Effect of fluid dynamics and device mechanism on biofluid behaviour in microchannel systems: modelling biofluids in a microchannel biochip separator

Biofluid behaviour in microchannel systems is investigated in this paper through the modelling of a microfluidic biochip developed for the separation of blood plasma. Based on particular assumptions, the effects of some mechanical features of the microchannels on behaviour of the biofluid are explored. These include microchannel, constriction, bending channel, bifurcation as well as channel length ratio between the main and side channels. The key characteristics and effects of the microfluidic dynamics are discussed in terms of separation efficiency of the red blood cells with respect to the rest of the medium. The effects include the Fahraeus and Fahraeus-Lindqvist effects, the Zweifach-Fung bifurcation law, the cell-free layer phenomenon. The characteristics of the microfluid dynamics include the properties of the laminar flow as well as particle lateral or spinning trajectories. In this paper the fluid is modelled as a single-phase flow assuming either Newtonian or Non-Newtonian behaviours to investigate the effect of the viscosity on flow and separation efficiency. It is found that, for a flow rate controlled Newtonian flow system, viscosity and outlet pressure have little effect on velocity distribution. When the fluid is assumed to be Non-Newtonian more fluid is separated than observed in the Newtonian case, leading to reduction of the flow rate ratio between the main and side channels as well as the system pressure as a whole.

Defining seasonal marine microbial community dynamics

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.

Dynamics and Function of Langerhans Cells In Vivo: Dermal Dendritic Cells Colonize Lymph Node Areas Distinct from Slower Migrating Langerhans Cells

Langerhans cells (LCs) are prominent dendritic cells (DCs) in epithelia, but their role in immunity is poorly defined. To track and discriminate LCs from dermal DCs in vivo, we developed knockin mice expressing enhanced green fluorescent protein (EGFP) under the control of the langerin (CD207) gene. By using vital imaging, we showed that most EGFP(+) LCs were sessile under steady-state conditions, whereas skin inflammation induced LC motility and emigration to lymph nodes (LNs). After skin immunization, dermal DCs arrived in LNs first and colonized areas distinct from slower migrating LCs. LCs reaching LNs under steady-state or inflammatory conditions expressed similar levels of costimulatory molecules. Langerin and EGFP were also expressed on thymic DCs and on blood-derived, CD8alpha(+) DCs from all secondary lymphoid organs. By using a similar knockin strategy involving a diphtheria toxin receptor (DTR) fused to EGFP, we demonstrated that LCs were dispensable for triggering hapten-specific T cell effectors through skin immunization.

On the structure and dynamics of ionic liquids

The structure and dynamics of the ionic liquid 1-ethyl-3-methylimidazolium nitrate is studied by molecular dynamics simulations. We find long-range spatial correlations between the ions and a three-dimensional local structure that reflects the asymmetry of the cations. The main contribution to the configurational energy comes from the electrostatic interactions which leads to charge-ordering effects. Radial screening and threedimensional distribution of charge are also analyzed. The motion of a single ion is studied via velocity and reorientational correlation functions. It is found that ions "rattle" in a long-lived cage, while the orientational structure relaxes on a time scale longer than 200 ps. As in a supercooled liquid, the mean square displacements reveal a subdiffusive dynamics. In addition, the presence of dynamic heterogeneities can be detected by analyzing the non-Gaussian behavior of the van Hove correlation function and the spatial arrangement of the most mobile ions. The short-time collective dynamics is also studied through the electric current time correlation function.

Beyond Ehrenfest: correlated non-adiabatic molecular dynamics

A method for introducing correlations between electrons and ions that is computationally affordable is described. The central assumption is that the ionic wavefunctions are narrow, which makes possible a moment expansion for the full density matrix. To make the problem tractable we reduce the remaining many-electron problem to a single-electron problem by performing a trace over all electronic degrees of freedom except one. This introduces both one- and two-electron quantities into the equations of motion. Quantities depending on more than one electron are removed by making a Hartree-Fock approximation. Using the first-moment approximation, we perform a number of tight binding simulations of the effect of an electric current on a mobile atom. The classical contribution to the ionic kinetic energy exhibits cooling and is independent of the bias. The quantum contribution exhibits strong heating, with the heating rate proportional to the bias. However, increased scattering of electrons with increasing ionic kinetic energy is not observed. This effect requires the introduction of the second moment.

Molecular dynamics studies of trinucleotide repeat DNA involved in neurodegenerative disorders.

Expansion of trinucleotide repeat DNA of the classes CAG�·CTG, CGG�·CCG and GAA�·TTC are found to be associated with several neurodegenerative disorders. Different mechanisms have been attributed to the expansion of triplets, mainly involving the formation of alternate secondary structures by such repeats. This paper reports the molecular dynamics simulation of triplet repeat DNA sequences to study the basic structural features of DNA that are responsible for the formation of structures such as hairpins and slip-strand DNA leading to expansion. All the triplet repeat sequences studied were found to be more flexible compared to the control sequence unassociated with disease. Moreover, flexibility was found to be in the order CAG�·CTG > CGG�·CCG = GAA�·TTC, the highly flexible CAG�·CTG repeat being the most common cause of neurodegenerative disorders. In another simulation, a single G�·C to T�·A mutation at the 9th position of the CAG�·CTG repeat exhibited a reduction in bending compared to the pure 15-mer CAGâ�¢CTG repeat. EPM1 dodecamer repeat associated with the pathogenesis of progressive myoclonus epilepsy was also simulated and showed flexible nature suggesting a similar expansion mechanism.

