Ms Time Scale Research Articles

Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms - μs) dynamics in the C-terminal helix at the dimer interface.

The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the dynamics of the protein’s backbone in solution and accelerate the identification and mapping of ligand-binding surfaces through chemical shift perturbation studies, the backbone 1H, 13C, and 15N NMR chemical shifts for Nsp9 have been extensively assigned. These assignments were assisted by the preparation of an ~ 70% deuterated sample and residue-specific, 15N-labelled samples (V, L, M, F, and K). A major feature of the assignments was the “missing” amide resonances for N96-L106 in the 1H-15N HSQC spectrum, a region that comprises almost the complete C-terminal α-helix that forms a major part of the homodimer interface in the crystal structure of SARS-CoV-2 Nsp9, suggesting this region either undergoes intermediate motion in the ms to μs timescale and/or is heterogenous. These “missing” amide resonances do not unambiguously appear in the 1H-15N HSQC spectrum of SARS-CoV-2 Nsp9 collected at a concentration of 0.0007 mM. At this concentration, at the detection limit, native mass spectrometry indicates the protein is exclusively in the monomeric state, suggesting the intermediate motion in the C-terminal of Nsp9 may be due to intramolecular dynamics. Perhaps this intermediate ms to μs timescale dynamics is the physical basis for a previously suggested “fluidity” of the C-terminal helix that may be responsible for homophilic (Nsp9-Nsp9) and postulated heterophilic (Nsp9-Unknown) protein-protein interactions.

High time resolution measurements of droplet evaporation kinetics and particle crystallisation.

A refined technique for observing the complete evaporation behaviour of free-falling droplets, from droplet generation to complete solvent evaporation, with ultra-high time resolution is introduced and benchmarked. High-resolution phase-delay stroboscopic imaging is employed to simultaneously resolve the evolving droplet morphology, geometric and aerodynamic diameters, throughout the evaporative lifetime with a user-controlled < μs timescale. This allows rapid, complex morphological changes, such as crystallisation events, to be clearly observed and the corresponding mechanisms to be inferred. The dried particles are sampled for offline SEM analysis and the observed morphologies compared to the inflight imaging. Density changes can be calculated directly from the deviation between the geometric and aerodynamic diameters. The full capabilities of the new technique are demonstrated by examination of the different evaporation behaviours and crystallisation mechanisms for aqueous sodium chloride droplets evaporating under different ambient relative humidity (RH) conditions. The crystallisation window, defined as the time taken from initial to complete crystallisation, is shown to be RH dependent, extending from 0.03 s at 20% RH and 0.13 s at 40% RH. The different crystallisation mechanisms observed during the experiments are also clearly reflected in the final structure of the dry particles, with multi-crystal structures produced at low RH compared to single-crystal structures at higher RH. It is anticipated that this technique will unlock measurements which explore the evaporation behaviour and crystallisation mechanisms for rapid, complex droplet drying events, and with increasingly non-ideal solutions, relevant to industrial applications.

Torque-dense photomechanical actuation.

Contactless actuation powered using light is shown to generate torque densities approaching 10 N m kg-1 at angular velocities ∼102 rad s-1: metrics that compare favorably against tethered electromechanical systems. This is possible even though the extinction of actinic light limits the characteristic thickness of photoresponse in polymers to tens of μm. Confinement of molecularly patterned developable shells fabricated from azobenzene-functionalized liquid crystalline polymers encodes torque-dense photoactuation. Photostrain gradients from unstructured irradiation segment this geometry into two oppositely curved regions connected by a curved crease. A monolithic curved shell spontaneously bifurcates into a jointed, arm-like mechanism that generates flexure over sweep angles exceeding a radian. Strain focusing at the crease is hierarchical: an integral crease nucleates at smaller magnitudes of the prebiased curvature, while a crease decorated with point-like defects emerges at larger curvatures. The phase-space of morphogenesis is traceable to the competition between stretch and bending energies and is parameterizable as a function of the geometry. The framework for generating repetitive torque-dense actuation from slender light-powered actuators holds broader implications for the design of soft, remotely operated machines. Here, it is harnessed in illustrative mechanisms including levers, lifters and grabbers that are powered and regulated exclusively using light.

