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EphB4 angiogenic kinase over-expression in Mesothelioma cells relies upon a degradation rescue signal provided by autocrine IGF-II activation of Insulin Receptor A. However, the identity of the molecular machinery involved in EphB4 rapid degradation upon IGF-II signal deprivation are unknown. Using targeted proteomics, protein–protein interaction methods, PCR cloning, and 3D modeling approaches, we identified a novel ubiquitin E3 ligase complex recruited by the EphB4 C tail upon autocrine IGF-II signal deprivation. We show this complex to contain a previously unknown N-Terminal isoform of Deltex3 E3-Ub ligase (referred as “DTX3c”), along with UBA1(E1) and UBE2N(E2) ubiquitin ligases and the ATPase/unfoldase Cdc48/p97. Upon autocrine IGF-II neutralization in cultured MSTO211H (a Malignant Mesothelioma cell line that is highly responsive to the EphB4 degradation rescue IGF-II signal), the inter-molecular interactions between these factors were enhanced and their association with the EphB4 C-tail increased consistently with the previously described EphB4 degradation pattern. The ATPase/unfoldase activity of Cdc48/p97 was required for EphB4 recruitment. As compared to the previously known isoforms DTX3a and DTX3b, a 3D modeling analysis of the DTX3c Nt domain showed a unique 3D folding supporting isoform-specific biological function(s). We shed light on the molecular machinery associated with autocrine IGF-II regulation of oncogenic EphB4 kinase expression in a previously characterized IGF-II+/EphB4+ Mesothelioma cell line. The study provides early evidence for DTX3 Ub-E3 ligase involvement beyond the Notch signaling pathway.

Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i) heterogeneous DNA retraction and rezipping (f < 17pN), (ii) normal (17pN < f < 60pN) and (iii) anomalous (f > 60pN) drift-diffusive behavior. We show that the normal drift-diffusion regime can be effectively modelled as a one-dimensional stochastic process in a tilted periodic potential. We use the theory of stochastic processes to recover the potential from nonequilibrium unzipping trajectories and show that it corresponds to the free-energy landscape for single base-pairs unzipping. Applying this general approach to other single-molecule systems with periodic potentials ought to yield detailed free-energy landscapes from out-of-equilibrium trajectories., 6 pages, 4 figures

We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide long xrRNA from Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either one of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on timescales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, both for activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing-downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings ought to be useful as a reference to interpret and design future theoretical and experimental studies of RNA translocation.

Publisher Copyright: © 2022 The Authors. Small published by Wiley-VCH GmbH. The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+-free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.

The dataset presented here regard the analysis reported in the research article entitled “Comparison of different plasma actuation strategies for aeroelastic control on a linear compressor cascade” De Giorgi et al. (2021) [1] . These data are related to the Computational Fluid Dynamics (CFD) assessment of different plasma actuation strategies for the aeroelastic control of an aero engine compressor cascade in subsonic flow conditions. The authors evaluated the accuracy of numerical computations using experimental results. Here, both experimental and raw data of the CFD simulations are presented.

Propofol, one of the most commonly used intravenous general anesthetics, modulates neuronal function by interacting with ion channels. The mechanisms that link propofol binding to the modulation of distinct ion channel states, however, are not understood. To tackle this problem, we investigated the prokaryotic ancestors of eukaryotic voltage-gated Na+ channels (Navs) using unbiased photoaffinity labeling (PAL) with a diazirine derivative of propofol (AziPm), electrophysiological methods, and mutagenesis. AziPm inhibits Nav function in a manner that is indistinguishable from that of the parent compound by promoting activation-coupled inactivation. In several replicates (8/9) involving NaChBac and NavMs, we found adducts at residues located at the C-terminal end of the S4 voltage sensor, the S4-S5 linker, and the N-terminal end of the S5 segment. However, the non-inactivating mutant NaChBac-T220A yielded adducts that were different from those found in the wild-type counterpart, which suggested state-dependent changes at the binding site. Then, using molecular dynamics simulations to further elucidate the structural basis of Nav modulation by propofol, we show that the S4 voltage sensors and the S4-S5 linkers shape two distinct propofol binding sites in a conformation-dependent manner. Supporting the PAL and MD simulation results, we also found that Ala mutations of a subset of adducted residues have distinct effects on gating modulation of NaChBac and NavMs by propofol. The results of this study provide direct insights into the structural basis of the mechanism through which propofol binding promotes activation-coupled inactivation to inhibit Nav channel function.

