arXiv subjects

James Sharpe

Publications and source records attributed to James Sharpe.

6 recordsLinked to original sources

arXiv2023

The Core & Periphery Hypothesis: A Conceptual Basis for Generality in Cell and Developmental Biology

The discovery of general principles underlying the complexity and diversity of cellular and developmental systems is a central and long-standing aim of biology. Whilst new technologies collect data at an ever-accelerating rate, there is growing concern that conceptual progress is not keeping pace. We contend that this is due to a paucity of appropriate conceptual frameworks to serve as a basis for general theories of mesoscale biological phenomena. In exploring this issue, we have developed a foundation for one such framework, termed the Core and Periphery (C&P) hypothesis, which reveals hidden generality across the diverse and complex behaviors exhibited by cells and tissues. Here, we present the C&P concept, provide examples of its applicability across multiple scales, argue its consistency with evolution, and discuss key implications and open questions. We propose that the C&P hypothesis could unlock new avenues of conceptual progress in cell and developmental biology.

q-bio.CB↗

arXiv2023

The Probability Conflation: A Reply

We respond to Tetlock et al. (2022) showing 1) how expert judgment fails to reflect tail risk, 2) the lack of compatibility between forecasting tournaments and tail risk assessment methods (such as extreme value theory). More importantly, we communicate a new result showing a greater gap between the properties of tail expectation and those of the corresponding probability.

q-fin.RM↗

arXiv2021

Arrested coalescence of multicellular aggregates

Multicellular aggregates are known to exhibit liquid-like properties. The fusion process of two cell aggregates is commonly studied as the coalescence of two viscous drops. However, tissues are complex materials and can exhibit viscoelastic behaviour. It is known that elastic effects can prevent the complete fusion of two drops, a phenomenon known as arrested coalescence. Here we report the presence of this phenomenon in stem cell aggregates and provide a theoretical framework which agrees with the experiments. In addition, agent-based simulations show that cell protrusion activity controls a solid-to-fluid phase transition, revealing that arrested coalescence can be found in the vicinity of an unjamming transition. By analysing the dynamics of the fusion process and combining it with nanoindentation measurements, we obtain the effective viscosity, shear modulus and surface tension of the aggregates. More generally, our work provides a simple, fast and inexpensive method to characterize the mechanical properties of viscoelastic materials.

cond-mat.soft↗

arXiv2019

Calibration of the Pareto and related distributions -a reference-intrinsic approach

We study two Bayesian (Reference Intrinsic and Jeffreys prior) and two frequentist (MLE and PWM) approaches to calibrating the Pareto and related distributions. Three of these approaches are compared in a simulation study and all four to investigate how much equity risk capital banks subject to Basel II banking regulations must hold. The Reference Intrinsic approach, which is invariant under one-to-one transformations of the data and parameter, performs better when fitting a generalised Pareto distribution to data simulated from a Pareto distribution and is competitive in the case study on equity capital requirements

stat.ME↗

arXiv2017

Key features of Turing systems are determined purely by network topology

Turing's theory of pattern formation is a universal model for self-organization, applicable to many systems in physics, chemistry and biology. Essential properties of a Turing system, such as the conditions for the existence of patterns and the mechanisms of pattern selection are well understood in small networks. However, a general set of rules governing how network topology determines fundamental system properties and constraints has not be found. Here we provide a first general theory of Turing network topology, which proves why three key features of a Turing system are directly determined by the topology: the type of restrictions that apply to the diffusion rates, the robustness of the system, and the phase relations of the molecular species.

nlin.AO↗

arXiv2016

Kilombo: a Kilobot simulator to enable effective research in swarm robotics

The Kilobot is a widely used platform for investigation of swarm robotics. Physical Kilobots are slow moving and require frequent recalibration and charging, which significantly slows down the development cycle. Simulators can speed up the process of testing, exploring and hypothesis generation, but usually require time consuming and error-prone translation of code between simulator and robot. Moreover, code of different nature often obfuscates direct comparison, as well as determination of the cause of deviation, between simulator and actual robot swarm behaviour. To tackle these issues we have developed a C-based simulator that allows those working with Kilobots to use the same programme code in both the simulator and the physical robots. Use of our simulator, coined Kilombo, significantly simplifies and speeds up development, given that a simulation of 1000 robots can be run at a speed 100 times faster than real time on a desktop computer, making high-throughput pre-screening possible of potential algorithms that could lead to desired emergent behaviour. We argue that this strategy, here specifically developed for Kilobots, is of general importance for effective robot swarm research. The source code is freely available under the MIT license.

cs.RO↗