arXiv subjects

Cornelis Storm

Publications and source records attributed to Cornelis Storm.

At least 37 records · Page 2Linked to original sources

arXiv2015

Modeling the effect of intercalators on the high-force stretching behavior of DNA

DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that captures all relevant findings of recent force-extension experiments. Two predictions from our model are presented. The first suggests the existence of a novel hyper-stretching regime in the presence of intercalators and the second, a linear dependence of the overstretching force on intercalator concentration, is verified by re-analyzing available experimental data. Our model pins down the physical principles that govern intercalated DNA mechanics, providing a predictive understanding of its limitations and possibilities.

physics.bio-ph↗

arXiv2015

Actin Remodeling and Polymerization Forces Control Dendritic Spine Morphology

Dendritic spines are small membranous structures that protrude from the neuronal dendrite. Each spine contains a synaptic contact site that may connect its parent dendrite to the axons of neighboring neurons. Dendritic spines are markedly distinct in shape and size, and certain types of stimulation prompt spines to evolve, in fairly predictable fashion, from thin nascent morphologies to the mushroom-like shapes associated with mature spines. This striking progression is coincident with the (re)configuration of the neuronal network during early development, learning and memory formation, and has been conjectured to be part of the machinery that encodes these processes at the scale of individual neuronal connections. It is well established that the structural plasticity of spines is strongly dependent upon the actin cytoskeleton inside the spine. A general framework that details the precise role of actin in directing the transitions between the various spine shapes is lacking. We address this issue, and present a quantitative, model-based scenario for spine plasticity validated using realistic and physiologically relevant parameters. Our model points to a crucial role for the actin cytoskeleton. In the early stages of spine formation, the interplay between the elastic properties of the spine membrane and the protrusive forces generated in the actin cytoskeleton propels the incipient spine. In the maturation stage, actin remodeling in the form of the combined dynamics of branched and bundled actin is required to form mature, mushroom-like spines. Our model identifies additional factors that plausibly aid the stabilization and maintenance of spine morphology. Taken together, our model provides unique insights into the fundamental role of actin remodeling and polymerization forces during spine formation and maturation.

physics.bio-ph↗

arXiv2015

Self-assembling multiblock amphiphiles: Molecular design, supramolecular structure, and mechanical properties

We perform off-lattice, canonical ensemble molecular dynamics simulations of the self-assembly of long segmented copolymers consisting of alternating, tunably attractive and hydrophobic {\em binder} domains, connected by hydrophilic {\em linker} chains whose length may be separately controlled. In such systems, the molecular design of the molecule directly determines the balance between energetic and entropic tendencies. We determine the structural phase diagram of this system, which shows collapsed states (dominated by the attractive linkers' energies), swollen states (dominated by the random coil linkers' entropies) as well as intermediate network hydrogel phases, where the long molecules exhibit partial collapse to a {\em single molecule network} state. We present an analysis of the connectivity and spatial structure of this network phase, and relate its basic topology to mechanical properties, using a modified rubber elasticity model. The mechanical properties are further characterized in a direct computational implementation of oscillatory rheology measurements. We find that it is possible to optimize the mechanical performance by an appropriate choice of molecular design, which may point the way to novel synthetics that make optimal mechanical use of constituent polymers.

cond-mat.soft↗

arXiv2015

Crowding induced clustering under confinement

We present Langevin dynamics simulations that study the collective behavior of driven particles embedded in a densely packed background consisting of passive particles. Depending on the driving force, the densities of driven and passive particles, and the temperature we observe a dynamical phase separation of the driven particles, which cluster together in tight bands. We explore the mechanisms that drive this cluster formation, and determine the critical conditions for such phase separation. A simple physical picture explains the formation and subsequent growth of a jammed zone developing in front of the driven cluster. The model correctly captures the observed scaling with time. We analyze the implications of this clustering transition for the driven transport in dense particulate flows, which due to a non-monotonic dependence on the applied driving force is not straightforwardly optimized. We provide proof-of-concept for a direct application of the clustering effect, and propose a 'colloidal chromatograph'; a setup that permits the separation of colloids by mass or size.

cond-mat.soft↗

arXiv2015

Disorder, pre-stress and non-affinity in polymer 8-chain models

To assess the role of single-chain elasticity, non-affine strain fields and pre-stressed reference states we present and discuss the results of numerical and analytical analyses of modified 8-chain Arruda-Boyce model for cross-linked polymer networks. This class of models has proved highly successful in modeling the finite-strain response of flexible rubbers. We extend it to include the effects of spatial disorder and the associated non-affinity, and use it to assess the validity of replacing the constituent chain's nonlinear elastic response with equivalent linear, Hookean springs. Surprisingly, we find that even in the regime of linear response, the full polymer model gives very different results from its linearized counterpart, even though none of the chains are stretched beyond their linear regime. We demonstrate that this effect is due to the fact that the polymer models are under considerable pre-stress in their ground state. We show that pre-stress strongly suppresses non-affinity in these unit cell models, resulting in a marked stiffening of the bulk response. The effects of pre-stress we discuss may explain why fully affine mechanical models, in many cases, predict the bulk mechanical response of disordered stiff polymer networks so well.

