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E-raamat: Dynamics of Engineered Artificial Membranes and Biosensors

(University of Technology Sydney), (Cornell University, New York), (University of British Columbia, Vancouver)
  • Formaat: EPUB+DRM
  • Ilmumisaeg: 03-May-2018
  • Kirjastus: Cambridge University Press
  • Keel: eng
  • ISBN-13: 9781108530378
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Dynamics of Engineered Artificial Membranes and BiosensorsSuurem pilt
  • Formaat: EPUB+DRM
  • Ilmumisaeg: 03-May-2018
  • Kirjastus: Cambridge University Press
  • Keel: eng
  • ISBN-13: 9781108530378
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Learn about the state of the art in building artificial membranes and synthetic biological devices, and in constructing mathematical models for their dynamics at multiple time and spatial scales with this comprehensive book. Drawing on recent advances in bioengineering and biochemistry, it describes how to engineer tethered bilayer lipid membranes, bioelectronic interfaces, high-resolution biosensors, and diagnostic devices for non-invasive cellular measurements and electroporation. Multi-physics models combining atomistic (molecular dynamics and coarse-grained molecular dynamics), mesoscopic (PoissonNernstPlanck), and macroscopic (reaction-rate theory) dynamics provide a complete structure-to-function description of these devices. Experiments and dynamic models explain how anti-microbial peptides penetrate membranes, how molecular machine biosensors built out of artificial membranes can detect femtomolar concentrations, and how electroporation can be controlled. Supported by atomistic simulation code online, this is essential reading for researchers, students and professionals in bioengineering, chemical engineering, biophysics, applied mathematics, and electrical engineering.

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A state-of-the-art guide to building synthetic membranes for biological devices, covering their construction, measurement, and modelling.
Preface xv
List of Abbreviations xviii
Part I Introduction and Background
1 Motivation and Outline
3(6)
1.1 Why Membranes?
3(1)
1.2 Guided Tour of the Book
4(5)
2 Biochemistry for Engineers: A Short Primer
9(21)
2.1 Bonded and Nonbonded Molecular Interactions
9(3)
2.2 Lipids, Vesicles, and Bilayers
12(2)
2.3 Lipid Bilayers
14(2)
2.3.1 Archaebacteria and DphPC Bilayers
14(1)
2.3.2 Energetics of Lipid Bilayers
15(1)
2.3.3 Structure of Lipid Bilayers
16(1)
2.4 Peptides and Proteins
16(5)
2.5 Ion Channels
21(3)
2.6 Tethers, Spacers, and the Bioelectronic Interface
24(3)
2.6.1 Tethers
25(1)
2.6.2 Spacers
25(1)
2.6.3 Bioelectronic Interface
26(1)
2.7 How to Visualize Macromolecules
27(2)
2.8 Closing Remarks
29(1)
3 Engineered Artificial Membranes
30(31)
3.1 Membranes
30(2)
3.2 Artificial Membrane Architectures
32(3)
3.3 Engineered Artificial Tethered Membranes
35(4)
3.4 Sensing with Engineered Tethered Membranes
39(6)
3.4.1 Device 1: Ion-Channel Switch (ICS) Biosensor
41(1)
3.4.2 Device 2: Pore Formation Measurement Platform (PFMP)
42(1)
