Particle-based model of liquid crystal skyrmion dynamics.

Motivated by recent experimental results that reveal rich collective dynamics of thousands-to-millions of active liquid crystal skyrmions, we have developed a coarse-grained, particle-based model of the dynamics of skyrmions in a dilute regime. The basic physical mechanism of skyrmion motion is related to squirming undulations of domains with high director twist within the skyrmion cores when the electric field is turned on and off. The motion is not related to mass flow and is caused only by the reorientation dynamics of the director field. Based on the results of the "fine-grained" Frank-Oseen continuum model, we have mapped these squirming director distortions onto an effective force that acts asymmetrically upon switching the electrical field on or off. The resulting model correctly reproduces the skyrmion dynamics, including velocity reversal as a function of the frequency of a pulse width modulated driving voltage. We have also obtained approximate analytical expressions for the phenomenological model parameters encoding their dependence upon the cholesteric pitch and the strength of the electric field. This has been achieved by fitting coarse-grained skyrmion trajectories to those determined in the framework of the Frank-Oseen model.

Bioprospecting essential oils of exotic species as potential mitigations of ruminant enteric methanogenesis.

The inclusion of essential oils (EOs) in the diet of ruminants is one of the strategies used to alter ruminal microbial fermentation, improving feed efficiency, while simultaneously reducing enteric methane (CH4) production. This study aimed to evaluate the effects of three new EOs from plants exotic to the Azores, Pittosporum undulatum (PU), Hedychium gardnerianum (HG), and Cryptomeria japonica (CJ), on biogas production kinetics and in vitro CH4 production. Three levels of EOs (40, 80, and 120 µL/g dry matter (DM) were added to the basal diet to evaluate ruminal fermentation using the in vitro gas production technique. Added 800 mL of rumen inoculum with 5 g DM of the basal diet (BD) to all experimental units for 96 h, except for the blanks, to which only the inoculum was added. The total gas and CH4 produced by treatment incubation were recorded every hour after incubation until 96 h. The results showed that the gas production decreased significantly (P < 0.001) at 24 and 96 h after incubation, in the medium and high levels, with the essential oils PU, CJ, and HG treatment, when compared to the control treatment. The same significant differences (P < 0.001) were observed in in vitro CH4 production. The greatest reduction was noted with the addition of PUEO at the highest concentration (120 µL), which allowed a reduction in CH4 production at 24 h of 47% (P < 0.01). There was an interaction effect between EOs and concentration levels for all variables (P < 0.001). A decrease in total volatile fat acid (VFA) concentration (P < 0.05) was recorded compared to control, as well as the insoluble fraction and the potential degradation of the BD when EOs were included in the diet. In conclusion, the addition of EOs to the BD effectively reduced total enteric gas emissions and mitigated CH4 production. The most significant reduction of CH4 (47% in 24 h of incubation) occurs when 120 µL PUEO is added to each gram DM. The inclusion of OEs in the BD also affected the gas production kinetics and fermentation parameters.

Percolation in binary mixtures of linkers and particles: Chaining vs branching.

Equilibrium gels of colloidal particles can be realized through the introduction of a second species, a linker that mediates the bonds between colloids. A gel forming binary mixture whose linkers can self-assemble into linear chains while still promoting the aggregation of particles is considered in this work. The particles are patchy particles with fC patches of type C and the linkers are patchy particles with 2 patches of type A and fB patches of type B. The bonds between patches of type A (AA bonds) promote the formation of linear chains of linkers. Two different ways (model A and model B) of bonding the linkers to the particles-or inducing branching-are studied. In model A, there is a competition between chaining and branching, since the bonding between linkers and particles takes place through AC bonds only. In model B, the linkers aggregate to particles through bonds BC only, making chaining and branching independent. The percolation behavior of these two models is studied in detail, employing a generalized Flory-Stockmayer theory and Monte Carlo simulations. The self-assembly of linkers into chains reduces the fraction of particles needed for percolation to occur (models A and B) and induces percolation when the fraction of particles is high (model B). Percolation by heating and percolation loops in temperature-composition diagrams are obtained when the formation of chains is energetically favorable by increasing the entropic gain of branching (model A). Chaining and branching are found to follow a model dependent relation at percolation, which shows that, for the same composition, longer chains require less branching for percolation to occur.

Effect of anisotropy on the formation of active particle films.

