One of the fundamental problems in biology would be the method by which organisms can regulate a distribution in response to global information. For example, a cluster of organisms can regulate the proportion of individuals that perform various roles or modes as if each individual is aware of the overall situation without a leader. Slow or rapid self-organized pattern formations with time...
Circadian clocks control 24-hour rhythms in the human body, including glucose and insulin dynamics. Glucose tolerance changes depending on the time of day and misalignment between environmental stimuli such as light and food and internal circadian clocks, e.g., as observed in shiftwork, is associated with metabolic disturbances and diabetes. The mechanisms of these are poorly understood. A...
The walls of our blood vessels are under a constant mechanical load, introduced by the blood pulsating through our vessels. Recent years have seen a substantial increase in the understanding of the interplay between the dynamics of blood flow (haemodynamics) and vessel (vascular) morphology. Alterations in the homeostatic distribution of mechanical forces exerted by blood on the vessel wall is...
Macroecological patterns, such as the species area relationship (SAR), relative species abundance (RSA), and endemic area relationship (EAR) provide us useful information of ecosystem structures that can be applied to, for example, ecosystem conservations. To understand these patterns across spatial scales is one of the central challenges recent years. To tackle the challenge, we develop a...
The Human African Trypanosomiasis (HAT) parasite, which causes African Sleeping Sickness, is transmitted by the tsetse fly as a vector. It has several possible hosts, including humans and domestic animals. Because domestic animals can be a host for the parasite, it has long been assumed that keeping domestic animals near human populations increases the spread of the disease. However, several...
With a five dimensional system of ordinary differential equations based on the SIR model, we consider the dynamics of epidemics in a community which consists of residents and visitors/tourists over a short period of time. The total population size of the community is taken to be constant, ignoring its change due to any birth and death in the period under consideration. Also, the resident and...
We constructed an anatomically-accurate three-dimensional model of salivary fluid secretion from a cluster of parotid gland acinar cells.
Parotid acinar cells are responsible for the secretion of saliva. Olfactory and gustatory stimuli provoke the release of agonists that bind to the basal membranes of the acinar cells. This triggers a cascade of events that results in the production of IP3,...
Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colours. Leaf colour-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. We performed whole-genome resequencing and transcriptomic analysis of regulatory...
Direct-Acting antivirals (DAAs) target intracellular viral replication and have realized high effectiveness for hepatitis C virus (HCV) patients. Now, many kinds of DAA drugs have discovered and the HCV treatment is improving day by day. A popular strategy of HCV treatment is combination of double or triple DAA drugs with different action mechanisms. Mathematical model is used to analyze the...
Life-histories in organisms faced with various selection pressures such as heterogeneity, intra- and inter-specific competitions, and variable environment. Ecologists have thought that evolution maximizes different objects from each pressure. For example, in the absence of the competitions, conventional Darwinism asserts that the adaptive life history maximizes the population growth. On the...
Chemical reactions are traditionally modelled using deterministic methods such as ordinary differential equations. In biology, we also consider the effect of diffusion upon a reactive system. For small biological systems, it is necessary to use stochastic models. In this talk, we choose to use an agent-based model commonly known as Smoluchowski kinetics.
In the Smoluchowski model, two...
Reproducibility of results is a key part of the scientific method; in general, scientific communication aims to describe a result in enough detail that readers and reviewers are able to contextualise the result within their own knowledge, and to reproduce it themselves given the appropriate skills and resources. In the field of computational biology, readers and reviewers face special...
We present an optimal impulse control problem related to anti-cancer therapeutics. Our model takes into account both the instantaneous toxicities of the treatments and the adverse effects of targeted and non-targeted antineoplastic therapies.
Rabies is a fatal zoonotic disease and remains to be a priority health concern in the Philippines. Dogs remain to be the principal carrier of rabies and despite the fatality of rabies, it is a vaccine-preventable disease. Currently, the Philippine health officials have been conducting mass dog vaccination campaigns with the goal of having a rabies-free Philippines by the year 2020. However,...