3.4.3 Device 3: Electroporation Measurement Platform (EMP)
43(1)
3.4.4 Device 4: Electrophysiological Response Platform (ERP)
44(1)
3.5 Multiphysics Dynamic Models of Engineered Tethered Membranes
45(4)
3.5.1 Ab Initio Molecular Dynamics
46(1)
3.5.2 Molecular Dynamics
47(1)
3.5.3 Coarse-Grained Molecular Dynamics
47(1)
3.5.4 Continuum Theories
48(1)
3.5.5 Reaction-Rate Theory
48(1)
3.6 Electrolyte Dynamics: Steric Effects and Double-Layer Charging
49(2)
3.7 Future Technologies: Implantable Medical Devices, Diagnostics, and Therapeutics
51(7)
3.7.1 Cochlear and Retinal Implants
51(1)
3.7.2 In Vitro Medical Diagnostics (IVDs)
52(2)
3.7.3 Molecular Therapeutics
54(1)
3.7.4 Biological Neural Networks
54(1)
3.7.5 Microeletrodes and Single-Cell Measurements
55(3)
3.7.6 Summary
58(1)
3.8 Closing Remarks
58(3)
Part II Building Engineered Membranes, Devices, and Experimental Results
4 Formation of Engineered Tethered Membranes
61(22)
4.1 Introduction
61(3)
4.1.1 Engineered Tethered Membrane: Structure
62(1)
4.1.2 Overview of Tethered Device
63(1)
4.2 Building an Engineered Artificial Membrane
64(7)
4.2.1 Solvent-Exchange Technique
64(6)
4.2.2 Evaluating the Quality of the Engineered Membrane
70(1)
4.3 Inserting Proteins and Ion Channels into Engineered Artificial Membranes
71(5)
4.3.1 Spontaneous Insertion Method
72(1)
4.3.2 Electrochemical Insertion Method
72(2)
4.3.3 Proteoliposomal Insertion Method
74(2)
4.4 Laboratory Exercise: Tethered Membranes and Spontaneous Insertion of Gramicidin Channels
76(5)
4.4.1 Prepare the Engineered Tethered Membrane for Spontaneous gA Ion-Channel Insertion
77(2)
4.4.2 Spontaneous Insertion of gA Ion Channels
79(1)
4.4.3 Measuring Membrane Conductance Response
79(2)
4.5 Complements and Sources
81(1)
4.6 Closing Remarks
82(1)
5 Ion-Channel Switch (ICS) Biosensor
83(20)
5.1 Introduction
83(2)
5.2 ICS Biosensor: Construction and Formation
85(2)
5.3 Operation of the ICS Biosensor
87(3)
5.3.1 Large and Small Analyte Detection
87(1)
5.3.2 Impedance Response of ICS Biosensor for Digoxin and b-Fab
87(3)
5.4 ICS Biosensor: Flow Velocity, Binding-Site Density, and Specificity
90(5)
5.4.1 Flow Velocity and Binding-Site Density
91(3)
5.4.2 Specificity in Complex Environments
94(1)
5.5 Detection of Influenza A in Clinical Samples
95(2)
5.5.1 ICS Biosensor Preparation and Clinical Trials for Rapid Influenza A Diagnosis
95(1)
5.5.2 Influenza A Clinical Samples
96(1)
5.5.3 Results of Influenza A Clinical Trial
96(1)
5.6 ICS for Multianalyte Detection
97(4)
5.6.1 Biosensor Arrays
98(1)
5.6.2 Multi-Analyte Detection
99(2)
5.7 Complements and Sources
101(1)
5.8 Closing Remarks
102(1)
6 Physiochemical Membrane Platforms
103(15)
6.1 Introduction
103(1)
6.2 Device 1: Pore Formation Measurement Platform (PFMP)
104(3)
6.2.1 Pore Formation Measurement Platform: Introduction
104(1)
6.2.2 Pore Formation Measurement Platform: Construction
105(1)
6.2.3 Pore Formation Measurement Platform: Operation and Experimental Measurements
106(1)
6.3 Device 2: Electroporation Measurement Platform (EMP)
107(3)
6.3.1 Electroporation Measurement Platform: Introduction
107(1)
6.3.2 Electroporation Measurement Platform: Formation
