Note: Cover -- Half Title -- Series Page -- Title Page -- Copyright Page -- Dedication -- Table of Contents -- Series Preface -- About the Editor -- Contributors -- 1. Force Fields for Biomembranes Simulations -- 1 Introduction -- 2 Force Fields -- 3 Validation and Comparisons of Force Fields -- 4 Conclusions -- 2. Mesoscopic Particle-Based Modeling of Self-Assembled Lipid Membranes -- I Introduction -- II The Particle-Based Mesoscopic Approach -- III Explicit Solvent Modeling -- IV Implicit Solvent Modeling -- V Conclusion -- 3. Continuum Elastic Description of Processes in Membranes -- 1 Continuum Modeling Paradigms -- 2 Variables of a Continuum Model -- 3 Pushing the Limits of a Continuum Model -- 4 Molecular Modifications to Continuum Modeling -- 4. Water between Membranes: Structure and Dynamics -- I Introduction -- II Dynamics of Water Between Stacked Membranes at Different Hydration Levels -- III Dependence of Water Dynamics on Distance to Membrane -- IV Effect of Temperature on the Hydration Water Dynamics -- V Extension of the Structural Effect of the Membrane on Interfacial Water -- VI Conclusions -- 5. Simulation Approaches to Short-Range Interactions between Lipid Membranes -- 1 Introduction -- 2 Thermodynamics of Membrane Interactions -- 3 Simulations of Interacting Membranes -- 4 Insights into Short-Range Interactions between Lipid Membranes -- 5 Summary and Outlook -- 6. Free-Energy Calculations of Pore Formation in Lipid Membranes -- 1 Introduction -- 2 Membrane Pores from Experiments -- 3 Modeling Pores in Molecular Dynamics Simulations -- 4 Reaction Coordinates for Free-Energy Calculations of Pore Formation: A Comparison -- 5 Longer Lipid Tails Increase the Free Energy of Pore Formation -- 6 Relative Volume of Lipid Head to Lipid Tails Determines the Metastability of the Pore. , 7 Practical Consideration for PMF Calculations with the Chain Coordinate -- 8 Summary and Outlook -- 7. Free Energy Calculation of Membrane Translocation: What Works When, and Why? -- 1 Introduction -- 2 Methods for Free Energy Calculations -- 3 Translocation of Specific Solutes -- 4 Implications and Recommendations -- 8. Theories and Algorithms for Molecular Permeation through Membranes -- I Introduction -- II Passive Permeation: Definition, Measurements, and Modeling -- III Solubility Diffusion Model -- IV Milestoning -- V Permeation of Blocked Tryptophan with Milestoning -- VI Fluctuations of Membrane Density with Milestoning -- VII Difference of Permeation of Positive and Negative Charged Molecules -- VIII Conclusions -- 9. Nanoparticle-Membrane Interactions: Surface Effects -- 1 Introduction -- 2 Experimental Data in Search for a Molecular-Scale Interpretation -- 3 What We Understood So Far Using Computational Tools -- 4 Perspectives -- 10. Simulations of Membranes Containing General Anesthetics -- 1 Introduction -- 2 Studies Involving Chemically Similar Molecules -- 3 Position of the Anesthetics in the Membrane -- 4 Change of Various Membrane Properties -- 5 Pressure Reversal -- 6 Concluding Remarks -- 11. Cation-Mediated Nanodomain Formation in Mixed Lipid Bilayers -- 1 Introduction -- 2 Methods -- 3 Model Validation -- 4 Results and Discussions -- 5 Conclusion -- 12. Molecular Dynamics Simulations of Gram-Negative Bacterial Membranes -- Slow Diffusion and Importance of Divalent Cations -- Different Dynamics, Not Just Slower -- Specific Binding -- Asymmetric Energetic Barriers for Permeation of Small Molecules -- Larger Simulation Systems: Correlated Lipid Motion -- Summary and Outlook -- Index.

Note: Front Cover -- Algal Ecology: Freshwater Benthic Ecosystems -- Copyright Page -- Contents -- Contributors -- Preface -- Acknowledgments -- SECTION ONE: PATTERNS OF BENTHIC ALGAE IN AQUATIC ECOSYSTEMS -- Chapter 1. An Introduction to Algal Ecology in Freshwater Benthic Habitats -- I. The Diversity of Benthic Algae and Their Habitats in Fresh Waters -- II. The Niche of Freshwater Benthic Algae -- III. Methods for Characterizing Freshwater Benthic Algae -- IV. Conceptual Frameworks for Benthic Algal Community Ecology -- References -- Chapter 2. Patterns in Benthic Algae of Streams -- I. Introduction -- II. Temporal Patterns -- III. Spatial Patterns -- IV. Benthic Algal Proliferations -- V. Concluding Remarks -- References -- Chapter 3. Periphyton Patterns in Lakes -- I. Introduction -- II. The Lentic Periphyton Community -- III. Important Influential Factors -- IV. Conclusions and Missing Pieces -- References -- Chapter 4. Pattern in Wetlands -- I. Introduction -- II. Algal Assemblages in Wetlands -- III. The Role of Algae in Wetlands -- IV. Species Composition of Wetland Algae -- V. Algal Production in Wetlands -- VI. Factors Affecting Algal Production -- VII. Conceptual Model of Wetland Algae -- VIII. Conclusion -- References -- SECTION TWO: FACTORS AFFECTING BENTHIC ALGAE -- Chapter 5. Effects of Light -- I. Introduction -- II. Photosynthetic Processes -- III. Benthic Light Environments -- IV. Photosynthesis-Irradiance Relations -- V. Ecological Effects of Light Intensity -- VI. Ecological Effects of Light Quality -- VII. Ultraviolet Radiation -- VIII. Summary -- References -- Chapter 6. Periphyton Responses to Temperature at Different