arXiv subjects

Matthew S. Turner

Publications and source records attributed to Matthew S. Turner.

At least 37 records · Page 2Linked to original sources

arXiv2017

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these systems arise due to topological interactions between polymers, or between the polymers and the environment, and it is often challenging to describe this quantitatively. Here we review recent research which suggests that a key role is played by inter-ring threadings (or penetrations), which become more abundant as the ring size increases. As we discuss, the physical consequences of such threadings are far-reaching: for instance, they lead to a topologically-driven glassy behaviour of ring polymer melts under pinning perturbations, while they can also account for the shape of experimentally observed patterns in two-dimensional gel electrophoresis of DNA knots.

cond-mat.soft↗

arXiv2016

A Topologically Driven Glass in Ring Polymers

The static and dynamic properties of ring polymers in concentrated solutions remains one of the last deep unsolved questions in Polymer Physics. At the same time, the nature of the glass transition in polymeric systems is also not well understood. In this work we study a novel glass transition in systems made of circular polymers by exploiting the topological constraints that are conjectured to populate concentrated solutions of rings. We show that such rings strongly inter-penetrate through one another, generating an extensive network of topological interactions that dramatically affects their dynamics. We show that a kinetically arrested state can be induced by randomly pinning a small fraction of the rings. This occurs well above the classical glass transition temperature at which microscopic mobility is lost. Our work demonstrates both the existence of long-lived inter-ring penetrations and also realises a novel, topologically-induced, glass transition.

cond-mat.soft↗

arXiv2015

Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension

The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations and hence the drag, measurements of diffusivity can be used to infer--- via an elastic model of the protein--- how conformation is changed by tension. Motivated by recent experimental results [Quemeneur et al., Proc. Natl. Acad. Sci. USA, 111 5083 (2014)] we focus on KvAP, a voltage-gated potassium channel. The conformation of KvAP is found to change considerably due to tension, with its `walls', where the protein meets the membrane, undergoing significant angular strains. The torsional stiffness is determined to be 26.8 kT at room temperature. This has implications for both the structure and function of such proteins in the environment of a tension-bearing membrane.

cond-mat.soft↗

arXiv2015

The Role of Optical Projection in the Analysis of Membrane Fluctuations

We propose a methodology to measure the mechanical properties of membranes from their fluctuations and apply this to optical microscopy measurements of giant unilamellar vesicles of lipids. We analyze the effect of the projection of thermal shape undulations across the focal depth of the microscope. We derive an analytical expression for the mode spectrum that varies with the focal depth and accounts for the projection of fluctuations onto the equatorial plane. A comparison of our model with existing approaches, that use only the apparent equatorial fluctuations without averaging out of this plane, reveals a significant and systematic reduction in the inferred value of the bending rigidity. Our results are in full agreement with the values measured through X-ray scattering and other micromechanical manipulation techniques, resolving a long standing discrepancy with these other experimental methods.

cond-mat.soft↗

arXiv2015

Composition variation and underdamped mechanics near membrane proteins and coats

We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both undergo a transition from over-damped to under-damped spatial variation, well before the membrane becomes unstable in the bulk. This transition is associated with a change in the sign of the thermodynamic energy and hence has the unusual features that it can favour the early stages of coat assembly necessary for vesiculation (budding), while suppressing the activity of mechanosensitive membrane channels and transporters. Our results also suggest an approach to obtain physical parameters that are otherwise difficult to measure.

cond-mat.soft↗

arXiv2014

Rings in Random Environments: Sensing Disorder Through Topology

In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby generating a disordered environment. Changes in the microscopic structure of the gel are captured by measuring the electrophoretic mobility of ring polymers moving through the medium, while their linear counterparts provide a control system as we show they are insensitive to these changes. We show that ring polymers provide a novel non-invasive way of exploiting topology to sense microscopic disorder. Finally, we compare the results from the simulations with an analytical model for the non-equilibrium differential mobility, and find a striking agreement between simulation and theory