We used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.

DNA origami technology allows for the precise nanoscale assembly of chemical entities that give rise to sophisticated functional materials. We have created a versatile DNA origami nanofork antenna (DONA) by assembling Au or Ag nanoparticle dimers with different gap sizes down to 1.17 nm, enabling signal enhancements in surface-enhanced Raman scattering (SERS) of up to 1011. This allows for single-molecule SERS measurements, which can even be performed with larger gap sizes to accommodate differently sized molecules, at various excitation wavelengths. A general scheme is presented to place single analyte molecules into the SERS hot spots using the DNA origami structure exploiting covalent and noncovalent coupling schemes. By using Au and Ag dimers, single-molecule SERS measurements of three dyes and cytochrome c and horseradish peroxidase proteins are demonstrated even under nonresonant excitation conditions, thus providing long photostability during time-series measurement and enabling optical monitoring of single molecules.

We characterize equilibrium properties and relaxation dynamics of a two-dimensional lattice containing, at each site, two particles connected by a double-well potential (dumbbell). Dumbbells are oriented in the orthogonal direction with respect to the lattice plane and interact with each other through a Lennard-Jones potential truncated at the nearest neighbor distance. We show that the system's equilibrium properties are accurately described by a two-dimensional Ising model with an appropriate coupling constant. Moreover, we characterize the coarsening kinetics by calculating the cluster size as a function of time and compare the results with Monte Carlo simulations based on Glauber or reactive dynamics rate constants.

Understanding the biophysical mechanisms that govern the combination of protein domains into viable proteins is essential for advancing synthetic biology and biomedical engineering. Here, we use massively parallel genotype/phenotype assays to determine cell surface expression of over 300,000 variants of the inward rectifier K+ channel Kir2.1 recombined with hundreds of protein motifs. We use machine learning to derive a quantitative biophysical model and practical rules for domain recombination. Insertional fitness depends on nonlinear interactions between the biophysical properties of inserted motifs and the recipient protein, which adds a new dimension to the rational design of fusion proteins. Insertion maps reveal a generalizable hierarchical organization of Kir2.1 and several other ion channels that balances stability needed for folding and dynamics required for function.SummaryMassively parallel assays reveal interactions between donor domains and recipient proteins govern domain compatibility

Propofol, one of the most commonly used intravenous general anesthetics, modulates neuronal function by interacting with ion channels. The mechanisms that link propofol binding to the modulation of distinct ion channel states, however, are not understood. To tackle this problem, we investigated prokaryotic ancestors of eukaryotic voltage-gated Na+ channels (Navs) using unbiased photoaffinity labeling with a photoacitivatable propofol analog (AziPm), electrophysiological methods and mutagenesis. The results directly demonstrate conserved propofol binding sites involving the S4 voltage sensors and the S4-S5 linkers in NaChBac and NavMs, and also suggest state-dependent changes at these sites. Then, using molecular dynamics simulations to elucidate the structural basis of propofol modulation, we show that the S4 voltage sensors and the S4-S5 linkers shape two distinct propofol binding sites in a conformation-dependent manner. These interactions help explain how propofol binding promotes activation-coupled inactivation to inhibit Nav channel function.

