arXiv subjects

Jef Hooyberghs

Publications and source records attributed to Jef Hooyberghs.

16 recordsLinked to original sources

arXiv2026

Performance of Nanoring-based Transparent Conductors: a Computational Investigation

Metallic nanoring networks can serve as promising flexible transparent electrodes. These materials are crucial components in a wide range of applications, including solar cells, touchscreens and displays. In this work, a computational investigation considers in detail (i) the electrical conductance and optical performance of nanoring networks and (ii) the breakdown of these networks due to electrical damage. The electrical resistance of both the nanorings and the contacts between the rings (junctions) is taken into account. In part (i), the effects of 5 parameters on the electrical sheet resistance and optical transparency are presented. It is shown that several parameter combinations achieve better performance in comparison to indium tin oxide, currently the most widely used transparent electrode. In part (ii), due to electrical damage, the nanoring systems display the formation of a crack, running parallel to the vertical terminals, where a voltage difference is applied. The network degradation is measured by its sheet resistance, and a universal effect is observed: networks with varying filling factors exhibit the same degradation profile.

cond-mat.mtrl-sci↗

arXiv2026

Impedance in Periodically Driven Stochastic Systems

We study the time-dependent currents arising in periodically driven stochastic systems. In the linear regime of small driving, a closed expression is obtained for the impedance/admittance associated with these currents. This expression leads directly to an interpretation in terms of an equivalent electrical circuit. For a stochastic system with $N$ states, the electrical circuit consists of precisely $N$ parallel branches, with each branch comprising a resistor and a capacitor in series. The low- and high-frequency limits of these currents are calculated, and the results are generalized to more general current expressions. We demonstrate our findings across several archetypal settings, illustrating the potential to detect specific broken symmetries or the graph topology associated with the stochastic process.

cond-mat.stat-mech↗

arXiv2026

DNA handles bias force-dependent looping times

DNA loop formation is a key mechanism in gene regulation, and looping kinetics are sensitive to mechanical tension acting on the DNA. In both single-molecule experiments and biological settings, this tension is typically transmitted through DNA segments flanking the looping region, rather than acting directly at the looping sites. How this indirect force transmission affects the looping time has not been systematically investigated. Using molecular dynamics simulations of a wormlike chain, we show that such flanking segments significantly steepen the force dependence of the looping time, an effect that is insensitive to their length once it exceeds the persistence length, and vanishes when the junction to the looping region is made flexible. We develop an analytical framework that accounts for this effect through a force-dependent shift in the effective free energy landscape of the looping segment. In the limit of small forces, this shift reduces to a zero-force equilibrium average, after which the entire force dependence of the looping time follows analytically. Applying this framework using a coarse-grained DNA model that treats individual bases as rigid bodies, we obtain predictions in quantitative agreement with experimental looping data. Our results demonstrate that the geometry of force transmission has a significant and predictable effect on looping kinetics, with direct implications for the interpretation of tension-dependent looping in both single-molecule experiments and gene regulatory contexts.

physics.bio-ph↗

arXiv2024

Polymer dynamics under tension: mean first passage time for looping

This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous theoretical approaches to polymer looping under tension have relied on barrier escape methods, which assume local equilibrium, an assumption that may not always hold. As a starting point we use an analytical expression for the equilibrium looping probability as a function of the number of monomers and applied force, predicting an inverse relationship between looping time and looping probability. Using molecular dynamics simulations the predictions of this theoretical approach are validated within the numerical precision achieved. We compare our predictions to those of the barrier escape approach, by way of a calculation of the mean first passage time (MFPT) for the ends of a polymer to cross. For this purpose, we derive the exact free energy landscape, but resulting temporal predictions do not agree with the observed inverse scaling. We conclude that the traditional barrier escape approach does not provide satisfactory predictions for polymer looping dynamics and that the inverse scaling with looping probability offers a more reliable alternative.

cond-mat.stat-mech↗

arXiv2024

Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+

Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs. all-atom models using stiffness matrices in Fourier space ($q$-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version cgDNA+. Our analysis shows that while cgDNA+ follows closely the $q$-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables which are rather strong in the $q \to 0$ (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects which manifest themselves at longer length scales. In particular, cgDNA performs poorly on the twist stiffness with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist is strongly length scale dependent: DNA is torsionally soft at a few base pair distances, but becomes more rigid at distances of a few dozens base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.

cond-mat.soft↗

arXiv2019

Enhancing the performance of DNA surface-hybridization biosensors through target depletion

DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large and have high affinity for the target, the DNA in solution may get depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration $c_2$) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration $c_1 \gg c_2$). We show that depletion can give rise to a strongly-enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations $c_2/c_1$ that are up to three orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich, and exhibits a non-monotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence.

q-bio.BM↗

arXiv2018

DNA capture into the ClyA nanopore: diffusion-limited versus reaction-limited processes

The capture and translocation of biomolecules through nanometer-scale pores are processes with a potential large number of applications, and hence they have been intensively studied in the recent years. The aim of this paper is to review existing models of the capture process by a nanopore, together with some recent experimental data of short single- and double-stranded DNA captured by Cytolysin A (ClyA) nanopore. ClyA is a transmembrane protein of bacterial origin which has been recently engineered through site-specific mutations, to allow the translocation of double- and single-stranded DNA. A comparison between theoretical estimations and experiments suggests that for both cases the capture is a reaction-limited process. This is corroborated by the observed salt dependence of the capture rate, which we find to be in quantitative agreement with the theoretical predictions.

cond-mat.soft↗

arXiv2012

Probing Hybridization parameters from microarray experiments: nearest neighbor model and beyond