Recent studies have shown that pathogens can alter the behaviour of hosts or vectors to improve their transmission power. This happens not only in animal pathosystems but in plant pathosystems. While animal pathogens can alter the behaviour of both hosts and vectors in ways that increase frequency of host-host or host-vector encounters, in plant pathosystems the host does not have mobility, so...
p53, a cellular damage response regulator, is mutated in 50% of all cancers. We have constructed a mathematical model showing how different p53 dynamics after UV radiation and $\gamma$-irradiation exposure allows cells to respond properly to both slowly and quickly detected damage. We extend this model with an apoptosis module accounting for the transcription-dependent and -independent...
In Noor Asih et al. (2016) already given mathematical modelling as the dynamic of HPV infection on cervical cancer. Also given five scenarios for the existence of equilibrium points and their local stability. From the analysis of the system it is found the basic reproduction number is depends on the infection rate, the number of new virion that produce by infected cells, the death rate of...
Avian malaria is a mosquito-borne parasitic disease of birds caused by protists of the genera Plasmodium, most notably Plasmodium relictum. This disease has been identified as a primary cause of the drastic decline and extinctions of endemic birds on Pacific Islands. In this work, we formulate an epizootiological model of the transmission dynamics of avian malaria between a generic bird...
Bond graphs are an energy-based framework for modelling physical systems while adhering to thermodynamic and physical constraints, and they have recently been extended and applied to biochemical and electrophysiological systems. Here we describe a bond graph model of the cardiac action potential and use it to explore the issue of drift in mathematical models of electrophysiology, which is a...
Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. But how robust are these methods to future information? If additional species are added to the original set of trees, will the expanded consensus tree simply be an expansion of the original consensus tree? In this talk I will formalise and answer this...
Interspecies comparisons of physiological energetics are possible only through the prism of a formal metabolic approach such as the Dynamic Energy Budget (DEB) theory which uniformly describes how individuals of different species acquire and utilise energy. We used the DEB theory to infer the energy budgets of three commercial tuna species (skipjack, Pacific bluefin, and Atlantic bluefin)...
IUCN criteria are the most authoritative and objective to assess the conservation status of animal species. Although IUCN criteria are purely descriptive in nature, they can be interpreted as e.g. the relative size of the annual population growth factor (λ, the dominant eigenvalue of a projection matrix). This enables quantitative assessment based on demographic data (survival and...
The construction of effective and informative landscapes for stochastic dynamical systems has proven a long-standing and complex problem, including for biological systems. Such landscapes may refer to a true energy function for cases such as protein folding or to a phenomenological metaphor in the case of Waddington’s epigenetic landscape. In many situations, constructing a landscape comes...
Maintaining physiological levels of oxygen (O$_2$) and carbon dioxide (CO$_2$) in the blood is crucial for survival and is achieved by sophisticated neural control mechanisms affecting both the breathing pattern and heart rate. Neural activity, originated in the brainstem, drives the respiratory muscles, providing air flow into and out of the lungs where gas exchange takes place and also...
Hematopoietic system is maintained by hematopoietic stem cells (HSCs) with dual abilities of long-term self-renewal and differentiation to all types of blood cells. Recently, using a single-cell transplantation system and mice expressing a fluorescent protein, myeloid-restricted progenitors with long-term repopulating activity (MyRPs) were found. Moreover, by using paired daughter cell assay,...
Cellular adaptation to varying signal strengths has been observed in the innate immune cells responses to external and internal challenges. Monocytes persistently challenged with low levels of external stimulants, can be skewed into a low-grade ‘primed’ state, while persistent challenges with high levels of external stimulants will skew them into to a ‘tolerant’ state. Based on experimental...
