arXiv subjects

Mauro Chinappi

Publications and source records attributed to Mauro Chinappi.

15 recordsLinked to original sources

arXiv2025

A nanopore-gated sub-attoliter silicon nanocavity for single-molecule trapping and analysis

Biomolecules exhibit dynamic conformations critical to their functions, yet observing these processes at the single-molecule level under native conditions remains a formidable challenge. While surface immobilization has been widely used to extend observation times, it could disrupt molecular dynamics and impede biological function. Moreover, the study of weak molecular interactions requires high local concentrations, often leading to problems with signal saturation in fluorescence-based approaches. Recent advancements in single-molecule trapping techniques have addressed some limitations, but achieving precise, controllable, long-term trapping in a molecularly crowded environment without external forces remains difficult. Here, we introduce a nanopore-gated sub-attoliter silicon nanocavity that enables precise, non-perturbative trapping of individual biomolecules for extended observation times, eliminating the need for external forces. Using nucleosomes as model systems, we demonstrate single-molecule Förster resonance energy transfer (smFRET) to monitor relative distances. Our data also show that an applied electric field can modulate the conformational properties of macromolecules, emphasizing a key advantage of our device: it does not require an electric field to retain trapped molecules. We envision this nanocavity platform as a powerful tool for interrogating molecular dynamics in physiologically relevant environments, offering unperturbed access to weak and transient interactions that are central to biological regulation.

physics.ins-det↗

arXiv2025

Dynamics of DNA-Templated Ultrafine Silver Nanowires Formation

Recent research on silver nanowires prepared on DNA templates has focused on two fundamental applications: nano-scale circuits and sensors. Despite its broad potential, the formation kinetics of DNA-templated silver nanowires remains unclear. Here, we present an experimental demonstration of the formation of silver nanowires with a diameter of 2.2+0.4 nm at the single-molecule level through chemical reduction. We conducted equilibrium and perturbation kinetic experiments to measure force spectroscopy during the formation of Ag+ -DNA complexes and Ag-DNA complexes, using optical tweezers combined with microfluidics. The addition of AgNO3 resulted in an increase in force of 5.5-7.5 pN within 2 minutes, indicating that Ag+ compacts the DNA structure. In contrast, the addition of hydroquinone caused the force to decrease by 4-5 pN. Morphological characterization confirmed the presence of a dense structure formed by silver atoms bridging the DNA strands, and revealed conformational differences before and after metallization. We compare our experimental data with Brownian dynamics simulations using a coarse-grained double-stranded DNA (dsDNA) model that provides insights on the dependency of the force on the persistence length.

physics.app-ph↗

arXiv2024

Ionic Current Rectification in Nanopores: Effects of Nanopore Material, Electrolyte and Surface Treatment

Ionic Current Rectification (ICR) can appear in nanopores, causing a diode-like behavior that originates from different efficiency of ion transport through the pore channel with respect to the applied voltage bias polarity. This effect is particularly interesting for nanopores with a short channel length, that is smaller than 500 nm, because then the dependence of the ion current on the direction along which the ions pass through the channel is determined by the geometry and material of the nanopore, and by the ion concentration in the electrolyte. Surface charges can play an important role, and therefore nanopores consisting of multiple materials can induce ICR because of different charge distributions at the nanopore-electrolyte interface for the different material sections. In this work, we study four solid-state nanopore designs considering different geometries of charge distributions along the inner and outer surfaces of nanopores, and evaluate their impact on ICR with six different electrolytes. The direct comparison between experimental data and modeling enables to understand how the different surface charge configurations impact the ICR.

physics.app-ph↗

arXiv2023

Hydrophobically gated memristive nanopores for neuromorphic applications

Brain-inspired computing has the potential to revolutionise the current von Neumann architecture, advancing machine learning applications. Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor \tr{and construct a synaptic device capable of learning and forgetting}. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.

cond-mat.mes-hall↗

arXiv2023

Assessment of heat transfer and Mach number effects on high-speed turbulent boundary layers