Self-propulsion droplet induced via periodic explosive boiling

When a droplet is placed on a surface with a temperature higher than Leidenfrost temperature, it will be levitated on its own vapor cushion, which makes the droplet have amazing mobility. Generally, the vapor flow under the droplet is corrected by constructing asymmetry micro/nano textured surfaces to realize the self-propulsion of the droplet. However, the control of droplet dynamics becomes uncertain due to the complicated interaction among liquid-vapor-solid phases, and the direction of droplet motion and droplet transport velocity (10－40 cm/s) have limitations. Leidenfrost heat transfer surface and impact surface are constructed in this experiment. When the surface of Leidenfrost heat transfer for droplet levitation contacts the droplet which the sufficient energy flows towards, the rough ring surface acts as an igniter. When a warm Leidenfrsot droplet (&lt;i&gt;fuel&lt;/i&gt;) contacts skirt ring (&lt;i&gt;igniter&lt;/i&gt;), abundant micro/nano cavities of rough skirt ring not only generate additional radiation heat flux towards droplet but also provide nucleation sites to trigger explosive boiling on a ～10 ms time scale. The thrust force &lt;i&gt;F&lt;/i&gt;&lt;sub&gt;th&lt;/sub&gt; generated by periodic explosive boiling realizes the self-propulsion of droplets. In the initial stage of droplet motion, the inertial force &lt;i&gt;F&lt;/i&gt;&lt;sub&gt;i&lt;/sub&gt; is dominant, and the droplet impact is mostly specular reflection, and the droplet trajectory is chaotic. With the decrease of droplet diameter, the pulsed thrust &lt;i&gt;F&lt;/i&gt;&lt;sub&gt;th&lt;/sub&gt; is dominant, and the droplet trajectory passes through the center of the Leidenfrost heat transfer surface. Our experimental results show that the droplet passes through the center of the Leidenfrost heat transfer surface in a wide diameter range (&lt;i&gt;D&lt;/i&gt; = 0.671－1.576 mm). For the last (150&lt;sup&gt;th&lt;/sup&gt;) collision with the rough ring, the curved trajectory exists instead of line trajectory with &lt;inline-formula&gt;&lt;tex-math id="Z-20211217122516-1"&gt;\begin{document}$ D \sim 0.105 $\end{document}&lt;/tex-math&gt;&lt;alternatives&gt;&lt;graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="24-20211386_Z-20211217122516-1.jpg"/&gt;&lt;graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="24-20211386_Z-20211217122516-1.png"/&gt;&lt;/alternatives&gt;&lt;/inline-formula&gt; mm. For a very small droplet, the drag force &lt;i&gt;F&lt;/i&gt;&lt;sub&gt;d&lt;/sub&gt; is dominant, which prevents the droplet from continuing to move. The droplet is followed by sessile droplet evaporation until it totally disappears. At the same time, the droplet transport velocity is as high as 68.91 cm/s, which has not been realized before. The present work provides a new method to manipulate droplet motion at a high temperature. Our Leidenfrost system is simple, cost-effective and lasts long-term operation because it does not depend on complicated micro/nano fabrications, which is expected to be used in microfluidic and heat transfer two-phase systems.

Omega-3 versus Omega-6 fatty acid availability is controlled by hydrophobic site geometries of phospholipase A2s