108(1)
6.3.3 Electroporation Measurement Platform: Operation and Experimental Measurements
109(1)
6.4 Device 3: Electrophysiological Response Platform (ERP)
110(5)
6.4.1 Electrophysiological Response Platform: Overview
110(2)
6.4.2 Electrophysiological Response Platform: Formation
112(2)
6.4.3 Electrophysiological Response Platform: Operation and Experimental Measurements
114(1)
6.5 Complements and Sources
115(2)
6.6 Closing Remarks
117(1)
7 Experimental Measurement Methods for Engineered Membranes
118(21)
7.1 Introduction
118(1)
7.2 Electrical Response of Engineered Membranes
118(9)
7.2.1 Electrical Impedance Measurements
120(2)
7.2.2 Time-Dependent Electrical Measurements
122(3)
7.2.3 Interpretation of Measured Current Response
125(2)
7.3 Spectroscopy and Imaging Techniques for Engineered Tethered Membranes
127(7)
7.3.1 X-Ray Reflectometry for Measuring Area per Lipid
128(1)
7.3.2 Nuclear Magnetic Resonance Measurements of the Conformation and Orientation of Gramicidin A
129(1)
7.3.3 Fluorescence Recovery after Photobleaching for Measuring Lipid Diffusion
129(2)
7.3.4 Neutron Reflectometry for Measuring Membrane Thickness and Reservoir Thickness
131(2)
7.3.5 Summary
133(1)
7.4 Complements and Sources
134(1)
7.5 Closing Remarks
135(4)
Part III Dynamic Models for Artificial Membranes: From Atoms to Device
8 Reaction-Rate-Constrained Models for Engineered Membranes
139(20)
8.1 Introduction
139(1)
8.2 Fractional-Order Macroscopic Model
140(10)
8.2.1 Fractional-Order Derivatives: Double-Layer Capacitance and Charging Dynamics
144(3)
8.2.2 Fractional-Order Macroscopic Model: Sinusoidal and Time-Varying Excitation Potential
147(1)
8.2.3 Determining the Quality of an Engineered Membrane Using the Fractional-Order Macroscopic Model
148(2)
8.3 Experimental Measurements: Fractional-Order Macroscopic Model
150(4)
8.3.1 Spacer Surface and Electrolyte Concentration
151(1)
8.3.2 Variation in Membrane Types and Tether Density
152(1)
8.3.3 Estimating the Dielectric Constant of the Membrane
152(2)
8.4 Modeling Membranes with Sterol Components
154(3)
8.4.1 Fractional-Order Model for Cholesterol in Engineered Membranes
154(2)
8.4.2 Impedance Analysis of Engineered Membranes Containing Sterol Molecules
156(1)
8.5 Complements and Sources
157(1)
8.6 Closing Remarks
158(1)
9 Reaction-Rate-Constrained Models for the ICS Biosensor
159(15)
9.1 Introduction
159(2)
9.2 Detection of Analyte Species in the Reaction-Rate Regime
161(6)
9.2.1 Aside: From Chemical Equations to Reaction-Rate Differential Equations
161(1)
9.2.2 Reaction-Rate Model of the ICS Biosensor
162(3)
9.2.3 Singular Perturbation Analysis of Dimer Concentration
165(1)
9.2.4 Detection of Human Chorionic Gonadotropin (hCG)
166(1)
9.3 Microelectrode ICS (mICS) Biosensor and Hidden Markov Model (HMM)
167(5)
9.3.1 Hidden Markov Model for mICS Biosensor
168(2)
9.3.2 Hidden Markov Model Statistical Signal Processing
170(1)
9.3.3 Detection of Monoterpene Oxidation Product (MTOP)
171(1)
9.4 Complements and Sources
172(1)
9.5 Closing Remarks
172(2)
10 Diffusion-Constrained Continuum Models of Engineered Membranes
174(38)
10.1 Introduction
