arXiv subjects

Richard G. Morris

Publications and source records attributed to Richard G. Morris.

30 records · Page 2Linked to original sources

arXiv2019

Noise-Induced Schooling of Fish

We report on the dynamics of collective alignment in groups of the cichlid fish, Etroplus suratensis. Focusing on small-to-intermediate sized groups ($10<N<100$), we demonstrate that schooling (highly polarised and coherent motion) is noise-induced, arising from the intrinsic stochasticity associated with finite numbers of interacting fish. The fewer the fish, the greater the (multiplicative) noise and therefore the likelihood of alignment. Such empirical evidence is rare, and tightly constrains the possible underlying interactions between fish: computer simulations indicate that E. suratensis align with each other one at a time, which is at odds with the canonical mechanism of collective alignment, local direction-averaging. More broadly, our results confirm that, rather than simply obscuring otherwise deterministic dynamics, noise is fundamental to the characterisation of emergent collective behaviours, suggesting a need to re-appraise aspects of both collective motion and behavioural inference.

cond-mat.stat-mech↗

arXiv2019

Deriving mesoscopic models of collective behaviour for finite populations

Animal groups exhibit emergent properties that are a consequence of local interactions. Linking individual-level behaviour to coarse-grained descriptions of animal groups has been a question of fundamental interest. Here, we present two complementary approaches to deriving coarse-grained descriptions of collective behaviour at so-called mesoscopic scales, which account for the stochasticity arising from the finite sizes of animal groups. We construct stochastic differential equations (SDEs) for a coarse-grained variable that describes the order/consensus within a group. The first method of construction is based on van Kampen's system-size expansion of transition rates. The second method employs Gillespie's chemical Langevin equations. We apply these two methods to two microscopic models from the literature, in which organisms stochastically interact and choose between two directions/choices of foraging. These `binary-choice' models differ only in the types of interactions between individuals, with one assuming simple pair-wise interactions, and the other incorporating higher-order effects. In both cases, the derived mesoscopic SDEs have multiplicative, or state-dependent, noise. However, the different models demonstrate the contrasting effects of noise: increasing order in the pair-wise interaction model, whilst reducing order in the higher-order interaction model. Although both methods yield identical SDEs for such binary-choice, or one-dimensional, systems, the relative tractability of the chemical Langevin approach is beneficial in generalizations to higher-dimensions. In summary, this book chapter provides a pedagogical review of two complementary methods to construct mesoscopic descriptions from microscopic rules and demonstrates how resultant multiplicative noise can have counter-intuitive effects on shaping collective behaviour.

q-bio.PE↗

arXiv2017

Covariant Active Hydrodynamics of Shape-Changing Epithelial Monolayers

During the early-stages of embryo development, morphogenesis--- the emergence of shape and form in living organisms--- is almost exclusively associated with monolayers of tightly bound epithelial cells. To understand how such tissues change their shape, we construct a fully covariant active-hydrodynamic theory. At the cellular scale, stresses arise from apical contractility, mechanical response and the constraint of constant cell volume. Tissue-scale deformations emerge due to the balance between such cell-autonomous stresses and the displacement and shear of a low Reynolds number embedding fluid. Tissues with arbitrary curvature or shape can be described, providing a general framework for epithelial monolayer morphology. Analysis of the stability of flat monolayers reveals two generic shape instabilities: passive constrained-buckling, and actively-driven tissue deformation. The active instability can be further categorised into two types, corresponding to cell shape changes that are either "squamous to columnar" or "regular-prism to truncated-pyramid". The deformations resulting from the latter qualitatively reproduce in vivo observations of the onset of both mesoderm and posterior midgut invaginations, which take place during gastrulation in the fruit fly Drosophila melanogaster.

cond-mat.soft↗

arXiv2017

Signatures of Mechanosensitive Gating

The question of how mechanically-gated membrane channels open and close is notoriously difficult to address, especially if the protein structure is not available. This perspective highlights the relevance of micropipette-aspirated single-particle tracking--- used to obtain a channel's diffusion coefficient, $D$, as a function of applied membrane tension, $σ$--- as an indirect assay for determining functional behaviour in mechanosensitive channels. Whilst ensuring that the protein remains integral to the membrane, such methods can be used to identify not only the gating mechanism of a protein, but also associated physical moduli, such as torsional- and dilational-rigidity, which correspond to the protein's effective shape change. As an example, three distinct $D$ versus $σ$ "signatures" are calculated, corresponding to gating by dilation, gating by tilt, and a combination of both dilation and tilt. Both advantages and disadvantages of the approach are discussed.

physics.bio-ph↗

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↗

arXiv2014

A Hierarchical Multi-Output Nearest Neighbor Model for Multi-Output Dependence Learning

Multi-Output Dependence (MOD) learning is a generalization of standard classification problems that allows for multiple outputs that are dependent on each other. A primary issue that arises in the context of MOD learning is that for any given input pattern there can be multiple correct output patterns. This changes the learning task from function approximation to relation approximation. Previous algorithms do not consider this problem, and thus cannot be readily applied to MOD problems. To perform MOD learning, we introduce the Hierarchical Multi-Output Nearest Neighbor model (HMONN) that employs a basic learning model for each output and a modified nearest neighbor approach to refine the initial results.

