scholarly journals Computer Simulations of DNA Packing inside Bacteriophages: Elasticity, Electrostatics and Entropy

2008 ◽  
Vol 9 (3-4) ◽  
pp. 317-325 ◽  
Author(s):  
D. Marenduzzo

There is now a considerable literature on computer simulations of DNA packaging inside bacteriophage capsids. While most studies have reached a semiquantitative or qualitative agreement with single molecule packaging and ejection studies, several quantitative answers are to date still lacking, needing either more accurate measurements or more realistic or difficult simulations. Here, I briefly review the outstanding questions in this field and report some new numerical results on DNA packaging inside the phi29 phage, modelled either as a capped sphero-cylinder or as a sphere with the same internal volume. These simulations include electrostatics and a realistic genome length, and contribute to seriously questioning the inverse spool model, which arises from a purely continuum mechanics view of the problem, and is still commonly adopted to describe the shape of the packaged genome.

2016 ◽  
Vol 110 (3) ◽  
pp. 46a ◽  
Author(s):  
Li Dai ◽  
Digvijay Singh ◽  
Reza Vafabakhsh ◽  
Marthandan Mahalingam ◽  
Vishal Kottadiel ◽  
...  

2012 ◽  
Vol 102 (3) ◽  
pp. 643a
Author(s):  
Reza Vafabakhsh ◽  
Kiran Kondabagil ◽  
Li Dai ◽  
Zhihong Zhang ◽  
Venigalla B. Rao ◽  
...  

2007 ◽  
Vol 26 (2) ◽  
pp. 527-537 ◽  
Author(s):  
Dan Shu ◽  
Hui Zhang ◽  
Jiashun Jin ◽  
Peixuan Guo

Author(s):  
Oleg N. Dmitrochenko ◽  
Bassam A. Hussein ◽  
Ahmed A. Shabana

The effect of the absolute nodal coordinate formulation (ANCF)–coupled deformation modes on the accuracy and efficiency when higher order three-dimensional beam and plate finite elements are used is investigated in this study. It is shown that while computational efficiency can be achieved in some applications by neglecting the effect of some of the ANCF-coupled deformation modes, such modes introduce geometric stiffening/softening effects that can be significant in the case of very flexible structures. As shown in previous publications, for stiff structures, the effect of the ANCF-coupled deformation modes can be neglected. For such stiff structures, the solution does not strongly depend on some of the ANCF-coupled deformation modes, and formulations that include these modes lead to numerical results that are in good agreement with formulations that exclude them. In the case of a very flexible structure, on the other hand, the inclusion of the ANCF-coupled deformation modes becomes necessary in order to obtain an accurate solution. In this case of very flexible structures, the use of the general continuum mechanics approach leads to an efficient solution algorithm and to more accurate numerical results. In order to examine the effect of the elastic force formulation on the efficiency and the coupling between different modes of deformation, three different models are used again to formulate the elastic forces in the absolute nodal coordinate formulation. These three methods are the general continuum mechanics approach, the elastic line (midsurface) approach, and the elastic line (midsurface) approach with the Hellinger–Reissner principle. Three-dimensional absolute nodal coordinate formulation beam and plate elements are used in this study. In the general continuum mechanics approach, the coupling between the cross section deformation and the beam centerline or plate midsurface displacement is considered, while in the approaches based on the elastic line and the Hellinger–Reissner principle, this coupling is neglected. In addition to the fully parametrized beam element used in this study, three different plate elements, two fully parametrized and one reduced order thin plate elements, are used. The numerical results obtained using different finite elements and elastic force formulations are compared in this study.


Models of the form X n+1 =λ (X n ) + Z n+1 are considered for time-series {X n }, where {Z n } is an impulse sequence and λ is a nonlinear function. These processes extend the range of behaviour available with linear autoregressivemoving average models. Methods for approximating the stationary distributions of the processes are considered and expressions are found by which the exact moments, joint moments and densities of stationary processes can be obtained. Moments and densities of conditional (predictive) distributions are also found. The results of these methods have been verified by computer simulations and these and other numerical results are given. The extension of the methods obtained to treat multivariate processes of the same form is indicated briefly.


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