Extensional Response and Equilibrium Kinetics of Torsionally Relaxed dsDNA Under Tension: A Brownian Dynamics Study

2016 ◽  
Vol 12 (3) ◽  
Author(s):  
Ikenna D. Ivenso
Keyword(s):  
Single Molecule ◽  
Brownian Dynamics ◽  
Thermal Fluctuations ◽  
Aqueous Environment ◽  
Chain Model ◽  
Full Extension ◽  
Applied Tension ◽  
Dynamics Simulations ◽  
Kinetics Of ◽  
Insight Into

Deoxyribonucleic acid (DNA) is a long flexible polyelectrolyte that is housed in the aqueous environment within the cell of an organism. When a length of torsionally relaxed (untwisted) DNA is held in tension, such as is the case in many single molecule experiments, the thermal fluctuations arising from the constant bombardment of the DNA by the surrounding fluid molecules induce bending in it, while the applied tension tends to keep it extended. The combined effect of these influences is that DNA is never at its full extension but eventually attains an equilibrium value of end-to-end extension under these influences. An analytical model was developed to estimate the tension-dependent value of this extension. This model, however, does not provide any insight into the dynamics of the extensional response of DNA to applied tension nor the kinetics of DNA at equilibrium under said tension. This paper reports the results of Brownian dynamics simulations using a discrete wormlike-chain model of DNA that provide some insight into these dynamics and kinetics.

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 Dynamics of Tpm1.8 domains on actin filaments with single molecule resolution

2020 ◽  
Author(s):  
Ilina Bareja ◽  
Hugo Wioland ◽  
Miro Janco ◽  
Philip R. Nicovich ◽  
Antoine Jégou ◽  
...  
Keyword(s):  
Actin Filament ◽  
Single Molecule ◽  
Actin Filaments ◽  
High Probability ◽  
Actin Binding ◽  
Single Molecule Level ◽  
Filament Dynamics ◽  
Kinetics Of ◽  
Insight Into

ABSTRACTTropomyosins regulate dynamics and functions of the actin cytoskeleton by forming long chains along the two strands of actin filaments that act as gatekeepers for the binding of other actin-binding proteins. The fundamental molecular interactions underlying the binding of tropomyosin to actin are still poorly understood. Using microfluidics and fluorescence microscopy, we observed the binding of fluorescently labelled tropomyosin isoform Tpm1.8 to unlabelled actin filaments in real time. This approach in conjunction with mathematical modeling enabled us to quantify the nucleation, assembly and disassembly kinetics of Tpm1.8 on single filaments and at the single molecule level. Our analysis suggests that Tpm1.8 decorates the two strands of the actin filament independently. Nucleation of a growing tropomyosin domain proceeds with high probability as soon as the first Tpm1.8 molecule is stabilised by the addition of a second molecule, ultimately leading to full decoration of the actin filament. In addition, Tpm1.8 domains are asymmetrical, with enhanced dynamics at the edge oriented towards the barbed end of the actin filament. The complete description of Tpm1.8 kinetics on actin filaments presented here provides molecular insight into actin-tropomyosin filament formation and the role of tropomyosins in regulating actin filament dynamics.

Kinetics of empty viral capsid assembly in a minimal model

Soft Matter ◽  
2019 ◽  
Vol 15 (36) ◽  
pp. 7166-7172 ◽  
Author(s):  
D. Reguera ◽  
J. Hernández-Rojas ◽  
J. M. Gomez Llorente
Keyword(s):  
Minimal Model ◽  
Brownian Dynamics ◽  
Viral Capsid ◽  
Capsid Assembly ◽  
Optimal Efficiency ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Kinetics Of

The kinetics and conditions to achieve optimal efficiency of empty viral capsid assembly are studied performing Brownian Dynamics simulations of a minimal model.

scholarly journals Polymer-like model to study the dynamics of dynamin filaments on deformable membrane tubes

2019 ◽  
Author(s):  
Jeffrey K. Noel ◽  
Frank Noé ◽  
Oliver Daumke ◽  
Alexander S. Mikhailov
Keyword(s):  
Thermal Fluctuations ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Chain Model ◽  
Dependent Manner ◽  
Membrane Tube ◽  
Elastic Filament ◽  
Intrinsic Shape ◽  
Deformable Membrane ◽  
Dynamics Simulations