High-speed vehicles experience a highly challenging environment in which the free-stream Mach number and surface temperature greatly influence aerodynamic drag and heat transfer. The interplay of these two parameters strongly affects the near-wall dynamics of high-speed turbulent boundary layers in a non-trivial way, breaking similarity arguments on velocity and temperature fields, typically derived for adiabatic cases. In this work, we present direct numerical simulations of flat-plate zero-pressure-gradient turbulent boundary layers spanning three free-stream Mach numbers [2,4,6] and four wall temperature conditions (from adiabatic to very cold walls), emphasising the choice of the diabatic parameter $\mathitΘ$ (Zhang, Bi, Hussain & She, J. Fluid Mech., vol. 739, pp. 392-420) to recover a similar flow organisation at different Mach numbers. We link qualitative observations on flow patterns to first- and second-order statistics to explain the strong decoupling of temperature-velocity fluctuations that occurs at reduced wall temperatures and high Mach numbers. For these cases, we find that the mean temperature gradient in the near-wall region can reach such a strong intensity that it promotes the formation of a secondary peak of thermal production in the viscous sublayer, which is in direct contrast with the monotonic behaviour of adiabatic profiles. We propose different physical mechanisms induced by wall-cooling and compressibility that result in apparently similar flow features, such as a higher peak in the streamwise velocity turbulence intensity, and distinct ones, such as the separation of turbulent scales.

physics.flu-dyn↗

arXiv2022

Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores

Selectivity towards positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and results to be completely inverted when reverting the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we demonstrate that unidirectional electroosmosis also occurs for a biological pore whose structure presents a coaxial cavity surrounding the pore constriction. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may open the way to a more flexible design of selective membranes.

physics.flu-dyn↗

arXiv2022

Electroosmosis in nanopores: Computational methods and technological applications

Electroosmosis is a fascinating effect where liquid motion is induced by an applied electric field. Counter ions accumulate in the vicinity of charged surfaces, triggering a coupling between liquid mass transport and external electric field. In nanofluidic technologies, where surfaces play an exacerbated role, electroosmosis is thus of primary importance. Its consequences on the transport properties in biological and synthetic nanopores are subtle and intricate. Thorough understanding is therefore challenging yet crucial to fully assess the mechanisms at play. Here, we review recent progress on computational techniques for the analysis of electroosmosis and discuss technological applications, in particular for sensing devices.

physics.flu-dyn↗

arXiv2022

EH-DPD: a Dissipative Particle Dynamics approach to Electro-Hydrodynamics

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.

physics.flu-dyn↗

arXiv2021

Base flow decomposition for complex moving objects in linear hydrodynamics: application to helix-shaped flagellated microswimmers

The 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.

physics.flu-dyn↗

arXiv2020

Effects of surface nanostructure and wettability on pool boiling: A molecular dynamics study

We study the role of surface topology, surface chemistry, and wall superheat temperature on the onset of boiling, bubble nucleation and growth, and the possible formation of an insulating vapour film by means of large-scale MD simulations. In the numerical experiments, we control the system pressure by imposing a constant force on a moving piston. The simulations reveal that the presence of a nanostructure triggers the bubble formation, determines the nucleation site and facilitates the energy transfer from the hot substrate to the water. The surface chemistry, on the other hand, governs the shape of the formed bubble. A hydrophilic surface chemistry accelerates the bubble nucleation, however, decelerates the bubble expansion, thus postponing the formation of the film of vapour. Therefore, a hydrophilic surface provides better energy transfer from the hot wall to the water. By analysing the system energy, we show that irrespective of wall topology and chemistry, there is a wall temperature for which the amount of transferred energy is maximum.

cond-mat.soft↗

arXiv2018

Charge polarization, local electroneutrality breakdown and eddy formation due to electroosmosis in varying-section channels

We 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.

