments Section 4: Quantum Chemistry The Super Instruction Architecture 1. Introduction 2. Productivity for Electronic Structure Science and Engineering 3. Productivity for Method Developers 4. Outlook Acknowledgments Section 5: Chemical Education Electronically Excited States in Interstellar Chemistry 1. Introduction 2. Theoretical Details of Coupled Cluster Excited States 3. Excited States in the ISM: Radicals, Cations, and Anions, Oh My! 4. Conclusions Acknowledgments Computational Chemistry of Vision in Vertebrates and Invertebrates 1. Introduction 2. Retinal Proteins 3. Theoretical Framework 4. Spectral Tuning 5. Conclusion Acknowledgments A Class Project Combining Organic Chemistry, Quantum Chemistry, and Statistics 1. Background 2. Results and Discussion 3. Conclusions Notes and Acknowledgment