DNA origami technology allows for the precise nanoscale assembly of chemical entities that give rise to new functional materials. We have created a versatile DNA Origami Nanofork Antenna (DONA) by assembling Au or Ag nanoparticle dimers with 1.17 ± 0.67 nm gap size, enabling signal enhancements in surface-enhanced Raman scattering (SERS) of up to 1011. This allows for single-molecule SERS measurements, which can even be performed with larger gap sizes to accommodate differently sized molecules, and at various excitation wavelengths. A general scheme is presented to place single analyte molecules into the SERS hot spots using the DNA origami structure exploiting covalent and non-covalent coupling schemes. By using Au and Ag dimers, single-molecule SERS measurements of three dyes and cytochrome c and horseradish peroxidase proteins are demonstrated even under non-resonant excitation conditions, thus providing long photostability during time-series measurement, and enabling unprecedented optical monitoring of single molecules and DNA origami based nanomachines.

xrRNAs from flaviviruses survive in host cells for their exceptional dichotomic response to the unfolding action of different enzymes. They can be unwound, and hence copied, by replicases, and yet can resist degradation by exonucleases. How the same stretch of xrRNA can encode such diverse responses is an open question. Here, by using atomistic models and translocation simulations, we uncover an elaborate and directional mechanism for how stress propagates when the two xrRNA ends, 5′ and 3′, are driven through a pore. Pulling the 3′ end, as done by replicases, elicits a progressive unfolding; pulling the 5′ end, as done by exonucleases, triggers a counterintuitive molecular tightening. Thus, in what appears to be a remarkable instance of intra-molecular tensegrity, the very pulling of the 5′ end is what boosts resistance to translocation and consequently to degradation. The uncovered mechanistic principle might be co-opted to design molecular meta-materials.

We study the stationary dynamics of an active interacting Brownian particle system. We measure the violations of the fluctuation dissipation theorem, and the corresponding effective temperature, in a locally resolved way. Quite naturally, in the homogeneous phases the diffusive properties and effective temperature are also homogeneous. Instead, in the inhomogeneous phases (close to equilibrium and within the MIPS sector) the particles can be separated in two groups with different diffusion properties and effective temperatures. Notably, at fixed activity strength the effective temperatures in the two phases remain distinct and approximately constant within the MIPS region, with values corresponding to the ones of the whole system at the boundaries of this sector of the phase diagram. We complement the study of the globally averaged properties with the theoretical and numerical characterization of the fluctuation distributions of the single-particle diffusion, linear response, and effective temperature in the homogeneous and inhomogeneous phases. We also distinguish the behavior of the (time-delayed) effective temperature from the (instantaneous) kinetic temperature, showing that the former is independent of the friction coefficient.

Polyamines regulate K+ efflux from cells by binding to K channels in a voltage-dependent manner. Suma et al. analyze how two polyamines, spermidine and spermine, bind and block the prokaryotic K channel MthK., Polyamines such as spermidine and spermine are found in nearly all cells, at concentrations ranging up to 0.5 mM. These cations are endogenous regulators of cellular K+ efflux, binding tightly in the pores of inwardly rectifying K+ (Kir) channels in a voltage-dependent manner. Although the voltage dependence of Kir channel polyamine blockade is thought to arise at least partially from the energetically coupled movements of polyamine and K+ ions through the pore, the nature of physical interactions between these molecules is unclear. Here we analyze the polyamine-blocking mechanism in the model K+ channel MthK, using a combination of electrophysiology and computation. Spermidine (SPD3+) and spermine (SPM4+) each blocked current through MthK channels in a voltage-dependent manner, and blockade by these polyamines was described by a three-state kinetic scheme over a wide range of polyamine concentrations. In the context of the scheme, both SPD3+ and SPM4+ access a blocking site with similar effective gating valences (0.84 ± 0.03 e0 for SPD3+ and 0.99 ± 0.04 e0 for SPM4+), whereas SPM4+ binds in the blocked state with an ∼20-fold higher affinity than SPD3+ (Kd = 28.1 ± 3.1 µM for SPD3+ and 1.28 ± 0.20 µM for SPM4+), consistent with a free energy difference of 1.8 kcal/mol. Molecular simulations of the MthK pore in complex with either SPD3+ or SPM4+ are consistent with the leading amine interacting with the hydroxyl groups of T59, at the selectivity filter threshold, with access to this site governed by outward movement of K+ ions. These coupled movements can account for a large fraction of the voltage dependence of blockade. In contrast, differences in binding energetics between SPD3+ and SPM4+ may arise from distinct electrostatic interactions between the polyamines and carboxylate oxygens on the side chains of E92 and E96, located in the pore-lining helix.