We propose a structured integro-difference equation model for an invasive marine species with a pelagic larval stage and examine the role of dispersal heterogeniety on the spreading speed. The spread of the green crab up the northwest coast of the Atlantic is used as a case study. We find that the relationship between spreading speed and demographic and dispersal parameters is similar to...
Motivated by in vitro time-lapse images of ovarian cancer spheroids inducing mesothelial cell clearance, the traditional agent–based model of cell migration, based on simple volume exclusion, was extended to include the possibility that a cell seeking to move into an occupied location may push the resident cell, and any cells neighbouring it, out of the way to occupy that location. In...
Obesity is the result of caloric imbalance and is mediated by genetic, behavioural, and environmental factors. Healthy lifestyle habits, including healthy eating and physical activity, can lower the risk of becoming obese and developing related diseases. The prevalence of obesity among Korean adolescents aged 13 to 18 years increased from 13.65% in 2007 to 19.3% in 2016 for boys.
We analyze...
Recent advances in understanding of complex interactions between the processes that maintain and control the physiological state of brain parenchyma open new possibilities and deliver new challenges for modelling studies on topic. Now it is clear that any significant deviation from normal conditions as well as natural alternations of activity of cortical neurons (say, during sleep-wake...
A deterministic model of biochemical reaction networks is not always appropriate. Gene expression, for example, often involves a small number of molecules which means that noise can significantly influence the dynamics. By discretising space into voxels and letting the molecule dynamics be governed by the reaction-diffusion master equation, it is possible to model the reaction and diffusion of...
The demographic hypothesis of cumulative cultural evolution claims that population size has been a crucial determinant of the rate of cumulative cultural evolution in humans rather than other factors such as environmental risk. The original version of this hypothesis does not distinguish the role of population size from that of social connectedness, i.e. the degree to which individuals in a...
The temporal and spectral characteristics of tonic-clonic seizures are investigated by using a neural field model of the corticothalamic system in the presence of a temporally varying connection strength between the cerebral cortex and thalamus. Increasing connection strength drives the system into 10 Hz seizure oscillations once a threshold is passed and a subcritical Hopf bifurcation occurs....
Projection matrix models are known to provide us with a plenty of population statistics, such as population growth rate, steady size-class distribution, and sensitivity and elasticity for population growth rate. Hundreds of academic papers using the model have been published these last forty years and a database on many of their matrices is now available on the internet (COMPADRE and COMADRE),...
Many large-scale high-throughput experiments use DNA barcodes—short DNA sequences prepended to DNA libraries—for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely-used error-correcting codes borrowed from computer...
Specific biomarkers can be identified in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) breast scans and quantified using pharmacokinetic models that return estimates of parameters related to tissue physiology including vessel perfusion and permeability ($K^{trans}$), the extravascular-extracellular volume fraction ($v_e$), the plasma volume fraction ($v_p$), and the efflux...
Cell proliferation is the most important cellular-level mechanism responsible for regulating cell population dynamics in living tissues. Modern experimental procedures show that the proliferation rates of individual cells can vary significantly within the same cell line. However, in the mathematical biology literature cell proliferation is typically modelled using a classical logistic equation...
In this research, we study feedback control problem in the context of deterministic epidemic models. Feedback control is obtained by solving Hamilton-Jacobi-Bellman(HJB) equation, which is employed to overcome limitations of previous work. There are three key factors in the implementation of this methodology, decoupling value function and control variables, truncation of unbounded domain, and...
Stochastic evolutionary game dynamics in finite populations has recently been examined not only for symmetric games [1] but also for bimatrix games [2]. While in these studies the fixation probabilities of pure strategies are investigated, this study examines the evolutionary dynamics of two-player 2 by 2 bimatrix games with mixed-strategies in finite populations under weak selection. The game...
Immunotherapy using checkpoint inhibitors has demonstrated clinical efficacy for cancers ranging from melanoma to non-small-cell lung cancer and other types. Despite some success, many patients do not respond to the therapy, and a subset of patients develops “hyper-progressive” disease. Biomarkers that predict response or toxicity to checkpoint inhibitors will help to select patients who are...