Human phospholipase A2s (PLA2) constitute a superfamily of enzymes that hydrolyze the sn-2 acyl-chain of glycerophospholipids, producing lysophospholipids and free fatty acids. Each PLA2 enzyme type contributes to specific biological functions based on its expression, subcellular localization, and substrate specificity. Among the PLA2 superfamily, the cytosolic cPLA2 enzymes, calcium-independent iPLA2 enzymes, and secreted sPLA2 enzymes are implicated in many diseases, but a central issue is the preference for double-bond positions in polyunsaturated fatty acids (PUFAs) occupying the sn-2 position of membrane phospholipids. We demonstrate that each PLA2 has a unique preference between the specific omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and the omega-6 arachidonic acid (AA), which are the precursors of most proinflammatory and anti-inflammatory or resolving eicosanoids and related oxylipins. Surprisingly, we discovered that human cPLA2 selectively prefers AA, whereas iPLA2 prefers EPA, and sPLA2 prefers DHA as substrate. We determined the optimal binding of each phospholipid substrate in the active site of each PLA2 to explain these specificities. To investigate this, we utilized recently developed lipidomics-based LC-MS/MS and GC/MS assays to determine the sn-2 acyl chain specificity in mixtures of phospholipids. We performed μs timescale molecular dynamics (MD) simulations to reveal unique active site properties, especially how the precise hydrophobic cavity accommodation of the sn-2 acyl chain contributes to the stability of substrate binding and the specificity of each PLA2 for AA, EPA, or DHA. This study provides the first comprehensive picture of the unique substrate selectivity of each PLA2 for omega-3 and omega-6 fatty acids.

Eu3+/Tb3+ supramolecular assembly hybrids for ultrasensitive and ratiometric detection of anthrax spore biomarker in water solution and actual spore samples

Rare earth (RE) complexes have found a variety of applications in materials science and biomedicine because of their unique luminescence properties. However, the poor stability and solubility in water of multicomponent RE assemblies significantly limit their practical applications. We rationally designed and developed a novel Eu3+/Tb3+ supramolecular assembly hybrids (Eu/Tb-SAH) by supramolecular host-guest recognition and coordination recognition with the excellent characteristics of water dispersion stability, biocompatibility and luminous properties. As anthrax spore biomarker, 2,6-pyridinedicarboxylic acid (DPA) can coordinate with Tb3+ and sensitize Tb3+, resulting in a proportional change of fluorescence intensity and lifetime on the ms timescales, thereby realizing rapid and sensitive detection of DPA in water media or actual spores. To confirm our prediction, accurate and selective detection of DPA was achieved with Eu/Tb-SAH as a nanoprobe through steady-state ratiometric fluorescence and time-resolved technology, of which the limit of detection (LOD) are 27.3 nM and 1.06 nM, respectively. This was obviously lower than the amount of anthrax spores infecting the human body (60 μM). Besides, the filter paper was used to carry out visual detection of DPA and read the corresponding data through smart phones. This work paves a new way to fabricate luminescent RE nanomaterials and provides new ideas for the design of ratiometic lifetime imaging biosensors in the meantime.

Terpyridine-Functionalized Calixarenes: Synthesis, Characterization and Anion Sensing Applications.

Lanthanide complexes have been developed and are reported herein. These complexes were derived from a terpyridine-functionalized calix[4]arene ligand, chelated with Tb3+ and Eu3+. Synthesis of these complexes was achieved in two steps from a calix[4]arene derivative: (1) amide coupling of a calix[4]arene bearing carboxylic acid functionalities and (2) metallation with a lanthanide triflate salt. The ligand and its complexes were characterized by NMR (1H and 13C), fluorescence and UV-vis spectroscopy as well as MS. The photophysical properties of these complexes were studied; high molar absorptivity values, modest quantum yields and luminescence lifetimes on the ms timescale were obtained. Anion binding results in a change in the photophysical properties of the complexes. The anion sensing ability of the Tb(III) complex was evaluated via visual detection, UV-vis and fluorescence studies. The sensor was found to be responsive towards a variety of anions, and large binding constants were obtained for the coordination of anions to the sensor.

Observation of giant persistent photoconductivity on vanadium dioxide thin film device

We report a giant persistent photoconductivity (GPPC) phenomenon in VO2 film device prepared on corning glass substrate. With a single pulse laser irradiation onto the device at bias voltages of 7 V and 8 V, the VO2 film makes an insulator-to-metal transition with a sharp increase of photo current. The photo current remained at a highly conductive state for long period, e.g. the photo current for VO2 device was decreased only ~1% in one day. The GPPC was found within the limit of critical voltages of the hysteresis loop in voltage vs current curve of the device. High speed time-current measurements on the device with a 20 ms single pulse laser irradiation revealed that the onset of abrupt photo current occurs in less than 1 ms time scale. The GPPC in VO2 device can contribute in realizing ultrafast optical remote control of advanced electronic devices i.e. optical memories, displays, and remote ultrafast switching devices.

