63 research outputs found
Charge Inversion of Divalent Ionic Solutions in Silica Channels
Recent experiments (F.H.J. Van Der Heyden et al., PRL 96, 224502 (2006)) of
streaming currents in silica nanochannels with divalent ions report charge
inversion, i.e. interfacial charges attracting counterions in excess of their
own nominal charge, in conflict with existing theoretical and simulation
results. We reveal the mechanism of charge inversion by using all-atomic
molecular dynamics simulations. Our results show excellent agreement with
experiments, both qualitatively and quantitatively. We further discuss the
implications of our study for the general problem of ionic correlations in
solutions as well as in regards of the properties of silica-water interfaces.Comment: 5 pages, 5 figure
Nonequilibrium corrections in the pressure tensor due to an energy flux
The physical interpretation of the nonequilibrium corrections in the pressure
tensor for radiation submitted to an energy flux obtained in some previous
works is revisited. Such pressure tensor is shown to describe a moving
equilibrium system but not a real nonequilibrium situation.Comment: 4 pages, REVTeX, Brief Report to appear in PRE Dec 9
Curvature-coupling dependence of membrane protein diffusion coefficients
We consider the lateral diffusion of a protein interacting with the curvature
of the membrane. The interaction energy is minimized if the particle is at a
membrane position with a certain curvature that agrees with the spontaneous
curvature of the particle. We employ stochastic simulations that take into
account both the thermal fluctuations of the membrane and the diffusive
behavior of the particle. In this study we neglect the influence of the
particle on the membrane dynamics, thus the membrane dynamics agrees with that
of a freely fluctuating membrane. Overall, we find that this curvature-coupling
substantially enhances the diffusion coefficient. We compare the ratio of the
projected or measured diffusion coefficient and the free intramembrane
diffusion coefficient, which is a parameter of the simulations, with analytical
results that rely on several approximations. We find that the simulations
always lead to a somewhat smaller diffusion coefficient than our analytical
approach. A detailed study of the correlations of the forces acting on the
particle indicates that the diffusing inclusion tries to follow favorable
positions on the membrane, such that forces along the trajectory are on average
smaller than they would be for random particle positions.Comment: 16 pages, 8 figure
Horizontal low gradient magnetophoresis behaviour of iron oxide nanoclusters at the different steps of the synthesis route
In this work the use of Horizontal Low Gradient Magnetic Field (HLGMF) (<100T/m) for filtration, control and separation of synthesized magnetic nanoparticles (NPs) is investigated. The characteristics of the suspension, size and type of the NPs are considered and discussed. For these purposes, Fe2O3 silica coated nanoclusters of about 150 nm are synthesized by co-precipitation, monodispersion and silica coating. SQUID, TEM, XRD, and z potential techniques were used to characterize the synthesized nanoclusters. An extensive magnetophoresis study was performed at different magnetophoretical conditions. Different reversible aggregation times were observed at different HLGMF, at each step of the synthesis route. In particular, differences of several orders of magnitude were observed when comparing citric acid modified NPs with silica coated nanoclusters . Reversible aggregation times are correlated to the properties of the NPs at different steps of synthesis route.Fundação para a Ciência e a Tecnologia (FCT) - Bolsa NANO/NMed-SD/0156/2007, PTCD/CTM/69316/2006
Variational Methods for Biomolecular Modeling
Structure, function and dynamics of many biomolecular systems can be
characterized by the energetic variational principle and the corresponding
systems of partial differential equations (PDEs). This principle allows us to
focus on the identification of essential energetic components, the optimal
parametrization of energies, and the efficient computational implementation of
energy variation or minimization. Given the fact that complex biomolecular
systems are structurally non-uniform and their interactions occur through
contact interfaces, their free energies are associated with various interfaces
as well, such as solute-solvent interface, molecular binding interface, lipid
domain interface, and membrane surfaces. This fact motivates the inclusion of
interface geometry, particular its curvatures, to the parametrization of free
energies. Applications of such interface geometry based energetic variational
principles are illustrated through three concrete topics: the multiscale
modeling of biomolecular electrostatics and solvation that includes the
curvature energy of the molecular surface, the formation of microdomains on
lipid membrane due to the geometric and molecular mechanics at the lipid
interface, and the mean curvature driven protein localization on membrane
surfaces. By further implicitly representing the interface using a phase field
function over the entire domain, one can simulate the dynamics of the interface
and the corresponding energy variation by evolving the phase field function,
achieving significant reduction of the number of degrees of freedom and
computational complexity. Strategies for improving the efficiency of
