Modeling of microscale transport in biological processes

Modeling of microscale transport in biological processes

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...

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Bibliographic Details
Other Authors: Becker, Sid, author (author), Becker, Sid M., editor (editor)
Format: eBook
Language:Inglés
Published: Amsterdam, Netherlands : Elsevier 2017.
Edition:1st edition
Subjects:
Becker, Sid M.
Microorganisms.
Microorganisms > Congresses.
See on Biblioteca Universitat Ramon Llull:https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009630280506719
Table of 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
  • References
  • 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
  • References
  • 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
  • Acknowledgements
  • Appendix A Along-the-Chord Collagen Fiber Tangent Modulus
  • Appendix B Microstructure of Aortic Media Layer
  • References
  • 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
  • Acknowledgements
  • References
  • 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
  • References
  • 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
  • References
  • 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
  • References
  • 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
  • References
  • 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
  • References
  • 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
  • References
  • 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
  • Acknowledgements
  • References
  • 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
  • References
  • Nomenclature
  • 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.

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