Ecological Levels -- I. Introduction -- II. Autecological Responses -- III. Population Responses -- IV. Community Structure -- V. Ecosystem Response -- VI. Global Temperature Changes -- VII. Synthesis -- References. , Chapter 7. Nutrients -- I. Introduction -- II. Conceptual Framework: Nutrient Uptake and Growth Kinetics -- III. Conceptual Framework: Microhydrodynamic Environment -- IV. Nutrient Limitation of Benthic Algae -- V. Nutrient Kinetics of Benthic Algae -- VI. Effects of Water Motion on Benthic Algal Nutrient Uptake and Nutrient-Limited Growth -- VII. Nutrient Competition -- References -- Chapter 8. Resource Competition and Species Coexistence in Freshwater Benthic Algal Assemblages -- I. Introductory Remarks -- II. Basic Theory and Predictions: The Lotka-Volterra Equations and the Competitive Exclusion Principle -- III. Limitations to Classical Theory: Equilibrium and Nonequilibrium Coexistence in Competitive Hierarchies -- IV. Adaptive Traits Conferring Competitive Dominance and Avoidance -- V. Summary and Recommendations for Future Research -- References -- Chapter 9. Interactions of Benthic Algae with Their Substrata -- I. Introduction: The Interface Niche of Benthic Algae -- II. Substratum Physical Influences -- III. The Challenge of Examining Substratum Chemical Influences -- IV. Known Influences of Substratum Composition -- V. Conclusions and Recommendations -- References -- Chapter 10. The Role of Heterotrophy in Algae -- I. Defining Autotrophy and Heterotrophy -- II. The Ecological Roles of Algal Heterotrophy in Benthic Assemblages -- III. Conclusions -- References -- Chapter 11. The Stimulation and Drag of Current -- I. Introduction -- II. Direct Effects -- III. Indirect Effects -- IV. Manifestations of Current Effects -- V. Conclusions -- References -- Chapter 12. Effects of Grazers on Freshwater Benthic Algae -- I. Introduction -- II. Conceptual Framework -- III. Algal Responses to Herbivory -- IV. Future Research Directions and Concerns -- References -- Chapter 13. Response of Benthic Algal Communities to Natural Physical Disturbance. , I. Introduction -- II. Factors Influencing Resistance to Scour -- III. Factors Influencing Resilience Following Scour -- IV. Factors Influencing Response to Emersion -- V. Factors Influencing Response to Light Deprivation and Burial -- VI. Concluding Remarks -- References -- Chapter 14. Ecotoxicology of Inorganic Chemical Stress to Algae -- I. Introduction -- II. Adsorption and Uptake -- III. Effects of Inorganic Chemical Stress on Algae -- IV. Mechanisms of Tolerance -- V. Environmental Factors Affecting Metal Toxicity and Uptake -- VI. Interactions among Inorganic Stressors -- VII. Response of Algal Communities to Inorganic Stressors -- VIII. Algal Bioassay of Inorganic Stressors -- References -- Chapter 15. Effects of Organic Toxic Substances -- I. Introduction -- II. Conceptual Framework -- III. Direct Effects -- IV. Indirect Effects -- V. Conclusions and Future Directions -- References -- Chapter 16. Acidification Effects -- I. Introduction -- II. General Responses to the Loss of the Acid-Neutralizing Capacities of Ecosystems -- III. Hypotheses Explaining Acidification Effects -- IV. Conclusions -- References -- SECTION THREE: THE NICHE OF BENTHIC ALGAE IN FRESHWATER ECOSYSTEMS -- Chapter 17. The Role of Periphyton in Benthic Food Webs -- I. Introduction -- II. Structure of "Macroscopic" Benthic Food Webs -- III. Periphyton in Aquatic Energy Budgets -- IV. Periphyton in Benthic Food Webs -- V. Top-down and Bottom-up Regulation of Benthic Food Webs -- VI. The Case for "Intermediate Regulation -- VII. General Conclusions and Directions for Future Research -- References -- Chapter 18. Algae in Microscopic Food Webs -- I. Introduction -- II. Algal-Bacterial Interaction -- III. Detection of Microbial Feeding Relationships -- IV. Algal and Bacterial Ingestion by Microconsumers. , V. Use of Other Food Resources, Intraguild Predation, and Links to Higher Organisms -- VI. Impact on Production and Standing Crops -- VII. Nutrient Regeneration -- VIII. Conclusions, Implications, and Research Needs -- References -- Chapter 19. Role in Nutrient Cycling in Streams -- I. Introduction -- II. Direct Effects: Nutrient Cycling Processes -- III. Indirect Effects -- IV. Nutrient Turnover Rates and Comparison with Other Ecosystems -- V. Summary and Conclusions -- References -- Chapter 20. Benthic Algae and Nutrient Cycling in Lentic Freshwater Ecosystems -- I. Introduction -- II. Nutrient Characteristics in Lentic Habitats -- III. Nutrient Gradients and Limitations -- IV. Summary and Conclusions -- References -- Chapter 21. Modeling Benthic Algal Communities: An Example from Stream Ecology -- I. Introduction -- II. A Modeling Approach -- III. The McIntire and Colby Stream Model -- IV. An Updated Herbivory Subsystem Model -- V. Behavior of the Herbivory Subsystem Model -- VI. Behavior of the Updated M & -- C Model -- VII. Hypothesis Generation -- VIII. Discussion and Conclusions -- References -- Chapter 22. Benthic Algal Communities as Biological Monitors -- I. Introduction -- II. Applications -- III. Methodology -- IV. Summary and Conclusions -- References -- Taxonomic Index -- Subject Index.