computational implementations and for extending applications to coarse-graining
or multiscale molecular simulations are outlined.Comment: 36 page
Superparamagnetic colloids in viscous fluids
The influence of a magnetic field on the aggregation process of superparamagnetic colloids has been well known on short time for a few decades. However, the influence of important parameters, such as viscosity of the liquid, has received only little attention. Moreover, the equilibrium state reached after a long time is still challenging on some aspects. Indeed, recent experimental measurements show deviations from pure analytical models in extreme conditions. Furthermore, current simulations would require several years of computing time to reach equilibrium state under those conditions. In the present paper, we show how viscosity influences the characteristic time of the aggregation process, with experimental measurements in agreement with previous theories on transient behaviour. Afterwards, we performed numerical simulations on equivalent systems with lower viscosities. Below a critical value of viscosity, a transition to a new aggregation regime is observed and analysed. We noticed this result can be used to reduce the numerical simulation time from several orders of magnitude, without modifying the intrinsic physical behaviour of the particles. However, it also implies that, for high magnetic fields, granular gases could have a very different behaviour from colloidal liquids
Calcium Triggered LÎą-H2 Phase Transition Monitored by Combined Rapid Mixing and Time-Resolved Synchrotron SAXS
BACKGROUND: Awad et al. reported on the Ca(2+)-induced transitions of dioleoyl-phosphatidylglycerol (DOPG)/monoolein (MO) vesicles to bicontinuous cubic phases at equilibrium conditions. In the present study, the combination of rapid mixing and time-resolved synchrotron small-angle X-ray scattering (SAXS) was applied for the in-situ investigations of fast structural transitions of diluted DOPG/MO vesicles into well-ordered nanostructures by the addition of low concentrated Ca(2+) solutions. METHODOLOGY/PRINCIPAL FINDINGS: Under static conditions and the in absence of the divalent cations, the DOPG/MO system forms large vesicles composed of weakly correlated bilayers with a d-spacing of approximately 140 A (L(alpha)-phase). The utilization of a stopped-flow apparatus allowed mixing these DOPG/MO vesicles with a solution of Ca(2+) ions within 10 milliseconds (ms). In such a way the dynamics of negatively charged PG to divalent cation interactions, and the kinetics of the induced structural transitions were studied. Ca(2+) ions have a very strong impact on the lipidic nanostructures. Intriguingly, already at low salt concentrations (DOPG/Ca(2+)>2), Ca(2+) ions trigger the transformation from bilayers to monolayer nanotubes (inverted hexagonal phase, H(2)). Our results reveal that a binding ratio of 1 Ca(2+) per 8 DOPG is sufficient for the formation of the H(2) phase. At 50 degrees C a direct transition from the vesicles to the H(2) phase was observed, whereas at ambient temperature (20 degrees C) a short lived intermediate phase (possibly the cubic Pn3m phase) coexisting with the H(2) phase was detected. CONCLUSIONS/SIGNIFICANCE: The strong binding of the divalent cations to the negatively charged DOPG molecules enhances the negative spontaneous curvature of the monolayers and causes a rapid collapsing of the vesicles. The rapid loss of the bilayer stability and the reorganization of the lipid molecules within ms support the argument that the transition mechanism is based on a leaky fusion of the vesicles
A comparative evaluation of a new fully automated assay for von Willebrand factor collagen binding activity to an established method
Introduction: Laboratory diagnosis of von Willebrand disease (VWD) is made by the measurement of von Willebrand factor (VWF) protein level and its activities. Current VWF activity tests include ristocetin cofactor and collagen binding (VWF:CB) assays. Aim: We have undertaken an evaluation of a new fully automated VWF:CB assay relative to an established enzyme-linked immunosorbent assay (ELISA) method. Methods: The two analytical systems operate with different detection principles: a chemiluminescent method performed on ACL AcuStar Analyzer (the former) and a colorimetric ELISA by Asserachrom Stago (the latter) (type III collagen from human placenta). The HemosIL AcuStar VWF:CB assay is a chemiluminescent 2-step immunoassay that uses magnetic particles coated with a type III collagen triple-helical peptide. VWF:CB levels were determined in 50 healthy subjects and 100 VWD patients (22 type 1, 73 type 2 and 5 type 3). Results: Eleven VWD samples reported VWF:CB values below the lower detection limit of one or both methods. The new method showed a good correlation with the ELISA method (r\uc2\ua0>.9, mean bias 3.85\uc2\ua0IU/dL) in both healthy and VWD samples. One of 150 samples gave inconsistent results using the two assays, leading to an uncertain diagnosis of VWD type 1 (ELISA method) or type 2 MCB (fully automated method). Conclusion: The new assay is rapid and simple to use, with its ready-to-use reagent cartridges. This VWF:CB assay, in addition to the measurement of VWF:Ag and VWF:RCo made on the same platform, gives additional information for the diagnosis of VWD in both nonspecialized and reference laboratories
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