stat.ML↗

arXiv2014

Growth-induced breaking and unbreaking of ergodicity in fully-connected spin systems

Two canonical models of statistical mechanics, the fully-connected voter and Glauber-Ising models, are modified to incorporate growth via the addition or replication of spins. The resulting behaviour is examined in a regime where the timescale of expansion cannot be separated from that of the internal dynamics. Depending on the model specification, growth radically alters the long-time dynamical behaviour by breaking or unbreaking ergodicity.

cond-mat.stat-mech↗

arXiv2014

Relaxation and curvature-induced molecular flows within multicomponent membranes

The quantitative understanding of membranes is still rooted in work performed in the 1970s by Helfrich and others, concerning amphiphilic bilayers. However, most biological membranes contain a wide variety of nonamphiphilic molecules too. Drawing analogy with the physics of nematic/non-nematic mixtures, we present a dynamical (out of equilibrium) description of such multicomponent membranes. The approach combines nematohydrodynamics in the linear regime and a proper use of (differential) geometry. The main result is to demonstrate that one can obtain equations describing a cross-diffusion effect (similar to the Soret and Dufour effects) between curvature and the (in-membrane) flow of amphiphilic molecules relative to nonamphiphilic ones. Surprisingly, the shape of a membrane relaxes according to a simple heat equation in the mean curvature, a process that is accompanied by a simultaneous boost to the diffusion of amphiphiles away from regions of high curvature. The model also predicts the inverse process, by which the forced bending of a membrane induces a flow of amphiphilic molecules towards areas of high curvature. In principle, numerical values for the relevant diffusion coefficients should be verifiable by experiment.

cond-mat.soft↗

arXiv2013

Interdependent networks: the fragility of control

Recent work in the area of interdependent networks has focused on interactions between two systems of the same type. However, an important and ubiquitous class of systems are those involving monitoring and control, an example of interdependence between processes that are very different. In this Article, we introduce a framework for modelling distributed supervisory control in the guise of an electrical network supervised by a distributed system of control devices. The system is characterised by degrees of freedom salient to real-world systems--- namely, the number of control devices, their inherent reliability, and the topology of the control network. Surprisingly, the behavior of the system depends crucially on the reliability of control devices. When devices are completely reliable, cascade sizes are percolation controlled; the number of devices being the relevant parameter. For unreliable devices, the topology of the control network is important and can dramatically reduce the resilience of the system.

cond-mat.dis-nn↗

arXiv2012

Transport on coupled spatial networks

Transport processes on spatial networks are representative of a broad class of real world systems which, rather than being independent, are typically interdependent. We propose a measure of utility to capture key features that arise when such systems are coupled together. The coupling is defined in a way that is not solely topological, relying on both the distribution of sources and sinks, and the method of route assignment. Using a toy model, we explore relevant cases by simulation. For certain parameter values, a picture emerges of two regimes. The first occurs when the flows go from many sources to a small number of sinks. In this case, network utility is largest when the coupling is at its maximum and the average shortest path is minimized. The second regime arises when many sources correspond to many sinks. Here, the optimal coupling no longer corresponds to the minimum average shortest path, as the congestion of traffic must also be taken into account. More generally, results indicate that coupled spatial systems can give rise to behavior that relies subtly on the interplay between the coupling and randomness in the source-sink distribution.

cond-mat.dis-nn↗

arXiv2011

Stability of growing vesicles

We investigate the stability of growing vesicles using the formalism of nonequilibrium thermodynamics. The vesicles are growing due to the accretion of lipids to the bilayer which forms the vesicle membrane. The thermodynamic description is based on the hydrodynamics of a water{/}lipid mixture together with a model of the vesicle as a discontinuous system in the sense of linear nonequilibrium thermodynamics. This formulation allows the forces and fluxes relevant to the dynamic stability of the vesicle to be identified. The method is used to analyze the stability of a spherical vesicle against arbitrary axisymmetric perturbations. It is found that there are generically two critical radii at which changes of stability occur. In the case where the perturbation takes the form of a single zonal harmonic, only one of these radii is physical and is given by the ratio $2 L_p / L_γ$, where $L_p$ is the hydraulic conductivity and $L_γ$ is the Onsager coefficient related to changes in membrane area due to lipid accretion. The stability of such perturbations is related to the value of $l$ corresponding to the particular zonal harmonic: those with lower $l$ are more unstable than those with higher $l$. Possible extensions of the current work and the need for experimental input are discussed.

cond-mat.soft↗

arXiv2010

Dynamical description of vesicle growth and shape change

We systematize and extend the description of vesicle growth and shape change using linear nonequilibrium thermodynamics. By restricting the study to shape changes from spheres to axisymmetric ellipsoids, we are able to give a consistent formulation which includes the lateral tension of the vesicle membrane. This allows us to generalize and correct a previous calculation. Our present calculations suggest that, for small growing vesicles, a prolate ellipsoidal shape should be favored over oblate ellipsoids, whereas for large growing vesicles oblates should be favored over prolates. The validity of this prediction is examined in the light of the various assumptions made in its derivation.

cond-mat.soft↗