Simulations of Stretching Single Stranded DNA

2011 ◽  
Vol 1301 ◽  
Author(s):  
Abhishek Singh ◽  
Yaroslava G. Yingling
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Stranded Dna ◽  
Folded Structure ◽  
Non Linear ◽  
Dna Strands ◽  
Dynamics Simulations ◽  
Force Profiles ◽  
Similar Force

ABSTRACTMolecular dynamics simulations were performed to estimate sequence dependent force required to stretch single stranded DNA (ssDNA) homo oligonucleotides. Simulations suggest that polyA and polyC oligonucleotides exhibit similar force profiles and corresponding elongation. Among single stranded DNA strands polyT is the most flexible and needs the most force to unwind from an equilibrium folded structure. In contrast, polyG had a very small recoverable deformation prior to a non-linear stretching. Our results indicate that mechanical properties of ssDNA chains are directly related to their sequence.

scholarly journals On the yielding of a point-defect-rich model crystal under shear: insights from molecular dynamics simulations

Soft Matter ◽  
2021 ◽  
Author(s):  
Gaurav Prakash Shrivastav ◽  
Gerhard Kahl
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Point Defect ◽  
Point Defects ◽  
Model Crystal ◽  
Non Linear ◽  
Linear Effects ◽  
Dynamics Simulations

In real crystals and at finite temperatures point defects are inevitable. Under shear their dynamics severely influence the mechanical properties of these crystals, giving rise to non-linear effects, such as...

scholarly journals Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

2013 ◽  
Vol 4 ◽  
pp. 429-440 ◽  
Author(s):  
Hlengisizwe Ndlovu ◽  
Alison E Ashcroft ◽  
Sheena E Radford ◽  
Sarah A Harris
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Steered Molecular Dynamics ◽  
Mechanical Failure ◽  
Structural Defects ◽  
Dynamics Simulations

We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.

scholarly journals Atomistic investigation into the mechanical behaviour of crystalline and amorphous TiO2 nanotubes

RSC Advances ◽  
2016 ◽  
Vol 6 (33) ◽  
pp. 28121-28129 ◽  
Author(s):  
Yanan Xu ◽  
Mingchao Wang ◽  
Ning Hu ◽  
John Bell ◽  
Cheng Yan
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Titanium Dioxide ◽  
Molecular Dynamics Simulations ◽  
Mechanical Behaviour ◽  
Tio2 Nanotubes ◽  
Amorphous Tio2 ◽  
Dynamics Simulations

The mechanical properties of titanium dioxide (TiO2) nanotubes are studied based on molecular dynamics simulations.

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