arXiv subjects

Wouter G. Ellenbroek

Publications and source records attributed to Wouter G. Ellenbroek.

At least 19 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↗

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↗

arXiv2022

Associative bond swaps in molecular dynamics

We implement a three-body potential to model associative bond swaps, and release it as part of the HOOMD-blue software. The use of a three-body potential to model swaps has been proven to be effective and has recently provided useful insights into the mechanics and dynamics of adaptive network materials such as vitrimers. It is elegant because it can be used in plain molecular dynamics simulations without the need for topology-altering Monte Carlo steps, and naturally represents typical physical features such as slip-bond behavior. It is easily tunable with a single parameter to control the average swap rate. Here, we show how associative bond swaps can be used to speed up the equilibration of systems that self-assemble by avoiding traps and pitfalls, corresponding to long-lived metastable configurations. Our results demonstrate the possibilities of these swaps not only for modeling systems that are associative by nature, but also for increasing simulation efficiency in other systems that are modellable in HOOMD-blue.

cond-mat.soft↗

arXiv2018

Self-stresses control stiffness and stability in overconstrained disordered networks

We investigate the interplay between pre-stress and mechanical properties in random elastic networks. To do this in a controlled fashion, we introduce an algorithm for creating random freestanding frames that support exactly one state of self stress. By multiplying all the bond tensions in this state of self stress by the same number---which with the appropriate normalization corresponds to the physical pre-stress inside the frame---we systematically evaluate the linear mechanical response of the frame as a function of pre-stress. After proving that the mechanical moduli of affinely deforming frames are rigourously independent of pre-stress, we turn to non-affinely deforming frames. In such frames, pre-stress has a profound effect on linear response: not only can it change the values of the linear modulus---an effect we demonstrate to be related to a suppressive effect of pre-stress on non-affinity---but pre-stresses also generically trigger bistable mechanical response. Thus, pre-stress can be leveraged to both augment the mechanical response of network architectures on the fly, and to actuate finite deformations. These control modalities may be of use in the design of both novel responsive materials and soft actuators.

cond-mat.dis-nn↗

arXiv2018

Harnessing entropy to enhance toughness in reversibly crosslinked polymer networks

Reversible crosslinking is a design paradigm for polymeric materials, wherein they are microscopically reinforced with chemical species that form transient crosslinks between the polymer chains. Besides the potential for self-healing, recent experimental work suggests that freely diffusing reversible crosslinks in polymer networks, such as gels, can enhance the toughness of the material without substantial change in elasticity. This presents the opportunity for making highly elastic materials that can be strained to a large extent before rupturing. Here, we employ Gaussian chain theory, molecular simulation, and polymer self-consistent field theory for networks to construct an equilibrium picture for how reversible crosslinks can toughen a polymer network without affecting its linear elasticity. Maximisation of polymer entropy drives the reversible crosslinks to bind preferentially near the permanent crosslinks in the network, leading to local molecular reinforcement without significant alteration of the network topology. In equilibrium conditions, permanent crosslinks share effectively the load with neighbouring reversible crosslinks, forming multi-functional crosslink points. The network is thereby globally toughened, while the linear elasticity is left largely unaltered. Practical guidelines are proposed to optimise this design in experiment, along with a discussion of key kinetic and timescale considerations.

cond-mat.soft↗

arXiv2018

Dynamics of vitrimers: defects as a highway to stress relaxation

We propose a coarse-grained model to investigate stress relaxation in star-polymer networks induced by dynamic bond exchange processes. We show how the swapping mechanism, once activated, allows the network to reconfigure, exploring distinct topological configurations, all of them characterised by complete extent of reaction. Our results reveal the important role played by topological defects in mediating the exchange reaction and speeding up stress relaxation. The model provides a representation of the dynamics in vitrimers, a new class of polymers characterized by bond swap mechanisms which preserve the total number of bonds, as well as in other bond-exchange materials.

