From microscopic to macroscopic descriptions of cell\ud migration on growing domains

Cell migration and growth are essential components of the development of multicellular organisms. The role of various cues in directing cell migration is widespread, in particular, the role of signals in the environment in the control of cell motility and directional guidance. In many cases, especially in developmental biology, growth of the domain also plays a large role in the distribution of cells and, in some cases, cell or signal distribution may actually drive domain growth. There is a ubiquitous use of partial differential equations (PDEs) for modelling the time evolution of cellular density and environmental cues. In the last twenty years, a lot of attention has been devoted to connecting macroscopic PDEs with more detailed microscopic models of cellular motility, including models of directional sensing and signal transduction pathways. However, domain growth is largely omitted in the literature. In this paper, individual-based models describing cell movement and domain growth are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge by making the lattice size variable over time. A reaction-diffusion master equation formalism is generalised to the case of growing lattices and used in the derivation of the macroscopic PDEs

Refining self-propelled particle models for collective behaviour

Swarming, schooling, flocking and herding are all names given to the wide variety of collective behaviours exhibited by groups of animals, bacteria and even individual cells. More generally, the term swarming describes the behaviour of an aggregate of agents (not necessarily biological) of similar size and shape which exhibit some emergent property such as directed migration or group cohesion. In this paper we review various individual-based models of collective behaviour and discuss their merits and drawbacks. We further analyse some one-dimensional models in the context of locust swarming. In specific models, in both one and two dimensions, we demonstrate how varying the parameters relating to how much attention individuals pay to their neighbours can dramatically change the behaviour of the group. We also introduce leader individuals to these models with the ability to guide the swarm to a greater or lesser degree as we vary the parameters of the model. We consider evolutionary scenarios for models with leaders in which individuals are allowed to evolve the degree of influence neighbouring individuals have on their subsequent motion

Going from microscopic to macroscopic on nonuniform growing domains

Throughout development, chemical cues are employed to guide the functional specification of underlying tissues while the spatiotemporal distributions of such chemicals can be influenced by the growth of the tissue itself. These chemicals, termed morphogens, are often modeled using partial differential equations (PDEs). The connection between discrete stochastic and deterministic continuum models of particle migration on growing domains was elucidated by Baker, Yates, and Erban [ Bull. Math. Biol. 72 719 (2010)] in which the migration of individual particles was modeled as an on-lattice position-jump process. We build on this work by incorporating a more physically reasonable description of domain growth. Instead of allowing underlying lattice elements to instantaneously double in size and divide, we allow incremental element growth and splitting upon reaching a predefined threshold size. Such a description of domain growth necessitates a nonuniform partition of the domain. We first demonstrate that an individual-based stochastic model for particle diffusion on such a nonuniform domain partition is equivalent to a PDE model of the same phenomenon on a nongrowing domain, providing the transition rates (which we derive) are chosen correctly and we partition the domain in the correct manner. We extend this analysis to the case where the domain is allowed to change in size, altering the transition rates as necessary. Through application of the master equation formalism we derive a PDE for particle density on this growing domain and corroborate our findings with numerical simulations

Reconciling transport models across scales: the role of volume exclusion

Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the role of volume exclusion, which can significantly alter diffusive transport, particularly within biological systems where the diffusing particles might occupy a significant fraction of the available space. In this work we use a random walk approach to provide a means to reconcile models that incorporate crowding effects on different spatial scales. Our work demonstrates that coarse-grained models incorporating simplified descriptions of excluded volume can be used in many circumstances, but that care must be taken in pushing the coarse-graining process too far

Analysis of nuclear waste disposal in space, phase 3. Volume 1: Executive summary of technical report

The objectives, approach, assumptions, and limitations of a study of nuclear waste disposal in space are discussed with emphasis on the following: (1) payload characterization; (2) safety assessment; (3) health effects assessment; (4) long-term risk assessment; and (5) program planning support to NASA and DOE. Conclusions are presented for each task

