Generalized Turing Patterns and Their Selective Realization in Spatiotemporal Systems

We consider the pattern formation problem in coupled identical systems after the global synchronized state becomes unstable. Based on analytical results relating the coupling strengths and the instability of each spatial mode (pattern) we show that these spatial patterns can be selectively realized by varying the coupling strengths along different paths in the parameter space. Furthermore, we discuss the important role of the synchronized state (fixed point versus chaotic attractor) in modulating the temporal dynamics of the spatial patterns.Comment: 9 pages, 3 figure

Frequency decomposition of conditional Granger causality and application to multivariate neural field potential data

It is often useful in multivariate time series analysis to determine statistical causal relations between different time series. Granger causality is a fundamental measure for this purpose. Yet the traditional pairwise approach to Granger causality analysis may not clearly distinguish between direct causal influences from one time series to another and indirect ones acting through a third time series. In order to differentiate direct from indirect Granger causality, a conditional Granger causality measure in the frequency domain is derived based on a partition matrix technique. Simulations and an application to neural field potential time series are demonstrated to validate the method.Comment: 18 pages, 6 figures, Journal publishe

Viral hijacking of cellular ubiquitination pathways as an anti-innate immunity strategy.

International audienceViruses are obligate parasites of host cells. Virus-host coevolution has selected virus for growth despite antiviral defenses set up by hosting cells and organisms. Ubiquitin conjugation onto proteins, through a cascade of reactions mediated by E1 (ubiquitin-activating enzyme) and E2 and E3 (ubiquitin- conjugating ligases), is one of the major regulatory systems that, in particular, tightly controls the concentration of cellular proteins by sorting them for degradation. The combined diversity of E2 and E3 ligases ensures the selective/specific ubiquitination of a large number of protein substrates within the cell interior. Therefore it is not surprising that several viruses encode proteins with E3 ubiquitin ligase activities that target cellular proteins playing a key role in innate antiviral mechanisms

Analyzing Stability of Equilibrium Points in Neural Networks: A General Approach

Networks of coupled neural systems represent an important class of models in computational neuroscience. In some applications it is required that equilibrium points in these networks remain stable under parameter variations. Here we present a general methodology to yield explicit constraints on the coupling strengths to ensure the stability of the equilibrium point. Two models of coupled excitatory-inhibitory oscillators are used to illustrate the approach.Comment: 20 pages, 4 figure

Wavefront correction enables vibrational imaging of bacteria with multimode fibre probes

Raman spectroscopy is a valuable tool for non-invasive and label-free identification of sample chemical composition. Recently a few miniaturized optical probes emerged driven by the need to address areas of difficult access, such as in endoscopy. However, imaging modality is still out of reach for most of them. Separately, recent advances in wavefront shaping enabled different microscopies to be applied in various complex media including multimode fibers. Here we present the first and thinnest to date Raman fiber imaging probe based on wavefront shaping through a single multimode fiber without use of any additional optics. We image agglomerates of bacteria and pharmaceuticals to demonstrate the capability of our method. This work paves the way towards compact and flexible Raman endoscopy. © (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.Publisher PD

Raman imaging through a single multimode fibre

UK Engineering and Physical Sciences Research Council (EPSRC) (EP/J01771/X); European Union project FAMOS (FP7 ICT no. 317744); PreDiCT-TB consortium (IMI 115337); European Union’s Horizon 2020 Marie Sklodowska-Curie Actions (MSCA) (707084).Vibrational spectroscopy is a widespread, powerful method of recording the spectra of constituent molecules within a sample in a label-free manner. As an example, Raman spectroscopy has major applications in materials science, biomedical analysis and clinical studies. The need to access deep tissues and organs in vivo has triggered major advances in fibre Raman probes that are compatible with endoscopic settings. However, imaging in confined geometries still remains out of reach for the current state of art fibre Raman systems without compromising the compactness and flexibility. Here we demonstrate Raman spectroscopic imaging via complex correction in single multimode fibre without using any additional optics and filters in the probe design. Our approach retains the information content typical to traditional fibre bundle imaging, yet within an ultra-thin footprint of diameter 125 µm which is the thinnest Raman imaging probe realised to date. We are able to acquire Raman images, including for bacteria samples, with fields of view exceeding 200 µm in diameter.Publisher PDFPeer reviewe

Is there an optimal basis to maximise optical information transfer?

We establish the concept of the density of the optical degrees of freedom that may be applied to any photonics based system. As a key example of this versatile approach we explore information transfer using optical communication. We demonstrate both experimentally, theoretically and numerically that the use of a basis set with fields containing optical vortices does not increase the telecommunication capacity of an optical system.Peer reviewe

Optical analysis of homocysteine metabolites using vibrational spectroscopy

Funding: Funding: European Union FAMOS project (FP7-ICT-317744); Engineering and Physical Sciences Research Council (EP/P030017/1); RS MacDonald Charitable Trust.Homocysteine (HCy) is a sulphur-containing amino acid that correlates with several maladaptive health conditions, including an enhanced risk of cardiovascular and neurodegenerative diseases. Detection of HCy and its potentially pathogenic metabolites are studied here for the first time, to the first of our knowledge, using Raman spectroscopy. This study shows that different HCy metabolites have distinct Raman spectra and that the limits of detection reach the sub-mM level for these compounds. This investigation paves the way for photonics–based approaches for detection of HCy–related fluids as predictive biomarkers of disease in blood, which would assist in early intervention for improved clinical outcomes.Publisher PDFPeer reviewe

Dynamics of a levitated microparticle in vacuum trapped by a perfect vortex beam : three-dimensional motion around a complex optical potential

We trap a single silica microparticle in a complex three dimensional optical potential with orbital angular momentum in vacuum. The potential is formed by the generation of a ``perfect vortex' in vacuum which, upon propagation, evolves to a Bessel light field. The optical gradient and scattering forces interplay with the inertial and gravitational forces acting on the trapped particle, including the rotational degrees of freedom. As a result the particle undergoes a complex trajectory, part of which is rotational motion in the plane of the "perfect vortex". As the particle explores the whole three dimensional volume and not solely restricted to one anchor point, we are able to determine the three dimensional optical potential in situ by tracking the particle. This represents the first demonstration of trapping a microparticle within a complex three dimensional optical potential in vacuum. This may open up new perspectives in levitated optomechanics with particle dynamics on complex trajectories.PostprintPeer reviewe