cond-mat.soft↗

arXiv2015

Curvature-induced cross-hatched order in two-dimensional semiflexible polymer networks

A recurring motif in the organization of biological tissues are networks of long, fibrillar protein strands effectively confined to cylindrical surfaces. Often, the fibers in such curved, quasi-2D geometries adopt a characteristic order: the fibers wrap around the central axis at an angle which varies with radius and, in several cases, is strongly bimodally distributed. In this Letter, we investigate the general problem of a 2D crosslinked network of semiflexible fibers confined to a cylindrical substrate, and demonstrate that in such systems the trade-off between bending and stretching energies, very generically, gives rise to cross-hatched order. We discuss its general dependency on the radius of the confining cylinder, and present an intuitive model that illustrates the basic physical principle of curvature-induced order. Our findings shed new light on the potential origin of some curiously universal fiber orientational distributions in tissue biology, and suggests novel ways in which synthetic polymeric soft materials may be instructed or programmed to exhibit preselected macromolecular ordering.

physics.bio-ph↗

arXiv2014

Forced transport of deformable containers through narrow constrictions

We study, numerically and analytically, the forced transport of deformable containers through a narrow constriction. Our central aim is to quantify the competition between the constriction geometry and the active forcing, regulating whether and at which speed a container may pass through the constriction and under what conditions it gets stuck. We focus, in particular, on the interrelation between the force that propels the container and the radius of the channel, as these are the external variables that may be directly controlled in both artificial and physiological settings. We present Lattice-Boltzmann simulations that elucidate in detail the various phases of translocation, and present simplified analytical models that treat two limiting types of these membrane containers: deformational energy dominated by the bending or stretching contribution. In either case we find excellent agreement with the full simulations, and our results reveal that not only the radius but also the length of the constriction determines whether or not the container will pass.

cond-mat.soft↗

arXiv2014

Confinement without boundaries: Anisotropic diffusion on the surface of a cylinder

Densely packed systems of thermal particles in curved geometries are frequently encountered in biological and microfluidic systems. In 2D systems, at sufficiently high surface coverage, diffusive motion is widely known to be strongly affected by physical confinement, e.g., by the walls. In this Letter, we explore the effects of confinement by shape, not rigid boundaries, on the diffusion of particles by confining them to the surface of a cylinder. We find that both the magnitude and the directionality of lateral diffusion is strongly influenced by the radius of the cylinder. An anisotropy between diffusion in the longitudinal and circumferential direction of the cylinder develops. We demonstrate that the origin of this effect lies in the fact that screw-like packings of mono- and oligodisperse discs on the surface of a cylinder induce preferential collective motions in the circumferential direction, but also show that even in polydisperse systems lacking such order an intrinsic finite size confinement effect increases diffusivity in the circumferential direction.

cond-mat.stat-mech↗

arXiv2013

Fluctuation-stabilized marginal networks and anomalous entropic elasticity

We study the elastic properties of thermal networks of Hookean springs. In the purely mechanical limit, such systems are known to have vanishing rigidity when their connectivity falls below a critical, isostatic value. In this work we show that thermal networks exhibit a non-zero shear modulus $G$ well below the isostatic point, and that this modulus exhibits an anomalous, sublinear dependence on temperature $T$. At the isostatic point, $G$ increases as the square-root of $T$, while we find $G \propto T^α$ below the isostatic point, where $α \simeq 0.8$. We show that this anomalous $T$ dependence is entropic in origin.

cond-mat.soft↗

arXiv2010

Off-lattice Monte Carlo Simulation of Supramolecular Polymer Architectures

We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational changes that exactly preserve fixed-length constraints of all bonds. The algorithm reproduces known end-to-end distance distributions for simple, analytically tractable systems of cross-linked stiff and freely jointed polymers flawlessly, and is used to determine the effective persistence length of short bundles of semi-flexible worm-like chains, cross-linked to each other. It reveals a possible regulatory mechanism in bundled networks: the effective persistence of bundles is controlled by the linker density.

cond-mat.soft↗

arXiv2010

Semiflexible Filamentous Composites

Inspired by the ubiquity of composite filamentous networks in nature we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains between the stiff and floppy fractions c_s and c_f, and reveal a non-trivial relationship between the mechanical behavior and the relative fraction of stiff polymer: when there are few stiff polymers, non-percolated stiff ``inclusions`` are protected from large deformations by an encompassing floppy matrix, while at higher fractions of stiff material the stiff network is independently percolated and dominates the mechanical response.