Analysis of nuclear waste disposal in space, phase 3. Volume 2: Technical report

The options, reference definitions and/or requirements currently envisioned for the total nuclear waste disposal in space mission are summarized. The waste form evaluation and selection process is documented along with the physical characteristics of the iron nickel-base cermet matrix chosen for disposal of commercial and defense wastes. Safety aspects of radioisotope thermal generators, the general purpose heat source, and the Lewis Research Center concept for space disposal are assessed as well as the on-pad catastrophic accident environments for the uprated space shuttle and the heavy lift launch vehicle. The radionuclides that contribute most to long-term risk of terrestrial disposal were determined and the effects of resuspension of fallout particles from an accidental release of waste material were studied. Health effects are considered. Payload breakup and rescue technology are discussed as well as expected requirements for licensing, supporting research and technology, and safety testing

Isotropic model for cluster growth on a regular lattice

There exists a plethora of mathematical models for cluster growth and/or aggregation on regular lattices. Almost all suffer from inherent anisotropy caused by the regular lattice upon which they are grown. We analyze the little-known model for stochastic cluster growth on a regular lattice first introduced by Ferreira Jr. and Alves [J. Stat. Mech. Theo. & Exp. (2006) P11007], which produces circular clusters with no discernible anisotropy. We demonstrate that even in the noise-reduced limit the clusters remain circular. We adapt the model by introducing a specific rearrangement algorithm so that, rather than adding elements to the cluster from the outside (corresponding to apical growth), our model uses mitosis-like cell splitting events to increase the cluster size. We analyze the surface scaling properties of our model and compare it to the behavior of more traditional models. In “1+1” dimensions we discover and explore a new, nonmonotonic surface thickness scaling relationship which differs significantly from the Family-Vicsek scaling relationship. This suggests that, for models whose clusters do not grow through particle additions which are solely dependent on surface considerations, the traditional classification into “universality classes” may not be appropriate

The importance of the Voronoi domain partition for position-jump reaction-diffusion processes on non-uniform rectilinear lattices

Position-jump processes are used for the mathematical modeling of spatially extended chemical and biological systems with increasing frequency. A large subset of the literature concerning such processes is concerned with modeling the effect of stochasticity on reaction-diffusion systems. Traditionally, computational domains have been divided into regular voxels. Molecules are assumed well mixed within each of these voxels and are allowed to react with other molecules within the same voxel or to jump to neighboring voxels with predefined transition rates. For a variety of reasons implementing position-jump processes on irregular grids is becoming increasingly important. However, it is not immediately clear what form an appropriate irregular partition of the domain should take if it is to allow the derivation of mean molecular concentrations that agree with a given partial differential equation for molecular concentrations. It has been demonstrated, in one dimension, that the Voronoi domain partition is the appropriate method with which to divide the computational domain. In this Brief Report, we investigate theoretically the propriety of the Voronoi domain partition as an appropriate method to partition domains for position-jump models in higher dimensions. We also provide simulations of diffusion processes in two dimensions in order to corroborate our results

Contextualizing and Expanding Conversational Queries without Supervision

Most conversational passage retrieval systems try to resolve conversational dependencies by using an intermediate query resolution step. To do so, they synthesize conversational data or assume the availability of large-scale question rewriting datasets. To relax those conditions, we propose a zero-shot unified resolution–retrieval approach, that (i) contextualizes and (ii) expands query embeddings using the conversation history and without fine-tuning on conversational data. Contextualization biases the last user question embeddings towards the conversation. Query expansion is used in two ways: (i) abstractive expansion generates embeddings based on the current question and previous history, whereas (ii) extractive expansion tries to identify history term embeddings based on attention weights from the retriever. Our experiments demonstrate the effectiveness of both contextualization and unified expansion in improving conversational retrieval. Contextualization does so mostly by resolving anaphoras to the conversation and bringing their embeddings closer to the important resolution terms that were omitted. By adding embeddings to the query, expansion targets phenomena of ellipsis more explicitly, with our analysis verifying its effectiveness on identifying and adding important resolutions to the query. By combining contextualization and expansion, we find that our zero-shot unified resolution–retrieval methods are competitive and can even outperform supervised methods