Modeling of microscale transport in biological processes / edited by Sid Becker.

Format:

Book

Author/Creator:

Becker, Sid, author.

Contributor:

Becker, Sid M., editor.

Language:

English

Subjects (All):

Becker, Sid M.

Microorganisms.

Microorganisms--Congresses.

Physical Description:

1 online resource (396 pages) : illustrations

Edition:

1st edition

Place of Publication:

Amsterdam, Netherlands : Elsevier, 2017.

System Details:

text file

Summary:

Modeling of Microscale Transport in Biological Processes provides a compendium of recent advances in theoretical and computational modeling of biotransport phenomena at the microscale. The simulation strategies presented range from molecular to continuum models and consider both numerical and exact solution method approaches to coupled systems of equations. The biological processes covered in this book include digestion, molecular transport, microbial swimming, cilia mediated flow, microscale heat transfer, micro-vascular flow, vesicle dynamics, transport through bio-films and bio-membranes, and microscale growth dynamics. The book is written for an advanced academic research audience in the fields of engineering (encompassing biomedical, chemical, biological, mechanical, and electrical), biology and mathematics. Although written for, and by, expert researchers, each chapter provides a strong introductory section to ensure accessibility to readers at all levels. Features recent developments in theoretical and computational modeling for clinical researchers and engineers Furthers researcher understanding of fluid flow in biological media and focuses on biofluidics at the microscale Includes chapters expertly authored by internationally recognized authorities in the fundamental and applied fields that are associated with microscale transport in living media

Contents:

