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"Numerical Analysis, Computer-Assisted."
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MATLAB : a practical introduction to programming and problem solving
MATLAB: A Practical Introduction to Programming and Problem Solving, Second Edition, is the only book that gives a full introduction to programming in MATLAB combined with an explanation of MATLAB's powerful functions, enabling engineers to fully exploit the software's power to solve engineering problems.
eBook
Three-dimensional manipulation of single cells using surface acoustic waves
The ability of surface acoustic waves to trap and manipulate micrometer-scale particles and biological cells has led to many applications involving “acoustic tweezers” in biology, chemistry, engineering, and medicine. Here, we present 3D acoustic tweezers, which use surface acoustic waves to create 3D trapping nodes for the capture and manipulation of microparticles and cells along three mutually orthogonal axes. In this method, we use standing-wave phase shifts to move particles or cells in-plane, whereas the amplitude of acoustic vibrations is used to control particle motion along an orthogonal plane. We demonstrate, through controlled experiments guided by simulations, how acoustic vibrations result in micromanipulations in a microfluidic chamber by invoking physical principles that underlie the formation and regulation of complex, volumetric trapping nodes of particles and biological cells. We further show how 3D acoustic tweezers can be used to pick up, translate, and print single cells and cell assemblies to create 2D and 3D structures in a precise, noninvasive, label-free, and contact-free manner.
Journal Article
Diffusion pseudotime robustly reconstructs lineage branching
Diffusion pseudotime (DPT) enables robust and scalable inference of cellular trajectories, branching events, metastable states and underlying gene dynamics from snapshot single-cell gene expression data.
The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.
Journal Article
Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data
Here I present the R package 'plantecophys', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO2 in the leaf. The 'plantecophys' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO2 response curves ('A-Ci curves'), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN.
Journal Article
Self-organization of active particles by quorum sensing rules
Many microorganisms regulate their behaviour according to the density of neighbours. Such quorum sensing is important for the communication and organisation within bacterial populations. In contrast to living systems, where quorum sensing is determined by biochemical processes, the behaviour of synthetic active particles can be controlled by external fields. Accordingly they allow to investigate how variations of a density-dependent particle response affect their self-organisation. Here we experimentally and numerically demonstrate this concept using a suspension of light-activated active particles whose motility is individually controlled by an external feedback-loop, realised by a particle detection algorithm and a scanning laser system. Depending on how the particles’ motility varies with the density of neighbours, the system self-organises into aggregates with different size, density and shape. Since the individual particles’ response to their environment is almost freely programmable, this allows for detailed insights on how communication between motile particles affects their collective properties.
Bacteria communicate and organize via quorum sensing which is determined by biochemical processes. Here the authors aim to reproduce this behaviour in a system of synthetic active particles whose motion is induced by an external beam which is in turn controlled by a feedback-loop which mimics quorum sensing.
Journal Article
Robustness and lethality in multilayer biological molecular networks
Robustness is a prominent feature of most biological systems. Most previous related studies have been focused on homogeneous molecular networks. Here we propose a comprehensive framework for understanding how the interactions between genes, proteins and metabolites contribute to the determinants of robustness in a heterogeneous biological network. We integrate heterogeneous sources of data to construct a multilayer interaction network composed of a gene regulatory layer, a protein–protein interaction layer, and a metabolic layer. We design a simulated perturbation process to characterize the contribution of each gene to the overall system’s robustness, and find that influential genes are enriched in essential and cancer genes. We show that the proposed mechanism predicts a higher vulnerability of the metabolic layer to perturbations applied to genes associated with metabolic diseases. Furthermore, we find that the real network is comparably or more robust than expected in multiple random realizations. Finally, we analytically derive the expected robustness of multilayer biological networks starting from the degree distributions within and between layers. These results provide insights into the non-trivial dynamics occurring in the cell after a genetic perturbation is applied, confirming the importance of including the coupling between different layers of interaction in models of complex biological systems.
Robustness is a prominent feature of most biological systems, but most of the current efforts have been focused on studying homogeneous molecular networks. Here the authors propose a comprehensive framework for understanding how the interactions between genes, proteins, and metabolites contribute to the determinants of robustness.
Journal Article
Cell separation using tilted-angle standing surface acoustic waves
Significance We have developed a unique approach for the separation of particles and biological cells through standing surface acoustic waves oriented at an optimum angle to the fluid flow direction in a microfluidic device. This experimental setup, optimized by systematic analyses, has been used to demonstrate effective separation based on size, compressibility, and mechanical properties of particles and cells. The potential of this method for biological–biomedical applications was demonstrated through the example of isolating MCF-7 breast cancer cells from white blood cells. The method offers a possible route for label-free particle or cell separation for many applications in research, disease diagnosis, and drug-efficacy assessment.
Journal Article
Generation of ECG signals from a reaction-diffusion model spatially discretized
We propose a model to generate electrocardiogram signals based on a discretized reaction-diffusion system to produce a set of three nonlinear oscillators that simulate the main pacemakers in the heart. The model reproduces electrocardiograms from healthy hearts and from patients suffering various well-known rhythm disorders. In particular, it is shown that under ventricular fibrillation, the electrocardiogram signal is chaotic and the transition from sinus rhythm to chaos is consistent with the Ruelle-Takens-Newhouse route to chaos, as experimental studies indicate. The proposed model constitutes a useful tool for research, medical education, and clinical testing purposes. An electronic device based on the model was built for these purposes
Journal Article
Epidemic spreading in modular time-varying networks
We investigate the effects of modular and temporal connectivity patterns on epidemic spreading. To this end, we introduce and analytically characterise a model of time-varying networks with tunable modularity. Within this framework, we study the epidemic size of Susceptible-Infected-Recovered, SIR, models and the epidemic threshold of Susceptible-Infected-Susceptible, SIS, models. Interestingly, we find that while the presence of tightly connected clusters inhibits SIR processes, it speeds up SIS phenomena. In this case, we observe that modular structures induce a reduction of the threshold with respect to time-varying networks without communities. We confirm the theoretical results by means of extensive numerical simulations both on synthetic graphs as well as on a real modular and temporal network.
Journal Article