scholarly journals Translocation time of a polymer chain through an energy gradient nanopore

2017 ◽  
Vol 12 (3) ◽  
Author(s):  
Meng-Bo Luo ◽  
Shuang Zhang ◽  
Fan Wu ◽  
Li-Zhen Sun
Keyword(s):  
Polymer Chain ◽  
Energy Gradient ◽  
Translocation Time

DYNAMICAL MODES OF POLYMER TRANSLOCATING THROUGH INTERACTING PORE UNDER CHEMICAL POTENTIAL DIFFERENCE

2011 ◽  
Vol 25 (25) ◽  
pp. 3345-3351 ◽  
Author(s):  
WEI-PING CAO ◽  
LI-ZHEN SUN ◽  
CHAO WANG ◽  
MENG-BO LUO
Keyword(s):  
Monte Carlo ◽  
Polymer Chain ◽  
Power Law ◽  
Chemical Potential ◽  
Monte Carlo Technique ◽  
Potential Difference ◽  
Nonequilibrium Process ◽  
Chemical Potential Difference ◽  
Translocation Time

The translocation of polymer chain through an interacting pore under chemical potential difference Δμ is simulated using Monte Carlo technique. Three translocation modes, dependent on the polymer–pore interaction ε and Δμ, are discovered. The translocation process is found to be an nonequilibrium process, which influences the dependence of translocation time τ on ε and Δμ. It is found that τ decreases in a power law relation with the increase of Δμ, and the exponent is dependent on the interaction.

Conformation of Polymer Chain in the Bulk

1976 ◽  
Vol 1 ◽  
pp. 112-121
Author(s):  
J. P. Cotton ◽  
D. Decker ◽  
H. Benoit ◽  
B. Farnoux ◽  
J. Higgins ◽  
...  
Keyword(s):  
Polymer Chain

Undulations of a Straight Polymer Chain Embedded in a Membrane

1996 ◽  
Vol 6 (12) ◽  
pp. 1743-1757
Author(s):  
M. Singh-Zocchi ◽  
M. M. Kozlov ◽  
W. Helfrich
Keyword(s):  
Polymer Chain

Molecular Dynamics Using Non-Variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model

2019 ◽  
Author(s):  
Pier Paolo Poier ◽  
Louis Lagardere ◽  
Jean-Philip Piquemal ◽  
Frank Jensen
Keyword(s):  
Boundary Conditions ◽  
Periodic Boundary ◽  
Force Fields ◽  
Periodic Boundary Conditions ◽  
Computational Effort ◽  
Polarizable Force Fields ◽  
Energy Models ◽  
Capacity Model ◽  
Energy Gradient ◽  
Polarization Models

<div> <div> <div> <p>We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations. </p><div> <div> <div> <p>By making use of a Lagrange formalism, however, this computational demanding task can be re- placed by solving a single equation similar to that for determining the electrostatic variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p><div><div><div> </div> </div> </div> <p> </p><div> <div> <div> <p>variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p> </div> </div> </div> </div> </div> </div> </div> </div> </div>

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