cond-mat.soft↗

arXiv2017

Geometry and the onset of rigidity in a disordered network

Disordered spring networks that are undercoordinated may abruptly rigidify when sufficient strain is applied. Since the deformation in response to applied strain does not change the generic quantifiers of network architecture - the number of nodes and the number of bonds between them - this rigidity transition must have a geometric origin. Naive, degree-of-freedom based mechanical analyses such as the Maxwell-Calladine count or the pebble game algorithm overlook such geometric rigidity transitions and offer no means of predicting or characterizing them. We apply tools that were developed for the topological analysis of zero modes and states of self-stress on regular lattices to two-dimensional random spring networks, and demonstrate that the onset of rigidity, at a finite simple shear strain $γ^\star$, coincides with the appearance of a single state of self stress, accompanied by a single floppy mode. The process conserves the topologically invariant difference between the number of zero modes and the number of states of self stress, but imparts a finite shear modulus to the spring network. Beyond the critical shear, we confirm previously reported critical scaling of the modulus. In the sub-critical regime, a singular value decomposition of the network's compatibility matrix foreshadows the onset of rigidity by way of a continuously vanishing singular value corresponding to nascent state of self stress.

cond-mat.soft↗

arXiv2017

Mechanics from Calorimetry: A New Probe of Elasticity for Responsive Hydrogels

Temperature-sensitive hydrogels based on polymers such as poly(N-isopropylacrylamide) (PNIPAM) undergo a volume phase transition in response to changes in temperature. During this transition, distinct changes in both thermal and mechanical properties are observed. Here, we illustrate and exploit the inherent thermodynamic link between thermal and mechanical properties by showing that the compressive elastic modulus of PNIPAM hydrogels can be probed using differential scanning calorimetry. We validate our approach by using conventional osmotic compression tests. Our method could be particularly valuable for determining the mechanical response of thermosensitive submicron-sized and/or oddly shaped particles, to which standard methods are not readily applicable.

cond-mat.soft↗

arXiv2015

Rigidity Loss in Disordered Systems: Three Scenarios

We reveal significant qualitative differences in the rigidity transition of three types of disordered network materials: randomly diluted spring networks, jammed sphere packings, and stress-relieved networks that are diluted using a protocol that avoids the appearance of floppy regions. The marginal state of jammed and stress-relieved networks are globally isostatic, while marginal randomly diluted networks show both overconstrained and underconstrained regions. When a single bond is added to or removed from these isostatic systems, jammed networks become globally overconstrained or floppy, whereas the effect on stress-relieved networks is more local and limited. These differences are also reflected in the linear elastic properties and point to the highly effective and unusual role of global self-organization in jammed sphere packings.

cond-mat.soft↗

arXiv2013

Stability of jammed packings I: the rigidity length scale

In 2005, Wyart et al. (Europhys. Lett., 72 (2005) 486) showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*.

cond-mat.soft↗

arXiv2011

Rigidity percolation on the square lattice

The square lattice with central forces between nearest neighbors is isostatic with a subextensive number of floppy modes. It can be made rigid by the random addition of next-nearest neighbor bonds. This constitutes a rigidity percolation transition which we study analytically by mapping it to a connectivity problem of two-colored random graphs. We derive an exact recurrence equation for the probability of having a rigid percolating cluster and solve it in the infinite volume limit. From this solution we obtain the rigidity threshold as a function of system size, and find that, in the thermodynamic limit, there is a mixed first-order-second-order rigidity percolation transition at the isostatic point.

cond-mat.stat-mech↗

arXiv2010

Rotational and Translational Phonon Modes in Glasses Composed of Ellipsoidal Particles

The effects of particle shape on the vibrational properties of colloidal glasses are studied experimentally. 'Ellipsoidal glasses' are created by stretching polystyrene spheres to different aspect ratios and then suspending the resulting ellipsoidal particles in water at high packing fraction. By measuring displacement correlations between particles, we extract vibrational properties of the corresponding "shadow" ellipsoidal glass with the same geometric configuration and interactions as the 'source' suspension but without damping. Low frequency modes in glasses composed of ellipsoidal particles with major/minor axis aspect ratios $\sim$1.1 are observed to have predominantly rotational character. By contrast, low frequency modes in glasses of ellipsoidal particles with larger aspect ratios ($\sim$3.0) exhibit a mix of rotational and translational character. All glass samples were characterized by a distribution of particles with different aspect ratios. Interestingly, even within the same sample it was found that small-aspect-ratio particles participate relatively more in rotational modes, while large-aspect-ratio particles tend to participate relatively more in translational modes.

