scholarly journals Internal friction can be measured with the Jarzynski equality

2019 ◽  
Author(s):  
R. Kailasham ◽  
Rajarshi Chakrabarti ◽  
J. Ravi Prakash
Keyword(s):  
Friction Coefficient ◽  
Internal Friction ◽  
Single Molecule ◽  
Brownian Dynamics ◽  
Single Mode ◽  
Optical Tweezer ◽  
Jarzynski Equality ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Internal Friction Coefficient

AbstractA simple protocol for the extraction of the internal friction coefficient of polymers is presented. The proposed scheme necessitates repeatedly stretching the polymer molecule, and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the hypothetical limit of zero solvent viscosity. The validity of the protocol is established through Brownian dynamics simulations of a single-mode spring-dashpot model for a polymer. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally.

scholarly journals Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

2020 ◽  
Author(s):  
Govardhan Reddy ◽  
D. Thirumalai
Keyword(s):  
Single Molecule ◽  
Brownian Dynamics ◽  
Structural Changes ◽  
Building Blocks ◽  
Self Organized ◽  
End Distance ◽  
Transcription Regulators ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Brownian Dynamics Simulations

AbstractNucleosomes, the building blocks of chromosomes, are also transcription regulators. Single molecule pulling experiments have shown that nucleosomes unwrap in two major stages, releasing nearly equal length of DNA in each stage. The first stage, attributed to the rupture of the outer turn is reversible, occurs at low forces (≈ (3 - 5) pNs) whereas in the second stage the inner turn ruptures irreversibly at high forces (between ≈ (9 - 15) or higher) pNs. We show that Brownian dynamics simulations using the Self-Organized Polymer model of the nucleosome capture the experimental findings, thus permitting us to discern the molecular details of the structural changes not only in DNA but also in the Histone Protein Core (HPC). Upon unwrapping of the outer turn, which is independent of the pulling direction, there is a transition from 1.6 turns to 1.0 turn DNA wound around the HPC. In contrast, the rupture of the inner turn, leading to less than 0.5 turn DNA around the HPC, depends on the pulling direction, and is controlled by energetic and kinetic barriers. The latter arises because the mechanical force has to produce sufficient torque to rotate (in an almost directed manner) the HPC by 180°. In contrast, during the rewrapping process, HPC rotation is stochastic, with the quenched force fQ playing no role. Interestingly, if fQ = 0 the HPC rotation is not required for rewrapping because the DNA ends are unconstrained. The assembly of the outer wrap upon force quench, as assessed by the decrease in the end-to-end distance (Ree) of the DNA, nearly coincides with the increase in Ree as force is increased, confirming the reversible nature of the 1.6 turns to 1.0 turn transition. The asymmetry in HPC rotation during unwrapping and rewrapping accounts for the observed hysteresis in the stretch-release cycles in single molecule pulling experiments. Experiments that could validate the prediction that HPC rotation, which gives rise to the kinetic barrier in the unwrapping process, are proposed.

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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