Kink Motion Research Articles

О движении кинка ДНК под действием постоянного торсионного момента

The influence of the torsion moment on the DNA kink motion is studied by the methods of mathematical modeling. Time dependence of the kink coordinate, velocity, size, and energy on the different values of the parameters of the external torsion moment have been found. It has been shown that by changing the parameters, by switching on and off of the external action, one could regulate the velocity and the direction of the kink movement. Estimation of the torque value necessary for the kink (open state) movement with the velocity comparable to the transcription velocity, has been made.

FORWARD MODELING OF STANDING KINK MODES IN CORONAL LOOPS. I. SYNTHETIC VIEWS

ABSTRACT Kink magnetohydrodynamic (MHD) waves are frequently observed in various magnetic structures of the solar atmosphere. They may contribute significantly to coronal heating and could be used as a tool to diagnose the solar plasma. In this study, we synthesize the Fe ix λ171.073 Å emission of a coronal loop supporting a standing kink MHD mode. The kink MHD wave solution of a plasma cylinder is mapped into a semi-torus structure to simulate a curved coronal loop. We decompose the solution into a quasi-rigid kink motion and a quadrupole term, which dominate the plasma inside and outside of the flux tube, respectively. At the loop edges, the line of sight integrates relatively more ambient plasma, and the background emission becomes significant. The plasma motion associated with the quadrupole term causes spectral line broadening and emission suppression. The periodic intensity suppression will modulate the integrated intensity and the effective loop width, which both exhibit oscillatory variations at half of the kink period. The quadrupole term can be directly observed as a pendular motion at the front view.

Segmented strings in AdS 3

We study segmented strings in flat space and in $AdS_3$. In flat space, these well known classical motions describe strings which at any instant of time are piecewise linear. In $AdS_3$, the worldsheet is composed of faces each of which is a region bounded by null geodesics in an $AdS_2$ subspace of $AdS_3$. The time evolution can be described by specifying the null geodesic motion of kinks in the string at which two segments are joined. The outcome of collisions of kinks on the worldsheet can be worked out essentially using considerations of causality. We study several examples of closed segmented strings in $AdS_3$ and find an unexpected quasi-periodic behavior. We also work out a WKB analysis of quantum states of yo-yo strings in $AdS_3$ and find a logarithmic term reminiscent of the logarithmic twist of string states on the leading Regge trajectory.

Yield stress, polymorphic transformation, and spall fracture of shock-loaded iron in various structural states and at various temperatures

The response of polycrystalline 99.5% pure iron was studied in a series of planar impact experiments, with samples of different thickness having an initial temperature that ranged between 300 and 1233 K. The free surface velocity histories of the shocked samples were recorded in the course of the experiments. Almost all recorded histories are characterized by a three-wave structure containing an elastic precursor Pel and two plastic, P1 and P2, waves. It was found that at 300, 900, and 1039 K (some 5 K away from iron's Curie point), the decay of the Pel wave with propagation distance is characterized by two different regimes; a fast one that corresponds to plastic strain rates above ∼105 s−1 and a slower one at lower strain rates. Since the shear stress at which the change-over takes place is very close to the Peierls stress of iron, we assume that above this stress the decay is governed by the phonon-damped over-barrier dislocation motion, while below it, the thermally activated generation and motion of the dislocation kinks is the governing mechanism. Based on the parameters of the P1 and P2 waves, both the initial and the maximum rates of the α→ε transformation in iron have been estimated. The results indicate that the approach to the Curie point is associated with a substantial, by 2–3 times, increase of the transformation rate.

Model of Deep Nonvolcanic Tremor Part II: Episodic Tremor and Slip

Bursts of tremor accompany a moving slip pulse in Episodic Tremor and Slip (ETS) events. The sources of this non-volcanic tremor (NVT) are largely unknown. We have developed a model describing the mechanism of NTV generation. According to this model, NTV is a reflection of resonant-type oscillations excited in a fault at certain depth ranges. From a mathematical viewpoint, tremor (phonons) and slip pulses (solitons) are two different solutions of the sine-Gordon equation describing frictional processes inside a fault. In an ETS event, a moving slip pulse generates tremor due to interaction with structural heterogeneities in a fault and to failures of small asperities. Observed tremor parameters, such as central frequency and frequency attenuation curve, are associated with fault parameters and conditions, such as elastic modulus, effective normal stress, penetration hardness and friction. Model prediction of NTV frequency content is consistent with observations. In the framework of this model it is possible to explain the complicated pattern of tremor migration, including rapid tremor propagation and reverse tremor migration. Migration along the strike direction is associated with movement of the slip pulse. Rapid tremor propagation in the slip-parallel direction is associated with movement of kinks along a 2D slip pulse. A slip pulse, pinned in some places, can fragment into several pulses, causing tremor associated with some of these pulse fragments to move opposite to the main propagation direction. The model predicts that the frequency content of tremor during an ETS event is slightly different from the frequency content of ambient tremor and tremor triggered by earthquakes.

