The transportation of mass is an inherently `non-equilibrium' process, relying on a current of mass between two or more locations. Life exists by necessity out of equilibrium and non-equilibrium transport processes are seen at all levels in living organisms, from DNA replication up to animal foraging. As such, biological processes are ideal candidates for modelling using non-equilibrium stochastic processes, but, unlike with equilibrium processes, there is as of yet no general framework for their analysis. In the absence of such a framework we must study specific models to learn more about the behaviours and bulk properties of systems that are out of equilibrium. In this work I present the analysis of three distinct models of non-equilibrium mass transport processes. Each transport process is conceptually distinct but all share close connections with each other through a set of fundamental nonequilibrium models, which are outlined in Chapter 2. In this thesis I endeavour to understand at a more fundamental level the role of stochasticity and fluctuations in non-equilibrium transport processes. In Chapter 3 I present a model of a diffusive search process with stochastic resetting of the searcher's position, and discuss the effects of an imperfection in the interaction between the searcher and its target. Diffusive search process are particularly relevant to the behaviour of searching proteins on strands of DNA, as well as more diverse applications such as animal foraging and computational search algorithms. The focus of this study was to calculate analytically the effects of the imperfection on the survival probability and the mean time to absorption at the target of the diffusive searcher. I find that the survival probability of the searcher decreases exponentially with time, with a decay constant which increases as the imperfection in the interaction decreases. This study also revealed the importance of the ratio of two length scales to the search process: the characteristic displacement of the searcher due to diffusion between reset events, and an effective attenuation depth related to the imperfection of the target. The second model, presented in Chapter 4, is a spatially discrete mass transport model of the same type as the well-known Zero-Range Process (ZRP). This model predicts a phase transition into a state where there is a macroscopically occupied `condensate' site. This condensate is static in the system, maintained by the balance of current of mass into and out of it. However in many physical contexts, such as traffic jams, gravitational clustering and droplet formation, the condensate is seen to be mobile rather than static. In this study I present a zero-range model which exhibits a moving condensate phase and analyse it's mechanism of formation. I find that, for certain parameter values in the mass `hopping' rate effectively all of the mass forms a single site condensate which propagates through the system followed closely by a short tail of small masses. This short tail is found to be crucial for maintaining the condensate, preventing it from falling apart. Finally, in Chapter 5, I present a model of an interface growing against an opposing, diffusive membrane. In lamellipodia in cells, the ratcheting effect of a growing interface of actin filaments against a membrane, which undergoes some thermal motion, allows the cell to extrude protrusions and move along a surface. The interface grows by way of polymerisation of actin monomers onto actin filaments which make up the structure that supports the interface. I model the growth of this interface by the stochastic polymerisation of monomers using a Kardar-Parisi-Zhang (KPZ) class interface against an obstructing wall that also performs a random walk. I find three phases in the dynamics of the membrane and interface as the bias in the membrane diffusion is varied from towards the interface to away from the interface. In the smooth phase, the interface is tightly bound to the wall and pushes it along at a velocity dependent on the membrane bias. In the rough phase the interface reaches its maximal growth velocity and pushes the membrane at this speed, independently of the membrane bias. The interface is rough, bound to the membrane at a subextensive number of contact points. Finally, in the unbound phase the membrane travels fast enough away from the interface for the two to become uncoupled, and the interface grows as a free KPZ interface. In all of these models stochasticity and fluctuations in the properties of the systems studied play important roles in the behaviours observed. We see modified search times, strong condensation and a dramatic change in interfacial properties, all of which are the consequence of just small modifications to the processes involved.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:712367 |
| Date | January 2016 |
| Creators | Whitehouse, Justin |
| Contributors | Evans, Martin ; Blythe, Richard |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/20998 |
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