AbstractPeripheral membrane proteins with intrinsic curvature can act both as sensors of membrane curvature and shape modulators of the underlying membranes. A well-studied example of such proteins is the mechano-chemical GTPase dynamin that assembles into helical filaments around membrane tubes and catalyzes their scission in a GTPase-dependent manner. It is known that the dynamin coat alone, without GTP, can constrict membrane tubes to radii of about 10 nanometers, indicating that the intrinsic shape and elasticity of dynamin filaments should play an important role in membrane remodeling. However, molecular and dynamic understanding of the process is lacking. Here, we develop a dynamical polymer-chain model for a helical elastic filament bound on a deformable membrane tube of conserved mass, accounting for thermal fluctuations in the filament and lipid flows in the membrane. The model is based on a locally-cylindrical helix approximation for dynamin. We obtain the elastic parameters of the dynamin filament by molecular dynamics simulations of its tetrameric building block and also from coarse-grained structure-based simulations of a 17-dimer filament. The results show that the stiffness of dynamin is comparable to that of the membrane. We determine equilibrium shapes of the filament and the membrane, and find that mostly the pitch of the filament, not its radius, is sensitive to variations in membrane tension and stiffness. The close correspondence between experimental estimates of the inner tube radius and those predicted by the model suggests that dynamin’s “stalk” region is responsible for its GTP-independent membrane-shaping ability. The model paves the way for future mesoscopic modeling of dynamin with explicit motor function.

scholarly journals Stretching Wormlike Chains in Narrow Tubes of Arbitrary Cross-Sections

Polymers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2050
Author(s):  
Ming Li ◽  
Jizeng Wang
Keyword(s):  
Cross Sections ◽  
Brownian Dynamics ◽  
Statistical Physics ◽  
Polymer Chains ◽  
Chain Model ◽  
Mode Decomposition ◽  
Dynamics Simulations ◽  
Single Formula ◽  
Wormlike Chain Model ◽  
Confined Polymer Chains

We considered the stretching of semiflexible polymer chains confined in narrow tubes with arbitrary cross-sections. Based on the wormlike chain model and technique of normal mode decomposition in statistical physics, we derived a compact analytical expression on the force-confinement-extension relation of the chains. This single formula was generalized to be valid for tube confinements with arbitrary cross-sections. In addition, we extended the generalized bead-rod model for Brownian dynamics simulations of confined polymer chains subjected to force stretching, so that the confinement effects to the chains applied by the tubes with arbitrary cross-sections can be quantitatively taken into account through numerical simulations. Extensive simulation examples on the wormlike chains confined in tubes of various shapes quantitatively justified the theoretically derived generalized formula on the force-confinement-extension relation of the chains.

Magnetic tweezers: a sensitive tool to study DNA and chromatin at the single-molecule level

2003 ◽  
Vol 81 (3) ◽  
pp. 151-159 ◽  
Author(s):  
Jordanka Zlatanova ◽  
Sanford H Leuba
Keyword(s):  
Single Molecule ◽  
Magnetic Tweezers ◽  
Biological Macromolecules ◽  
High Definition ◽  
Single Molecule Level ◽  
Applied Tension ◽  
Sensitive Tool ◽  
Different Types ◽  
Distinct Features ◽  
Insight Into

The advent of single-molecule biology has allowed unprecedented insight into the dynamic behavior of biological macromolecules and their complexes. Unexpected properties, masked by the asynchronous behavior of myriads of molecules in bulk experiments, can be revealed; equally importantly, individual members of a molecular population often exhibit distinct features in their properties. Finally, the single-molecule approaches allow us to study the behavior of biological macromolecules under applied tension or torsion; understanding the mechanical properties of these molecules helps us understand how they function in the cell. In this review, we summarize the application of magnetic tweezers (MT) to the study of DNA behavior at the single-molecule level. MT can be conveniently used to stretch DNA and introduce controlled levels of superhelicity into the molecule and to follow to a high definition the action of different types of topoisomerases. Its potential for chromatin studies is also enormous, and we will briefly present our first chromatin results.Key words: single-molecules, chromatin, topoisomerases, magnetic tweezers, force.

Direct Mechanical Measurement of Organised Water and the Influence of Adjacent Surface Chemistry Using Atomic Force Microscopy (Keynote)

2005 ◽  
Author(s):  
M. J. Higgins ◽  
M. Polcik ◽  
T. Fukuma ◽  
J. E. Sader ◽  
S. P. Jarvis
Keyword(s):  
Single Molecule ◽  
Structural Changes ◽  
High Selectivity ◽  
Biological Function ◽  
Aqueous Environment ◽  
Force Microscopy ◽  
Molecular Adhesion ◽  
Atomic Force ◽  
Membrane Recognition ◽  
Insight Into

Directly measuring structural changes in water with a mechanical probe of lateral dimensions comparable to that of a single molecule provides an invaluable insight into how and why bio-molecules behave with high selectivity or why certain surfaces promote or inhibit bio-molecular adhesion. In the immediate vicinity of the molecule, continuum models break down and the aqueous environment will often form a discrete layered structure depending on the nature of the molecule. The absence or presence of such structure may be fundamental in influencing the promotion or inhibition of protein adsorption, biological function and membrane recognition.

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