Active colloids belong to a class of nonequilibrium systems where energy uptake, conversion, and dissipation occur at the level of individual colloidal particles, which can lead to particles' self-propelled motion and surprising collective behavior. Examples include coexistence of vapor- and liquid-like steady states for active particles with repulsive interactions only, phenomena known as motility-induced phase transitions. Similarly to motile unicellular organisms, active colloids tend to accumulate at confining surfaces forming dense adsorbed films. In this work, we study the structure and dynamics of aggregates of self-propelled particles near confining solid surfaces, focusing on the effects of the particle anisotropic interactions. We performed Langevin dynamics simulations of two complementary models for active particles: ellipsoidal particles interacting through the Gay-Berne potential and rodlike particles composed of several repulsive Lennard-Jones beads. We observe a nonmonotonic behavior of the structure of clusters formed along the confining surface as a function of the particle aspect ratio, with a film spreading when particles are near-spherical, compact clusters with hedgehog-like particle orientation for more elongated active particles, and a complex dynamical behavior for an intermediate aspect ratio. The stabilization time of cluster formation along the confining surface also displays a nonmonotonic dependence on the aspect ratio, with a local minimum at intermediate values. Additionally, we demonstrate that the hedgehog-like aggregates formed by Gay-Berne ellipsoids exhibit higher structural stability as compared to the ones formed by purely repulsive active rods, which are stable due to the particle activity only.

Kidney Injury Molecule-1 in the detection of early kidney injury in dogs with leptospirosis.

Renal damage, a common feature in canine leptospirosis, ranges from a subclinical affection to kidney dysfunction and death. Chances of recovery can be improved by early intervention. However, traditional biomarkers (serum urea and creatinine) have limited relevance for precocity. Kidney Injury Molecule-1 (KIM-1) is a transmembrane protein upregulated in early stages of tubular injury. This study evaluated the use of urinary KIM-1 to detect early renal injury in naturally occurring canine leptospirosis. This exploratory research included 30 dogs divided into two groups: (1) dogs with leptospirosis (n = 25) and (2) healthy dogs (n = 5). Leptospira sp. infection was diagnosed through urine PCR and/or direct bacteriologic culture and/or serology (single MAT titters ≥800). Additionally, stage of infection was further characterized in acute and subacute phases based on the onset of clinical symptoms from 3 to 7 days. Urinary KIM-1 (uKIM-1) concentrations were measured in both groups with a commercial canine ELISA kit. uKIM-1 levels were statistically different (P < 0.01) between the studied groups, especially in non-azotemic dogs (P = 0.0042). The biomarker showed 88 % sensibility to diagnosis of kidney injury at> 1.49 ng/mL cut-off. Urine KIM-1 was negatively correlated with urine specific gravity (USG) but accompanied histopathological evidence of renal degeneration, necrosis and regeneration processes, extending information on kidney health. Measurement of KIM-1 in the urine of canine patients was able to detect naturally occurring acute and subacute leptospirosis accompanied by tubular injury in early non-azotemic infections.

Wetting of a solid surface by active matter.

A lattice model is used to study repulsive active particles at a planar surface. A rejection-free Kinetic Monte Carlo method is employed to characterize the wetting behaviour. The model predicts a motility-induced phase separation of active particles, and the bulk coexistence of dense liquid-like and dilute vapour-like steady states is determined. An "ensemble", with a varying number of particles, analogous to a grand canonical ensemble in equilibrium, is introduced. The formation and growth of the liquid film between the solid surface and the vapour phase is investigated. At constant activity, as the system is brought towards coexistence from the vapour side, the thickness of the adsorbed film exhibits a divergent behaviour regardless of the activity. This suggests a complete wetting scenario along the full coexistence curve.

Modeling of Cell-Mediated Self-Assembled Colloidal Scaffolds.

A critical step in tissue engineering is the design and synthesis of 3D biocompatible matrices (scaffolds) to support and guide the proliferation of cells and tissue growth. The most existing techniques rely on the processing of scaffolds under controlled conditions and then implanting them in vivo, with questions related to biocompatibility and implantation that are still challenging. As an alternative, it was proposed to assemble the scaffolds in loco through the self-organization of colloidal particles mediated by cells. To overcome the difficulty to test experimentally all the relevant parameters, we propose the use of large-scale numerical simulation as a tool to reach useful predictive information and to interpret experimental results. Thus, in this study, we combine experiments, particle-based simulations, and mean-field calculations to show that, in general, the size of the self-assembled scaffold scales with the cell-to-particle ratio. However, we have found an optimal value of this ratio, for which the size of the scaffold is maximal when the cell-cell adhesion is suppressed. These results suggest that the size and structure of the self-assembled scaffolds may be designed by tuning the adhesion between cells in the colloidal suspension.