We study synaptically coupled neuronal networks to identify the role of coupling delays in network's synchronized behaviours. We consider a network of excitable, relaxation oscillator neurons where two distinct populations, one excitatory and one inhibitory, are coupled and interact with each other. The excitatory population is uncoupled, while the inhibitory population is tightly coupled. A...
Improving crop yield is essential to meet increasing global food demands. Crop yields depend on the coordinated acquisition of carbon and nitrogen by the leaves and roots respectively and the use of these nutrients within each part of the plant. Changes in environmental conditions cause fluctuations in carbon and nitrogen availability. This leads to crosstalk between the signalling pathways...
The Hybrid Agent–based Library (HAL) is a Java Library made of simple, efficient, generic components which can be used to model complex spatial systems. HAL's components can broadly be classified into: on and off lattice agent containers, finite difference diffusion fields, a GUI building system, and additional tools and utilities for computation and collecting data. These components were...
The aim of this research was to explore the potential of profile likelihoods for identifiability analysis in the context of real enzyme kinetics data, collected ourselves.
Parameter identifiability concerns the question of whether the type of experimental data we have collected properly determines the parameters of our mathematical models. Identifiability issues arise because not all biological...
In genetics, enhancer regions are short non-coding strands of DNA belonging to a class of elements known as cis-regulatory. These regions, typically in intergenic regions, encompass binding sites for proteins (transcription factors) that regulate gene expression. Changes to the DNA sequence in these enhancer regions are thought to provide a mechanism to explain changes of gene expression even...
We consider a setup in which $n$ particles are initially released into a domain and diffuse freely. Part of the boundary consists of absorbing "escape" regions, where the particles can escape the domain, and reflecting regions. The rest of boundary consists of "capture" regions (receptors), that can switch between being reflecting and absorbing. Specifically, after capturing a particle, the...
Information transfer is thought to play a key role in adaptive complex systems such as social insects, brain and human society, while epidemic spreading through interactions can impact on survival in the individuals and society. Social insects such as ants and bees are one of the most sophisticated complex systems exhibiting collective decision making, providing us the opportunity of studying...
Carnitine is a fundamental compound for humans. Mainly introduced via nutrition, but also synthetized in the body, this metabolite allows the transport of long-chain fatty acids in the mitochondria, where they can undergo β -oxidation. Lately, the attention on carnitine and acyl-carnitine, carnitine derivatives, has increased since it has been proposed that insulin resistance may be linked to...
Primates exhibit an array of mating behaviours and arrangements, from monogamy to promiscuity, or mate-guarding to multiple-mating. We have previously explored the role of adult sex ratio in determining the likelihood of males choosing either promiscuity or monogamy, but many questions remain open. In particular, do (and, if so, how do) longevity and life history contribute to the choice of...
The unmarried rate of Japanese people is rising year by year, and countermeasures are required. We modelled male and female marriage decision-making models based on male’s willingness to cooperate on housework and childcare. We assume that male marriage utility function decreases as male’s willingness to cooperate on housework and childcare increases, while female marriage utility function...
True slime mold Physarum polycepharum is a large uni-cellular amoeba-like organism and it can sense environmental information and change its behaviours. Large true slime mold extends its frontal parts for foraging. To study its exploration strategy, we observed how physarum spreads in a binary-tree-shaped maze. We found that slime mold changes its searching strategies when its total mass...
Asthma is a chronic lung disease of reversible airway constriction. Imaging experiments show that during an asthma attack, the asthmatic's lung exhibits what is known as clustered ventilation defects, which is the hallmark trait of asthma. This phenomenon is when there are some regions of the lung where the airways are closed, and some regions where they are open. These clusters vary from...