Small engines will be finding increasing applications in unmanned aerial vehicles (UAVs), drones and helicopters. However, their turbomachines exhibit lower efficiencies than those of large scale engines. In this context, the aerodynamic losses in the low-pressure turbines (LPTs) are largely accountable to flow separation at low Reynolds numbers operation, i.e. in cruise conditions. Active flow control is a promising technology to suppress separation, thus reducing losses, fuel consumption rates and therefore emissions. The present paper is focused on the experimental investigation of the potentialities of a Single Dielectric Barrier Discharge Plasma Actuator (SDBDPA) to reattach the separated flow at a Reynolds number of 2 ⋅ 10 4 . The influence of the high voltage (HV) waveform supplying the SDBDPA on both flow separation control and device power dissipation was studied. The investigated SDBDPA was manufactured by microfabrication techniques. Photolithography ensured thin metal deposition with high manufacturing reliability control. Due to the possible device degradation during operation, emphasis was put in selecting thin film materials that could withstand the plasma environment. Schott alkali-free borosilicate glass substrate was chosen as dielectric, while a multilayer tungsten (W)/titanium nitride (TiN) as electrode material. The experimental approach comprised the actuator testing over a curved wall plate, designed with a shape to reproduce the suction surface of a LPT rotor blade and installed in closed loop wind tunnel test section. The SDBDPA was located at the front side of the adverse pressure gradient area, in order to control flow separation. Different HV excitation waveforms (sinus, triangle and square) and amplitudes were tested and compared, aiming to identify the input signal that gave the best flow control authority and device energy conversion efficiency. The applied voltage and the discharge current were acquired in order to determine the actuator dissipated power. Two-dimensional (2-D) flow velocity measurements were carried out by laser Doppler velocimetry (LDV) and particle image velocimetry (PIV). Velocity results showed that the extension of the separation area was reduced by actuation. Moreover, when the actuator was on, the boundary layer thickness and the negative velocity magnitude decreased. Their reduction increased with the applied voltage (i.e. higher power dissipations). At comparable peak-to-peak applied voltages, the sinus waveforms slightly outperformed the other waveforms; however, while the sinus and triangle ones had comparable power dissipation, the square wave always dissipated the most.

The objective of this paper is to investigate the effects of Dielectric Barrier Discharge (DBD) plasma actuators on the aeroelastic control of a subsonic compressor cascade, for unsteady load mitigation and enhancement in the cascade aeroelastic response. Numerical simulations of the blades oscillating in traveling wave mode are performed with the commercial solver Ansys FLUENT®. Results are then validated through comparison with experimental data to assess the stability and convergence of the reference grid. Aeroelastic control is achieved by means of two AC-DBD plasma actuators installed on the trailing edge of the compressor blades, one on the suction side and one on the pressure side. Alleviation of the blade load is realized by operating alternately the actuators through a cosinusoidal function. Moreover, the effect of the actuation force phase on the blade load control is evaluated. Based on the actuation phase, results show that it is possible to manipulate effectively the unsteady lift and moment coefficients, stabilizing the compressor performance, alleviating fatigue phenomena and enlarging the flutter limits of the cascade. Plasma actuators confirm to be a very promising technology for active flow control in turbomachines and aeronautical applications.

Different input waveforms applied to a Single Dielectric Barrier Discharge Plasma Actuator (SDBDPA) were compared for flow separation control on low-pressure turbines (LPTs). The investigated Reynolds number (Re) was 2·104. The work aim was the device optimization in terms of materials and excitation conditions for enhancing its durability and performances. The SDBDPA was manufactured by microfabrication techniques. Device materials that could withstand the plasma environment were selected. Sine, square and triangle waveforms were compared in terms of actuator dissipated power and induced velocity. At comparable peak-to-peak applied voltage, the sinus outperformed the other waveforms, while the square dissipated the most.

