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