174(2)
10.2 Mass Transport versus Reaction-Rate-Limited Kinetics
176(2)
10.2.1 Damkohler and Peclet Numbers
176(1)
10.2.2 Characterization of Operating Regime
177(1)
10.3 Mass-Transport-Limited Model of the ICS Biosensor Dynamics
178(9)
10.3.1 Poisson's Equation: Electrostatics
180(1)
10.3.2 Nernst-Planck Equation: Advection and Diffusion
181(1)
10.3.3 Poisson-Nernst-Planck Equation
182(3)
10.3.4 Estimating the Reaction Rates in the ICS Biosensor
185(1)
10.3.5 Experimental Results: Streptavidin, TSH, Ferritin, and hCG
186(1)
10.4 Biosensor Arrays: Numerical Case Study
187(8)
10.4.1 Biosensor Array Model
189(1)
10.4.2 Mass-Transport Phase Diagram
190(3)
10.4.3 Sensor Array Can Mitigate Mass-Transport Limits
193(2)
10.5 Pore Formation Dynamics: Models for PGLa Antimicrobial Peptides
195(8)
10.5.1 Generalized Reaction-Diffusion Equation
197(1)
10.5.2 Analyte and Surface Reaction Mechanism of PGLa
197(2)
10.5.3 Dynamic Model of Electrolyte and Surface Diffusion of PGLa
199(2)
10.5.4 Experimental Results: Reaction Dynamics of PGLa
201(2)
10.6 Asymptotic Poisson-Nernst-Planck Model and Lumped Circuit Parameters
203(5)
10.6.1 Double-Layer Capacitance and Electrolyte Resistance for Blocking Electrode
204(2)
10.6.2 Double-Layer Capacitance for Reaction-Limited Electrode
206(2)
10.7 Complements and Sources
208(3)
10.7.1 Poisson-Nernst-Planck (PNP) Model
208(1)
10.7.2 ICS Biosensor Arrays and Multicompartment Models
208(1)
10.7.3 Parameter Estimation and System Identification
209(2)
10.8 Closing Remarks
211(1)
11 Electroporation Models in Engineered Artificial Membranes
212(38)
11.1 Introduction
212(5)
11.1.1 Applications of Electroporation
212(1)
11.1.2 What Is Electroporation?
213(1)
11.1.3 Mesoscopic Model of Electroporation
214(2)
11.1.4 Organization of This
Chapter
216(1)
11.2 Smoluchowski-Einstein Equation
217(5)
11.2.1 Source Term and Energy Term of the Smoluchowski-Einstein Equation
219(3)
11.2.2 Summary
222(1)
11.3 Multiphysics (Mesoscopic) Model of Electroporation
222(5)
11.3.1 Equivalent Circuit Model of Electroporation
222(2)
11.3.2 Singular Perturbation Approximation and Electrical Dynamics
224(3)
11.4 Continuum Model of Electroporation: Aqueous Pore Conductance and Double-Layer Capacitance
227(8)
11.4.1 Continuum Model 1: Generalized Poisson-Nernst-Planck (GPNP) Equation
229(3)
11.4.2 Continuum Model 2: Poisson-Fermi-Nernst-Planck (PFNP) Equation
232(3)
11.5 Computing Engineered Tethered-Membrane Parameters from Continuum Theory
235(7)
11.5.1 Computing Pore Conductance
235(1)
11.5.2 Electrical Potential Energy for Pore Formation
236(1)
11.5.3 Computing Pore Capacitance
237(1)
11.5.4 Double-Layer Capacitance
238(1)
11.5.5 Detection Tests for Ionic Correlation Effects
238(4)
11.6 Faradic Reactions at the Bioelectronic Interface
242(5)
11.6.1 Faradic Reactions and Double-Layer Charging at the Bioelectronic Interface
242(2)
11.6.2 Faradic Reaction Boundary Conditions for the PFNP Continuum Model
244(3)
11.7 Complements and Sources
247(1)
11.8 Closing Remarks
248(2)
12 Electroporation Measurements in Engineered Membranes
250(32)
12.1 Introduction
250(3)
