Structure and Dynamics of Confined Polymers

1. Front Matter

   Pages i-xvii

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2. Profound Implications for Biophysics of the Polymer Threading a Membrane Transition

   • Edmund A. DiMarzio

   Pages 1-21

3. Phage DNA Transport Across Membranes

   • Lucienne Letellier

   Pages 23-36

4. Translocation of Macromolecules across Membranes and Through Aqueous Channels

   • Sanford M. Simon

   Pages 37-66

5. Protein Translocation Across the Outer Membrane of Mitochondria

   • Stephan Nussberger, Walter Neupert

   Pages 67-84

6. Protein Translocation Channels in Mitochondria

   • Kathleen W. Kinnally

   Pages 85-95

7. Sizing Channels with Neutral Polymers

   • O. V. Krasilnikov

   Pages 97-115

8. Dynamic Partitioning of Neutral Polymers into a Single Ion Channel

   • Sergey M. Bezrukov, John J. Kasianowicz

   Pages 117-130

9. Branched Polymers inside Nanoscale Pores

   • C. Gay, P.-G. de Gennes, E. Raphaël, F. Brochard-Wyart

   Pages 131-139

10. Physics of DNA Threading through a Nanometer Pore and Applications to Simultaneous Multianalyte Sensing

    • John J. Kasianowicz, Sarah E. Henrickson, Martin Misakian, Howard H. Weetall, Baldwin Robertson, Vincent Stanford

    Pages 141-163

11. Mechanism of Ionic Current Blockades during Polymer Transport through Pores of Nanometer Dimensions

    • David W. Deamer, Hugh Olsen, Mark A. Akeson, John J. Kasianowicz

    Pages 165-175

12. Using Nanopores to Discriminate between Single Molecules of DNA

    • Daniel Branton, Amit Meller

    Pages 177-185

13. Use of a Nanoscale Pore to Read Short Segments within Single Polynucleotide Molecules

    • Mark Akeson, David W. Deamer, Wenonah Vercoutere, Rebecca Braslau, Hugh Olsen

    Pages 187-200

14. Polymer Dynamics in Microporous Media

    • Björn Åkerman

    Pages 201-225

15. Entropic Barrier Theory of Polymer Translocation

    • Murugappan Muthukumar

    Pages 227-239

16. Polymer Translocation through a “Complicated” Pore

    • David K. Lubensky

    Pages 241-259

17. The Polymer Barrier Crossing Problem

    • Wokyung Sung, Pyeong Jun Park

    Pages 261-280

18. Brownian Ratchets and Their Application to Biological Transport Processes and Macromolecular Separation

    • Imre Derényi, R. Dean Astumian

    Pages 281-294

19. Composition and Structural Dynamics of Vertebrate Striated Muscle Thick Filaments

    • Zoya A. Podlubnaya

    Pages 295-309

20. Force-Driven Folding and Unfolding Transitions in Single Titin Molecules

    • Miklós S. Z. Kellermayer, Steven Smith, Carlos Bustamante, Henk L. Granzier

    Pages 311-326

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.

• Biophysics
• Copolymer
• DNA
• Nucleotide
• REM
• STEM
• fluorescence
• polymer
• proteins

• Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, USA

  John J. Kasianowicz

• Department of Biophysics, Pécs University Medical School, Pécs, Hungary

  Miklós S. Z. Kellermayer

• Biophysics Laboratory, Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA

  David W. Deamer

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