We study the large deviations of the distribution P(W_\tau) of the work associated with the propulsion of individual active brownian particles in a time interval \tau, in the region of the phase diagram where macroscopic phase separation takes place. P(W_\tau) is characterised by two peaks, associated to particles in the gaseous and in the clusterised phases, and two separate non-convex branches. Accordingly, the generating function of W_\tau cumulants displays a double singularity. We discuss the origin of such non-convex branches in terms of the peculiar dynamics of the system phases, and the relation between the observation time \tau and the typical persistence times of the particles in the two phases., Comment: 7 pages, 5 figures

The purpose of this paper is to perform a numerical study regarding the implementation of dielectric barrier discharge plasma micro-actuators for load alleviation on a NACA 23012 oscillating blade in a freestream flow. The work aims to evaluate the feasibility of using multiple dielectric barrier discharge (multi-DBD PAs) plasma actuators as a novel approach for load alleviation and stability control of airfoils in unsteady flow. A 6-actuators configuration, positioned at the trailing edge, is designed and tested. In this configuration, half of the actuators operate on the suction surface and the others on the pressure surface. In particular, the actuators located on the suction surface reduce the airfoil lift force if the induced body force is in a direction that is opposite of the main flow, because they lead to a slight and local increment of pressure on the surface. Instead, when actuators produce a body force aligned with the streamwise direction, they lead to a slight reduction of pressure, increasing lift. Contrarily, the actuators located on the pressure surface increase the lift, if the induced body force is in the direction opposite of the flow and reduce the lift in the opposite case. The effects of plasma actuators on the flow are incorporated into Navier–Stokes equations as a body force vector into the momentum equation. Different switching on/off laws of the actuators have been are compared, in order to reduce the loads amplitude of the airfoil, and to increase the stability of the blade response to the flow, and thus, alleviating fatigue phenomena on the blade and enhancing its aeroelastic stability. The effect of the phase of the plasma actuators switching law was evaluated for different pitching oscillation reduced frequencies, ranging from 0.1 to 0.5. The results underline the capability of DBD-PAs to control and reduce unsteady loads on an oscillating airfoil, improving also the airfoil stability if the phase of the actuation force is optimized for each pitching oscillation reduced frequency.

The present work focuses on the impact of dielectric barrier discharge (DBD) plasma actuators (PAs) on non-premixed lifted flame stabilization in a methane CH4-air Bunsen burner. Two coaxial DBD-PA configurations are considered. They are composed of a copper corona, installed on the outer surface of a quartz tube and powered with a high voltage sinusoidal signal, and a grounded needle installed along the burner axis. The two configurations differ in the standoff distance value, which indicates the positioning of the high frequency/high voltage (HV) electrode&rsquo, s upper edge with respect to the needle tip. Experimental results highlight that flame reattachment is obtained at a lower dissipated power when using a negative standoff distance (i.e., placing the needle upstream with respect to the corona). At 11 kV peak-to-peak voltage and 20 kHz frequency, plasma actuation allowed for reattaching the flame with a very low dissipated power (of about 0.05 W). Numerical simulations of the electrostatic field confirmed that this negative standoff configuration has a beneficial effect on the momentum sources, which oppose the flow and show that the highest electric field extends into the inner quartz tube, as confirmed by experimental visualization close to the needle tip. The modeling predicted an increase in the gas temperature of about 21.8 &deg, C and a slight modification of the fuel composition at the burner exit. This impacts the flame speed with a 10% increase close to the stoichiometric conditions with respect to the clean configuration.

Airfoils shelf life is strongly reduced by the application of unsteady loads, which can bring to fatigue phenomena and non-stable performance of the device. In this context, this paper carries out an evaluation of an unsteady application of Dielectric Barrier Discharge Plasma Actuator (DBD-PA) to reduce loads variability on a pitching airfoil, with the aim to increase the aerodynamic profiles durability and thus to increase airfoil stability. The comparison, in order to evaluate the effect of actuators dimensions, involves two different devices, with a high voltage electrode length one order of magnitude different.

