arXiv subjects

Wout Laeremans

Publications and source records attributed to Wout Laeremans.

5 recordsLinked to original sources

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↗

arXiv2026

Synthetic design of force-responsive hydrogels with ring-forming catch bonds

Catch bonds are interactions whose lifetimes increase under mechanical load, a counterintuitive behaviour that underlies diverse biological processes. Translating this mechanism to synthetic materials offers the potential to create systems that are compliant at low stress but stiffen under applied force, with applications ranging from impact-responsive materials to dynamic tissue scaffolds. However, engineering materials with tunable, force-dependent interactions remains challenging, and existing conceptual designs are limited. Here, we present a minimal synthetic framework for catch bond behaviour in dynamic hydrogels, based on reversible ring-forming polymers. Using coarse-grained molecular dynamics simulations, we show that hydrogels with such a chemistry undergo fewer bond-breaking reactions as the stress increases and can even display a non-monotonic dependence of the strain rate on the applied stress. Our results highlight the potential of reversible ring formation as a versatile platform for designing mechanically adaptive materials with tunable durability and responsiveness.

cond-mat.soft↗

arXiv2025

Theoretical Models for Tension-Dependent DNA Looping Time

The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly review the predictions of those models and propose a novel model that demonstrates exceptional agreement with simulations for long semiflexible chains. Additionally, we elucidate the relationship between our result and that of the previously proposed two-state model, highlighting the distinct interpretative approach that underpins our framework. Our findings offer predictive insights that pave the way for future experimental validation.

cond-mat.stat-mech↗

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↗