12.2 Aqueous Pore Conductance, Capacitance, and Electrical Energy
253(7)
12.2.1 Aqueous Pore Conductance
254(2)
12.2.2 Aqueous Pore Electrical Energy
256(3)
12.2.3 Aqueous Pore Capacitance
259(1)
12.3 Pore Radii and Membrane Conductance Dynamics
260(1)
12.4 Sensitivity of Current Response to Model Parameters
260(2)
12.5 Effect of Tether Density of Membrane Electroporation Dynamics
262(3)
12.6 Heterogeneous Membrane Mixtures
265(2)
12.7 Membranes with Sterol Inclusions
267(2)
12.8 Estimating Hydration Ion Size and Faradic Reaction Rates
269(2)
12.9 Electrical Double-Layer Charging Dynamics
271(5)
12.9.1 Spatially Dependent Dielectric Constant at the Bioelectronic Interface
272(3)
12.9.2 Voltage-Dependent Double-Layer Capacitance
275(1)
12.10 Large Excitation Potentials and Double-Layer Charging Dynamics
276(3)
12.11 Complements and Sources
279(2)
12.12 Closing Remarks
281(1)
13 Electrophysiological Response of Ion Channels and Cells
282(13)
13.1 Introduction
282(2)
13.2 Dynamic Model of Embedded Ion Channels
284(1)
13.3 Electrophysiological Response of a Voltage-Gated Ion Channel
285(1)
13.4 Dynamic Model of Electrophysiological Response of Cells
286(5)
13.4.1 Macroscopic Model of the Electrophysiological Response Platform
287(2)
13.4.2 Cellular Membrane Conductance and Charging Dynamics
289(2)
13.5 Electrophysiological Response of Skeletal Myoblasts
291(1)
13.6 Complements and Sources
292(1)
13.7 Closing Remarks
293(2)
14 Coarse-Grained Molecular Dynamics
295(58)
14.1 Introduction
295(4)
14.2 Basics of Coarse-Grained Molecular Dynamics
299(2)
14.2.1 From an Atomistic to a Mesoscopic Coarse-Grained Description of Engineered Membranes
300(1)
14.3 Atomistic-to-Observable Model of Tethered Membranes
301(4)
14.4 Aside: The Fokker-Planck Equation
305(5)
14.4.1 Kolmogorov and Fokker-Planck Equations
306(2)
14.4.2 First-Passage Time and the Arrhenius Equation
308(2)
14.5 Coarse-Grained Molecular Dynamics Model for the Bioelectronic Interface and Water
310(12)
14.5.1 Percus-Yevick Equation and Water Density at the Bioelectronic Interface
311(4)
14.5.2 Density Profile of Water at the Bioelectronic Interface
315(2)
14.5.3 Fokker-Planck Equation: Spatially Dependent Water Diffusion Coefficient
317(3)
14.5.4 Diffusion Tensor of Water in Tethering Reservoir
320(1)
14.5.5 Summary
321(1)
14.6 Tethered Membrane Dynamics and Energetics
322(10)
14.6.1 Lipid Energetics and Pore Density
322(3)
14.6.2 Line Tension and Surface Tension
325(3)
14.6.3 Deuterium Order Parameter
328(1)
14.6.4 Lipid Lateral Diffusion
328(2)
14.6.5 Geometric Properties of Tethered Membranes
330(2)
14.6.6 Summary
332(1)
14.7 Control of Tethered-Membrane Properties by Sterol Inclusions
332(4)
14.7.1 Lateral Diffusion Dynamics of Lipids and Cholesterol
333(1)
14.7.2 Biomechanics of Lipids and Cholesterol
334(2)
14.8 Molecular Diffusion and Langevin's Equation
336(5)
14.8.1 Langevin's Equation and Diffusion of Molecules
336(3)
14.8.2 Nonstationary Lipid Diffusion with Sterol Inclusions
339(2)
14.9 Case Study: Atomistic-to-Observable Model PGLa Pore Formation in Tethered Membranes
341(7)
14.9.1 Coarse-Grained Molecular Dynamics Simulation of Tethered Membrane Containing PGLa
