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Modeling and simulation of the mechanical response from nanoindentation test of DNA-filled viral capsids

Ahadi, Aylin LU ; Johansson, Dan LU and Evilevitch, Alex LU (2013) In Journal of Biological Physics 39(2). p.183-199
Abstract
Viruses can be described as biological objects composed mainly of two parts: a stiff protein shell called a capsid, and a core inside the capsid containing the nucleic acid and liquid. In many double-stranded DNA bacterial viruses (aka phage), the volume ratio between the liquid and the encapsidated DNA is approximately 1:1. Due to the dominant DNA hydration force, water strongly mediates the interaction between the packaged DNA strands. Therefore, water that hydrates the DNA plays an important role in nanoindentation experiments of DNA-filled viral capsids. Nanoindentation measurements allow us to gain further insight into the nature of the hydration and electrostatic interactions between the DNA strands. With this motivation, a... (More)
Viruses can be described as biological objects composed mainly of two parts: a stiff protein shell called a capsid, and a core inside the capsid containing the nucleic acid and liquid. In many double-stranded DNA bacterial viruses (aka phage), the volume ratio between the liquid and the encapsidated DNA is approximately 1:1. Due to the dominant DNA hydration force, water strongly mediates the interaction between the packaged DNA strands. Therefore, water that hydrates the DNA plays an important role in nanoindentation experiments of DNA-filled viral capsids. Nanoindentation measurements allow us to gain further insight into the nature of the hydration and electrostatic interactions between the DNA strands. With this motivation, a continuum-based numerical model for simulating the nanoindentation response of DNA-filled viral capsids is proposed here. The viral capsid is modeled as large- strain isotropic hyper-elastic material, whereas porous elasticity is adopted to capture the mechanical response of the filled viral capsid. The voids inside the viral capsid are assumed to be filled with liquid, which is modeled as a homogenous incompressible fluid. The motion of a fluid flowing through the porous medium upon capsid indentation is modeled using Darcy's law, describing the flow of fluid through a porous medium. The nanoindentation response is simulated using three-dimensional finite element analysis and the simulations are performed using the finite element code Abaqus. Force-indentation curves for empty, partially and completely DNA-filled capsids are directly compared to the experimental data for bacteriophage lambda. Material parameters such as Young's modulus, shear modulus, and bulk modulus are determined by comparing computed force-indentation curves to the data from the atomic force microscopy (AFM) experiments. Predictions are made for pressure distribution inside the capsid, as well as the fluid volume ratio variation during the indentation test. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Capsid nanoindentation, AFM, Darcy's law, Finite element simulations, Spring constant, DNA-filled capsid
in
Journal of Biological Physics
volume
39
issue
2
pages
183 - 199
publisher
Kluwer
external identifiers
  • wos:000319387700004
  • scopus:84878736770
ISSN
0092-0606
DOI
10.1007/s10867-013-9297-9
language
English
LU publication?
yes
id
52560e11-c6c9-43ba-ab5c-b5febdf79a0f (old id 3931281)
date added to LUP
2013-07-15 15:23:34
date last changed
2019-10-13 03:51:14
@article{52560e11-c6c9-43ba-ab5c-b5febdf79a0f,
  abstract     = {Viruses can be described as biological objects composed mainly of two parts: a stiff protein shell called a capsid, and a core inside the capsid containing the nucleic acid and liquid. In many double-stranded DNA bacterial viruses (aka phage), the volume ratio between the liquid and the encapsidated DNA is approximately 1:1. Due to the dominant DNA hydration force, water strongly mediates the interaction between the packaged DNA strands. Therefore, water that hydrates the DNA plays an important role in nanoindentation experiments of DNA-filled viral capsids. Nanoindentation measurements allow us to gain further insight into the nature of the hydration and electrostatic interactions between the DNA strands. With this motivation, a continuum-based numerical model for simulating the nanoindentation response of DNA-filled viral capsids is proposed here. The viral capsid is modeled as large- strain isotropic hyper-elastic material, whereas porous elasticity is adopted to capture the mechanical response of the filled viral capsid. The voids inside the viral capsid are assumed to be filled with liquid, which is modeled as a homogenous incompressible fluid. The motion of a fluid flowing through the porous medium upon capsid indentation is modeled using Darcy's law, describing the flow of fluid through a porous medium. The nanoindentation response is simulated using three-dimensional finite element analysis and the simulations are performed using the finite element code Abaqus. Force-indentation curves for empty, partially and completely DNA-filled capsids are directly compared to the experimental data for bacteriophage lambda. Material parameters such as Young's modulus, shear modulus, and bulk modulus are determined by comparing computed force-indentation curves to the data from the atomic force microscopy (AFM) experiments. Predictions are made for pressure distribution inside the capsid, as well as the fluid volume ratio variation during the indentation test.},
  author       = {Ahadi, Aylin and Johansson, Dan and Evilevitch, Alex},
  issn         = {0092-0606},
  keyword      = {Capsid nanoindentation,AFM,Darcy's law,Finite element simulations,Spring constant,DNA-filled capsid},
  language     = {eng},
  number       = {2},
  pages        = {183--199},
  publisher    = {Kluwer},
  series       = {Journal of Biological Physics},
  title        = {Modeling and simulation of the mechanical response from nanoindentation test of DNA-filled viral capsids},
  url          = {http://dx.doi.org/10.1007/s10867-013-9297-9},
  volume       = {39},
  year         = {2013},
}