arXiv subjects

See-Chen Ying

Publications and source records attributed to See-Chen Ying.

15 recordsLinked to original sources

arXiv2023

Electronic Noise of a Single Skyrmion

To enable the practical use of skyrmion-based devices, it is essential to achieve a balance between energy efficiency and thermal stability, while also ensuring reliable electrical detection against noise. Understanding how a skyrmion interacts with material disorder and external perturbations is thus essential. Here we investigate the electronic noise of a single skyrmion under the influence of thermal fluctuations and spin currents in a magnetic thin film. We detect the thermally induced noise with a 1/f signature in the strong pinning regime but a random telegraph noise in the intermediate pinning regime. Both the thermally dominated and current-induced telegraph-like signals are detected in the weak pinning regime. Our results provide a comprehensive electronic noise picture of a single skyrmion, demonstrating the potential of noise fluctuation as a valuable tool for characterizing the pinning condition of a skyrmion. These insights could also aid in the development of low-noise and reliable skyrmion-based devices.

cond-mat.mes-hall↗

arXiv2015

Consistent Hydrodynamics for Phase Field Crystals

We use the amplitude expansion in the phase field crystal framework to formulate an approach where the fields describing the microscopic structure of the material are coupled to a hydrodynamic velocity field. The model is shown to reduce to the well known macroscopic theories in appropriate limits, including compressible Navier-Stokes and wave equations. Moreover, we show that the dynamics proposed allows for long wavelength phonon modes and demonstrate the theory numerically showing that the elastic excitations in the system are relaxed through phonon emission.

cond-mat.stat-mech↗

arXiv2009

Driven polymer translocation through nanopores: slow versus fast dynamics

We investigate the dynamics of polymer translocation through nanopores under external driving by 3D Langevin Dynamics simulations, focusing on the scaling of the average translocation time $τ$ versus the length of the polymer, $τ\sim N^α$. For slow translocation, i.e., under low driving force and/or high friction, we find $α\approx 1+ν\approx 1.588$ where $ν$ denotes the Flory exponent. In contrast, $α\approx 1.37$ is observed for fast translocation due to the highly deformed chain conformation on the trans side, reflecting a pronounced non-equilibrium situation. The dependence of the translocation time on the driving force is given by $τ\sim F^{-1}$ and $τ\sim F^{-0.80}$ for slow and fast translocation, respectively. These results clarify the controversy on the magnitude of the scaling exponent $α$ for driven translocation.

cond-mat.soft↗

arXiv2009

Polymer translocation out of confined environments

We consider the dynamics of polymer translocation out of confined environments. Analytic scaling arguments lead to the prediction that the translocation time scales like $τ\sim N^{β+ν_{2D}}R^{1+(1-ν_{2D})/ν}$ for translocation out of a planar confinement between two walls with separation $R$ into a 3D environment, and $τ\sim N^{β+1}R$ for translocation out of two strips with separation $R$ into a 2D environment. Here, $N$ is the chain length, $ν$ and $ν_{2D}$ are the Flory exponents in 3D and 2D, and $β$ is the scaling exponent of translocation velocity with $N$, whose value for the present choice of parameters is $β\approx 0.8$ based on Langevin dynamics simulations. These scaling exponents improve on earlier predictions.

cond-mat.soft↗

arXiv2008

Scaling exponents of Forced Polymer Translocation through a nano-pore

We investigate several scaling properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulation in three dimension (3D). Specifically motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we determine the chain length dependence of the scaling exponents of the average translocation time, the average velocity of the center of mass, $ $, the effective radius of gyration during the translocation process, and the scaling exponent of the translocation coordinate ($s$-coordinate) as a function of the translocation time. We further discuss the possibility that in the case of driven translocation the finite pore size and its geometry could be responsible that the veclocity scaling exponent is less than unity and discuss the dependence of the scaling exponents on the pore geometry for the range of $N$ studied here.

cond-mat.soft↗

arXiv2008

Dynamics of DNA translocation through an attractive nanopore

We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases $A$ and $C$, having different base-pore interactions, {\textit e.g.}, a strong (weak) attractive force between the pore and the base $A$ ($C$) inside the pore. From a series of studies on hetero-DNAs with repeat units $A_mC_n$, we find that the translocation time decreases exponentially as a function of the volume fraction $f_C$ of the base $C$. %($ε_{pC} < ε_{pA}$). For longer $A$ sequences with $f_C \le 0.5$, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length $N$ with repeat units $A_mC_n$, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of $m$, $n$ and $N$ respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection technic.

cond-mat.soft↗

arXiv2008

Translocation Dynamics with Attractive Nanopore-Polymer Interactions

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $τ\approx τ_1+τ_2+τ_3$ corresponding to the initial filling of the pore, transfer of polymer from the \textit{cis} side to the \textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $τ_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $τ$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {\it vs.} that for the natural $α$-hemolysin channel.

cond-mat.soft↗

arXiv2007

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {\em block length} $2n$ as well as on the {\em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.

