Modeling the Abrupt Buckling Transition in dsDNA During Supercoiling

2016 ◽  
Vol 11 (6) ◽  
Author(s):  
Ikenna D. Ivenso
Keyword(s):  
Brownian Dynamics ◽  
Dna Supercoiling ◽  
Transition Regime ◽  
Extended State ◽  
Wormlike Chain ◽  
End To End ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

When deoxyribonucleic (DNA), held at a fixed tension, is subjected to torsional deformations, it responds by forming plectonemic supercoils accompanied by a reduction in its end-to-end extension. This transition from the extended state to the supercoiled state is marked by an abrupt buckling of the DNA accompanied by a rapid “hopping” of the DNA between the extended and supercoiled states. This transition is studied by means of Brownian dynamics simulations using a discrete wormlike-chain (dWLC) model of DNA. The simulations reveal, among other things, the distinct regimes that occur during DNA supercoiling and the probabilities of states within the buckling transition regime.

The Dynamics of DNA Supercoiling: A Brownian Dynamics Study

2015 ◽  
Author(s):  
Ivenso Ikenna ◽  
Todd D. Lillian
Keyword(s):  
Brownian Dynamics ◽  
Linear Trend ◽  
Dna Supercoiling ◽  
Torsional Deformation ◽  
Torsional Response ◽  
Double Stranded Dna ◽  
End To End ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

Induced torsional stresses lead to an increase in the magnitude of torque sustained by double stranded DNA. There exists a critical magnitude of torque at which the DNA buckles signaling the beginning of the formation of a plectonemically supercoiled domain in the DNA. Further torsional deformation leads to an increase in the size of the supercoiled domain while the torque sustained by the DNA remains constant. The formation of the supercoiled domain also leads to a reduction in the end-to-end extension of the DNA starting with an abrupt reduction at the onset of buckling. Experiments have shown that this reduction in extension follows a linear trend. We investigate, by means of Brownian dynamics simulations, the extensional and torsional response of dsDNA to induced torsional stresses.

scholarly journals Structure evolution of suspensions under time-dependent electric or magnetic field

2021 ◽  
Author(s):  
Konstantinos Manikas ◽  
Markus Hütter ◽  
Patrick D. Anderson
Keyword(s):  
Magnetic Field ◽  
Field Strength ◽  
Brownian Dynamics ◽  
Thermal Fluctuations ◽  
Time Dependent ◽  
Structure Evolution ◽  
Strength Increase ◽  
Large Rotation ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

AbstractThe effect of time-dependent external fields on the structures formed by particles with induced dipoles dispersed in a viscous fluid is investigated by means of Brownian Dynamics simulations. The physical effects accounted for are thermal fluctuations, dipole-dipole and excluded volume interactions. The emerging structures are characterised in terms of particle clusters (orientation, size, anisotropy and percolation) and network structure. The strength of the external field is increased in one direction and then kept constant for a certain amount of time, with the structure formation being influenced by the slope of the field-strength increase. This effect can be partially rationalized by inhomogeneous time re-scaling with respect to the field strength, however, the presence of thermal fluctuations makes the scaling at low field strength inappropriate. After the re-scaling, one can observe that the lower the slope of the field increase, the more network-like and the thicker the structure is. In the second part of the study the field is also rotated instantaneously by a certain angle, and the effect of this transition on the structure is studied. For small rotation angles ($$\theta \le 20^{{\circ }}$$ θ ≤ 20 ∘ ) the clusters rotate but stay largely intact, while for large rotation angles ($$\theta \ge 80^{{\circ }}$$ θ ≥ 80 ∘ ) the structure disintegrates and then reforms, due to the nature of the interactions (parallel dipoles with perpendicular inter-particle vector repel each other). For intermediate angles ($$20<\theta <80^{{\circ }}$$ 20 < θ < 80 ∘ ), it seems that, during rotation, the structure is altered towards a more network-like state, as a result of cluster fusion (larger clusters). The details provided in this paper concern an electric field, however, all results can be projected into the case of a magnetic field and paramagnetic particles.

scholarly journals Influence of size polydispersity on magnetic field tunable structures in magnetic nanofluids containing superparamagnetic nanoparticles.

2021 ◽  
Author(s):  
Dillip Kumar Mohapatra ◽  
Philip James Camp ◽  
John Philip
Keyword(s):  
Magnetic Field ◽  
Particle Size ◽  
Light Scattering ◽  
Optical Microscopy ◽  
Brownian Dynamics ◽  
Phase Contrast ◽  
Superparamagnetic Nanoparticles ◽  
Magnetic Nanofluids ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

We probe the influence of particle size polydispersity on field-induced structures and structural transitions in magnetic fluids (ferrofluids) using phase contrast optical microscopy, light scattering and Brownian dynamics simulations. Three...

scholarly journals Hard discs under steady shear: comparison of Brownian dynamics simulations and mode coupling theory

2009 ◽  
Vol 367 (1909) ◽  
pp. 5033-5050 ◽  
Author(s):  
Oliver Henrich ◽  
Fabian Weysser ◽  
Michael E. Cates ◽  
Matthias Fuchs
Keyword(s):  
Brownian Dynamics ◽  
Mode Coupling ◽  
Transition Density ◽  
Two Dimensions ◽  
Coupling Theory ◽  
Mode Coupling Theory ◽  
Stationary Structure ◽  
Homogeneous Shear Flow ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

Brownian dynamics simulations of bidisperse hard discs moving in two dimensions in a given steady and homogeneous shear flow are presented close to and above the glass transition density. The stationary structure functions and stresses of shear-melted glass are compared quantitatively to parameter-free numerical calculations of monodisperse hard discs using mode coupling theory within the integration through transients framework. Theory qualitatively explains the properties of the yielding glass but quantitatively overestimates the shear-driven stresses and structural anisotropies.

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