cond-mat.soft↗

arXiv2014

Topology Regulation during Replication of the Kinetoplast DNA

We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a marginally linked network of rings with only one connected component. During cell division each mini-circle is removed from the network, duplicated and then re-attached, along with its progeny. We study this process under the hypothesis that there is a coupling between the topological state of the mini-circles and the expression of genetic information encoded on them, leading to the production of Topoisomerase. This model describes a self-regulating system capable of full replication that reproduces several previous experimental findings. We find that the fixed point of the system depends on a primary free parameter of the model: the ratio between the rate of removal of mini-circles from the network (R) and their (re)attachment rate (A). The final topological state is found to be that of a marginally linked network structure in which the fraction of mini-circles linked to the largest connected component approaches unity as R/A decreases. Finally we discuss how this may suggest an evolutionary trade-off between the speed of replication and the accuracy with which a fully topologically linked state is produced.

cond-mat.soft↗

arXiv2014

Differentiating swarming models by mimicking a frustrated anti-Ferromagnet

Self propelled particle (SPP) models are often compared with animal swarms. However, the collective behaviour observed in experiments usually leaves considerable unconstrained freedom in the structure of these models. To tackle this degeneracy, and better distinguish between candidate models, we study swarms of SPPs circulating in channels (like spins) where we permit information to pass through windows between neighbouring channels. Co-alignment between particles then couples the channels (antiferromagnetically) so that they tend to counter-rotate. We study channels arranged to mimic a geometrically frustrated antiferromagnet and show how the effects of this frustration allow us to better distinguish between SPP models. Similar experiments could therefore improve our understanding of collective motion in animals. Finally we discuss how the spin analogy can be exploited to construct universal logic gates and therefore swarming systems that can function as Turing machines.

q-bio.PE↗

arXiv2014

The Role of Projection in the Control of Bird Flocks

Swarming is a conspicuous behavioural trait observed in bird flocks, fish shoals, insect swarms and mammal herds. It is thought to improve collective awareness and offer protection from predators. Many current models involve the hypothesis that information coordinating motion is exchanged between neighbors. We argue that such local interactions alone are insufficient to explain the organization of large flocks of birds and that the mechanism for the exchange of long-ranged information necessary to control their density remains unknown. We show that large flocks self-organize to the maximum density at which a typical individual is still just able to see out of the flock in many directions. Such flocks are marginally opaque - an external observer can also just still see a substantial fraction of sky through the flock. Although seemingly intuitive we show that this need not be the case; flocks could easily be highly diffuse or entirely opaque. The emergence of marginal opacity strongly constrains how individuals interact with each other within large swarms. It also provides a mechanism for global interactions: An individual can respond to the projection of the flock that it sees. This provides for faster information transfer and hence rapid flock dynamics, another advantage over local models. From a behavioural perspective it optimizes the information available to each bird while maintaining the protection of a dense, coherent flock.

q-bio.QM↗

arXiv2014

Density regulation in strictly metric-free swarms

There is now experimental evidence that nearest-neighbour interactions in flocks of birds are metric free, i.e. they have no characteristic interaction length scale. However, models that involve interactions between neighbours that are assigned topologically are naturally invariant under spatial expansion, supporting a continuous reduction in density towards zero, unless additional cohesive interactions are introduced or the density is artificially controlled, e.g. via a finite system size. We propose a solution that involves a metric-free motional bias on those individuals that are topologically identified to be on an edge of the swarm. This model has only two primary control parameters, one controlling the relative strength of stochastic noise to the degree of co-alignment and another controlling the degree of the motional bias for those on the edge, relative to the tendency to co-align. We find a novel power-law scaling of the real-space density with the number of individuals N as well as a familiar order-to-disorder transition.

q-bio.QM↗

arXiv2014

Dynamics of Self-Threading Ring Polymers in a Gel

We study of the dynamics of ring polymers confined to diffuse in a background gel at low concentrations. We do this in order to probe the inter-play between topology and dynamics in ring polymers. We develop an algorithm that takes into account the possibility that the rings hinder their own motion by passing through themselves, i.e. "self-threading". Our results suggest that the number of self-threadings scales extensively with the length of the rings and that this is substantially independent of the details of the model. The slowing down of the rings' dynamics is found to be related to the fraction of segments that can contribute to the motion. Our results give a novel perspective on the motion of ring polymers in gel, for which a complete theory is still lacking, and may help us to understand the irreversible trapping of ring polymers in gel electrophoresis experiments.