Alzheimer’s disease (AD) is a devastating illness affecting over 40 million people globally. The accumulation of AD associated Amyloid beta (Aβ) oligomers can trigger aberrant intracellular calcium signals by disrupting calcium regulatory mechanism within neurons. These disruptions can cause changes in homeostasis levels that can have detrimental effects on cell function and survival. Although...
Biofilms are sessile communities of bacteria housed in a self-produced adhesive matrix consisting of extracellular polymeric substances (EPS), including polysaccharides, proteins, lipids, and DNA. [1]. Biofilm provokes chronic bacterial infection, infection on medical devices, deterioration of water quality, and the contamination of food [2]. On the other hand, biofilm can be used for...
The occurrence of distant metastases greatly reduces or even removes the possibilities of curative treatment for cancer patients. The development of tools for predicting and diagnosing the onset of secondary tumours has long been a significant subject of cancer research effort. Moreover, it is widely known that while in some tissues cancer cells exhibit higher proliferation, in others they are...
Intracellular phase transitions are an emerging mechanism for cell organization. These membrane-less compartments are formed via liquid-liquid demixing and subsequent concentration of cellular components in a specific region. By undergoing these localized phase separations, cells are able to create dynamic compartments that help maintain the regulation of biomolecular interactions and...
Tissue engineering is a rapidly growing field, attracting a huge concentration of research effort. An important subfield of tissue engineering focuses on the use of bioreactors, devices that attempt to simulate a physiological environment in order to promote the growth of functional cell or tissue in vivo. In this talk we present a mathematical model to simulate both nutrient transport and...
Cancer is one of the leading causes of morbidity and mortality worldwide. Many of the disease related events, such as metastatic progression, treatment resistance, and overall survival, generate much uncertainty and are oftentimes viewed as random. Applying current modelling techniques and methodologies to existing data can produce a forecasting framework that can be leveraged to predict these...
The human species is unique in its tendency towards monogamy, a trait which can be traced back to hunter-gathering societies. Traditional explanations for this evolution have focused on the presence of paternal care and the needs of our offspring. However, recent research has challenged this claim, contending that the significant effects of mating competition on male choice result in...
Agricultural systems throughout the world are threatened by a variety of pest species, including insects, pathogens and weeds. Conventional control methods often have limited success, notably in the case of pesticide use due to the ubiquitous development of resistance. Novel control approaches are therefore needed to improve management of these pest populations. Gene drive strategies, based on...
The human brain consists of folds (gyri) and valleys (sulci) that vary dramatically in their size, extent, and shape across individuals. There is considerable debate among biologists as to how the folding patterns develop and if the folding patterns can be used to diagnose disease. In this presentation, I will discuss some of the mathematical and modelling approaches my research group is...
Empty homes, called Akiya in Japanese, due to an aging population and declining birthrate is very serious problem in the aging society of modern Japan. The current proportion of empty home in Japan is 13.5%, but it is expected to be increased up to 30.2% nationwide in 2033, implying that Akiya will have a serious impact on the economy as well as the national finance. Indeed, Detroit city in...
An endoplasmic reticulum (ER) is a tubular organelle observed in cells of eukaryote including the plants and animals. Interacting with flow of actin cytoskeleton, the net-like pattern organized by ER in plant cells is continuously moving.
For the understanding of this system, we constructed a mathematical model based on a partial differential equation (PDE). By combining two spatially...
Calcium is a universal messenger that participates in a great variety of physiological functions including muscle contraction, neuronal plasticity and immune responses. There is now compelling evidence that transient changes in the intracellular calcium concentration are key for achieving such versatility.
To date, most of these findings have been obtained from constant stimulation or step...
We constructed a dynamical model of a salivary gland acinar cell with the objective of investigating the role of two plasma membrane (PM) anion exchangers, the Ae2 (Slc4a2) and Ae4 (Slc4a9), in primary fluid secretion. Transepithelial chloride (Cl$^-$) movement drives water transport in salivary gland acinar cells. Basolateral PM mechanisms accumulate Cl$^-$ to levels well above its...
