1,721,054 research outputs found
Charge polarization, local electroneutrality breakdown and eddy formation due to electroosmosis in varying-section channels
No full textWe characterize the dynamics of an electrolyte embedded in a varying-section channel under the action of a constant external electrostatic field. By means of molecular dynamics simulations we determine the stationary density, charge and velocity profiles of the electrolyte. Our results show that when the Debye length is comparable to the width of the channel bottlenecks a concentration polarization along with two eddies sets inside the channel. Interestingly, upon increasing the external field, local electroneutrality breaks down and charge polarization sets leading to the onset of net dipolar field. This novel scenario, that cannot be captured by the standard approaches based on local electroneutrality, opens the route for the realization of novel micro and nano-fluidic devices
RELAXATION DYNAMICS OF CONFINED DNA: A MESOSCALE SIMULATION
No full textThe fast development of microfluidic devices are helping to realize the possibility of flow control in biological applications
e.g. DNA separation or single molecule mapping. However, for the efficient design of such device also a detailed knowledge
of the molecules dynamics must be at hand. In this respect, a number of experiments analyzing the relaxation dynamics
of DNA both in confined and non confined geometry have been recently presented. In this contribution we propose a
numerical study of DNA relaxation in a slitlike geometry obtained via a mesoscopic model both for the solvent and the
single chain. We confirm the existence of two relaxation regimes at different extensions as have been observed in a recent
experiment by Balducci et al.[1]
EH-DPD: a dissipative particle dynamics approach to electrohydrodynamics
Full text linkAbstract: Electrohydrodynamics is crucial in many nanofluidic and biotechnological applications. In such small scales, the complexity due to the coupling of fluid dynamics with the dynamics of ions is increased by the relevance of thermal fluctuations. Here, we present a mesoscale method based on the Dissipative Particle Dynamics (DPD) model of the fluid. Two scalar quantities, corresponding to the number of positive and negative ions carried by each DPD particle, are added to the standard DPD formulation. We introduced a general framework that, given the definition of the free-energy of the DPD particle, allows to derive a fluctuation-dissipation relation and the expression for ionic fluxes between the DPD particles. This provides a link between the dynamics of the system and its equilibrium properties. The model is then validated simulating a planar electroosmotic flow for the cases of overlapping and non overlapping electric double layers. It is shown that using a Van der Waals equation of state the effect of ionic finite size can be accounted, leading to significant effects on the concentration and velocity profiles with respect to the ideal solution case. Graphic abstract: [Figure not available: see fulltext.]
Nanopore tweezers: Voltage-controlled trapping and releasing of analytes
No full textSeveral devices for single-molecule detection and analysis employ biological and artificial nanopores as core elements. The performance of such devises strongly depends on the amount of time the analytes spend into the pore. This residence time needs to be long enough to allow the recording of a high signal-to-noise ratio analyte-induced blockade. We propose a simple approach, dubbed nanopore tweezing, for enhancing the trapping time of molecules inside the pore via a proper tuning of the applied voltage. This method requires the creation of a strong dipole that can be generated by adding a positive and a negative tail at the two ends of the molecules to be analyzed. Capture rate is shown to increase with the applied voltage while escape rate decreases. In this paper we rationalize the essential ingredients needed to control the residence time and provide a proof of principle based on atomistic simulations
Flow simulations with multi-particle collision dynamics
No full textMulti-particle collision dynamics (MPCD) is a particle based Navier-Stokes solver and in the last ten years it has been largely used to analyze mesoscopic systems where both hydrodynamics and thermal effects have to be taken into account, typical examples being colloidal suspensions and polymer solutions. Though the soundness of this approach is well documented, only a few studies present a systematic validation of the method as a Navier-Stokes solver for relatively complex flows (e.g. unsteady, non-uniform). In this study we use MPCD to simulate an unsteady periodic flow (second Stokes' problem) and a two dimensional flow (lid-driven cavity). Quantitative comparisons with analytical and finite difference results show that MPCD is able to correctly reproduce the hydrodynamics of these systems in a wide range of numerical parameter values, allowing the applications of MPCD to the analysis of complex fluids in confined geometries such as in Lab-On-a-Chip microfluidic devices. Discrepancies for certain parameter ranges and in specific flow conditions are singled out and discussed
Base flow decomposition for complex moving objects in linear hydrodynamics: application to helix-shaped flagellated microswimmers
No full textThe motion of microswimmers in complex flows is ruled by the interplay between swimmer propulsion and the dynamics induced by the fluid velocity field. Here we study the motion of a chiral microswimmer whose propulsion is provided by the spinning of a helical tail with respect to its body in a simple shear flow. Thanks to an efficient computational strategy that allowed us to simulate thousands of different trajectories, we show that the tail shape dramatically affects the swimmer's motion. In the shear dominated regime, the swimmers carrying an elliptical helical tail show several different Jeffery-like (tumbling) trajectories depending on their initial configuration. As the propulsion torque increases, a progressive regularization of the motion is observed until, in the propulsion dominated regime, the swimmers converge to the same final trajectory independently on the initial configuration. Overall, our results show that elliptical helix swimmer presents a much richer variety of trajectories with respect to the usually studied circular helix tails
Translocation intermediates of ubiquitin through an α-hemolysin nanopore: Implications for detection of post-translational modifications
No full textNanopore based sensors constitute a promising approach to single molecule protein characterization being able, in principle, to detect sequences, structural elements and folding states of proteins and polypeptide chains. In narrow nanopores, one of the open issues concerns the coupling between unfolding and translocation. Here, we studied the ubiquitin translocation in an -hemolysin nanopore, the most widely used pore for nanopore sensing, via all-atom molecular dynamics simulations. We completely characterize the co-translocational unfolding pathway finding that robust translocation intermediates are associated with the rearrangement of secondary structural elements, as also confirmed by coarse grained simulations. An interesting recurrent pattern is the clogging of the -hemolysin constriction by an N-terminal -hairpin. This region of ubiquitin is the target of several post-translational modifications. We propose a strategy to detect post-translational modifications at the N-terminal using the -hemolysin nanopore based on the comparison of the co-translocational unfolding signals associated with modified and unmodified proteins
Protein transport across nanopores: A statistical mechanical perspective from coarse-grained modeling and approaches
No full textA multiparticle collision model for fluid mechanics application
No full textA new particle-based mesoscopic model for fluid dynamics with continuos velocities and a multi-particle collision dynamics has recently introduced. Even though the model has been mainly
developed for simulating a multiscale, though simplified, dynamics for solvent-solute interaction in complex fluids such as polymers in solution, when appropriately used it can be proven to show correct hydrodynamic behaviour in flows at low Reynolds number
Flagellated microswimmers: Hydrodynamics in thin liquid films
No full textThe hydrodynamics of a flagellated microswimmer moving in thin films is discussed. The fully resolved hydrodynamics is exploited by solving the Stokes equations for the actual geometry of the swimmer. Two different interfaces are used to confine the swimmer: a bottom solid wall and a top air-liquid interface, as appropriate for a thin film. The swimmer follows curved clockwise trajectories that can converge towards an asymptotically stable circular path or can result in a collision with one of the two interfaces. A bias towards the air-liquid interface emerges. Slight changes in the swimmer geometry and film thickness strongly affect the resulting dynamics suggesting that a very reach phenomenology occurs in the presence of confinement. Under specific conditions, the swimmer follows a "crown-like" path. Implications for the motion of bacteria close to an air bubble moving in a microchannel are discussed
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