Overview

This book will be written with all these audiences in mind - touching equally on each of these unique perspectives and goals. The topics discussed will be grounded in physics, but at a level accessible to researchers in other fields and consequently will discuss relevance and applicability to cellular biology and materials science. Key Features • 1. Detailed protocols for creating and tuning biopolymer networks, including video protocols. • 2. Description of methods for measuring mechanics, structure, and dynamics of biopolymer networks with a focus on optical tweezers micro rheology and differential dynamic microscopy (two valuable techniques that are not widely used due to lack of understanding) • 3. Freeware Python code for data analysis (available through GitHub repositories) • 4. Discussion of networks of topologically-novel polymer networks – the underlying physics, how to create, and open questions • 5. Discussion of biopolymer networks as active matter – the frontier of soft matter and materials science research. • 6. Written to be highly interdisciplinary, suitable for relevant audiences in physics, biophysics, biology, chemistry, engineering, materials science

Full Product Details

Author:   Rae M Robertson-Anderson
Publisher:   Institute of Physics Publishing
Imprint:   Institute of Physics Publishing
Dimensions:   Width: 17.80cm , Height: 2.40cm , Length: 25.40cm
Weight:   0.960kg
ISBN:  

9780750350358

ISBN 10:   0750350350
Pages:   300
Publication Date:   02 October 2023
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   In Print  
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Table of Contents