Smoluchowski equations for linker-mediated irreversible aggregation.

We developed a generalized Smoluchowski framework to study linker-mediated aggregation, where linkers and particles are explicitly taken into account. We assume that the bonds between linkers and particles are irreversible, and that clustering occurs through limited diffusion aggregation. The kernel is chosen by analogy with single-component diffusive aggregation but the clusters are distinguished by their number of particles and linkers. We found that the dynamics depends on three relevant factors, all tunable experimentally: (i) the ratio of the diffusion coefficients of particles and linkers; (ii) the relative number of particles and linkers; and (iii) the maximum number of linkers that may bond to a single particle. To solve the Smoluchoski equations analytically we employ a scaling hypothesis that renders the fraction of bondable sites of a cluster independent of the size of the cluster, at each instant. We perform numerical simulations of the corresponding lattice model to test this hypothesis. We obtain results for the asymptotic limit, and the time evolution of the bonding probabilities and the size distribution of the clusters. These findings are in agreement with experimental results reported in the literature and shed light on unexplained experimental observations.

Optimal number of linkers per monomer in linker-mediated aggregation.

We study the dynamics of diffusion-limited irreversible aggregation of monomers, where bonds are mediated by linkers. We combine kinetic Monte Carlo simulations of a lattice model with a mean-field theory to study the dynamics when the diffusion of aggregates is negligible and only monomers diffuse. We find two values of the number of linkers per monomer which maximize the size of the largest aggregate. We explain the existence of the two maxima based on the distribution of linkers per monomer. This observation is well described by a simple mean-field model. We also show that a relevant parameter is the ratio of the diffusion coefficients of monomers and linkers. In particular, when this ratio is close to ten, the two maxima merge at a single maximum.

Posterior urethral valves: comparison of clinical outcomes between postnatal and antenatal cohorts.

BACKGROUND: Posterior urethral valves (PUVs) constitute the most common infravesical urinary obstruction in boys and are often accompanied by severe consequences to the lower and upper urinary tract. Currently, about two-thirds of diagnosis of PUVs has been suspected by prenatal ultrasonography findings. The aim of this study was to compare long-term clinical outcomes in two groups of patients with PUVs, with antenatal vs. postnatal diagnosis. STUDY DESIGN: This was a retrospective cohort study of 173 patients with PUVs systematically followed up in a tertiary center. Median follow-up time was 66.5 months (interquartile range [IQ], 11.4-147.9 months) for those patients who survived neonatal period. Seventy-nine (45.6%) patients were followed up for more than 5 years and 55 (32%) for more than 10 years. For analysis, the cohort was stratified into two groups according to the clinical presentation (prenatal vs. postnatal). The events of interest were urinary tract infection (UTI), surgical interventions, proteinuria, hypertension, chronic kidney disease (CKD), and death. Survival analyses were performed to evaluate time until occurrence of the events. RESULTS: Sixty-two patients (35.8%) were diagnosed by fetal sonography. Patients of postnatal group presented a higher incidence rate of UTI episodes (6.5, 95% confidence interval [CI], 4.9-8.3) than antenatal group (1.2, 95% CI, 0.4-2.7) (P < 0.001). Thirty-six patients (21%) presented hypertension, and 77 (44.5%) had persistent mild proteinuria. There was no significant difference in the estimated incidence of hypertension (P = 0.28) and proteinuria (P = 0.78) between antenatal and postnatal groups. The cumulative incidence of CKD stage ≥3 was estimated to be about 37% at 10 years of age, and 56% at 18 years of age. By survival analysis, there was no significant difference in the estimated incidence of CKD stage ≥3 (log-rank = 0.32, P = 0.57) and CKD stage 5 (log-rank = 1.08, P = 0.28, Figure) between antenatal and postnatal groups. Of 173 patients included in the analysis, 13 (7.5%) died during follow-up with a median age of 2.6 months (IQ, 15 days-62 months). Survival analyses have not shown any significant difference in the estimated incidence of death between antenatal and postnatal groups (log-rank = 1.38, P = 0.24). CONCLUSION: The study findings did not corroborate the initial hypothesis that the rates of renal function declining in patients with PUVs would be attenuated by an early diagnosis and intervention after antenatal diagnosis.

