Translocation of polymers out of confined geometries

We consider the free energy of confinement for a flexible self-avoiding polymer inside a spherical cavity. Accurate numerical calculations allow us to arbitrate between competing scaling predictions. We find that, for moderate confinement, the free energy exhibits a power-law dependence on cavity size that is different from what is observed for planar and cylindrical confinement. At high monomer concentrations, crossover to another scaling regime occurs. One of the consequences of these findings is a new prediction for the escape time of a polymer from a spherical confinement. By means of additional simulations, we confirm that the translocation time can be described by a scaling law that exhibits a nonlinear dependence on the degree of polymerization that is sensitive to the nature of the confining geometry. The geometry dependence contradicts earlier predictions but is in quantitative agreement with findings for the free energy of confinement.

[1]  D. Lubensky,et al.  Driven polymer translocation through a narrow pore. , 1999, Biophysical journal.

[2]  Confinement-driven translocation of a flexible polymer. , 2006, Physical review letters.

[3]  M. Muthukumar,et al.  Polymer translocation through a hole , 1999 .

[4]  Erik Luijten,et al.  Self-avoiding flexible polymers under spherical confinement. , 2006, Nano letters.

[5]  P. Gennes Scaling Concepts in Polymer Physics , 1979 .

[6]  H. Stanley,et al.  Statistical physics of macromolecules , 1995 .

[7]  Polymer Chains in Confined Spaces and Flow-Injection Problems: Some Remarks , 2005, cond-mat/0506803.

[8]  Mehran Kardar,et al.  Anomalous dynamics of forced translocation. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[9]  A. Ravve,et al.  Principles of Polymer Chemistry , 1995 .

[10]  D Thirumalai,et al.  Simulations of β-hairpin folding confined to spherical pores using distributed computing , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Sung,et al.  Polymer Translocation through a Pore in a Membrane. , 1996, Physical review letters.

[12]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[13]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[14]  Chuan Yi Tang,et al.  A 2.|E|-Bit Distributed Algorithm for the Directed Euler Trail Problem , 1993, Inf. Process. Lett..

[15]  E. Casassa Equilibrium distribution of flexible polymer chains between a macroscopic solution phase and small voids , 1967 .

[16]  S. Edwards,et al.  The entropy of a confined polymer. I , 1969 .

[17]  M. Muthukumar,et al.  Translocation of a confined polymer through a hole. , 2001, Physical review letters.

[18]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[19]  Anomalous dynamics of translocation. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[20]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[21]  C. Tanford Macromolecules , 1994, Nature.