The vector-borne Dengue fever poses a major health issue in tropic environments, which includes areas such as far-north Queensland. Historically, attempts at curtailing the spread of dengue have focused on controlling the size and spread of mosquito populations that carry the virus. Several factors make this an astronomically difficult task to accomplish on any reasonable scale, however, and...
Tuberculosis (TB) is one of the top 10 causes of death worldwide, and the WHO’s EndTB strategy requires developing an effective vaccine. The H56 vaccine is a candidate currently in phase I/IIa trials as a boost to Bacillus Calmette-Guérin (BCG, the TB vaccine that is currently used in most countries world-wide). We build a multi-compartment, hybrid multi-scale model to 1) improve our...
The mammalian circadian rhythm is governed by the principal clock which is located in the suprachiasmatic nucleus (SCN). This clock is composed of tens of thousands of neurons and their connection to one another is essential to important roles of SCN: synchronization, entrainment to light, etc. Previous studies about the SCN network used the maximal information coefficient (MIC) statistic to...
A mathematical standard structure of a binary digit of memory in a cell is presented. This is based on a kind of frequency model with scale effect. This model has ability of "on-off" switching property, and moreover, this is affected by scale effect to make the memorable ability be reinforced. This property is derived from multiple covalent modification cites inducing important enzyme...
Physiological levels of oxygen and carbon dioxide in the blood are tightly regulated by varying the pattern of breathing, but this can be achieved with different combinations of amplitude and frequency. Why a specific combination of amplitude and frequency of breathing is observed remains a mystery. The aim of this study is to explore the hypothesis that the particular combination realised is...
Barreto et al. (2017) studied the rock-paper-scissors games (or cyclic competition games) by the dynamics of phenotypic and genotypic frequencies corresponding to three morphs of lizards. In their model they show that both dynamics have equal internal equilibrium but the genotypic model has wider parameter range for its stability compared to the phenotypic model.
Here, first of all, we...
The apical-basal cell polarity endows epithelial tissues with distinct biochemical and mechanical properties at the apical, basal, and lateral sides of tissues. Mounting evidence shows that remodelling of epithelial cell polarity, where polarity regulators redistribute their locations on the cell membrane, causes changes of cell shapes that drives tissue morphogenesis during embryonic...
The activated sludge process (ASP) is the most widely used process for the biological treatment of both domestic and industrial wastewaters. Wastewater treatment plants (WWTPs) based on the ASP are in widespread use in both developed and developing countries.
The ASP uses microorganisms which grow by consuming organic pollutants that are present in the wastewater. This produces new organisms...
Species eradications and reintroductions are drastic management actions that alter ecosystem structure with the end goal of conserving or restoring one or more species of interest. Because of the complexity of ecosystem food webs, these actions can have unintended consequences on other parts of the ecosystem. Even with the best available data, predicting future trajectories of the ecosystem...
The placement of stomata on the leaf surface is regulated by a number of things: coordinated asymmetric cellular division, genetic regulation, and distribution of extracellular signalling molecules.
It has been noted that the number of stomata per non-stomatal epidermal cell can vary between plants which have the same spatial distribution of stomata, which suggests that in some circumstances...
Error threshold being the forefront of the issue for computationally-intensive methodologies and statistical models based on Kingman’s coalescent, six main points arise: (i) discrepancy between the exact and linearized non-coalescence probability; (ii) validity of the linearized coalescence probability; (iii) conditional probabilities of single-pair and multi-coalescences given at least one...
Since many kinds of Direct Acting Antivirals (DAA) have become the main treatment instead of interferon-α (IFN-α) against hepatitis C virus (HCV), combinations of these DAA are now standard treatment strategies. These treatments are very effective, however, at the same time, this provokes the problems which drug combination is more or most effective for each patient. Therefore, we established...
