arXiv subjects

G. T. Barkema

Publications and source records attributed to G. T. Barkema.

At least 19 recordsLinked to original sources

arXiv2019

Approximate dynamical eigenmodes of the Ising model with local spin-exchange moves

We establish that the Fourier modes of the magnetization serve as the dynamical eigenmodes for the two-dimensional Ising model at the critical temperature with local spin-exchange moves, i.e., Kawasaki dynamics. We obtain the dynamical scaling properties for these modes, and use them to calculate the time evolution of two dynamical quantities for the system, namely the autocorrelation function and the mean-square deviation of the line magnetizations. At intermediate times $1 \lesssim t \lesssim L^{z_c}$, where $z_c=4-η=15/4$ is the dynamical critical exponent of the model, we find that the line magnetization undergoes anomalous diffusion. Following our recent work on anomalous diffusion in spin models, we demonstrate that the Generalized Langevin Equation (GLE) with a memory kernel consistently describes the anomalous diffusion, verifying the corresponding fluctuation-dissipation theorem with the calculation of the force autocorrelation function.

cond-mat.stat-mech↗

arXiv2016

Finite-size scaling at infinite-order phase transitions

For systems with infinite-order phase transitions, in which an order parameter smoothly becomes nonzero, a new observable for finite-size scaling analysis is suggested. By construction this new observable has the favourable property of diverging at the critical point. Focussing on the example of the F-model we compare the analysis of this observable with that of another observable, which is also derived from the order parameter but does not diverge, as well as that of the associated susceptibility. We discuss the difficulties that arise in the finite-size scaling analysis of such systems. In particular we show that one may reach incorrect conclusions from large-system size extrapolations of observables that are not known to diverge at the critical point. Our work suggests that one should base finite-size scaling analyses for infinite-order phase transitions only on observables that are guaranteed to diverge.

cond-mat.stat-mech↗

arXiv2016

Skyrmions in square-lattice antiferromagnets

The ground states of square lattice two-dimensional antiferromagnets with anisotropy in an external magnetic field are determined using Monte Carlo simulations and compared to theoretical analysis. We find a new phase in between the spin-flop and spiral phase that shows strong similarity to skyrmions in ferromagnetic thin films. We show that this phase arises as a result of the competition between Zeeman and Dzyaloshinskii-Moriya interaction energies of the magnetic system. Moreover, we find that isolated (anti-)skyrmions are stabilized in finite-sized systems, even at higher temperatures. The existence of thermodynamically stable skyrmions in square-lattice antiferromagnets provides an appealing alternative over skyrmions in ferromagnets as data carriers.

cond-mat.mes-hall↗

arXiv2015

Degeneracies and fluctuations of Néèl skyrmions in confined geometries

The recent discovery of tunable Dzyaloshinskii-Moriya interactions in layered magnetic materials with perpendicular magnetic anisotropy makes them promising candidates for stabilization and manipulation of skyrmions at elevated temperatures. In this article, we use Monte Carlo simulations to investigate the robustness of skyrmions in these materials against thermal fluctuations and finite-size effects. We find that in confined geometries and at finite temperatures skyrmions are present in a large part of the phase diagram. Moreover, we find that the confined geometry favors the skyrmion over the spiral phase when compared to infinitely large systems. Upon tuning the magnetic field through the skyrmion phase, the system undergoes a cascade of transitions in the magnetic structure through states of different number of skyrmions, elongated and half-skyrmions, and spiral states. We consider how quantum and thermal fluctuations lift the degeneracies that occur at these transitions, and find that states with more skyrmions are typically favored by fluctuations over states with less skyrmions. Finally, we comment on electrical detection of the various phases through the topological and anomalous Hall effects.

cond-mat.mes-hall↗

arXiv2014

KPZ universality class and the anchored Toom interface

We revisit the anchored Toom interface and use KPZ scaling theory to argue that the interface fluctuations are governed by the Airy_1 process with the role of space and time interchanged. There is no free parameter. The predictions are numerically well confirmed for space-time statistics in the stationary state. In particular the spatial fluctuations of the interface are given by the GOE edge distribution of Tracy and Widom.