cond-mat.soft↗

arXiv2017

Hydrodynamics of flagellated microswimmers near free-slip interfaces

The hydrodynamics of a flagellated microorganism is investigated when swimming close to a planar free-slip surface by means of numerical solu- tions of the Stokes equations obtained via a Boundary Element Method. Depending on the initial condition, the swimmer can either escape from the free-slip surface or collide with the boundary. Interestingly, the mi- croorganism does not exhibit a stable orbit. Independently of escape or attraction to the interface, close to a free-slip surface, the swimmer fol- lows a counter-clockwise trajectory, in agreement with experimental find- ings, [15]. The hydrodynamics is indeed modified by the free-surface. In fact, when the same swimmer moves close to a no-slip wall, a set of initial conditions exists which result in stable orbits. Moreover when moving close to a free-slip or a no-slip boundary the swimmer assumes a different orientation with respect to its trajectory. Taken together, these results contribute to shed light on the hydrodynamical behaviour of microorgan- isms close to liquid-air interfaces which are relevant for the formation of interfacial biofilms of aerobic bacteria.

physics.flu-dyn↗

arXiv2017

Mobility tensor of a sphere moving on a super-hydrophobic wall: application to particle separation

The paper addresses the hydrodynamic behavior of a sphere close to a micro-patterned superhydrophobic surface described in terms of alternated no-slip and perfect-slip stripes. Physically, the perfect-slip stripes model the parallel grooves where a large gas cushion forms between fluid and solid wall, giving rise to slippage at the gas-liquid interface. The potential of the boundary element method (BEM) in dealing with mixed no-slip/perfect-slip boundary conditions is exploited to systematically calculate the mobility tensor for different particle-to-wall relative positions and for different particle radii. The particle hydrodynamics is characterized by a non trivial mobility field which presents a distinct near wall behavior where the wall patterning directly affects the particle motion. In the far field, the effects of the wall pattern can be accurately represented via an effective description in terms of a homogeneous wall with a suitably defined apparent slippage. The trajectory of the sphere under the action of an external force is also described in some detail. A resonant regime is found when the frequency of the transversal component of the force matches a characteristic crossing frequency imposed by the wall pattern. It is found that, under resonance, the particle undergoes a mean transversal drift. Since the resonance condition depends on the particle radius the effect can in principle be used to conceive devices for particle sorting based on superhydrophobic surfaces.

physics.flu-dyn↗

arXiv2015

Driven diffusion against electrostatic or effective energy barrier across Alpha-Hemolysin

We analyze the translocation of a charged particle across an Alpha-Hemolysin (aHL) pore in the framework of a driven diffusion over an extended energy barrier generated by the electrical charges of the aHL. A one-dimensional electrostatic potential is extracted from the full 3D solution of the Poisson's equation. We characterize the particle transport under the action of a constant forcing by studying the statistics of the translocation time. We derive an analytical expression of translocation time average that compares well with the results from Brownian dynamic simulations of driven particles over the electrostatic potential. Moreover, we show that the translocation time distributions can be perfectly described by a simple theory which replaces the true barrier by an equivalent structureless square barrier. Remarkably our approach maintains its accuracy also for low-applied voltage regimes where the usual inverse-Gaussian approximation fails. Finally we discuss how the comparison between the simulated time distributions and their theoretical prediction results to be greatly simplified when using the notion of the empirical Laplace transform technique.

q-bio.BM↗

arXiv2015

Modulation of current through a nanopore induced by a charged globule: implications for DNA-docking

The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of the two events. However, at low voltages a clear distinction of the two phases is lost. By using numerical simulations we clarify how the current signature associated to the docking events depends on the applied voltage. The simulations show that at small voltage the DNA globule enhances the pore conductance due to an enrichment of charge carriers. At high voltage, the globule drains substantial charge carriers from the pore region, thereby reducing the overall conductance. The results provide a new interpretation to the experimental data on conductance and show how docking interferes with the translocation signal, of potential interest for sequencing applications.

physics.bio-ph↗