Interpersonal Entrainment in Music Performance

Interpersonal musical entrainment—temporal synchronization and coordination between individuals in musical contexts—is a ubiquitous phenomenon related to music’s social functions of promoting group bonding and cohesion. Mechanisms other than sensorimotor synchronization are rarely discussed, while little is known about cultural variability or about how and why entrainment has social effects. In order to close these gaps, we propose a new model that distinguishes between different components of interpersonal entrainment: sensorimotor synchronization—a largely automatic process manifested especially with rhythms based on periodicities in the 100–2000 ms timescale—and coordination, extending over longer timescales and more accessible to conscious control. We review the state of the art in measuring these processes, mostly from the perspective of action production, and in so doing present the first cross-cultural comparisons between interpersonal entrainment in natural musical performances, with an exploratory analysis that identifies factors that may influence interpersonal synchronization in music. Building on this analysis we advance hypotheses regarding the relationship of these features to neurophysiological, social, and cultural processes. We propose a model encompassing both synchronization and coordination processes and the relationship between them, the role of culturally shared knowledge, and of connections between entrainment and social processes.

Charge separation and singlet fission in covalently linked diketopyrrolopyrrole derivatives and triphenylamine triad in solution

A covalently linked push-pull type triad containing two unsymmetrical electron donors, triphenylamine (TPA) and benzothiophene (BT), and diketopyrrolopyrrole (DPP), an electron acceptor, through thiophene spacer has been synthesized (BT-DPP-TPA(7)) and ultrafast relaxation dynamics of the triad has been explored in solution phase by various spectroscopic methods. Steady-state and time-resolved emission studies show the efficient fluorescence quenching of the DPP entity of as prepared BT-DPP-TPA(7) triad. The negative free energy values comprising the redox potentials and singlet state energy of BT-DPP-TPA(7) revealed the probability of electron transfer from the singlet ground state of TPA to the excited singlet state of DPP. Femtosecond transient absorption (fsTA) spectroscopic studies confirmed the formation of charge separation state by detecting triphenylamine radical cation as electron-transfer transients. The rate of charge separation, kCS, is (109−108 s−1) observed to be increasing from nonpolar to polar solvents and the rate of charge recombination, kCR, was found to be slower (μs time scale) in polar solvents like DMF and chloroform, than that in hexane, non-polar solvent (ns time scale). This novel aspect could be due to asymmetrically designed push-pull type triad, a feature that was not evident in push-pull triad constructed using symmetric TPA as electron donors. Furthermore, fsTA studies also demonstrate, for the first time, that the DPP derivatives, TDPP(4) and BT-DPP-TPA(7), both undergo singlet fission (SF) event (S→TT) in 100−200 ps time scale in solution phase for the solution of concentration above ∼100 μM. These results may pave the new avenue for device design comprising DPP derivatives.

Plasma activation of N2, CH4 and CO2: an assessment of the vibrational non-equilibrium time window

Vibrational excitation potentially enhances the energy efficiency of plasma dissociation of stable molecules and may open new routes for energy storage and process electrification. Electron, vibrational and rotational temperatures were measured by in situ Thomson and Raman scattering in order to assess the opportunities and limitations of the essential vibration-translation non-equilibria in N2, CO2 and CH4 plasma. Electron temperatures of 1.1–2.8 eV were measured in N2 and CH4. These are used to confirm predominant energy transfer to vibrations after an initial phase of significant electronic excitation and ionization. The vibrational temperatures initially exceed rotational temperatures by almost 8000 K in N2, by 900 K in CO2, and by 300 K in CH4. Equilibration is observed at the 0.1 ms timescale. Based on the vibrational temperatures, the vibrational loss rates for different channels are estimated. In N2, vibrational quenching via N atoms is identified as the dominant equilibration mechanism. Atomic nitrogen population reaches a mole fraction of more than 1%, as inferred from the afterglow emission decay, and explains a gas heating rate of 25 K μs−1. CH4 equilibration at 1200 K is predominantly caused by vibrational-translational relaxation in CH4–CH4 collisions. As for CO2, vibrational-translational relaxation via parent molecules is responsible for a large fraction of the observed heating, whereas product-mediated VT relaxation is not significantly contributing. It is suggested that electronic excitation, followed by dissociation or quenching contributes to the remaining heat generation. In conclusion, the time window to profit from vibrational excitation under the present conditions is limiting practical application.

