Richard E. Spinney
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View article: Stochastic Multistability of Clonallike States in the Eigen Model: a Fidelity Catastrophe
Stochastic Multistability of Clonallike States in the Eigen Model: a Fidelity Catastrophe Open
The Eigen model is a prototypical toy model of evolution that is synonymous with the so-called error catastrophe: when mutation rates are sufficiently high, the genetic variant with the largest replication rate does not occupy the largest …
View article: Non-Stationary Critical Phenomena: Expanding The Critical Point
Non-Stationary Critical Phenomena: Expanding The Critical Point Open
A prototypical model of symmetry-broken active matter -- biased quorum-sensing active particles (bQSAPs) -- is used to extend notions of dynamic critical phenomena to the paradigmatic setting of driven transport, where characteristic behav…
View article: A Dean–Kawasaki equation for reaction diffusion systems driven by Poisson noise
A Dean–Kawasaki equation for reaction diffusion systems driven by Poisson noise Open
We derive a stochastic partial differential equation that describes the fluctuating behaviour of reaction-diffusion systems of N particles, undergoing Markovian, unary reactions. This generalises the work of Dean (1996 J. Phys. A: Math. an…
View article: A Dean-Kawasaki equation for reaction diffusion systems driven by Poisson noise
A Dean-Kawasaki equation for reaction diffusion systems driven by Poisson noise Open
We derive a stochastic partial differential equation that describes the fluctuating behaviour of reaction-diffusion systems of N particles, undergoing Markovian, unary reactions. This generalises the work of Dean [J. Phys. A: Math. and Gen…
View article: Geometrical patterning of receptor sites controls kinetics via many-body effects in bivalent systems
Geometrical patterning of receptor sites controls kinetics via many-body effects in bivalent systems Open
We report on the geometrical patterning of receptor sites in bi- and multi-valent systems as a modality for controlling kinetic behaviors, in both synthetic and biological contexts, that is independent of the underlying chemistry. Explorin…
View article: The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure
The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure Open
The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood.…
View article: Bivalent Kinetics: Insights from Many Body Physics
Bivalent Kinetics: Insights from Many Body Physics Open
Bivalency confers several concentration-dependent phenomena, including avidity, competitive exchange and multi-site competitive exchange. Since these concepts are crucial for a wide variety of topics in cell and molecular biology, their ex…
View article: Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor
Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor Open
Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular…
View article: Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure
Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure Open
The kinetics of DNA hybridisation are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridise at different rates are not well understood.…
View article: Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data
Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data Open
Transfer entropy (TE) is a widely used measure of directed information flows in a number of domains including neuroscience. Many real-world time series for which we are interested in information flows come in the form of (near) instantaneo…
View article: Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data
Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data Open
Transfer entropy (TE) is a widely used measure of directed information flows in a number of domains including neuroscience. Many real-world time series in which we are interested in information flows come in the form of (near) instantaneou…
View article: Phase Transitions in Spatial Connectivity during Influenza Pandemics
Phase Transitions in Spatial Connectivity during Influenza Pandemics Open
We investigated phase transitions in spatial connectivity during influenza pandemics, relating epidemic thresholds to the formation of clusters defined in terms of average infection. We employed a large-scale agent-based model of influenza…
View article: Irreversibility and emergent structure in active matter
Irreversibility and emergent structure in active matter Open
Active matter is rapidly becoming a key paradigm of out-of-equilibrium soft matter exhibiting complex collective phenomena, yet the thermodynamics of such systems remain poorly understood. In this article we study the dynamical irreversibi…
View article: Entropy production during collective motion of active Brownian particles undergoing phase separation and alignment
Entropy production during collective motion of active Brownian particles undergoing phase separation and alignment Open
We study the entropy production rate in a system of active Brownian particles interacting via volume exclusion and alignment, described by under-damped dynamics. Using numerical simulations, we build the phase diagram of the system and ide…
View article: A thermodynamically consistent model of finite-state machines
A thermodynamically consistent model of finite-state machines Open
Finite-state machines (FSMs) are a theoretically and practically important model of computation. We propose a general, thermodynamically consistent model of FSMs and characterize the resource requirements of these machines. We model FSMs a…
View article: Entropy balance and information processing in bipartite and nonbipartite composite systems
Entropy balance and information processing in bipartite and nonbipartite composite systems Open
Information dynamics is an emerging description of information processing in\ncomplex systems which describes systems in terms of intrinsic computation,\nidentifying computational primitives of information storage and transfer. In\nthis pa…
View article: Information ratchets exploiting spatially structured information reservoirs
Information ratchets exploiting spatially structured information reservoirs Open
Fully mechanized Maxwell's demons, also called information ratchets, are an important conceptual link between computation, information theory, and statistical physics. They exploit low-entropy information reservoirs to extract work from a …
View article: Characterizing information-theoretic storage and transfer in continuous time processes
Characterizing information-theoretic storage and transfer in continuous time processes Open
The characterization of information processing is an important task in complex systems science. Information dynamics is a quantitative methodology for modeling the intrinsic information processing conducted by a process represented as a ti…
View article: A thermodynamically consistent model of finite state machines
A thermodynamically consistent model of finite state machines Open
Finite state machines (FSMs) are a theoretically and practically important model of computation. We propose a general, thermodynamically consistent model of FSMs and characterise the resource requirements of these machines. We model FSMs a…
View article: Associations between the Objectively Measured Office Environment and Workplace Step Count and Sitting Time: Cross-Sectional Analyses from the Active Buildings Study
Associations between the Objectively Measured Office Environment and Workplace Step Count and Sitting Time: Cross-Sectional Analyses from the Active Buildings Study Open
Office-based workers spend a large proportion of the day sitting and tend to have low overall activity levels. Despite some evidence that features of the external physical environment are associated with physical activity, little is known …
View article: Thermodynamics and computation during collective motion near criticality
Thermodynamics and computation during collective motion near criticality Open
We study self-organization of collective motion as a thermodynamic phenomenon in the context of the first law of thermodynamics. It is expected that the coherent ordered motion typically self-organises in the presence of changes in the (ge…
View article: Thermodynamics and the dynamics of information in distributed computation
Thermodynamics and the dynamics of information in distributed computation Open
Information dynamics is an emerging description of information processing in complex systems. In this paper we make a formal analogy between information dynamics and stochastic thermodynamics. As stochastic dynamics increasingly concerns i…
View article: Transfer entropy in continuous time, with applications to jump and neural spiking processes
Transfer entropy in continuous time, with applications to jump and neural spiking processes Open
Transfer entropy has been used to quantify the directed flow of information between source and target variables in many complex systems. While transfer entropy was originally formulated in discrete time, in this paper we provide a framewor…
View article: Indoor Tracking to Understand Physical Activity and Sedentary Behaviour: Exploratory Study in UK Office Buildings
Indoor Tracking to Understand Physical Activity and Sedentary Behaviour: Exploratory Study in UK Office Buildings Open
Little is known of the patterns of physical activity, standing and sitting by office workers. However, insight into these behaviours is of growing interest, notably in regard to public health priorities to reduce non-communicable disease r…