The present work shows a preliminary investigation of the impact of plasma actuation on lifted flame stabilization in a methane CH4-air Bunsen burner at ambient conditions. A high voltage (HV)/high frequency sinusoidal signal has been considered for the investigation. Also, different plasma actuator configurations have been tested, which differently ionized the flame detachment region immediately outside the Bunsen outlet and affected the flame behavior and reattachment. Experimental investigations were complemented by a numerical study, which allowed explaining the effect of each actuator configuration on the flow. Therefore, once the best actuator configuration was selected, the efficiency of the plasma actuation has been evaluated in terms of flame anchoring capability and actuator dissipated power (while keeping the fuel-to-air equivalence ratio ? fixed around 0.035). In particular, iorder to change the actuator power dissipation, different peak-to-peak voltages Vpp were tested, while the actuation frequency was kept equal to 20 kHz. Results showed that the plasma actuation allowed reattaching the flame with a negligible dissipated power (about 0.05 W). Other equivalence ratios were then tested by increasing the air flow rate and keeping constant the fuel flow rate. Results showed that we can operate at very lean conditions (? around 0.021) with a power dissipation lower than 0.1 W.

The aim of this study is to investigate the performance of dielectric barrier discharge plasma actuators (DBD-PAs) applied to control the aeroelastic response of a compressor cascade in subsonic flow conditions. Simulations involve a cascade composed by 7-blade, 3 of which show a not-synchronous pitching behaviour. Two different inter blade phase angle (IBPA) have been tested and compared. Actuators capabilities in terms of load alleviation and instability control have been evaluated through the measurement of mean value, standard deviation and hysteresis area of the airfoil response in terms of lift and moment coefficients.

The flame stabilization represents a relevant issue in aero-engine design. In fact, the growing demand of pollutant emissions reduction without significant losses of the combustion efficiency has driven the efforts of the scientific community towards lean flames. Lean fuel mixtures, characterized by low temperature flames, could manifest an unstable behaviour which can easily lead to the flame extinction due to the establishment of the blowout condition. This requires the implementation of control systems to avoid flame instability occurrence. The present work shows an investigation of the impact of dielectric barrier discharge (DBD) plasma actuation on lifted flame stabilization in a methane CH4-air Bunsen burner at ambient conditions. Two different plasma actuator configurations, powered with a high voltage (HV)/high frequency sinusoidal signal, have been investigated. Once the best actuator configuration was selected, the efficiency of the plasma actuation has been evaluated in terms of the flame lift-off distance, length and shape. In particular, in order to change the actuator power dissipation, different peak-to-peak voltages Vpp were tested, while the actuation frequency was kept equal to 20 kHz. The application of plasma discharges to flame stabilization leads to plasma-attached flames or plasma-enhanced lifted flames, depending on the air and fuel flow rates. At air flow rate of 1.54 g/s, plasma actuation allowed to decrease the lift-off height until the fuel jet velocity was below about 0.05 m/s thanks to the extension of the flame region upstream, toward the burner exit section. Beyond this value, it had no significant impact on the flame lift-off height, even though the amplitude of the lift-off height oscillations reduced coupled with a more stable behaviour of the lifting flame. The benefit of the plasma actuation increased by reducing the air flow rate to 1.35 g/s. In this condition, plasma-assisted flame reattachment was evident at each fuel velocity, in combination with an increasing flame height proportionally to the fuel jet velocity.