The unprecedented accumulation of high-throughput single-cell RNAseq data provides an essential opportunity for researchers to study the dynamics of biological systems. At the same time, it raises new questions and grand challenges in view of the key characteristics of these data that include high-dimensionality and heterogeneity. In response, we develop a data-driven computational framework...
To gain deep insights into the interactions among major types of cells, such as healthy, tumour, and immune cells, in a tumour-bearing host, we propose a mathematical model consisting of four delay differential equations by considering the inherent delay in the tumour cells’ life cycle. When choosing model parameters, sensitivity analysis justified previous assumptions had been...
One of the challenging questions in Ecology is how spatial structure influences the formation of biodiversity patterns. Here, we explore networks that represent population connectivity including cases where dispersal is symmetric and asymmetric, looking for the relationship between population connectivity network structure and biodiversity patterns therein. In this metapopulation system, we...
There are large differences between men and women of child-bearing age in the expression level of 5 key enzymes in one-carbon metabolism almost certainly caused by the sex hormones. These male-female differences in one-carbon metabolism are greatly accentuated in during pregnancy. Thus, understanding the origin and consequences of sex differences in one-carbon metabolism is important for...
Many species of animals, plants, cyanobacteria, and fungi are reported to have circadian clocks, that is, gene regulatory and biochemical network in a cell exhibiting endogenous oscillatory dynamics with a period close to 24 hours. There is diversity in the members of the circadian system, but all clocks share similar features such as temperature-compensated circadian period. Therefore,...
Human papillomavirus, or HPV, is a sexually transmissible virus infection, which is necessary risk factor for developing cervical cancer, most common type of cancer in working age women in Moldova. We observe both behavioural change (increase in sexual partner acquisition rates) and demographical change (population ageing and massive emigration, but still very young), which both corresponding...
Gene expression and genetic regulatory networks (GRNs) have become important areas of study because they play an important role in solving issues related to human health such as cancer diseases. Cancers can be hard to recognise and the best way to improve their defected is to understand the underlying mechanisms of genetic regulatory dynamics. This means introducing and improving...
The spatio-temporal intra- and interspecific competition of two diffusing similar populations is considered. The growth of both populations is either logistic or shows an Allee effect. Conditions of spatial segregation without mixing are investigated. Furthermore, the impact of density-dependent environmental noise on the occurring stationary fronts is studied. A special focus is set on the...
Fluorescent cell cycle labelling in cell biology experiments provides real time information about the location of individual cells, as well as the phase of the cell cycle of individual cells. We develop a stochastic, lattice-based random walk model of a two-dimensional scratch assay where the total population is composed of three distinct subpopulations which we visualise as red, yellow and...
Using a simple lattice model describing infectious tree disease dynamics on a homogeneous landscape we can observe an Epiphytotic phase transition from local confinement of the pathogen to a global epidemic through the forest. The phase transition can be understood in terms of the forest tree density and the pathogen virulence. One interesting application of the model involves capturing the...
Pattern formation by Delta-Notch interaction has been well studied experimentally and theoretically. The Delta-Notch system is observed in various pattern formation process such as somitogenesis, neuroendocrine cell differentiation in lung, T cell differentiation and blood vessel development. Recent studies have shown endothelial cell proliferation and movement happen during this process....
Seasonality and contact patterns due to environmental fluctuations and social behaviour affect the dynamics of disease outbreaks. Recent studies applied to deterministic epidemic models with periodic environments have shown that the average basic reproduction number is not sufficient to predict an outbreak. We extend these studies to stochastic epidemic models with periodic environments to...
Tethered enzymatic reactions are a key component in signalling transduction pathways. It is found that many surface receptors rely on the tethering of cytoplasmic kinase to initiate and integrate signalling. A key factor to such reaction is the molecular reach; however, the role of it is incompletely understood. To date, a large number of compartment-based ODE and stochastic models have been...
Negative feedback and buffering, the use of reservoirs of molecules to maintain concentrations of key molecular species, are the primary known mechanisms for robust homeostatic regulation. However, the fundamental principles behind their combined effect have not been elucidated. Here, I will present our recent research on the interplay between buffering and negative feedback in the context of...
