Ebook: Structure and Dynamics of Confined Polymers

Polymers are essential to biology because they can have enough stable degrees of freedom to store the molecular code of heredity and to express the sequences needed to manufacture new molecules. Through these they perform or control virtually every function in life. Although some biopolymers are created and spend their entire career in the relatively large free space inside cells or organelles, many biopolymers must migrate through a narrow passageway to get to their targeted destination. This suggests the questions: How does confining a polymer affect its behavior and function? What does that tell us about the interactions between the monomers that comprise the polymer and the molecules that confine it? Can we design and build devices that mimic the functions of these nanoscale systems? The NATO Advanced Research Workshop brought together for four days in Bikal, Hungary over forty experts in experimental and theoretical biophysics, molecular biology, biophysical chemistry, and biochemistry interested in these questions. Their papers collected in this book provide insight on biological processes involving confinement and form a basis for new biotechnological applications using polymers. In his paper Edmund DiMarzio asks: What is so special about polymers? Why are polymers so prevalent in living things? The chemist says the reason is that a protein made of N amino acids can have any of 20 different kinds at each position along the chain, resulting in 20 N different polymers, and that the complexity of life lies in this variety.

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The primary goal of this book is to explore the physical properties of polymers in confined spaces at the nanometer scale, with a particular emphasis on determining the mechanisms by which polymers are transported through narrow interstices. A variety of pore structures that polymers can penetrate have recently been discovered, and it is now possible to probe the dynamics of the interactions between polymers and the penetrating molecules.
The experimental and theoretical advances discussed include:

- Mechanical properties of single molecules;
- Detection & characterization of single polymers transported through narrow ion channels;
- Direct measurement of the energetics and dynamics of polymer transport through a pore;
- Statistical mechanical theories for single polymer transport through a narrow pore;
- Novel polymer separations techniques not based on cross-linked gels;
- Physics of polymer-protein interactions. The book also explores potential scientific and technological applications that can exploit these systems, with the aim of stimulating new research in this highly multidisciplinary field.

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The primary goal of this book is to explore the physical properties of polymers in confined spaces at the nanometer scale, with a particular emphasis on determining the mechanisms by which polymers are transported through narrow interstices. A variety of pore structures that polymers can penetrate have recently been discovered, and it is now possible to probe the dynamics of the interactions between polymers and the penetrating molecules.
The experimental and theoretical advances discussed include:

- Mechanical properties of single molecules;
- Detection & characterization of single polymers transported through narrow ion channels;
- Direct measurement of the energetics and dynamics of polymer transport through a pore;
- Statistical mechanical theories for single polymer transport through a narrow pore;
- Novel polymer separations techniques not based on cross-linked gels;
- Physics of polymer-protein interactions. The book also explores potential scientific and technological applications that can exploit these systems, with the aim of stimulating new research in this highly multidisciplinary field.

Content:
Front Matter....Pages i-xvii
Profound Implications for Biophysics of the Polymer Threading a Membrane Transition....Pages 1-21
Phage DNA Transport Across Membranes....Pages 23-36
Translocation of Macromolecules across Membranes and Through Aqueous Channels....Pages 37-66
Protein Translocation Across the Outer Membrane of Mitochondria....Pages 67-84
Protein Translocation Channels in Mitochondria....Pages 85-95
Sizing Channels with Neutral Polymers....Pages 97-115
Dynamic Partitioning of Neutral Polymers into a Single Ion Channel....Pages 117-130
Branched Polymers inside Nanoscale Pores....Pages 131-139
Physics of DNA Threading through a Nanometer Pore and Applications to Simultaneous Multianalyte Sensing....Pages 141-163
Mechanism of Ionic Current Blockades during Polymer Transport through Pores of Nanometer Dimensions....Pages 165-175
Using Nanopores to Discriminate between Single Molecules of DNA....Pages 177-185
Use of a Nanoscale Pore to Read Short Segments within Single Polynucleotide Molecules....Pages 187-200
Polymer Dynamics in Microporous Media....Pages 201-225
Entropic Barrier Theory of Polymer Translocation....Pages 227-239
Polymer Translocation through a “Complicated” Pore....Pages 241-259
The Polymer Barrier Crossing Problem....Pages 261-280
Brownian Ratchets and Their Application to Biological Transport Processes and Macromolecular Separation....Pages 281-294
Composition and Structural Dynamics of Vertebrate Striated Muscle Thick Filaments....Pages 295-309
Force-Driven Folding and Unfolding Transitions in Single Titin Molecules....Pages 311-326
Dynamics of Actin Filaments in Motility Assays....Pages 327-332
Conformation-Dependent Sequence Design of Copolymers....Pages 333-350
Single Molecule Nucleic Acid Analysis by Fluorescence Flow Cytometry....Pages 351-370
Fluorescence Energy Transfer Reagents for DNA Sequencing and Analysis....Pages 371-383
Back Matter....Pages 385-390