cond-mat.soft↗

arXiv2014

Finite size effects in non-equilibrium membrane phase separation

The formation of dynamical clusters of proteins is ubiquitous in cellular membranes and is in part regulated by the recycling of membrane components. Mean-field models of out-of-equilibrium cluster formation with recycling predict a broad cluster size distribution for infinite systems and must be corrected for finite-size effects for small systems such as cellular organelles. We show, using stochastic simulations and analytic modelling, that tuning the system size is an efficient way to control the size of lateral membrane heterogeneities. We apply these findings to a chain of enzymatic reaction sensitive to membrane protein clustering. The reaction efficiency is found to be a non-monotonic function of the system size, and can be optimal for sizes comparable to those of cellular organelles.

cond-mat.soft↗

arXiv2010

Microphase separation in nonequilibrium biomembranes

Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be driven by fluctuating forces. We show that the membrane steady state is not only controlled by the strength of the forces and how they couple to the membrane, but also by their dynamics: In a simple class of models this is captured by a single a correlation time. We conclude that the coupling of membrane composition to normal mechanical forces, such as might be exerted by polymerizing cytoskeleton filaments, could play an important role in controlling the steady state of a cell membrane that exhibits transient microphase separation on lengthscales in the 10-100 nm regime.

q-bio.SC↗

arXiv2010

Force transduction by the microtubule-bound Dam1 ring

The coupling between the depolymerization of microtubules (MTs) and the motion of the Dam1 ring complex is now thought to play an important role in the generation of forces during mitosis. Our current understanding of this motion is based on a number of detailed computational models. Although these models realize possible mechanisms for force transduction, they can be extended by variation of any of a large number of poorly measured parameters and there is no clear strategy for determining how they might be distinguished experimentally. Here we seek to identify and analyze two distinct mechanisms present in the computational models. In the first the splayed protofilaments at the end of the depolymerizing MT physically prevent the Dam1 ring from falling off the end, in the other an attractive binding secures the ring to the microtubule. Based on this analysis, we discuss how to distinguish between competing models that seek to explain how the Dam1 ring stays on the MT. We propose novel experimental approaches that could resolve these models for the first time, either by changing the diffusion constant of the Dam1 ring (e.g., by tethering a long polymer to it) or by using a time varying load.

q-bio.SC↗

arXiv2005

Budded membrane microdomains as regulators for cellular tension

We propose a mechanism for mechanical regulation at the membrane of living cells, based on the exchange of membrane area between the cell membrane and a membrane reservoir. The reservoir is composed of invaginated membrane microdomains which are liable to flatten upon increase of membrane strain, effectively controlling membrane tension. We show that the domain shape transition is first order, allowing for coexistence between flat and invaginated domains. During coexistence, the membrane tension is controlled by the domains elasticity and by the kinetics of the shape transition. We show that the tension of the plasma membrane of living cells is inherently transient and dynamical, and that valuable insights into the organization of the cell membrane can be obtained by studying the variation of the cell membrane tension upon mechanical perturbation.

q-bio.SC↗

arXiv2005

Sequence Dependence of Electronic Transport in DNA

We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe small, but significant differences between lambda-DNA, centromeric DNA, promoter sequences as well as random-ATGC DNA.

cond-mat.soft↗

arXiv2005

Electronic Transport in DNA

We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which electrons travel. Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA and lambda-DNA. We find that random and lambda-DNA have localisation lengths allowing for electron motion among a few dozen base pairs only. A novel enhancement of localisation lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence dependent charge transfer in DNA.

q-bio.GN↗

arXiv2005

Non-equilibrium raft-like membrane domains under continuous recycling

We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domains have a broad power-law distribution with an average radius that scales with the 1/4 power of the domain lifetime when the line tension at the domain edges is large. For biologically reasonable recycling and diffusion rates the average domain radius is in the tens of nm range, consistent with observations. This represents one possible link between signaling (involving rafts) and traffic (recycling) in cells. Finally, we present evidence that suggests that the average raft size may be the same for all scale-free recycling schemes.

cond-mat.soft↗