A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

In this work, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equation is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.

Simulating acoustic emission: The noise of collapsing domains

Microstructural changes during mechanical shear of a ferroelastic or martensitic material and their signature in acoustic emission (AE) spectroscopy during strain-induced yield and detwinning are investigated by computer simulation. Complex domain patterns are generated during the main yield event, which leads to large displacements of surface atoms and emission of acoustic waves. Loading beyond the yield point leads, eventually, to a simplification of the domain patterns by local movements of needle domains, the nucleation and movement of kinks in domain walls, and the collapse of domains spanning the entire sample (from surface to surface). These microstructural changes lead to much weaker acoustic emissions than those near the yield point. Nucleation/collapse during a yield event involves an energy drop of some 3.7 meV/atom; the collapse of spanning domains releases 0.56 meV/atom, a kink crashing into the surface changes the energy by 0.017 meV/atom, and the collapsing vertical needle changes the energy by 0.017 meV/atom. All these energy bursts can, in principle, be seen by AE. The large energy spread means that AE spectroscopy measures a mixture of events whereby weak and strong signals may signify smaller and bigger events of the same kind or different microstructural changes with intrinsically different signal strengths. In order to disentangle the various contributions, other observables are needed, such as the time-dependent strain matrix of the deformed sample.

THE TRANSVERSE AND ROTATIONAL MOTIONS OF MAGNETOHYDRODYNAMIC KINK WAVES IN THE SOLAR ATMOSPHERE

Magnetohydrodynamic (MHD) kink waves have now been observed to be ubiquitous throughout the solar atmosphere. With modern instruments, they have now been detected in the chromosphere, interface region, and corona. The key purpose of this paper is to show that kink waves do not only involve purely transverse motions of solar magnetic flux tubes, but the velocity field is a spatially and temporally varying sum of both transverse and rotational motion. Taking this fact into account is particularly important for the accurate interpretation of varying Doppler velocity profiles across oscillating structures such as spicules. It has now been shown that, as well as bulk transverse motions, spicules have omnipresent rotational motions. Here we emphasize that caution should be used before interpreting the particular MHD wave mode/s responsible for these rotational motions. The rotational motions are not necessarily signatures of the classic axisymmetric torsional Alfven wave alone, because kink motion itself can also contribute substantially to varying Doppler velocity profiles observed across these structures. In this paper, the displacement field of the kink wave is demonstrated to be a sum of its transverse and rotational components, both for a flux tube with a discontinuous density profile at its boundary, and one with a more realistic density continuum between the internal and external plasma. Furthermore, the Doppler velocity profile of the kink wave is forward modeled to demonstrate that, depending on the line of sight, it can either be quite distinct or very similar to that expected from a torsional Alfven wave.

Simulation of a kink movement in homogeneous and heterogeneous DNA sequences taking into account the dissipation

AbstractThe problem of modelling the movement of a nonlinear conformational perturbation (i.e., kink) along a DNA molecule is considered taking into account the dissipation. The study of movement peculiarities is performed using a homogeneous sequence of nucleotides and a heterogeneous one consisting of two homogeneous parts separated by a boundary. Using analytic and numerical methods, it is shown that the effect of dissipation leads to a decrease of the energy of kink E, its velocity v, and the mass M. It is also shown that the consideration of the dissipation near the boundary leads to a smoothing of kink motion trajectories in the plane {z, t} in comparison with trajectories calculated without taking into account the dissipation and characterized by a sharp bend on the boundary caused by effects of reflection from the boundary or by a passage through the boundary with an increase or decrease of motion velocity.

STOCHASTIC DYNAMICS OF DC AND AC DRIVEN DISLOCATION KINKS

Dynamics of a pinned dislocation kink controlled by the acting DC and AC forces is studied analytically. The motion of the kink, described by sine-Gordon (sG) equation, is explored within the framework of McLaughlin–Scott perturbation theory. Assuming weakness of the acting AC force, the equation of motion of the dislocation kink in the pinning potential is linearized. Based on the equations derived, we study stochastic behavior of the kink, and determine the probability of its depinning. The dependencies of the depinning probability on DC and AC forces are analyzed in detail.

Solid solution softening and hardening by mobile solute atoms with special focus on hydrogen

Mobile solute atoms will affect both kink formation and kink motion. Softening occurs if solute atoms segregate to kinks and if the rate determining step is the formation of kink pairs. Then double kink formation energy is reduced, which can be shown within thermodynamics. With increasing solute concentration the rate of dislocation motion will finally be determined by kink motion. Kink motion is retarded by solute drag, which increases by adding more solute. Under these circumstances hardening is observed.

