Dan Nicolau

Queensland University of Technology | QUT · School of Mathematics, Science and Technology Education

Cancer is a leading cause of death in the world. However, cancer may not be life threatening if we can identify it in its early stages. By studying the complexity of the tumour microenvironment (TME), we can identify how tumour cells become invasive under different circumstances. In this study, we observe tumour cell behaviour under cellular stress...

Filamentous fungi have developed highly efficient strategies for space searching, which are essential to their survival, both as individuals and as species. Using purposefully designed microfluidics networks with maze geometries is was shown that the individual hyphae of several species of fungi use a ’master program’ with two ’slave subroutines’,...

Cancer occurs when abnormal cells grow in an uncontrolled way. Interaction between tumour cells and the tumour microenvironment (TME) is affects tumour cell progression and metastasis. It represents protocognitive abilities of tumour cells. Understanding this process is a key to blocking or slowing the spread of cancer cells and to developing bette...

Quantitative modelling is increasingly important in cancer research, helping to integrate myriad diverse experimental data into coherent pictures of the disease and able to discriminate between competing hypotheses or suggest specific experimental lines of enquiry and new approaches to therapy. Here, we review a diverse set of mathematical models o...

Actin and tubulin are key structural elements of Eukaryotes’ cytoskeleton. The networks of actin filaments and tubulin microtubules are substrates for cells’ motility and mechanics, intra-cellular transport and cell-level learning. Ideas of information processing taking place on a cytoskeleton network, especially in neurons, have been proposed by S...

We propose a road-map to experimental implementation of cytoskeleton-based computing devices. An overall concept is described in the following. Collision-based cytoskeleton computers implement logical gates via interactions between travelling localisation (voltage solitons on AF/MT chains and AF/MT polymerisation wave fronts). Cytoskeleton networks...

This review presents a brief overview of breast cancer, focussing on its heterogeneity and the role of mathematical modelling and simulation in teasing apart the underlying biophysical processes. Following a brief overview of the main known pathophysiological features of ductal carcinoma, attention is paid to differential equation-based models (bot...

Experimental studies have shown that fungi use a natural program for searching the space available in micro-confined networks, e.g., mazes. This natural program, which comprises two subroutines, i.e., collision-induced branching and directional memory, has been shown to be efficient compared with the suppressing one, or both subroutines. The presen...

The reliable response to weak biological signals requires that they be amplified with fidelity. In E. coli, the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P, but how this works is not well understood. A recently proposed allosteric model based on c...

One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics...

Complex Cooperativity Cooperativity in multisubunit protein complexes is classically understood in terms of either a concerted model, in which all subunits switch conformation simultaneously, or a sequential model, in which a subunit switches conformation whenever a ligand binds. More recently, a “conformational spread” model has suggested that a c...

E. coli does chemotaxis by performing a biased random walk composed of alternating periods of swimming (runs) and reorientations (tumbles). Tumbles are typically modelled as complete directional randomisations but it is known that in wild type E. coli, successive run directions are actually weakly correlated, with a mean directional difference of ∼...

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We present a general-purpose optimization algorithm inspired by "run-and-tumble", the biased random walk chemotactic swimming strategy used by the bacterium Escherichia coli to locate regions of high nutrient concentration The method uses particles (corresponding to bacteria) that swim through the variable space (corresponding to the attractant con...

One of the most important aspects of Computational Cell Biology is the understanding of the complicated dynamical processes that take place on plasma membranes. These processes are often so complicated that purely temporal models cannot always adequately capture the dynamics. On the other hand, spatial models can have large computational overheads....

A stochastic random walk model of protein molecule diffusion on a cell membrane was used to investigate the fundamental causes of anomalous diffusion in two-dimensional biological media. Three different interactions were considered: collisions with fixed obstacles, picket fence posts, and capture by, or exclusion from, lipid rafts. If motion is imp...

The dynamic lateral segregation of signaling proteins into microdomains is proposed to facilitate signal transduction, but the constraints on microdomain size, mobility, and diffusion that might realize this function are undefined. Here we interrogate a stochastic spatial model of the plasma membrane to determine how microdomains affect protein dyn...

In earlier work, we proposed "computing with bio-agents", a new model of computation, of the distributed parallel type, based on the notion that motions of biological objects such as bacteria or protein molecular motors in confined spaces can be regarded as computations. Beginning with the observation that the geometric nature of the physical struc...

Many crucial cellular processes take place at the plasma membrane. The latter is a complex, two-dimensional medium exhibiting significant lateral structure. As a result, a number of non-classical processes, including anomalous diffusion, compartimentalisation and fractal kinetics take place at the membrane surface. The evaluation of various hypothe...

The identification and differentiation of colours is a relatively problematic task for colour-impaired and partially vision-impaired persons and an impossible one for completely blind. In various contexts, this leads to a loss of independence or an increased risk of harm. The identification of colour using optoelectronic devices, on the other hand,...

The non-invasive or minimally invasive real-time spectral analysis of tissue and biological fluids in vivo would be of great assistance for diagnosis and monitoring of a wide range of diseases. We propose here a novel microdevice capable of determining the reflectance spectrum of a sample using a set of micrometer-sized light emitting diodes and a...

Predicting protein adsorption from solution to a surface is a perennial problem in biomedicine and related fields. Despite constant attention in the literature, it is not currently possible to predict quantitatively the amount of adsorbed protein given environment, protein and surface parameters. In previous work, we presented the Biomolecular Adso...

Investigation of protein-polymeric surface interaction requires reliable practical techniques for evaluation of the efficiency of protein immobilization. In this study the efficiency of protein immobilization was evaluated using three different techniques: (1) protein-binding assay with fluorescent detection and (2) quantification, and (3) atomic f...

Hybrid devices based on wholly bio-organic systems being interfaced with wholly inorganic systems are now being conceived of and constructed. A hypothetical device is likely to have some dynamic attributes and its dimensions will optimally be comparable with those of the current state of the art in microfabrication. While there are many established...

The adsorption of biomolecules on surfaces is dependent on biomolecule molecular descriptors, surface descriptors and environment descriptors. Of these descriptors, the biomolecular-related are the most complex and arguably the most important, as being related to both adsorption and possible denaturation on surfaces. The criticality of biomolecule...

The absorption of biomolecules on surfaces is a perennial and general problem relevant to fields as different as biomaterials, biosensors, microarrays for proteomics and microfluidics. The 'responsiveness-to-surfaces' character of the proteins augments the difficulty of the general problem of biomolecule adsorption on surfaces. This complexity of p...