Gradual compaction of the nascent peptide during cotranslational folding on the ribosome.

Nascent polypeptides begin to fold in the constrained space of the ribosomal peptide exit tunnel. Here we use force-profile analysis (FPA) and photo-induced energy-transfer fluorescence correlation spectroscopy (PET-FCS) to show how a small α-helical domain, the N-terminal domain of HemK, folds cotranslationally. Compaction starts vectorially as soon as the first α-helical segments are synthesized. As nascent chain grows, emerging helical segments dock onto each other and continue to rearrange at the vicinity of the ribosome. Inside or in the proximity of the ribosome, the nascent peptide undergoes structural fluctuations on the µs time scale. The fluctuations slow down as the domain moves away from the ribosome. Mutations that destabilize the packing of the domain's hydrophobic core have little effect on folding within the exit tunnel, but abolish the final domain stabilization. The results show the power of FPA and PET-FCS in solving the trajectory of cotranslational protein folding and in characterizing the dynamic properties of folding intermediates.

Real-Time Detection of Long Lived Near Infrared luminescence from Colourless Cubic Zirconia by Time-Gated Imaging

Here, we report a long-lived ms time scale decay luminescing in the near infrared &gt;800 nm present in productions of ‘white’ colourless, facetted yttrium stabilized cubic zirconia and observed using time-gated imaging. The spectrum of the strong luminescing feature also has characteristics of Neodymium (Nd3+) and has a multiexponential decay behaviour. Real-time detection of cubic zirconia mounted in diamond jewellery containing very small stones (≤0.01 ct) is made possible, where observation by loupe is more challenging or other conventional techniques impractical and or slow to implement. The near infrared observed can be excited using a low-cost and eye/skin safe-visible green LED light source and the time-gated imaging of the luminescence using a machine vision monochrome camera. The use of near infrared, time-gated detection in combination with other verification instruments increases the robustness of screening diamond parcels. Therefore, it is recommended that any stone exhibiting strong delayed luminescence in the near infrared be treated with caution, as this is not a typical feature found in this precious gemstone. In this case, the instrument developed was expanded to incorporate a white LED illumination ring as a viewfinder, in order to aid the inspection of loose and mounted configurations.

Passive Internalization of Bioactive β-Casein Peptides into Phospholipid (POPC) Bilayers. Free Energy Landscapes from Unbiased Equilibrium MD Simulations at μs-Time Scale

Absorption of bioactive peptides in the intestinal epithelium take place in the apical or the basolateral tight junctions of the cells. Depending on the peptide size and hydrophobicity, translocation mechanisms involve processes of passive diffusion, active transport by peptide-cotransporters such as members of the PepT family, and transcytosis by internalization vesicles. In this work, we investigated passive diffusion of bioactive peptides of 6, 17, and 30 amino acids into lipid bilayers of (POPC) phospholipid molecules. We initially selected these three peptides because such fragments are produced by partial hydrolysis of β-casein (BCN), and because of their physiological functions: BCN6 is an agonist of opioid receptors; BCN17 is an inhibitor of thrombin and angiotensin-converting enzymes, and BCN30 promotes secretion of the protective mucin barrier in the intestine. Our computational set up consisted of unbiased equilibrium molecular dynamics simulations, at the μs-time scale, using an all-atom force field. Each peptide was allowed to freely fold and unfold, as well as enter and exit the lipid bilayer, which allows determination of peptide affinity for the bilayer interface and hydrophobic core. Passive internalization of BCN6 (YPVEPF), BCN17 (YQEPVLGPVR GPFPIIV), and BCN30 (GVSKVKEAMA PKHKEMPFPK YPVEPFTESQ) displayed different dynamics at the bilayer interface: the BCN6 peptide attached and detached throughout the simulation trajectory; BCN17 and BCN30 attached irreversibly to the bilayer interface, respectively, with N- and C-terminus fragments in close contact with lipid molecules. Quenching of tyrosine fluorescence data suggest interfacial interactions of BCN6, BCN17 and BCN30 in POPC lipid bilayers, consistent with the proposed modeling set up. This approach gave valuable information of peptide insertion and folding at a lipid bilayer, allowing to explore the initial stages of the peptide adsorption at the interface, and providing a model for evaluation of amphipathic properties of potential biofunctional peptides.