q-bio.BM↗

arXiv2007

Accurate determination of elastic parameters for multi-component membranes

Heterogeneities in the cell membrane due to coexisting lipid phases have been conjectured to play a major functional role in cell signaling and membrane trafficking. Thereby the material properties of multiphase systems, such as the line tension and the bending moduli, are crucially involved in the kinetics and the asymptotic behavior of phase separation. In this Letter we present a combined analytical and experimental approach to determine the properties of phase-separated vesicle systems. First we develop an analytical model for the vesicle shape of weakly budded biphasic vesicles. Subsequently experimental data on vesicle shape and membrane fluctuations are taken and compared to the model. The combined approach allows for a reproducible and reliable determination of the physical parameters of complex vesicle systems. The parameters obtained set limits for the size and stability of nanodomains in the plasma membrane of living cells.

cond-mat.soft↗

arXiv2004

Fission of a multiphase membrane tube

A common mechanism for intracellular transport is the use of controlled deformations of the membrane to create spherical or tubular buds. While the basic physical properties of homogeneous membranes are relatively well-known, the effects of inhomogeneities within membranes are very much an active field of study. Membrane domains enriched in certain lipids in particular are attracting much attention, and in this Letter we investigate the effect of such domains on the shape and fate of membrane tubes. Recent experiments have demonstrated that forced lipid phase separation can trigger tube fission, and we demonstrate how this can be understood purely from the difference in elastic constants between the domains. Moreover, the proposed model predicts timescales for fission that agree well with experimental findings.

physics.bio-ph↗

arXiv2004

Nonlinear Elasticity in Biological Gels

Unlike most synthetic materials, biological materials often stiffen as they are deformed. This nonlinear elastic response, critical for the physiological function of some tissues, has been documented since at least the 19th century, but the molecular structure and the design principles responsible for it are unknown. Current models for this response require geometrically complex ordered structures unique to each material. In this Article we show that a much simpler molecular theory accounts for strain stiffening in a wide range of molecularly distinct biopolymer gels formed from purified cytoskeletal and extracellular proteins. This theory shows that systems of semi-flexible chains such as filamentous proteins arranged in an open crosslinked meshwork invariably stiffen at low strains without the need for a specific architecture or multiple elements with different intrinsic stiffnesses.

cond-mat.soft↗

arXiv2004

Fast DNA translocation through a solid-state nanopore

We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm pore. We find a power-law scaling of the translocation time versus length, with an exponent of 1.26 $\pm$ 0.07. This behavior is qualitatively different from the linear behavior observed in similar experiments performed with protein pores. We address the observed nonlinear scaling in a theoretical model that describes experiments where hydrodynamic drag on the section of the polymer outside the pore is the dominant force counteracting the driving. We show that this is the case in our experiments and derive a power-law scaling with an exponent of 1.18, in excellent agreement with our data.

q-bio.BM↗

arXiv2003

Weakly nonlinear subcritical instability of visco-elastic Poiseuille flow

It is well known that the Poiseuille flow of a visco-elastic polymer fluid between plates or through a tube is linearly stable in the zero Reynolds number limit, although the stability is weak for large Weissenberg numbers. In this paper we argue that recent experimental and theoretical work on the instability of visco-elastic fluids in Taylor-Couette cells and numerical work on channel flows suggest a scenario in which Poiseuille flow of visco-elastic polymer fluids exhibits a nonlinear "subcritical" instability due to normal stress effects, with a threshold which decreases for increasing Weissenberg number. This proposal is confirmed by an explicit weakly nonlinear stability analysis for Poiseuille flow of an UCM fluid. Our analysis yields explicit predictions for the critical amplitude of velocity perturbations beyond which the flow is nonlinearly unstable, and for the wavelength of the mode whose critical amplitude is smallest. The nonlinear instability sets in quite abruptly at Weissenberg numbers around 4 in the planar case and about 5.2 in the cylindrical case, so that for Weissenberg numbers somewhat larger than these values perturbations of the order of a few percent in the wall shear stress suffice to make the flow unstable. We have suggested elsewhere that this nonlinear instability could be an important intrinsic route to melt fracture and that preliminary experiments are both qualitatively and quantitatively in good agreement with these predictions.

cond-mat.stat-mech↗

arXiv2003

Sources, sinks and holes in a one-dimensional traveling wave convection experiment

We study dynamical behavior of local structures, such as sources and holes, in traveling wave patterns in a very long (2 m) heated wire convection experiment. The {\em sources} undergo a transition from stable coherent behavior to erratic behavior when the driving parameter $ε$ is {\em decreased}. This transition, as well as the scaling of the average source width in the erratic regime, are both qualitatively and quantitatively in accord with earlier theoretical predictions. We also present new results for the {\em holes} sent out by the erratic sources.

cond-mat.stat-mech↗

arXiv2002

The bend stiffness of S-DNA

We formulate and solve a two-state model for the elasticity of nicked, double-stranded DNA that borrows features from both the Worm Like Chain and the Bragg--Zimm model. Our model is computationally simple, and gives an excellent fit to recent experimental data through the entire overstretching transition. The fit gives the first value for the bending stiffness of the overstretched state as about 10 nm*kbt, a value quite different from either B-form or single-stranded DNA.

physics.bio-ph↗