math-ph↗

arXiv2012

Critical exponents of the pair contact process with diffusion

We study the pair contact process with diffusion (PCPD) using Monte Carlo simulations, and concentrate on the decay of the particle density $ρ$ with time, near its critical point, which is assumed to follow $ρ(t) \approx ct^{-δ} +c_2t^{-δ_2}+...$. This model is known for its slow convergence to the asymptotic critical behavior; we therefore pay particular attention to finite-time corrections. We find that at the critical point, the ratio of $ρ$ and the pair density $ρ_p$ converges to a constant, indicating that both densities decay with the same powerlaw. We show that under the assumption $δ_2 \approx 2 δ$, two of the critical exponents of the PCPD model are $δ= 0.165(10)$ and $β= 0.31(4)$, consistent with those of the directed percolation (DP) model.

cond-mat.stat-mech↗

arXiv2010

Unwinding dynamics of double-stranded polymers

We consider the unwinding of two lattice polymer strands of length N that are initially wound around each other in a double-helical conformation and evolve through Rouse dynamics. The problem relates to quickly bringing a double-stranded polymer well above its melting temperature, i.e., the binding interactions between the strands are neglected, and the strands separate from each other as it is entropically favorable for them to do so. The strands unwind by rotating around each other until they separate. We find that the process proceeds from the ends inward; intermediate conformations can be characterized by a tightly wound inner part, from which loose strands are sticking out, with length l~t^0.39. The total time needed for the two strands to unwind scales as a power of N as tu~N^(2.57+-0.03). We present a theoretical argument, which suggests that during this unwinding process, these loose strands are far out of equilibrium.

cond-mat.soft↗

arXiv2009

Non-Markovian dynamics of clusters during nucleation

Most theories of homogeneous nucleation are based on a Fokker-Planck-like description of the behavior of the mass of clusters. Here we will show that these approaches are incomplete for a large class of nucleating systems, as they assume the effective dynamics of the clusters to be Markovian, i.e., memoryless. We characterize these non-Markovian dynamics and show how this influences the dynamics of clusters during nucleation. Our results are validated by simulations of a three-dimensional Ising model with locally conserved magnetization.

cond-mat.stat-mech↗

arXiv2008

Monte Carlo study of multiply crosslinked semiflexible polymer networks

We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their persistent directionality through the crosslinks. A Monte Carlo scheme is employed to obtain isotropic, homogeneous networks that minimize the free energy, and for which all of the relevant parameters can be varied: the persistence length, the contour length as well as the crosslinking length may be chosen at will. We also provide an initial survey of the mechanical properties of our networks subjected to shear strains, showing them to display the expected non-linear stiffening behavior. Also, a key role for non-affinity and its relation to order in the network is uncovered.

cond-mat.soft↗

arXiv2008

Monte Carlo studies of extensions of the Blume-Emery-Griffiths model

We extend the Blume-Emery-Griffiths (BEG) model to a two-component BEG model in order to study 2D systems with two order parameters, such as magnetic superconductors or two-component Bose-Einstein condensates. The model is investigated using Monte Carlo simulations, and the temperature-concentration phase diagram is determined in the presence and absence of an external magnetic field. This model exhibits a rich phase diagram, including a second-order transition to a phase where superconductivity and magnetism coexist. Results are compared with experiments on Cerium-based heavy-fermion superconductors. To study cold atom mixtures, we also simulate the BEG and two-component BEG models with a trapping potential. In the BEG model with a trap, there is no longer a first order transition to a true phase-separated regime, but a crossover to a kind of phase-separated region. The relation with imbalanced fermi-mixtures is discussed. We present the phase diagram of the two-component BEG model with a trap, which can describe boson-boson mixtures of cold atoms. Although there are no experimental results yet for the latter, we hope that our predictions could help to stimulate future experiments in this direction.

cond-mat.stat-mech↗

arXiv2008

Universality class of the pair contact process with diffusion

The pair contact process with diffusion (PCPD) is studied with a standard Monte Carlo approach and with simulations at fixed densities. A standard analysis of the simulation results, based on the particle densities or on the pair densities, yields inconsistent estimates for the critical exponents. However, if a well-chosen linear combination of the particle and pair densities is used, leading corrections can be suppressed, and consistent estimates for the independent critical exponents delta=0.16(2), beta=0.28(2) and z=1.58 are obtained. Since these estimates are also consistent with their values in directed percolation (DP), we conclude that PCPD falls in the same universality class as DP.

