An immersed boundary method for Brownian dynamics simulation of polymers in complex geometries: Application to DNA flowing through a nanoslit with embedded nanopits

Zhang, Yu; de Pablo, Juan J.; Graham, Michael D.

doi:doi:10.1063/1.3672103

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Self-metalation of 2H-tetraphenylporphyrin on Cu(111): An x-ray spectroscopy study

The bonding and the temperature-driven metalation of 2H-tetraphenylporphyrin (2H-TPP) on the Cu(111) surface under ultrahigh vacuum conditions were investigated by a combination of x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy with density functional theory calculations. Thin films were prepared by organic molecular beam epitaxy and subsequent annealing. Our systematic study provides an understanding of the changes of the spectroscopic...

Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we s...

This work presents an immersed boundary method that allows fast Brownian dynamics simulation of solutions of polymer chains and other Brownian objects in complex geometries with fluctuating hydrodynamics. The approach is based on the general geometry Ewald-like method, which solves the Stokes equation with distributed regularized point forces in O(N) or O(NlogN) operations, where N is the number of point forces in the system. Time-integration is performed using a midpoint algorithm and Chebyshev polynomial approximation proposed by Fixman. This approach is applied to the dynamics of a genomic DNA molecule driven by flow through a nanofluidic slit with an array of nanopits on one wall of the slit. The dynamics of the DNA molecule was studied as a function of the Péclet number and chain length (the base case being λ-DNA). The transport characteristics of the hopping dynamics in this device differ at low and high Péclet number, and for long DNA, relative to the pit size, the dynamics is governed by the segments residing in the pit. By comparing with results that neglect them, hydrodynamic interactions are shown to play an important quantitative role in the hopping dynamics.

Article Outline

INTRODUCTION
METHODS FOR HYDRODYNAMICS OF CONFINED POLYMER SOLUTIONS
POLYMER MODEL AND SIMULATION METHOD
1. Model and governing equations
2. Governing equations
3. Mobility tensor and time-integration algorithm
4. Chebyshev approximation
5. Fast Stokes solver with complex boundary conditions
  1. Immersed boundary method
  2. Periodic GGEM
  3. Local velocity field
  4. Global velocity field
  5. Validation: GGEM
  6. Validation: IBM
DNA FLOWING ACROSS AN ARRAY OF NANOPITS
1. Dynamics at low Péclet number
2. Dynamics at high Péclet number
CONCLUSIONS

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KEYWORDS and PACS

Keywords

biological fluid dynamics, boundary-value problems, Brownian motion, Chebyshev approximation, DNA, fluctuations, genomics, hydrodynamics, molecular biophysics, molecular configurations, nanobiotechnology, polymers

PACS

87.15.hj

Transport dynamics
87.15.B-

Structure of biomolecules
87.15.A-

Theory, modeling, and computer simulation
05.40.Jc

Brownian motion
87.85.Rs

Nanotechnologies-applications
87.18.Wd

Genomics

ARTICLE DATA

Digital Object Identifier

http://dx.doi.org/10.1063/1.3672103

PUBLICATION DATA

ISSN

0021-9606 (print)

1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef

American Institute of Physics

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