Sub-fossil Insects and ecosystem dynamics in wetlands; implications for biodiversity and conservation.

We review the uses of fossil insects, particularly Coleoptera (beetles) and Chironomidae (non-biting midges) from ancient deposits to inform the study of wetland ecosystems and their ecological and restoration processes. In particular, we focus on two contrasting ecosystems, drawing upon research undertaken by us on British raised mire peats and shallow lake systems, one an essentially terrestrial ecosystem, the other aquatic, but in which wetland insects play an important and integral part. The study of raised mire peats suggests that faunal stability is a characteristic of these wetland systems, over what appear to be extensive periods of time (up to several millennia), whilst studies of shallow lake ecosystems over recent timescales indicates that faunal instability appears to be more common, usually driven by increasing eutrophication. Drawing upon a series of fossil Coleoptera records spanning several thousand years from Hatfield Moors, south Yorkshire, we reconstruct in some detail the mire’s ontogeny and fluctuations in site hydrology and vegetation cover, illustrating the intimate association between substrate, topography and peat development. A comparison between fossil and modern beetle populations indicates that the faunal characteristics of this mire and its adjacent neighbour, Thorne Moors, become established during the early phases of peat development, including its rare endemics, and that the faunal biodiversity on the sites today is dictated by complex site histories. The over-riding characteristic of these faunas is of stability over several thousand years, which has important implications for the restoration of degraded sites, especially those where refugial areas are limited. In contrast, analyses of fossil Chironomidae from shallow lakes allow researchers to track changes in limnological status and while attempts have been made to reconstruct changes in nutrient levels quantitatively, the chironomids respond indirectly to such changes, typically mediated through complex ecosystem dynamics such as changes in fish and/or macrophyte communities. These changes are illustrated via historic chironomid stratigraphies and diversity indices from a range of shallow lakes located across Britain: Slapton Ley, Frensham Great Pond, Fleet Pond, Kyre Pool and Barnes Loch. These sites have shown varying degrees of eutrophication over recent timescales which tends to be associated with a decline in chironomid diversity. While complex functional processes exist within these ecosystems, our evidence suggests that one of the key drivers in the loss of shallow lake chironomid diversity appears to be the loss of aquatic macrophytes. Overall, while chironomids do show a clear response to altered nutrient regimes, multi-proxy reconstructions are recommended for a clear interpretation of past change. We conclude that if we are to have a better understanding of biota at the ecosystem level we need to know more of the complex interactions between different insect groups as well as with other animal and plant communities. A palaeoecological approach is thus crucial in order to assess the role of insect groups in ecosystem processes, both in the recent past and over long time scales, and is essential for wetland managers and conservation organisations involved in long term management and restoration of wetland systems.

Haptic information stabilizes and destabilizes coordination dynamics

Goal-directed, coordinated movements in humans emerge from a variety of constraints that range from 'high-level' cognitive strategies based oil perception of the task to 'low-level' neuromuscular-skeletal factors such as differential contributions to coordination from flexor and extensor muscles. There has been a tendency in the literature to dichotomize these sources of constraint, favouring one or the other rather than recognizing and understanding their mutual interplay. In this experiment, subjects were required to coordinate rhythmic flexion and extension movements with an auditory metronome, the rate of which was systematically increased. When subjects started in extension on the beat of the metronome, there was a small tendency to switch to flexion at higher rates, but not vice versa. When subjects: were asked to contact a physical stop, the location of which was either coincident with or counterphase to the auditor) stimulus, two effects occurred. When haptic contact was coincident with sound, coordination was stabilized for both flexion and extension. When haptic contact was counterphase to the metronome, coordination was actually destabilized, with transitions occurring from both extension to flexion on the beat and from flexion to extension on the beat. These results reveal the complementary nature of strategic and neuromuscular factors in sensorimotor coordination. They also suggest the presence of a multimodal neural integration process-which is parametrizable by rate and context - in which intentional movement, touch and sound are bound into a single, coherent unit.

The influence of Notches on Domain Dynamics in Ferroelectric Nanowires

The extent to which notches inhibit axial switching of polarization in ferroelectric nanowires was investigated by monitoring the switching behavior of single crystal BaTiO(3) wires before and after patterning triangular notches along their lengths. Static zero-field domain patterns suggested a strong domain-notch interaction, implying that notches should act as pinning sites for domain wall propagation. Surprisingly though, notches appeared to assist, rather than inhibit, polar switching. The origin of this effect was rationalized using finite element modeling of the electric field distribution along the notched wire; it was found that the air gap associated with the notch acted to enhance the local field, both in the air, and in the adjacent region of the ferroelectric. It seems that this local field enhancement outweighs any pinning interactions.