cond-mat.soft↗

arXiv2010

Low-frequency vibrations of soft colloidal glasses

We conduct experiments on two-dimensional packings of colloidal thermosensitive hydrogel particles whose packing fraction can be tuned above the jamming transition by varying the temperature. By measuring displacement correlations between particles, we extract the vibrational properties of a corresponding "shadow" system with the same configuration and interactions, but for which the dynamics of the particles are undamped. The vibrational spectrum and the nature of the modes are very similar to those predicted for zero-temperature idealized sphere models and found in atomic and molecular glasses; there is a boson peak at low frequency that shifts to higher frequency as the system is compressed above the jamming transition.

cond-mat.soft↗

arXiv2010

Electrostatic cluster formation in lipid monolayers

We study phase separation in mixed monolayers of neutral and highly negatively charged lipids, induced by the addition of divalent positively charged counterions. We find good agreement between experiments on mixtures of pip2 and sopc and simulations of a simplified model in which only the essential electrostatic interactions are retained. Thus, our results support an interpretation of pip2 clustering as governed primarily by electrostatic interactions, in which divalent ions such as calcium mediate an effective attraction between like-charged lipids. Surprisingly, the mediated attractions are strong enough to give nearly complete phase separation, so that clusters can even form when the overall concentration of pip2 is low, as is the case in the cell membrane.

cond-mat.soft↗

arXiv2009

Jammed frictionless discs: connecting local and global response

By calculating the linear response of packings of soft frictionless discs to quasistatic external perturbations, we investigate the critical scaling behavior of their elastic properties and non-affine deformations as a function of the distance to jamming. Averaged over an ensemble of similar packings, these systems are well described by elasticity, while in single packings we determine a diverging length scale $\ell^*$ up to which the response of the system is dominated by the local packing disorder. This length scale, which we observe directly, diverges as $1/Δz$, where $Δz$ is the difference between contact number and its isostatic value, and appears to scale identically to the length scale which had been introduced earlier in the interpretation of the spectrum of vibrational modes. It governs the crossover from isostatic behavior at the small scale to continuum behavior at the large scale; indeed we identify this length scale with the coarse graining length needed to obtain a smooth stress field. We characterize the non-affine displacements of the particles using the \emph{displacement angle distribution}, a local measure for the amount of relative sliding, and analyze the connection between local relative displacements and the elastic moduli.

cond-mat.soft↗

arXiv2009

Non-affine response: jammed packings versus spring networks

We compare the elastic response of spring networks whose contact geometry is derived from real packings of frictionless discs, to networks obtained by randomly cutting bonds in a highly connected network derived from a well-compressed packing. We find that the shear response of packing-derived networks, and both the shear and compression response of randomly cut networks, are all similar: the elastic moduli vanish linearly near jamming, and distributions characterizing the local geometry of the response scale with distance to jamming. Compression of packing-derived networks is exceptional: the elastic modulus remains constant and the geometrical distributions do not exhibit simple scaling. We conclude that the compression response of jammed packings is anomalous, rather than the shear response.

cond-mat.soft↗

arXiv2007

The tail of the contact force distribution in static granular materials

We numerically study the distribution P(f) of contact forces in frictionless bead packs, by averaging over the ensemble of all possible force network configurations. We resort to umbrella sampling to resolve the asymptotic decay of P(f) for large f, and determine P(f) down to values of order 10^{-45} for ordered and disordered systems in two and three dimensions. Our findings unambiguously show that, in the ensemble approach, the force distributions decay much faster than exponentially: P(f) ~ exp(-f^α), with alpha \approx 2.0 for 2D systems, and alpha \approx 1.7 for 3D systems.

cond-mat.stat-mech↗