Sections (I-IV) and Chapters (1-10): Let’s Get Started 1. Introduction to Biopolymers and Networks. The chapter will cover what biopolymers are and why they are important. It will introduce the most important and widely studied biopolymers (nucleic acids, cytoskeleton filaments, proteins, and polysaccharides) and the key physical properties of each. The chapter will conclude with a discussion of biopolymer networks, including their importance in biology, physics, and materials science, key features and considerations, and open questions in the field. 2. Polymer physics for everyone. This chapter will cover the theoretical frameworks and tools needed to understand biopolymer network dynamics, structure and rheological properties. The purpose of the chapter is to provide a high-level overview of theoretical concepts that are necessary to understand polymer networks, but that can be understood by an interdisciplinary audience that may include biologists, chemists, and engineers, as well as advanced physics undergraduates. Some of the key theoretical concepts and models that will be discussed are: polymer flexibility (freely-jointed chain, worm-like chain, and rigid rod models), free-energy-minimizing conformations (random coils, etc), the Zimm model and hydrodynamic effects, the Rouse model and polymer overlap, the reptation model and steric entanglements, viscoelasticity, linear and nonlinear rheological properties, crosslinking and rigidity percolation theory. II. Making, Measuring and Making Sense 3. Biopolymer network design: protocols and considerations. This chapter will discuss the most widely studied types of biopolymer networks, classified by the type of biopolymer, their interactions and the network morphology. A unique feature of this chapter will be the inclusion of detailed protocols to create various networks, as well as links to video protocols and movies of the networks. The biopolymers that will be focused on will include DNA, actin and microtubules. The interactions and morphologies discussed will include steric entanglements, crosslinking, bundling, and nematic alignment. This chapter will also discuss the design of 2D networks and surface interactions, as well as networks encapsulated in cell-sized droplets and vesicles. Finally, the chapter will briefly discuss methods for fluorescent-labelling biopolymers for various imaging and microscopy modalities. eBook Project Approval Meeting title information sheet v3.0 4. Measuring mechanics, dynamics and structure. This chapter will discuss current methods for measuring transport properties, dynamics, viscoelastic properties, and structural features of biopolymer networks. Techniques that will be highlighted will include: epifluorescence microscopy, multi-spectral confocal microscopy, light-sheet microscopy, passive and active micro rheology, optical tweezers force spectroscopy, dynamic light scattering, traction force microscopy, STORM, and opto-rheology. Because nearly all of these methods require imaging microsphere probes embedded in the networks or the biopolymers themselves, this chapter will also discuss labeling methods for different biopolymers and measurement techniques, as well as considerations for choosing and preparing the optimal probes. Some unique features will include schematics for building novel instrumentation, videos of networks imaged using the different microscopy methods discussed. 5. Analysis methods, algorithms, and deliverables. This chapter will build upon the previous chapter by discussing the various methods for analysing data acquired using the methods described in Chapter 4 to determine biopolymer transport properties, single�molecule and ensemble dynamics, and network structure. The analysis methods will include: particle-tracking, single-molecule conformational tracking (SMCT), differential dynamic microscopy (DDM), particle-image velocimetry (PIV), Generalized-Stokes-Einstein Relation (GSER) approach to determining linear viscoelastic moduli, and spatial image autocorrelation analysis. A unique feature of this chapter will be the inclusion of links to GitHub repositories with Python algorithms for DDM, SMCT, SIA, PIV and GSER analyses. It may also include links to videos showing the use of freeware Fiji to post-process images for different analysis methods. Beyond the Basics - Novel and complex networks 6. Networks with topologically novel biopolymers. Polymer physics theory is largely devoted to linear polymers and their networks; yet biopolymers naturally exist in multiple topologies such as torsionally-strained and twisted (i.e., supercoiled), circular (i.e., ring), and branched. This chapter will discuss the effect of polymer topology on polymer transport and conformations in networks, as well as network dynamics, rheology and structure. It will cover theoretical principles, recent experimental findings, and open questions. A unique feature of the chapter will be protocols for creating networks of circular and supercoiled DNA. 7. Biopolymer composites, blends and crowding. While the focus of polymer physics theory and materials science has largely been on single-component polymer networks, cells take advantage of composite biopolymer systems, such as the cytoskeleton, to enable emergent dynamical and structural properties. Composites are of interest in industry and commercial applications as they can exhibit scale-dependent rheological properties and emergent low-weight and high-strength. This chapter will discuss composite networks and blends comprising two or more distinct polymers, as well as crowded environments comprising multiple types of macromolecules including synthetic polymers and colloids. It will describe the dynamics, mechanical properties and structure of composite networks, the emergent properties that they confer, and design considerations for preparing composites. Specific examples of networks that will be discussed include composites of: DNA and actin, DNA and microtubules, actin and microtubules, actin and intermediate filaments, and DNA and dextran. The effect of polymer concentrations, sizes, topologies, stiffnesses and crosslinking will be discussed, as well as design considerations, sample protocols, and open questions. 8. Active, responsive, and reconfigurable networks. The frontier of materials design and soft matter physics is active, responsive and reconfigurable non-equilibrium materials, for which biopolymer networks are ideal candidates. In the cytoskeleton of cells, molecular motors generate forces and restructure networks of cytoskeletal biopolymers. In the nucleus, enzymes wind, unwind, cleave, and concatenate DNA, changing the viscoelastic properties of the crowded biopolymer network. Changes to the dynamics and structure of biopolymer networks (polymerization, bundling, etc) can also be triggered by variations in the chemical environment. This chapter will discuss in vitro realizations of eBook Project Approval Meeting title information sheet v3.0 active biopolymer networks inspired by these biological feats, including network design, non-equilibrium dynamics, and mechanical properties. Key examples of active and responsive biopolymer networks that will be discussed include actomyosin networks, salt�mediated bundling of cytoskeleton networks, kinesin-microtubule active nematics, motor�driven cytoskeleton composites, and enzyme-driven DNA systems. Unique features of this chapter will include protocols for designing and characterizing a few of the examples discussed, as well as microscopy videos of the actively restructuring networks. 9. Heterogeneous networks and liquid-liquid phase separation. In crowded biological cells, entropically-driven depletion interactions drive biopolymer networks to adopt heterogeneous structures and connectivity over different length and time scales. These interactions also lead to liquid-liquid phase separation (LLPS) of interacting biopolymer networks - a phenomenon now recognized as the key driver of the spatial organization of cells. This chapter will discuss these novel heterogeneous networks, covering key examples of each, the underlying physics driving the heterogeneous organization or LLPS, the associated mechanical and structural properties of the networks, and the open questions that remain. IV. What now? 10. Future Directions, Applications, and Crowding-Sourcing. This chapter will summarize the previous chapters and discuss the big open questions in the field. It will highlight the most recent technological advances, and what is needed for further progress, including high-throughput analysis methods and machine-learning. This chapter will also discuss applications of biopolymer networks in industry, and will invite readers to contribute to the publicly-available soft matter database (of which a link will be provided) that will serve as a repository for biopolymer network protocols and properties to advance the use of biopolymer networks in materials discovery.

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Author Information

Rae M Robertson-Anderson is Professor of Physics and Biophysics and Associate Provost for Engaged Scholarship at the University of San Diego, where she has established an internationally recognized research program to elucidate macromolecular dynamics and microscale mechanics of bio-inspired soft and active matter systems. Robertson-Anderson is a leading expert in the design of novel microrheology methods and complex biopolymer composites to address critical questions in soft matter physics and cell biology. She is equally passionate about promoting and advancing undergraduate research and education, and building community among diverse scientists and with the general public. Robertson-Anderson has been awarded over $5M in grants to support her research, and her 74 publications feature 85 undergraduate co-authors.

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