Understanding the dependence on the pulling speed of the unfolding pathway of proteins

The dependence of the unfolding pathway of proteins on the pulling speed is investigated. This is done by introducing a simple one-dimensional chain comprising $N$ units, with different characteristic bistable free energies. These units represent either each of the modules in a modular protein or each of the intermediate "unfoldons" in a protein domain, which can be either folded or unfolded. The system is pulled by applying a force to the last unit of the chain, and the units unravel following a preferred sequence. We show that the unfolding sequence strongly depends on the pulling velocity $v_{p}$. In the simplest situation, there appears a critical pulling speed $v_{c}$: for pulling speeds $v_{p}v_{c}$ it is the pulled unit that unfolds first. By means of a perturbative expansion, we find quite an accurate expression for this critical velocity.Comment: accepted for publication in JSTA

How to Increase Reading Motivation among Elementary Children Based on Teachers’ Perspectives and Teaching Methods

This study investigates the way children react to reading based on teachers\u27 beliefs and teaching methods. Interviews were conducted with teachers and administration in an elementary school and asked various questions regarding different aspects about reading. Also, children were observed during reading instruction. After the data was collected, it was reviewed and analyzed based on a constant comparison method. The results showed that children are more motivated to read when there is parental involvement in the school and with reading. Teachers used many reading techniques learned through professional development throughout the school year. The professional development ultimately increased reading motivation in children. Also, reading motivation increased in children when the reading curriculum was constantly changing. Lastly, reading motivation increased in children when reading was enjoyable

Swimming and rafting of E.coli microcolonies at air–liquid interfaces

The dynamics of swimming microorganisms is strongly affected by solid-liquid and air-liquid interfaces. In this paper, we characterize the motion of both single bacteria and microcolonies at an air-liquid interface. Both of them follow circular trajectories. Single bacteria preferentially show a counter-clockwise motion, in agreement with previous experimental and theoretical findings. Instead, no preferential rotation direction is observed for microcolonies suggesting that their motion is due to a different physical mechanism. We propose a simple mechanical model where the microcolonies move like rafts constrained to the air-liquid interface. Finally, we observed that the microcolony growth is due to the aggregation of colliding single-swimmers, suggesting that the microcolony formation resembles a condensation process where the first nucleus originates by the collision between two single-swimmers. Implications of microcolony splitting and aggregation on biofilm growth and dispersion at air-liquid interface are discussed

EH-DPD: a dissipative particle dynamics approach to electrohydrodynamics

Abstract: 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.]

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 a novel setup for large-scale MD simulations. To minimise the effects of the system size on the bubble growth and the formation of the vapour film, we perform simulations in a box larger than those previously considered. The effect of the system pressure on bubble nucleation and growth is isolated by imposing a constant force on a moving piston and mechanically controlling the pressure. The simulations reveal that the presence of a nanostructure 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 accelerates the bubble nucleation, however, decelerates the bubble expansion, thus postponing the formation of the film of vapour. Hence, 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 from the wall is maximum

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

Thin front propagation in random shear flows

Front propagation in time dependent laminar flows is investigated in the limit of very fast reaction and very thin fronts, i.e. the so-called geometrical optics limit. In particular, we consider fronts evolving in time correlated random shear flows, modeled in terms of Ornstein-Uhlembeck processes. We show that the ratio between the time correlation of the flow and an intrinsic time scale of the reaction dynamics (the wrinkling time $t_w$) is crucial in determining both the front propagation speed and the front spatial patterns. The relevance of time correlation in realistic flows is briefly discussed in the light of the bending phenomenon, i.e. the decrease of propagation speed observed at high flow intensities.Comment: 5 Revtex4 pages, 4 figures include

Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores

Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter's ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge, and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus alpha-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements

Reversible Cavitation-Induced Junctional Opening in an Artificial Endothelial Layer.

Targeting pharmaceuticals through the endothelial barrier is crucial for drug delivery. In this context, cavitation-assisted permeation shows promise for effective and reversible opening of intercellular junctions. A vessel-on-a-chip is exploited to investigate and quantify the effect of ultrasound-excited microbubbles-stable cavitation-on endothelial integrity. In the vessel-on-a-chip, the endothelial cells form a complete lumen under physiological shear stress, resulting in intercellular junctions that exhibit barrier functionality. Immunofluorescence microscopy is exploited to monitor vascular integrity following vascular endothelial cadherin staining. It is shown that microbubbles amplify the ultrasound effect, leading to the formation of interendothelial gaps that cause barrier permeabilization. The total gap area significantly increases with pressure amplitude compared to the control. Gap opening is fully reversible with gap area distribution returning to the control levels 45 min after insonication. The proposed integrated platform allows for precise and repeatable in vitro measurements of cavitation-enhanced endothelium permeability and shows potential for validating irradiation protocols for in vivo applications