First Constraints on Compact Dark Matter from Fast Radio Burst Microstructure

Abstract Despite existing constraints, it remains possible that up to 35% of all dark matter is comprised of compact objects, such as the black holes in the 10–100 M ⊙ range whose existence has been confirmed by LIGO. The strong gravitational lensing of transients such as fast radio bursts (FRBs) and gamma-ray bursts has been suggested as a more sensitive probe for compact dark matter than intensity fluctuations observed in microlensing experiments. Recently the Australian Square Kilometre Array Pathfinder has reported burst substructure down to 15 μs timescales in FRBs in the redshift range 0.3–0.5. We investigate here the implications of this for the detectability of compact dark matter by FRBs. We find that a sample size of ∼130 FRBs would be required to constrain compact dark matter to less than the existing 35% limit with 95% confidence, if it were distributed along ≳1 Gpc-long FRB sightlines through the cosmic web. Conversely, existing constraints on the fraction of compact dark matter permit as many as 1 in ≈40 of all z ≲ 0.4 FRBs to exhibit microlensed burst structure. Approximately 170 FRBs intercepting halos within ∼50 kpc would be required to exclude the fraction of compact dark matter in each intercepted halo to a similar level. Furthermore, we consider the cumulative effects of lensing of the FRB signal by a macroscopic dark matter distribution. We conclude that lensing from a uniform distribution of compact objects is likely not observable, but suggest that FRBs may set meaningful limits on power-law distributions of dark matter.

Super-Resolution Microscopy and Single-Molecule Tracking Reveal Distinct Adaptive Dynamics of MreB and of Cell Wall-Synthesis Enzymes.

The movement of filamentous, actin-like MreB and of enzymes synthesizing the bacterial cell wall has been proposed to be highly coordinated. We have investigated the motion of MreB and of RodA and PbpH cell wall synthesis enzymes at 500 ms and at 20 ms time scales, allowing us to compare the motion of entire MreB filaments as well as of single molecules with that of the two synthesis proteins. While all three proteins formed assemblies that move with very similar trajectory orientation and with similar velocities, their trajectory lengths differed considerably, with PbpH showing shortest and MreB longest trajectories. These experiments suggest different on/off rates for RodA and PbpH at the putative peptidoglycan-extending machinery (PGEM), and during interaction with MreB filaments. Single molecule tracking revealed distinct slow-moving and freely diffusing populations of PbpH and RodA, indicating that they change between free diffusion and slow motion, indicating a dynamic interaction with the PGEM complex. Dynamics of MreB molecules and the orientation and speed of filaments changed markedly after induction of salt stress, while there was little change for RodA and PbpH single molecule dynamics. During the stress adaptation phase, cells continued to grow and extended the cell wall, while MreB formed fewer and more static filaments. Our results show that cell wall synthesis during stress adaptation occurs in a mode involving adaptation of MreB dynamics, and indicate that Bacillus subtilis cell wall extension involves an interplay of enzymes with distinct binding kinetics to sites of active synthesis.

A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.