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The primary goal of this book is to explore the physical properties of polymers in confined spaces at the nanometer scale, with a particular emphasis on determining the mechanisms by which polymers are transported through narrow interstices. A variety of pore structures that polymers can penetrate have recently been discovered, and it is now possible to probe the dynamics of the interactions between polymers and the penetrating molecules.
The experimental and theoretical advances discussed include:

- Mechanical properties of single molecules;
- Detection & characterization of single polymers transported through narrow ion channels;
- Direct measurement of the energetics and dynamics of polymer transport through a pore;
- Statistical mechanical theories for single polymer transport through a narrow pore;
- Novel polymer separations techniques not based on cross-linked gels;
- Physics of polymer-protein interactions. The book also explores potential scientific and technological applications that can exploit these systems, with the aim of stimulating new research in this highly multidisciplinary field.

Content:
Front Matter....Pages i-xvii
Profound Implications for Biophysics of the Polymer Threading a Membrane Transition....Pages 1-21
Phage DNA Transport Across Membranes....Pages 23-36
Translocation of Macromolecules across Membranes and Through Aqueous Channels....Pages 37-66
Protein Translocation Across the Outer Membrane of Mitochondria....Pages 67-84
Protein Translocation Channels in Mitochondria....Pages 85-95
Sizing Channels with Neutral Polymers....Pages 97-115
Dynamic Partitioning of Neutral Polymers into a Single Ion Channel....Pages 117-130
Branched Polymers inside Nanoscale Pores....Pages 131-139
Physics of DNA Threading through a Nanometer Pore and Applications to Simultaneous Multianalyte Sensing....Pages 141-163
Mechanism of Ionic Current Blockades during Polymer Transport through Pores of Nanometer Dimensions....Pages 165-175
Using Nanopores to Discriminate between Single Molecules of DNA....Pages 177-185
Use of a Nanoscale Pore to Read Short Segments within Single Polynucleotide Molecules....Pages 187-200
Polymer Dynamics in Microporous Media....Pages 201-225
Entropic Barrier Theory of Polymer Translocation....Pages 227-239
Polymer Translocation through a “Complicated” Pore....Pages 241-259
The Polymer Barrier Crossing Problem....Pages 261-280
Brownian Ratchets and Their Application to Biological Transport Processes and Macromolecular Separation....Pages 281-294
Composition and Structural Dynamics of Vertebrate Striated Muscle Thick Filaments....Pages 295-309
Force-Driven Folding and Unfolding Transitions in Single Titin Molecules....Pages 311-326
Dynamics of Actin Filaments in Motility Assays....Pages 327-332
Conformation-Dependent Sequence Design of Copolymers....Pages 333-350
Single Molecule Nucleic Acid Analysis by Fluorescence Flow Cytometry....Pages 351-370
Fluorescence Energy Transfer Reagents for DNA Sequencing and Analysis....Pages 371-383
Back Matter....Pages 385-390
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