cond-mat.soft↗

arXiv2007

Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''

One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $τ$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Molecular Dynamics methods confirm the original prediction $τ\sim N^{2ν+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.

cond-mat.soft↗

arXiv2007

Polymer translocation through a nanopore under a pulling force

We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length $N$ and the pulling force $F$ on the translocation time $τ$. The distribution of $τ$ is symmetric and narrow for strong $F$. We find that $τ\sim N^{2}$ and translocation velocity $v\sim N^{-1}$ for both moderate and strong $F$. For infinitely wide pores, three regimes are observed for $τ$ as a function of $F$. With increasing $F$, $τ$ is independent of $F$ for weak $F$, and then $τ\sim F^{-2+ν^{-1}}$ for moderate $F$, where $ν$ is the Flory exponent, which finally crosses over to $τ\sim F^{-1}$ for strong force. For narrow pores, even for moderate force $τ\sim F^{-1}$. Finally, the waiting time, for monomer $s$ and monomer $s+1$ to exit the pore, has a maximum for $s$ close to the end of the chain, in contrast to the case where polymer is driven by an external force within the pore.

cond-mat.soft↗

arXiv2007

Heteropolymer translocation through nanopores

We investigate the translocation dynamics of heteropolymers driven through a nanopore using a constant temperature Langevin thermostat. Specifically, we consider heteropolymers consisting of two types of monomers labeled A and B, which are distinguished by the magnitude of the driving force that they experience inside the pore. From a series of studies on polymers with sequences AnBn+m we identify both universal as well as sequence specific properties of the translocating chains. We find that the scaling of the average translocation time as a function of the chain length N remains unaffected by the heterogeneity, while the residence time of each bead is a strong function of the sequence for short repeat units. We further discover that for a symmetric heteropolymer AnBn of fixed length, the pattern exhibited by the residence time of the individual monomer has striking similarity with an interference pattern for an optical grating with N/(2n) slits. These results are relevant for designing nanopore based sequencing techniques.

cond-mat.soft↗

arXiv2006

Langevin Dynamics Simulations of Polymer Translocation through Nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time $τ_e$ required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that $τ_e$ scales with the chain length $N$ as $τ_e \sim N^{1+2ν}$, where $ν$ is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient $ξ$, the driving force $E$ and the length of the chain $N$ on the translocation time $τ$, which is defind as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and $τ\sim E^{-1}$. The influence of $ξ$ depends on the ratio between the driving and frictional forces. For intermediate $ξ$, we find a crossover scaling for $τ$ with $N$ from $τ\sim N^{2ν}$ for relatively short chains to $τ\sim N^{1 + ν}$ for longer chains. However, for higher $ξ$, only $τ\sim N^{1 + ν}$ is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing $ξ$ increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveals additional features of dependency on friction.

cond-mat.soft↗

arXiv2006

Polymer translocation through a nanopore under an applied external field

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength $E$, length of the chain $N$, and length of the pore $L$ on forced translocation. As our main result, we find a crossover scaling for the translocation time $τ$ with the chain length from $τ\sim N^{2ν}$ for relatively short polymers to $τ\sim N^{1 + ν}$ for longer chains, where $ν$ is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains $v \sim N^{- ν}$, which crosses over to $v \sim N^{- 1}$ for long polymers. The reason for this is that with increasing $N$ there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which $R_\parallel $, the radius of gyration $R_{g}$ along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large $N$, however, the asymptotic scaling $τ\sim N^{1 + ν}$ is recovered. In this regime, $τ$ is almost independent of $L$. We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for $R_\parallel \approx L$. We show here that this minimum persists for a weak fields $E$ such that $EL$ is less than some critical value, but vanishes for large values of $EL$.

cond-mat.soft↗

arXiv1996

Diffusion on a stepped substrate

We present results for collective diffusion of adatoms on a stepped substrate with a submonolayer coverage. We study the combined effect of the additional binding at step edge, the Schwoebel barrier, the enhanced diffusion along step edges, and the finite coverage on diffusion as a function of step density. In particular, we examine the crossover from step--dominated diffusion at high step density to terrace-dominated behavior at low step density in a lattice-gas model using analytical Green's function techniques and Monte Carlo simulations. The influence of steps on diffusion is shown to be more pronounced than previously anticipated.

cond-mat↗

arXiv1992

Theory of adsorbate induced surface reconstruction on W(100)

We report results of a theoretical study on an adsorbate induced surface reconstruction. Hydrogen adsorption on a W(100) surface causes a switching transition in the symmetry of the displacements of the W atoms within the ordered c(2x2) phase. This transition is modeled by an effective Hamiltonian, where the hydrogen degrees of freedom are integrated out. Based on extensive Monte Carlo renormalisation group calculations we show that the switching transition is of second order at high temperatures and of first order at low temperatures. This behavior is qualitatively explained in terms of an XY model where there is an interplay between four and eight fold anisotropy fields. We also compare the calculated phase diagrams with a simple mean field theory.

cond-mat↗