International audience; Recently, we characterized the complete phase transition diagram in the phgr-Pe parameter space for two models of active brownian particles in two dimensions. These models are composed of hard disks and dumbbells, respectively, the former being isotropic and the latter anisotropic. Here, we want to outline all the most significant features of these two paradigmatic models and compare them. Remarkably, the phase diagrams of the two models are affected differently by the introduction of activity. Disks present a two-stage melting scenario from Pe=0 to about Pe=3, with a first order phase transition between liquid and hexatic and a Berezinskii-Kosterlitz-Thouless transition between hexatic and solid. At higher activities, the three phases are still observed, but the transition between liquid and hexatic becomes a BKT transitions without a distinguishable coexistence region. Dumbbells, instead, present a macroscopic coexistence between hexatically ordered regions and disordered ones, over a finite interval of packing fractions, for all activities, included Pe=0, without any observable discontinuity in the behavior upon increasing Pe.

DNA polymerase θ (Polθ) is a unique polymerase-helicase fusion protein that promotes microhomology-mediated end-joining (MMEJ) of DNA double-strand breaks (DSBs). How full-length human Polθ performs MMEJ at the molecular level remains unknown. Using a biochemical approach, we find that the helicase is essential for Polθ MMEJ of long ssDNA overhangs which model resected DSBs. Remarkably, Polθ MMEJ of ssDNA overhangs requires polymerase-helicase attachment, but not the disordered central domain, and occurs independently of helicase ATPase activity. Using single-particle microscopy and biophysical methods, we find that polymerase-helicase attachment promotes multimeric gel-like Polθ complexes that facilitate DNA accumulation, DNA synapsis, and MMEJ. We further find that the central domain regulates Polθ multimerization and governs its DNA substrate requirements for MMEJ. These studies identify unexpected functions for the helicase and central domain and demonstrate the importance of polymerase-helicase tethering in MMEJ and the structural organization of Polθ., DNA polymerase θ is a polymerase-helicase essential for microhomology-mediated end-joining (MMEJ) or alternative end-joining of DNA. Here the authors use biochemical and biophysical methods to reveal how full-length human DNA polymerase θ performs MMEJ at the molecular level.

Knots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases.

International audience; With the help of molecular dynamics simulations we study an ensemble ofactive dumbbells in purely repulsive interaction. We derive the phase diagramin the density-activity plane and we characterise the various phases withliquid, hexatic and solid character. The analysis of the structural anddynamical properties, such as enstrophy, mean square displacement,polarisation, and correlation functions, shows the continuous character ofliquid and hexatic phases in the coexisting region when the activity isincreased starting from the passive limit.

Polyelectrolytes with strong counterion couplings are compact at low electric fields but switch to elongated forms at high ones. As yet, little is known from both nanomanipulation experiments and theory about the transition mechanisms between compact and extended states. Here, we systematically address this out-of-equilibrium conversion using molecular dynamics simulations of coarse-grained polyelectrolyte chains of 1000 and 1500 monomers in a salt buffer of about 20 000 and 80 000 charged particles, respectively. We find that compact-to-elongated transitions are smooth and fast in only half of the trajectories. In the other half, the elongation is jammed halfway by the formation of backfolded, needle-like states. These states, which have not been envisioned before, have lifetimes that are orders of magnitude larger than the chain’s relaxation time and ought to be detectable with current single-molecule experimental setups.

We study the statistics, in stationary conditions, of the work $W_\tau$ done by the active force in different systems of self-propelled particles in a time $\tau$. We show the existence of a critical value $W_\tau ^\dag$ such that fluctuations with $W_\tau >W_\tau ^\dag$ correspond to configurations where interaction between particles plays a minor role whereas those with $W_\tau < W_\tau ^\dag$ represent states with single particles dragged by clusters. This two-fold behavior is fully mirrored by the probability distribution $P(W_\tau)$ of the work, which does not obey the large-deviation principle for $W_\tau, Comment: 6 pages, 4 figures

We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.

We demonstrate that there is macroscopic co-existence between regions with hexatic order and regions in the liquid/gas phase over a finite interval of packing fractions in active dumbbell systems with repulsive power-law interactions in two dimensions. In the passive limit this interval remains finite, similarly to what has been found in bidimensional systems of hard and soft disks. We did not find discontinuous behaviour upon increasing activity from the passive limit., 5 pages, 5 figures. To be published in Physical Review Letters