Front Cover

Modeling of Microscale Transport in Biological Processes

Copyright

Contents

Contributors

Preface

1 Molecular Simulations of Complex Membrane Models

1.1 Introduction

1.1.1 Methods: Molecular Dynamics Simulations

1.2 Unsaturated Carbon Chains

1.3 Membrane Proteins

1.3.1 Ion Channel Functioning

1.3.2 Transmembrane Protein Clustering

1.3.3 Membrane Adaptation Around Protein Clusters

1.4 Sterols

1.5 Eukaryotic Membranes

1.6 Prokaryotic Membranes

1.7 Viral Membranes

1.8 Membrane Fusion

1.9 Graphitic Nanomaterials

1.10 Nanoparticles

1.11 On-Going Work

1.12 Outlook and Conclusion

References

2 Microbial Strategies for Oil Biodegradation

2.1 Introduction

2.2 Overview of the Biodegradation Process

2.2.1 Biosurfactant-Mediated Uptake of Oil Compounds

2.2.2 Transmembrane Transport of Oil Compounds

2.3 Microbial Growth Modes on Oily Substrates

2.3.1 Suspended Growth in the Aqueous Phase

2.3.2 Flatlander's (Interfacial) Growth at the Oil-Water Interface

2.3.3 Bio lm Growth Over the Oil-Water Interface

2.4 Microscale Modeling Considerations

2.5 Summary and Outlook

Acknowledgements

3 Modeling and Measurement of Biomolecular Transport and Sensing in Micro uidic Cell Culture and Analysis Systems

3.1 Introduction

3.2 Basic Principles of Microscale Cell Culture

3.3 Theory and Equations: Fluid Flow, Mass Transport, and Biochemical Reactions

3.3.1 Fluid Motion

3.3.2 Mass Transport in Fluids

3.3.3 Biochemical Reactions

3.3.4 Non-Dimensionalization

3.4 Review of Micro uidic Transport Models

3.4.1 Straight Microchannel with Biochemical Assay Reaction Site(s)

3.4.2 Straight Microchannel with Cell Monolayer

3.4.3 Alternative Geometries

3.5 Review of Theoretical Model Experimental Validation.

3.5.1 Experimental Validation of Micro uidic Biomolecular Transport and Sensing Models

3.5.2 Technological Advances in Micro uidic On-Chip Analysis

3.6 Summary and Conclusions

4 Coupling Microscale Transport and Tissue Mechanics: Modeling Strategies for Arterial Multiphysics

4.1 Introduction

4.2 Brief on Arterial Tissues

4.2.1 Histology and Mechanics of Arterial Tissues

4.2.2 Molecular Transport in Arterial Tissues

4.2.3 Extracellular Matrix Remodeling

4.3 Arterial Multiphysics Modeling

4.3.1 Geometric Description and General Notation

4.3.2 Multiphysics Modeling Rationale

4.3.3 Arterial Mechanical Problem

4.3.4 Molecular Transport Problem

4.3.5 Remodeling Laws

4.3.6 Integrated Computational Strategy: Towards an Analytical Solution

4.4 An Axisymmetric Case Study

4.4.1 Arterial Geometry and Structure

4.4.2 Quasi-Analytical Arterial Mechanics

4.4.3 Analytical Arterial Molecular Transport

4.4.4 Analytical Arterial Remodeling Induced by MMPs, TGF-ß, and IL

4.4.5 Results

4.5 Conclusions

Appendix A Along-the-Chord Collagen Fiber Tangent Modulus

Appendix B Microstructure of Aortic Media Layer

5 Modeling Cystic Fibrosis and Mucociliary Clearance

5.1 Mucociliary Clearance and Cystic Fibrosis

5.1.1 Airway Wall Environment and Mucociliary Clearance

5.1.2 The Cystic Fibrosis Pathology

5.1.3 Mathematical Modeling of Lung Wall Environment

5.2 Newtonian Models

5.2.1 Mathematical Analysis

5.2.2 Numerical Analysis

5.2.3 Numerical Computations of the Mucus Propelled by Ciliated Epithelium

5.2.4 Phenomena Analysis

5.3 Rheology of Mucus and Non-Newtonian Models

5.3.1 Rheometry Data on Lung Mucus from the Literature

5.3.2 Mucus Sample Analysis and Rheological Results.

5.3.3 Mathematical Modeling of the Rheology and Related Numerical Analysis

5.3.4 Medical Outcomes

5.4 Concluding Remarks

6 Intracellular Micro uid Transportation in Fast Growing Pollen Tubes

6.1 Introduction

6.2 Modeling Fluid Flow of Fountain Streaming in Pollen Tubes

6.2.1 Pollen Collection and Germination

6.2.2 Living Image and Observation

6.2.3 Hydrodynamics of Fountain Streaming

6.3 Modeling Intracellular Micro uid Transportation in Pollen Tubes

6.3.1 Analysis for the Properties of Micro uid Transportation in Pollen Tubes

6.3.2 Simulation for the Coupling Advection-Diffusion of Fountain Streaming

6.4 Results and Discussion

6.4.1 Hydrodynamics of Fountain Streaming in Pollen Tubes

6.4.2 Intracellular Transportation of Fountain Streaming in Pollen Tubes

6.5 Conclusions

7 Microorganisms and Their Response to Stimuli

7.1 Introduction

7.2 Swimming Dynamics

7.3 Response to Stimuli