Curved Josephson junction

The constant curvature one and quasi-one dimensional Josephson junction is considered. On the base of Maxwell equations, the sine–Gordon equation that describes an influence of curvature on the kink motion was obtained. It is showed that the method of geometrical reduction of the sine–Gordon model from three to lower dimensional manifold leads to an identical form of the sine–Gordon equation.

Dynamical behavior of the kink motion in carbon nanotubes

By performing molecular dynamics calculations, we studied the motion of the kink between two carbon nanotubes. Based on the sequential evaporation of the most energetic carbon atom, our calculations show that the kink has complex longitudinal and spiral motions, in good agreement with the experiments. The kink moves towards the nanotube of larger diameter, resulting in an overall diameter shrinking of the nanotubes without inducing any disorder or damage. The kink motions are found to be dependent on the chirality of the nanotubes. The kink connecting two zigzag nanotubes can have either a pseudoclimb or a spiral motion, while the kink between the armchair nanotubes has an interesting spiral motion with periodic split and recombination of the topological defects.

The Effect of Annealing on the Internal Friction in ECAP-Modified Ultrafine Grained Copper

A detailed study of anelastic effects in submicrocrystalline copper using resonance (~70 kHz, 2 K to 320 K) and sub-resonance (0.05-100 Hz, 300 K to 675 K) techniques was carried out. Several relaxation processes were found in the temperature range of 2 K - 675 K: the relaxation loss peaks (Q-1) near 35 (P1) and 90K (P2) with the activation energy and the pre-exponential factor (H1≈ 0.02 eV,το1≈ 10-9s andH2≈ 0.09 eV,το2≈ 10-11s) similar to those of the Bordoni and the Niblett-Wilks peaks in coarse-grained Cu. This suggests that the peaks are due to the thermally activated motion of dislocation kinks in the primary and secondary Peierls relief. The mean values of activation parameters (H3≈1.4-1.6 eV,το3≈10-17s) of a third thermally activated peak (P3), which was significantly broadened, can be interpreted as a grain boundary peak with uncoupled activation parametersH3*≈0.45 eV andτο3*≈10-14s. A pseudo peak PRis associated with irreversible recrystallization processes. The influence of annealing on the observed effects is also discussed.

Some numerical results on motion of kinks in some model of DNA torsional dynamics

We present numerical results about the dynamics of kinks in some discrete system of equations coming from simple mechanical models of DNA, including a celebrated model of L. Yakushevich, and whose continuous limit is, exaclty or modulo some approximation, the Sine-Gordon equation. In particular our results show that the Yakushevich model improves sustantially if we replace the pairing potential, which is considered harmonic in the distance between facing pairs of bases, with a Morse potential.

Axial Thermal Rotation of Slender Rods

Axial rotational diffusion of rodlike polymers is important in processes such as microtubule filament sliding and flagella beating. By imaging the motion of small kinks along the backbone of chains of DNA-linked colloids, we produce a direct and systematic measurement of axial rotational diffusivity of rods both in bulk solution and near a wall. The measured diffusivities decrease linearly with the chain length, irrespective of the distance from a wall, in agreement with slender-body hydrodynamics theory. Moreover, the presence of small kinks does not affect the chain's axial diffusivity. Our system and measurements provide insights into fundamental axial diffusion processes of slender objects, which encompass a wide range of entities including biological filaments and linear polymer chains.

The dynamics of the kink in curved large area Josephson junction

A formalism that allows description of the kink motion in an arbitrarily curved large area Josephson junction is proposed. A general formula for the lagrangian density that describes the curved Josephson junction, in small curvature regime, is obtained. Examples of propagation of the kink along the curved Josephson junction are considered.

Magnetic hysteresis and domain wall dynamics in single chain magnets with antiferromagneticinterchain coupling

Using Monte Carlo simulations we investigate magnetic hysteresis in two- andthree-dimensional systems of weakly antiferromagnetically coupled spin chains based on ascenario of domain wall (kink) motion within the chains. By adapting the model of walkersto simulate the domain wall dynamics and using the Ising-like dipole–dipole model, westudy the effects of interchain coupling, temperature and anisotropy axis direction onhysteresis curves.

Kink propagation in inhomogeneous systems driven by spatiotemporal perturbations

We investigate the propagation of kinks in inhomogeneous media. We show that the extended character of the kink, the internal mode instabilities and the phenomenon of disappearance of the translational mode can affect the kink motion in the presence of space-dependent external perturbations. We apply the results to the analysis of kink ratchets and the propagation of kinks driven by wave fields.

The studies on the motion of the sine‐Gordon kink on a curved surface

AbstractThe numerical studies of the kink motion on a curved manifold were performed. Examples of the curved surfaces are considered in detail. Enlarging the kink width in curved regions of the surface and reduction of its speed is confirmed. Reflection of the kink front from the large curvature areas is observed. The influence of the curvature on the speed of the Vachaspati waves is also observed.