342(3)
14.9.2 Diffusion of PGLa and Membrane Properties from Coarse-Grained Molecular Dynamics
345(1)
14.9.3 Surface Binding and Oligomerization of PGLa from Coarse-Grained Molecular Dynamics
346(2)
14.10 Complements and Sources
348(3)
14.11 Closing Remarks
351(2)
15 All-Atom Molecular Dynamics Simulation Models
353(37)
15.1 Introduction
353(1)
15.2 Basics of Molecular Dynamics
353(18)
15.2.1 Potential Energy Functions
355(3)
15.2.2 Macroscopic Parameters and Statistical Ensembles
358(7)
15.2.3 Numerical Methods for Molecular Dynamics
365(6)
15.3 MD Simulations for the Dynamics of Engineered Membranes
371(3)
15.4 Aqueous Pore Formation Dynamics in Tethered Membranes
374(2)
15.5 Capacitance and Dipole Potential of Tethered Membranes
376(2)
15.6 Modeling Ion Permeation and Channel Conductance
378(5)
15.6.1 Models for Ion Permeation: From Ab Initio to Reaction Rate
378(3)
15.6.2 Gramicidin Channel Conductance Estimation Using Distributional Molecular Dynamics
381(2)
15.7 Gramicidin A (gA) Dimer Dissociation and Reaction-Rate Estimation
383(4)
15.7.1 Molecular Reaction Dynamics of Gramicidin Channel Dissociation
384(1)
15.7.2 Gramicidin A Reaction Rates
385(2)
15.8 Complements and Sources
387(2)
15.9 Closing Remarks
389(1)
16 Closing Summary for Part III: From Atoms to Device
390(5)
Appendices
Appendix A Elementary Primer on Partial Differential Equations (PDEs)
395(9)
A.1 Linear, Semilinear, and Nonlinear Partial Differential Equations
395(1)
A.2 Linear Partial Differential Equations and Boundary Conditions
396(1)
A.3 Nondimensionalization of Partial Differential Equations
397(4)
A.4 Solutions of Partial Differential Equations
401(3)
Appendix B Tutorial on Coarse-Grained Molecular Dynamics with Peptides
404(8)
B.1 Constructing the All-Atom and Coarse-Grained Structure of a Peptide
404(2)
B.2 Construction of Coarse-Grained Lipid Bilayer
406(3)
B.3 How to Insert PGLa Peptides in the Transmembrane State
409(1)
B.4 Note on Publication-Quality Figures
410(2)
Appendix C Experimental Setup and Numerical Methods
412(9)
C.1 Ion-Channel Switch Biosensor
412(2)
C.2 Pore Formation Measurement Platform: PGLa
414(1)
C.3 Tethered-Membrane Parameters: Pore Conductance and Electrical Energy
415(1)
C.4 Coarse-Grained Molecular Dynamics (CGMD) Simulations
416(3)
C.5 CGMD Simulation Setup for PGLa
419(2)
C.5.1 Simulation Setup of All-Atom Molecular Dynamics
420(1)
Bibliography 421(26)
Index 447
William Hoiles is a Research Fellow in the Department of Electrical and Computer Engineering at the University of British Columbia, Vancouver. Vikram Krishnamurthy is a Professor in the School of Electrical and Computer Engineering and Cornell Tech at Cornell University, New York. He is a Fellow of the IEEE and the author of Partially Observed Markov Decision Processes (Cambridge, 2016). Bruce Cornell is an Adjunct Professor in the School of Life Sciences at the University of Technology Sydney, and at Western Sydney University. He is also the Principal Scientist at Surgical Diagnostics Pty Ltd and SDx Tethered Membranes Pty Ltd.
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