In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.

q-bio.BM↗

arXiv2011

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $ΔG$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $ΔG/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.

q-bio.BM↗

arXiv2011

Nonequilibrium wetting transition in a nonthermal 2D Ising model

Nonequilibrium wetting transitions are observed in Monte Carlo simulations of a kinetic spin system in the absence of a detailed balance condition with respect to an energy functional. A nonthermal model is proposed starting from a two-dimensional Ising spin lattice at zero temperature with two boundaries subject to opposing surface fields. Local spin excitations are only allowed by absorbing an energy quantum (photon) below a cutoff energy E_c. Local spin relaxation takes place by emitting a photon which leaves the lattice. Using Monte Carlo simulation nonequilibrium critical wetting transitions are observed as well as nonequilibrium first-order wetting phenomena, respectively in the absence or presence of absorbing states of the spin system. The transitions are identified from the behavior of the probability distribution of a suitably chosen order parameter that was proven useful for studying wetting in the (thermal) Ising model.

cond-mat.stat-mech↗

arXiv2009

Thermodynamics of histories for the one-dimensional contact process

The dynamical activity K(t) of a stochastic process is the number of times it changes configuration up to time t. It was recently argued that (spin) glasses are at a first order dynamical transition where histories of low and high activity coexist. We study this transition in the one-dimensional contact process by weighting its histories by exp(sK(t)). We determine the phase diagram and the critical exponents of this model using a recently developed approach to the thermodynamics of histories that is based on the density matrix renormalisation group. We find that for every value of the infection rate, there is a phase transition at a critical value of s. Near the absorbing state phase transition of the contact process, the generating function of the activity shows a scaling behavior similar to that of the free energy in an equilibrium system near criticality.

cond-mat.stat-mech↗

arXiv2008

DMRG-study of current and activity fluctuations near non-equilibrium phase transitions

Cumulants of a fluctuating current can be obtained from a free energy-like generating function which for Markov processes equals the largest eigenvalue of a generalized generator. We determine this eigenvalue with the DMRG for stochastic systems. We calculate the variance of the current in the different phases, and at the phase transitions, of the totally asymmetric exclusion process. Our results can be described in the terms of a scaling ansatz that involves the dynamical exponent z. We also calculate the generating function of the activity near the absorbing state transition of the contact process. Its scaling properties can be expressed in terms of known critical exponents.

cond-mat.stat-mech↗

arXiv2004

Absorbing state phase transitions with quenched disorder

Quenched disorder - in the sense of the Harris criterion - is generally a relevant perturbation at an absorbing state phase transition point. Here using a strong disorder renormalization group framework and effective numerical methods we study the properties of random fixed points for systems in the directed percolation universality class. For strong enough disorder the critical behavior is found to be controlled by a strong disorder fixed point, which is isomorph with the fixed point of random quantum Ising systems. In this fixed point dynamical correlations are logarithmically slow and the static critical exponents are conjecturedly exact for one-dimensional systems. The renormalization group scenario is confronted with numerical results on the random contact process in one and two dimensions and satisfactory agreement is found. For weaker disorder the numerical results indicate static critical exponents which vary with the strength of disorder, whereas the dynamical correlations are compatible with two possible scenarios. Either they follow a power-law decay with a varying dynamical exponent, like in random quantum systems, or the dynamical correlations are logarithmically slow even for weak disorder. For models in the parity conserving universality class there is no strong disorder fixed point according to our renormalization group analysis.

cond-mat.stat-mech↗

arXiv2003

Strong disorder fixed point in absorbing state phase transitions

The effect of quenched disorder on non-equilibrium phase transitions in the directed percolation universality class is studied by a strong disorder renormalization group approach and by density matrix renormalization group calculations. We show that for sufficiently strong disorder the critical behaviour is controlled by a strong disorder fixed point and in one dimension the critical exponents are conjectured to be exact: β=(3-\sqrt{5})/2 and ν_\perp=2. For disorder strengths outside the attractive region of this fixed point, disorder dependent critical exponents are detected. Existing numerical results in two dimensions can be interpreted within a similar scenario.

cond-mat.stat-mech↗

arXiv2001

The generalized contact process with n absorbing states

We investigate the critical properties of a one dimensional stochastic lattice model with n (permutation symmetric) absorbing states. We analyze the cases with $n \leq 4$ by means of the non-hermitian density matrix renormalization group. For n=1 and n=2 we find that the model is respectively in the directed percolation and parity conserving universality class, consistent with previous studies. For n=3 and n=4, the model is in the active phase in the whole parameter space and the critical point is shifted to the limit of one infinite reaction rate. We show that in this limit the dynamics of the model can be mapped onto that of a zero temperature n-state Potts model. On the basis of our numerical and analytical results we conjecture that the model is in the same universality class for all $n \geq 3$ with exponents $z = ν_\|/ν_\perp = 2$, $ν_\perp = 1$ and $β= 1$. These exponents coincide with those of the multispecies (bosonic) branching annihilating random walks. For n=3 we also show that, upon breaking the symmetry to a lower one ($Z_2$), one gets a transition either in the directed percolation, or in the parity conserving class, depending on the choice of parameters.

cond-mat.stat-mech↗

arXiv2000

The one-dimensional contact process: duality and renormalisation

We study the one-dimensional contact process in its quantum version using a recently proposed real space renormalisation technique for stochastic many-particle systems. Exploiting the duality and other properties of the model, we can apply the method for cells with up to 37 sites. After suitable extrapolation, we obtain exponent estimates which are comparable in accuracy with the best known in the literature.

cond-mat.stat-mech↗