Crossover from three- to six-fold symmetry of colloidal aggregates in circular traps.

At sufficiently low temperatures and high densities, repulsive spherical particles in two-dimensions (2d) form close-packed structures with six-fold symmetry. By contrast, when the interparticle interaction has an attractive anisotropic component, the structure may exhibit the symmetry of the interaction. We consider a suspension of spherical particles interacting through an isotropic repulsive potential and a three-fold symmetric attractive interaction, confined in circular potential traps in 2d. We find that, due to the competition between the interparticle and the external potentials, the particles self-organize into structures with three- or six-fold symmetry, depending on the width of the traps. For intermediate trap widths, a core-shell structure is formed, where the core has six-fold symmetry and the shell is three-fold symmetric. When the width of the trap changes periodically in time, the symmetry of the colloidal structure also changes, but it does not necessarily follow that of the corresponding static trap.

Dynamics of a network fluid within the liquid-gas coexistence region.

Low-density networks of molecules or colloids are formed at low temperatures when the interparticle interactions are valence limited. Prototypical examples are networks of patchy particles, where the limited valence results from highly directional pairwise interactions. We combine extensive Langevin simulations and Wertheim's theory of association to study these networks. We find a scale-free (relaxation) dynamics within the liquid-gas coexistence region, which differs from that usually observed for isotropic particles. While for isotropic particles the relaxation dynamics is driven by surface tension (coarsening), when the valence is limited, the slow relaxation proceeds through the formation of an intermediate non-equilibrium gel via a geometrical percolation transition in the Random Percolation universality class. We show that the slow dynamics is universal, being also observed outside the coexistence region at low temperatures in the single phase region.

Interaction anisotropy and the KPZ to KPZQ transition in particle deposition at the edges of drying drops.

The deposition process at the edge of evaporating colloidal drops varies with the shape of suspended particles. Experiments with prolate ellipsoidal particles suggest that the spatiotemporal properties of the deposit depend strongly on particle aspect ratio. As the aspect ratio increases, the particles form less densely-packed deposits and the statistical behavior of the deposit interface crosses over from the Kardar-Parisi-Zhang (KPZ) universality class to another universality class which was suggested to be consistent with the KPZ plus quenched disorder. Here, we numerically study the effect of particle interaction anisotropy on deposit growth. In essence, we model the ellipsoids, at the interface, as disk-like particles with two types of interaction patches that correspond to specific features at the poles and equator of the ellipsoid. The numerical results corroborate experimental observations and further suggest that the deposition transition can stem from interparticle interaction anisotropy. Possible extensions of our model to other systems are also discussed.

Dynamics of Patchy Particles in and out of Equilibrium.

We combine particle-based simulations, mean-field rate equations, and Wertheim's theory to study the dynamics of patchy particles in and out of equilibrium, at different temperatures and densities. We consider an initial random distribution of nonoverlapping three-patch particles, with no bonds, and analyze the time evolution of the breaking and bonding rates of a single bond. We find that the asymptotic (equilibrium) dynamics differs from the initial (out of equilibrium) one. These differences are expected to depend on the initial conditions, temperature, and density.

Dynamics of network fluids.

Network fluids are structured fluids consisting of chains and branches. They are characterized by unusual physical properties, such as, exotic bulk phase diagrams, interfacial roughening and wetting transitions, and equilibrium and nonequilibrium gels. Here, we provide an overview of a selection of their equilibrium and dynamical properties. Recent research efforts towards bridging equilibrium and non-equilibrium studies are discussed, as well as several open questions.

Relaxation dynamics of functionalized colloids on attractive substrates.