In this study, the maximal extent of future NPP uncertainties are explored by employing the conditional nonlinear optimal perturbation related to parameters (CNOP-P) approach and the Lund-Potsdam-Jena (LPJ) model based on future climate change assessments, which are provided by 10 general circulation models (GCMs) of the Coupled Model Intercomparison Project 5 (CMIP5) under the Representative...
Asymmetric cell division is one of the widespread mechanisms for generating cell diversity, for which a mother cell creates a polarity in both membrane and cytosol. In both experiment and theoretical approaches, PAR polarity of C. elegans embryo has been extensively well-studied and it was found that Anterior-Posterior (AP) polarity of cell membrane proteins plays a crucial role in...
Tuberculosis remains a widespread and deadly disease, infecting approximately two billion people worldwide. Gaining a better understanding of the immune response to Mycobacterium tuberculosis is crucial, and the increased prevalence of multi-drug resistant strains, the current complexity and length of treatment, and the inherent difficulties of experimental work each highlight the need for...
In silico prediction of the relationships between the protein structure and its physiological activity is an important research topic for drug design. Broad picture of my research is to construct a topological model to clarify the antibody-antigen recognition system, since immunotherapy is applied to wide range of severe diseases such as cancer [1].
To achieve the goal, we focus on a...
Infection with the bacteria Mycobacterium tuberculosis (Mtb) causes a dynamic immune response that spans multiple organs across multiple time scales. The infection may start with just a few Mtb infecting a few macrophages within the lungs, but sites of infection quickly experience local immune responses, and soon after draining lymph nodes become involved to mount an even greater defense....
Recently, it has been shown that intracellular transport of assembled intermediate filament proteins is one major determinant of their organization in cells. Based on experimental data, mathematical models of the spatio-temporal distribution of intermediate filaments in cells are developed to investigate the contributions of different types of transport such as retrograde flow of actin and...
It is an interesting topic to predict how dynamics change in disease progression. Our goal is to predict dynamics of the vital cells in the human immune system using the hierarchical HIV models. We assumed that the parameters are random variables with intra-level noise and inter-level noise. Individual-level parameters of HIV model are estimated by generalized least squares method based on the...
Tick-borne pathogens are transmitted when ticks take blood meals from vertebrate hosts. Ticks need to take blood meals to progress through immature life-stages and reach adulthood. For the most important zoonotic pathogens, including Borrelia burgdorferi (the causative agent of Lyme disease), two immature life-stages of the tick vector, termed larvae and nymphs, maintain the pathogens. Key...
Predicting the carbon balance of terrestrial plants, and its vulnerability to environmental change, is a fundamental problem common to agriculture, ecology and ecosystem science. Plant productivity is fuelled by the carbon taken up during photosynthesis, but other limitations to growth may restrict the ability of plants to utilise this carbon in production, a phenomenon known as sink...
The Proliferation-Invasion (PI) mathematical model of patient specific glioblastoma (GBM) growth utilizes T1 and T2-weighted/fluid attenuated inversion recovery (FLAIR) magnetic resonance (MR) images to estimate net proliferation (ρ) and net invasion (D) rates. We have previously developed methods to parametrize this model from these routine MRIs such that higher D/ρ tumours are considered...
The neutral theory in community ecology attempts to explain its species-abundance composition by the balance between local extinction of species due to demographic stochasticity and immigrational supply of new species from a meta-community. The original neutral theory is described by two parameters; the one (“theta”) that represents biodiversity in the meta-community, and the other (m) is the...
Increments in around-the-clock service in modern society yield increments in shift work. As a result, nowadays more than 20% of population in the world work in shifts. As shift work schedules inevitably have increased, the risks of shift work are also presenting including the increment of risk for disease, such as cardiovascular-disease and cancer. There have been several approaches to analyze...