cond-mat.stat-mech↗

arXiv2008

Unbiased computation of transition times by pathway recombination

In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these systems, direct simulation of phase space trajectories does not efficiently determine most physical quantities of interest. The last decade has seen the advent of methods circumventing brute force simulation. For most dynamical quantities, these methods all share the drawback of systematical errors. We present a novel method for generating ensembles of phase space trajectories. By sampling small pieces of these trajectories in different phase space domains and piecing them together in a smart way using equilibrium properties, we obtain physical quantities such as transition times. This method does not have any systematic error and is very efficient; the computational effort to calculate the first passage time across a free energy barrier does not increase with the height of the barrier. The strength of the method is shown in the Ising model. Accurate measurements of nucleation times span almost ten orders of magnitude and reveal corrections to classical nucleation theory.

cond-mat.other↗

arXiv2007

Modelling background intensity in Affymetrix Genechips

DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on the microarray surface onto which different probe sequences are grafted. One of the problems of the data analysis is that the signal contains a noisy background component due to non-specific binding. This paper presents a physical model for background estimation in Affymetrix Genechips. It combines two different approaches. The first is based on the sequence composition, specifically its sequence dependent hybridization affinity. The second is based on the strong correlation of intensities from locations which are the physical neighbors of a specific spot on the chip. Both effects are incorporated in a background functional which contains 24 free parameters, fixed by minimization on a training data set. In all data analyzed the sequence specific parameters, obtained by minimization, are found to strongly correlate with empirically determined stacking free energies for RNA/DNA hybridization in solution. Moreover, there is an overall agreement with experimental background data and we show that the physics-based model proposed in this paper performs on average better than purely statistical approaches for background calculations. The model thus provides an interesting alternative method for background subtraction schemes in Affymetrix Genechips.

q-bio.BM↗

arXiv2007

An analysis of the fluctuations of the geomagnetic dipole

The time evolution of the strength of the Earth's virtual axial dipole moment (VADM) is analyzed by relating it to the Fokker-Planck equation, which describes a random walk with VADM-dependent drift and diffusion coefficients. We demonstrate first that our method is able to retrieve the correct shape of the drift and diffusion coefficients from a time series generated by a test model. Analysis of the Sint-2000 data shows that the geomagnetic dipole mode has a linear growth time of 13 to 33 kyr, and that the nonlinear quenching of the growth rate follows a quadratic function of the type [1-(x/x0)^2]. On theoretical grounds, the diffusive motion of the VADM is expected to be driven by multiplicative noise, and the corresponding diffusion coefficient to scale quadratically with dipole strength. However, analysis of the Sint-2000 VADM data reveals a diffusion which depends only very weakly on the dipole strength. This may indicate that the magnetic field quenches the amplitude of the turbulent velocity in the Earth's outer core.

physics.geo-ph↗

arXiv2006

Comment on: ``Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"

In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco suggested that the "bright" mismatches observed in Affymetrix microarray experiments are caused by the fluorescent molecules used to label RNA target sequences, which would impede target-probe hybridization. Their conclusion is based on the observation of "unexpected" asymmetries in the affinities obtained by fitting microarray data from publicly available experiments. We point out here that the observed asymmetry is due to the inequivalence of RNA and DNA, and that the reported affinities are consistent with stacking free energies obtained from melting experiments of unlabeled nucleic acids in solution. The conclusion of Naef and Magnasco is therefore based on an unjustified assumption.

q-bio.BM↗

arXiv2006

Physics-based analysis of Affymetrix microarray data

We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and artificial origin. Our analysis is based on a recently introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433 (2006)] which takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a "collapse" of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained before for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin, rather than being a problem with the proposed model.

q-bio.BM↗

arXiv2006

Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.

q-bio.BM↗

arXiv2006

Spinodal decomposition in polymer mixtures via surface diffusion

We present experimental results for spinodal decomposition in polymer mixtures of gelatin and dextran. The domain growth law is found to be consistent with t^1/4-growth over extended time-regimes. Similar results are obtained from lattice simulations of a polymer mixture. This slow growth arises due to the suppression of the bulk mobility of polymers. In that case, spinodal decomposition is driven by the diffusive transport of material along domain interfaces, which gives rise to a t^1/4-growth law.

cond-mat.soft↗