We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables the modeling of four classes of artificial backbone units that are commonly used alongside natural α residues in blended or "heterogeneous" backbones: chirality-reversed D-α-residues, the Cα-methylated α-residue Aib, homologated β-residues (β3) bearing proteinogenic side chains, and two cyclic β residues (βcyc; APC and ACPC). The ff15ipq-m force field includes 472 unique atomic charges and 148 unique torsion terms. Consistent with the AMBER IPolQ lineage of force fields, the charges were derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of explicit solvent. To our knowledge, no general force field reported to date models the combination of artificial building blocks examined here. In addition, we have derived Karplus coefficients for the calculation of backbone amide J-coupling constants for β3Ala and ACPC β residues. The AMBER ff15ipq-m force field reproduces experimentally observed J-coupling constants in simple tetrapeptides and maintains the expected conformational propensities in reported structures of proteins/peptides containing the artificial building blocks of interest-all on the μs timescale. These encouraging results demonstrate the power and robustness of the IPolQ lineage of force fields in modeling the structure and dynamics of natural proteins as well as mimetics with protein-inspired artificial backbones in atomic detail.

Ultrafast Sweep-Tuned Spectrum Analyzer with Temporal Resolution Based on a Spin-Torque Nano-Oscillator.

We demonstrate that a spin-torque nano-oscillator (STNO) rapidly sweep-tuned by a bias voltage can be used to perform an ultrafast time-resolved spectral analysis of frequency-manipulated microwave signals. The critical reduction in the time of the spectral analysis comes from the naturally small-time constants of a nanosized STNO (1-100 ns). The demonstration is performed on a vortex-state STNO generating in a frequency range around 300 MHz, when frequency down-conversion and matched filtering is used for signal processing. It is shown that this STNO-based spectrum analyzer can perform analysis of frequency-agile signals, having multiple rapidly changing frequency components with temporal resolution in a μs time scale and frequency resolution limited only by the "bandwidth" theorem. Our calculations show that using uniform magnetization state STNOs it would be possible to increase the operating frequency of a spectrum analyzer to tens of GHz.

Dynamics of Single‐Stranded RNA Looping Probed and Photoregulated by Sulfonated Pyrene

AbstractRNAs especially the noncoding RNAs which lack protein‐coding capacity but have critical functions in a wide range of cellular processes have received increased attention. They are reported to be associated with normal development and physiology, and their disruption would cause cancer. RNAs are dynamic molecules and the structural transition of them is fundamental to many RNA‐involved cellular processes. The study of transition dynamics is critical to gaining knowledge on how the transition occurs, what factors govern the transition, and how to externally regulate the transition. Previously, we have reported the synthesis of sulfonated pyrene, SPy, and its application as a photoregulator for single‐stranded DNA (ssDNA) looping. Herein, we studied the dynamics of single‐stranded RNA (ssRNA) looping in aqueous solution by using SPy as both a probe and a photoregulator. The rate of end‐to‐end loop formation in ssRNA regulated by SPy upon photostimulation suggests a retarding impact of the ribose 2′‐OH. The results also attest that (rU)n sequences are endowed with higher flexibility compared with (dT)n sequences and demonstrate the slowing down effect of C5‐CH3 group in thymine base on the looping dynamics of polythymine sequences. The photoregulated ssRNA looping observed herein occurs at μs to tens of μs time scales. All the findings provide important insight into the flexibility and structural transition dynamics of oligonucleotides.

Effect of magnetic perturbations on turbulence-flow dynamics at the L-H transition on DIII-D

Detailed 2D turbulence measurements from the DIII-D tokamak provide an explanation for how resonant magnetic perturbations (RMPs) raise the L-H power threshold PLH [P. Gohil et al., Nucl. Fusion 51, 103020 (2011)] in ITER-relevant, low rotation, ITER-similar-shape plasmas with favorable ion ∇B direction. RMPs simultaneously raise the turbulence decorrelation rate ΔωD and reduce the flow shear rate ωshear in the stationary L-mode state preceding the L-H transition, thereby disrupting the turbulence shear suppression mechanism. RMPs also reduce the Reynolds stress drive for poloidal flow, contributing to the reduction of ωshear. On the ∼100 μs timescale of the L-H transition, RMPs reduce Reynolds-stress-driven energy transfer from turbulence to flows by an order of magnitude, challenging the energy depletion theory for the L-H trigger mechanism. In contrast, non-resonant magnetic perturbations, which do not significantly affect PLH, do not affect ΔωD and only slightly reduce ωshear and Reynolds-stress-driven energy transfer.