The challenge of revealing and tailoring the dynamics of radio-frequency plasmas

The complex dynamics of ionization and excitation mechanisms in capacitively coupled radio-frequency plasmas is discussed for single- and dual-frequency operations in low-pressure and atmospheric pressure plasmas. Electrons are energized through the dynamics of electric fields in the vicinity of the plasma boundary sheaths. Distinctly different power dissipation mechanisms can either co-exist or initiate mode transitions exhibiting characteristic spatio-temporal ionization structures. Phase resolved optical emission spectroscopy, in combination with adequate modelling of the population dynamics of excited states, and numerical simulations reveal dissipation associated with sheath expansion, sheath collapse, transient electron avalanches and wave–particle interactions. In dual-frequency systems the relative phase between the two frequency components provides additional strategies to tailor the plasma dynamics.

Track displacement and energy loss in a railway embankment

The mainline railway track between Dublin and Belfast was constructed during the 1850s, with substantial lengths of railway embankment constructed over soft, peaty soils. In recent years Northern Ireland Railways (NIR) has noticed that the sections of the railway track constructed on these peaty soils have been deteriorating at an increasing rate. Train speeds have been reduced in response to concerns that cyclic track displacements appear to be increasing over time in response to train loading. Track maintenance has also increased significantly. The research described in this paper was undertaken to quantify the response to cyclic train loading of two portions of this track founded on peaty soils. Track displacements were recorded using a sensor system specifically created for this project. The sensor consisted of a photosensitive array, mounted on the sleepers, and a laser, which was targeted onto the photosensitive array from a location outside the area of influence of train loading. Track deflections from 5 to 20 mm were measured under train speeds from near zero to over 120 km/h. The temporal variation in track displacement was used to calibrate an analytical (Winkler) model. This analysis suggests that the deformation of the embankment under train loading was not due to dynamic excitation but rather to static deformation of the poor-quality fill and soft foundation materials. As a consequence, the analytical model highlighted that train speed has limited effect on the magnitude of the deflection of the embankment within NIR operating speeds, but has the potential to significantly reduce the power lost to the damping within the embankment and subgrade.

Discrete solitons and vortices in hexagonal and honeycomb lattices: Existence, stability, and dynamics

We consider a prototypical dynamical lattice model, namely, the discrete nonlinear Schrodinger equation on nonsquare lattice geometries. We present a systematic classification of the solutions that arise in principal six-lattice-site and three-lattice-site contours in the form of both discrete multipole solitons and discrete vortices. Additionally to identifying the possible states, we analytically track their linear stability both qualitatively and quantitatively. We find that among the six-site configurations, the

Vortex line and ring dynamics in trapped Bose-Einstein condensates

Vortex dynamics in inhomogeneous Bose-Einstein condensates are studied numerically in two and three dimensions. We simulate the precession of a single vortex around the center of a trapped condensate, and use the Magnus force to estimate the precession frequency. Vortex ring dynamics in a spherical trap are also simulated, and we discover that a ring undergoes oscillatory motion around a circle of maximum energy. The position of this locus is calculated as a function of the number of condensed atoms. In the presence of dissipation, the amplitude of the oscillation will increase, eventually resulting in self-annihilation of the ring.

Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.

Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150–200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such quadruplex structures, with external TTA loops positioned to potentially interact with other macromolecules. This study reports on possible arrangements for these quadruplex dimers and tetramers, which can be formed from 8 or 16 telomeric DNA repeats, and on a methodology for modeling their interactions with small molecules. A series of computational methods including molecular dynamics, free energy calculations, and principal components analysis have been used to characterize the properties of these higher-order G-quadruplex dimers and tetramers with parallel-stranded topology. The results confirm the stability of the central G-tetrads, the individual quadruplexes, and the resulting multimers. Principal components analysis has been carried out to highlight the dominant motions in these G-quadruplex dimer and multimer structures. The TTA loop is the most flexible part of the model and the overall multimer quadruplex becoming more stable with the addition of further G-tetrads. The addition of a ligand to the model confirms the hypothesis that flat planar chromophores stabilize G-quadruplex structures by making them less flexible.

Population dynamics of the liver fluke, Fasciola hepatica: the effect of time and spatial separation on the genetic diversity of fluke populations in the Netherlands

An evaluation of the genetic diversity within Fasciola hepatica (liver fluke) may provide an insight into its potential to respond to environmental changes, such as anthelmintic use or climate change. In this study, we determined the mitochondrial DNA haplotypes of >400 flukes from 29 individual cattle, from 2 farms in the Netherlands, as an exemplar of fasciolosis in a European context. Analysis of this dataset has provided us with a measure of the genetic variation within infrapopulations (individual hosts) and the diversity between infrapopulations within a herd of cattle. Temporal sampling from one farm allowed for the measurement of the stability of genetic variation at a single location, whilst the comparison between the two farms provided information on the variation in relation to distance and previous anthelmintic regimes. We showed that the liver fluke population in this region is predominantly linked to 2 distinct clades. Individual infrapopulations contain a leptokurtic distribution of genetically diverse flukes. The haplotypes present on a farm have been shown to change significantly over a relatively short time-period.