A spatial multiscale mathematical model of Plasmodium vivax transmission.

The epidemiological behavior of Plasmodium vivax malaria occurs across spatial scales including within-host, population, and metapopulation levels. On the within-host scale, P. vivax sporozoites inoculated in a host may form latent hypnozoites, the activation of which drives secondary infections and accounts for a large proportion of P.

Temporal response patterns of Layer 4 rat barrel cortex neurons across various naturalistic whisker motions.

A central topic in neuroscience is the neural coding problem which aims to decipher how the brain signals sensory information through neural activity. Despite significant advancements in this area, the characterisation of information encoding through the precise timing of spikes in the somatosensory cortex is limited. Here, we utilised a comprehensive dataset from previous studies to identify and characterise temporal response patterns of Layer 4 neurons of the rat barrel cortex to five distinct stimuli with varying complexities: Basic, Contact, Whisking, Rough, and Smooth.

Enzyme kinetics simulation at the scale of individual particles.

Enzyme-catalyzed reactions involve two distinct timescales: a short timescale on which enzymes bind to substrate molecules to produce bound complexes and a comparatively long timescale on which the molecules of the complex are transformed into products. The uptake of the substrate in these reactions is the rate at which the product is made on the long timescale. Models often only consider the uptake to reduce the number of chemical species that need to be modeled and to avoid explicitly treating multiple timescales.

Two wrongs do not make a right: the assumption that an inhibitor acts as an inverse activator.

Models of biochemical networks are often large intractable sets of differential equations. To make sense of the complexity, relationships between genes/proteins are presented as connected graphs, the edges of which are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions in many cases by the identifying recurring of topological motifs, for example positive and negative feedback loops.

Antibody Dynamics for Plasmodium vivax Malaria: A Mathematical Model.

Malaria is a mosquito-borne disease that, despite intensive control and mitigation initiatives, continues to pose an enormous public health burden. Plasmodium vivax is one of the principal causes of malaria in humans. Antibodies, which play a fundamental role in the host response to P.

Delay-driven oscillations via Axin2 feedback in the Wnt/β-catenin signalling pathway.

The Wnt signalling pathway plays an important role in development, disease, and normal tissue function. Mathematical models for Wnt signalling have predominantly focused on quantitatively predicting changes in steady-state β-catenin concentrations (the main downstream protein regulated by canonical Wnt signalling). One of the genes targeted for expression by Wnt/β-catenin signalling is the negative Wnt regulator Axin2.

Parameter estimation for a point-source diffusion-decay morphogen model.

In this paper we present a novel method for finding unknown parameters for an unknown morphogen. We postulate the existence of an unknown morphogen in a given three-dimensional domain due to the spontaneous arrangement of a downstream species on the domain boundary for which data is known. Assuming a modified Helmholtz model for the morphogen and that it is produced from a single source in the domain, our method accurately estimates the source location and other model parameters.

An Activation-Clearance Model for Plasmodium vivax Malaria.

Malaria is an infectious disease with an immense global health burden. Plasmodium vivax is the most geographically widespread species of malaria. Relapsing infections, caused by the activation of liver-stage parasites known as hypnozoites, are a critical feature of the epidemiology of Plasmodium vivax.

Multi-resolution dimer models in heat baths with short-range and long-range interactions.

This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic springs (long-range). Two types of multi-resolution methodologies are considered in detail: (a) describing parts of the solvent far away from the dimer by a coarser approach; (b) describing each monomer of the dimer by using a model with different level of resolution.

A mathematical model of the use of supplemental oxygen to combat surgical site infection.

Infections are a common complication of any surgery, often requiring a recovery period in hospital. Supplemental oxygen therapy administered during and immediately after surgery is thought to enhance the immune response to bacterial contamination. However, aerobic bacteria thrive in oxygen-rich environments, and so it is unclear whether oxygen has a net positive effect on recovery.

A mathematical model for the induction of the mammalian ureteric bud.