Particle-based simulations are performed to study the post-relaxation dynamics of functionalized (patchy) colloids adsorbed on an attractive substrate. Kinetically arrested structures that depend on the number of adsorbed particles and the strength of the particle-particle and particle-substrate interactions are identified. The radial distribution function is characterized by a sequence of peaks, with relative intensities that depend on the number of adsorbed particles. The first-layer coverage is a non-monotonic function of the number of particles, with an optimal value around one layer of adsorbed particles. The initial relaxation towards these structures is characterized by a fast (exponential) and a slow (power-law) dynamics. The fast relaxation timescale is a linearly increasing function of the number of adsorbed particles in the submonolayer regime, but it saturates for more than one adsorbed layer. The slow dynamics exhibits two characteristic exponents, depending on the surface coverage.

Kinetic interfaces of patchy particles.

We study the irreversible adsorption of patchy particles on substrates in the limit of advective mass transport. Recent numerical results show that the interface roughening depends strongly on the particle attributes, such as, patch-patch correlations, bond flexibility and strength of the interactions, uncovering new absorbing phase transitions. Here, we revisit these results and discuss in detail the transitions. In particular, we present new evidence that the tricritical point, observed in systems of particles with flexible patches, is in the tricritical directed percolation universality class. A scaling analysis of the time evolution of the correlation length for the aggregation of patchy particles with distinct bonding energies confirms that the critical regime is in the Kardar-Parisi-Zhang with quenched disorder universality class.

Adsorbed films of three-patch colloids: continuous and discontinuous transitions between thick and thin films.

We investigate numerically the role of spatial arrangement of the patches on the irreversible adsorption of patchy colloids on a substrate. We consider spherical three-patch colloids and study the dependence of the kinetics on the opening angle between patches. We show that growth is suppressed below and above minimum and maximum opening angles, revealing two absorbing phase transitions between thick and thin film regimes. While the transition at the minimum angle is continuous, in the directed percolation class, that at the maximum angle is clearly discontinuous. For intermediate values of the opening angle, a rough colloidal network in the Kardar-Parisi-Zhang universality class grows indefinitely. The nature of the transitions was analyzed in detail by considering bond flexibility, defined as the dispersion of the angle between the bond and the center of the patch. For the range of flexibilities considered we always observe two phase transitions. However, the range of opening angles where growth is sustained increases with flexibility. At a tricritical flexibility, the discontinuous transition becomes continuous. The practical implications of our findings and the relation to other nonequilibrium transitions are discussed.

Mixtures of functionalized colloids on substrates.

Patchy particles are a class of colloids with functionalized surfaces. Through surface functionalization, the strength and directionality of the colloidal interactions are tunable allowing control over coordination of the particle. Exquisite equilibrium phase diagrams of mixtures of coordination two and three have been reported. However, the kinetics of self-organization and the feasibility of the predicted structures are still largely unexplored. Here, we study the irreversible aggregation of these mixtures on a substrate, for different fractions of two-patch particles. Two mechanisms of mass transport are compared: diffusion and advection. In the diffusive case, an optimal fraction is found that maximizes the density of the aggregate. By contrast, for advective transport, the density decreases monotonically with the fraction of two-patch colloids, in line with the behavior of the liquid density on the spinodal of the equilibrium phase diagram.

NAA and NAAG variation in neuronal activation during visual stimulation

N-acetyl-aspartyl-glutamate (NAAG) and its hydrolysis product N-acetyl-L-aspartate (NAA) are among the most important brain metabolites. NAA is a marker of neuron integrity and viability, while NAAG modulates glutamate release and may have a role in neuroprotection and synaptic plasticity. Investigating on a quantitative basis the role of these metabolites in brain metabolism in vivo by magnetic resonance spectroscopy (MRS) is a major challenge since the main signals of NAA and NAAG largely overlap. This is a preliminary study in which we evaluated NAA and NAAG changes during a visual stimulation experiment using functional MRS. The paradigm used consisted of a rest period (5 min and 20 s), followed by a stimulation period (10 min and 40 s) and another rest period (10 min and 40 s). MRS from 17 healthy subjects were acquired at 3T with TR/TE = 2000/288 ms. Spectra were averaged over subjects and quantified with LCModel. The main outcomes were that NAA concentration decreased by about 20% with the stimulus, while the concentration of NAAG concomitantly increased by about 200%. Such variations fall into models for the energy metabolism underlying neuronal activation that point to NAAG as being responsible for the hyperemic vascular response that causes the BOLD signal. They also agree with the fact that NAAG and NAA are present in the brain at a ratio of about 1:10, and with the fact that the only known metabolic pathway for NAAG synthesis is from NAA and glutamate.