7.3.1 Gyrotactic Phototrophs

7.3.2 Photosensitive Phototrophs

7.3.3 Chemotactic Microorganisms

7.4 Non-Flowing Suspensions

7.4.1 Gyrotactic Phototrophs

7.4.2 Photosensitive Phototrophs

7.4.3 Chemotaxis

7.5 Flowing Suspensions

7.5.1 Gyrotactic Focusing

7.5.2 Gyrotactic Plumes

7.5.3 Bioconvection

7.5.4 Bacterial Chemotaxis

7.5.5 Porous Media

7.6 Conclusions

8 Nano-Swimmers in Lipid-Bilayer Membranes

8.1 Introduction

8.2 Methods

8.2.1 Hybrid MD-MPCD Simulations for Fluid Lipid Bilayers in a Solvent

8.2.2 Simple Model for Membrane Swimmers

8.3 Results

8.4 Conclusions

9 Phase Field Modeling of Inhomogeneous Biomembranes in Flow

9.1 Motivation

9.2 Energy of the System

9.3 Hydrodynamic Models

9.4 Inhomogeneous Membranes

9.4.1 Separated Membrane Components.

9.4.2 Mixed Membrane Components

9.5 Numerical Methods

9.6 The Phase Field Method

9.6.1 Phase Field Equations

9.6.2 Inextensibility or Surface Elasticity

9.7 Phase Field Models for Inhomogeneous Membranes

9.7.1 Multicomponent Vesicles

9.7.2 Endocytosis

10 Modeling and Experimental Analysis of Thermal Therapy during Short Pulse Laser Irradiation

10.1 Introduction

10.2 Methods

10.2.1 Vascularized Tissue Phantom Preparation

10.2.2 Experimental Methods

10.2.3 Model Formulation

10.3 Results and Discussion

10.4 Conclusions

11 Micro-Scale Bio-Heat Diffusion Using Green's Functions

11.1 Introduction

11.2 Balance Equations

11.2.1 Heat Transfer and Blood Perfusion

11.2.2 Exact Uncoupling Procedure

11.2.3 Approximate Uncoupling Procedure

11.3 Dual-Phase Lag Bio-Heat Diffusion Equation

11.3.1 Phase Lag Times

11.3.2 Transformations of the Dependent Variable

11.4 Boundary and Initial Conditions

11.4.1 Impermeable Boundary Surfaces

11.4.2 Permeable Boundary Surfaces

11.4.3 Initial Conditions

11.4.4 Transformed Boundary and Initial Conditions

11.5 Temperature Solution with Homogeneous Boundary Conditions

11.5.1 Solution Due to Initial Conditions

11.5.2 Solution Due to a Heating Source

11.6 Temperature Solution with Non-Homogeneous Boundary Conditions

11.6.1 Alternative Solution

11.7 Green's Functions for Finite Regular Tissues

11.7.1 Dual-Phase Lag Green's Functions

11.7.2 DPL and Fourier-Type Green's Functions

11.7.3 DPL Alternative Green's Function Solution Equation

11.8 Temperature Distribution in a Laser-Irradiated Biological Tissue

11.8.1 De ning Equations for Highly Absorbed Laser Light

11.8.2 Temperature Solutions

11.8.3 Convergence of the Temperature Series-Solutions

11.8.4 Numerical Results.

11.9 Conclusions

Appendix A

Appendix B

Nomenclature

12 Microstructural In uences on Growth and Transport in Biological Tissue-A Multiscale Description

12.1 Introduction

12.2 Formulation: Nutrient-Limited Microscale Growth of a Porous Medium

12.2.1 Microscale Governing Equations and Boundary Conditions

12.2.2 Non-dimensionalization

12.3 Multiple Scales Analysis

12.3.1 Microscale Flow and Transport

12.3.2 Macroscale Flow and Transport

12.4 Results

12.4.1 Microscale Numerical Experiments

12.4.2 Macroscale Dynamics

12.5 Discussion

13 How Dense Core Vesicles Are Delivered to Axon Terminals - A Review of Modeling Approaches

13.1 Introduction

13.2 Review of Relevant Literature

13.2.1 Dense Core Vesicles and Their Cargos

13.2.2 Accumulation and Release of DCVs

13.2.3 DCV Transport in Axon Terminals

13.2.4 Link to Neurodegenerative Disorders

13.2.5 Importance of Mathematical Modeling for Better Understanding of Biological Issues Related to DCV Transport and Release

13.2.6 Modeling of DCV Transport

13.3 Mathematical Models of DCV Transport and Accumulation in Axon Terminals

13.3.1 Morphology of Axon Terminals

13.3.2 Simulated Geometry and Major Assumptions of the Model

13.3.3 Governing Equations

13.3.4 Estimation of Parameter Values

13.4 Results and Discussion

13.5 Future Work

13.6 Conclusions

Acknowledgement

14 Modeling of Food Digestion

14.1 Introduction

14.2 The Complexity of Food Digestion and Absorption

14.2.1 Chemical Processes

14.2.2 Physical Processes

14.2.3 Biological Processes

14.3 Development of Digestion and Absorption Modeling

14.3.1 Drug Absorption

14.3.2 Animal Feed Digestion and Absorption.

14.4 Microscale Modeling of Food Digestion and Absorption.

Notes:

Includes bibliographical references and index.

Description based on print version record.

ISBN:

0-12-804619-8

0-12-804595-7