Congenital abnormalities of the kidney and urinary tract collectively form the most common type of prenatally diagnosed malformations. Whilst many of the crucial genes that direct the kidney developmental program are known, the mechanisms by which kidney organogenesis is achieved is still largely unclear. In this paper, we propose a mathematical model for the localisation of the ureteric bud, the precursor to the ureter and collecting duct system of the kidney.

The pseudo-compartment method for coupling partial differential equation and compartment-based models of diffusion.

Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs), which assumes there are sufficient densities of particles that a continuum approximation is valid. However, owing to recent advances in computational power, the simulation and therefore postulation, of computationally intensive individual-based models has become a popular way to investigate the effects of noise in reaction-diffusion systems in which regions of low copy numbers exist.

Adaptive two-regime method: application to front propagation.

The Adaptive Two-Regime Method (ATRM) is developed for hybrid (multiscale) stochastic simulation of reaction-diffusion problems. It efficiently couples detailed Brownian dynamics simulations with coarser lattice-based models. The ATRM is a generalization of the previously developed Two-Regime Method [Flegg et al.

A deconvolution method for deriving the transit time spectrum for ultrasound propagation through cancellous bone replica models.

The acceptance of broadband ultrasound attenuation for the assessment of osteoporosis suffers from a limited understanding of ultrasound wave propagation through cancellous bone. It has recently been proposed that the ultrasound wave propagation can be described by a concept of parallel sonic rays. This concept approximates the detected transmission signal to be the superposition of all sonic rays that travel directly from transmitting to receiving transducer.

Multiscale stochastic reaction-diffusion modeling: application to actin dynamics in filopodia.

Two multiscale (hybrid) stochastic reaction-diffusion models of actin dynamics in a filopodium are investigated. Both hybrid algorithms combine compartment-based and molecular-based stochastic reaction-diffusion models. The first hybrid model is based on the models previously developed in the literature.

Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release.

The intracellular release of calcium from the endoplasmic reticulum is controlled by ion channels. The resulting calcium signals exhibit a rich spatio-temporal signature, which originates at least partly from microscopic fluctuations. While stochasticity in the gating transition of ion channels has been incorporated into many models, the distribution of calcium is usually described by deterministic reaction-diffusion equations.

Wound healing angiogenesis: the clinical implications of a simple mathematical model.

Nonhealing wounds are a major burden for health care systems worldwide. In addition, a patient who suffers from this type of wound usually has a reduced quality of life. While the wound healing process is undoubtedly complex, in this paper we develop a deterministic mathematical model, formulated as a system of partial differential equations, that focusses on an important aspect of successful healing: oxygen supply to the wound bed by a combination of diffusion from the surrounding unwounded tissue and delivery from newly formed blood vessels.

The two-regime method for optimizing stochastic reaction-diffusion simulations.

Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches to less detailed compartment-based simulations. Compartment-based approaches yield quick and accurate mesoscopic results, but lack the level of detail that is characteristic of the computationally intensive molecular-based models.

Monitoring and analysis of combustion aerosol emissions from fast moving diesel trains.

In this paper we report the results of the detailed monitoring and analysis of combustion emissions from fast moving diesel trains. A new highly efficient monitoring methodology is proposed based on the measurements of the total number concentration (TNC) of combustion aerosols at a fixed point (on a bridge overpassing the railway) inside the violently mixing zone created by a fast moving train. Applicability conditions for the proposed methodology are presented, discussed and linked to the formation of the stable and uniform mixing zone.

Exact solution for stochastic degradation and fragmentation processes in arbitrary chain and ring aggregates with multiple bonds.

This paper presents a statistical theory of stochastic evaporation and degradation processes in complex polymerlike ring and chain aggregates with multiple degrading bonds between the primary particles (monomers). The exact kinetic solution fully describing fragmentation processes is obtained for such aggregates with arbitrary number of primary particles (monomers) and bonds between them. The effects of additional interaction of multiple bonds with each other is shown to have a drastic impact on the predicted kinetic processes and time-dependent particle size distributions during aggregate degradation.