Intermediate Length Research Articles

Heat fluctuations in chemically active systems.

Chemically active systems such as living cells are maintained out of thermal equilibrium due to chemical events which generate heat and lead to active fluctuations. A key question is to understand on which time and length scales active fluctuations dominate thermal fluctuations. Here, we formulate a stochastic field theory with Poisson white noise to describe the heat fluctuations which are generated by stochastic chemical events and lead to active temperature fluctuations. We find that on large length- and timescales, active fluctuations always dominate thermal fluctuations. However, at intermediate length- and timescales, multiple crossovers exist which highlight the different characteristics of active and thermal fluctuations. Our work provides a framework to characterize fluctuations in active systems and reveals that local equilibrium holds at certain length- and timescales.

Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods.

Proteolysis targeting chimera (PROTAC) is a novel drug modality that facilitates the degradation of a target protein by inducing proximity with an E3 ligase. In this work, we present a new computational framework to model the cooperativity between PROTAC-E3 binding and PROTAC-target binding principally through protein-protein interactions (PPIs) induced by the PROTAC. Due to the scarcity and low resolution of experimental measurements, the physical and chemical drivers of these non-native PPIs remain to be elucidated. We develop a coarse-grained (CG) approach to model interactions in the target-PROTAC-E3 complexes, which enables converged thermodynamic estimations using alchemical free energy calculation methods despite an unconventional scale of perturbations. With minimal parametrization, we successfully capture fundamental principles of cooperativity, including the optimality of intermediate PROTAC linker lengths that originates from configurational entropy. We qualitatively characterize the dependency of cooperativity on PROTAC linker lengths and protein charges and shapes. Minimal inclusion of sequence- and conformation-specific features in our current force field, however, limits quantitative modeling to reproduce experimental measurements, but further development of the CG model may allow for efficient computational screening to optimize PROTAC cooperativity.

Interval follow up for intermediate cervical length (26 - 29mm) identified during routine anatomy scan

Identifying patients at risk for spontaneous preterm birth (sPTB) remains a challenge because most have no history. For patients with a singleton gestation and no history of sPTB, some institutions offer universal cervical length (CL) screening via transvaginal ultrasound (TVUS). Those with a CL ≤ 25mm may receive vaginal progesterone (VP). Patients with an intermediate CL (26 – 29mm) also have increased risk for sPTB, however there are no management recommendations. This study aims to determine an appropriate TVUS follow-up (f/u) interval for patients with an intermediate CL. This is a 5 year retrospective cohort of patients with a singleton gestation, no sPTB history, an intermediate CL seen during CL screening, and with ≥1 f/u TVUS at ≤ 24 6/7 weeks gestation. The primary outcome measure is incidence of short cervix. An intermediate CL was found in 157 patients. 61 (38%) had no sPTB history and ≥1 f/u TVUS. The mean f/u interval was 18.3 ± 10.0 days, with 77 total f/u TVUS. At follow up, 19 patients (31%) were diagnosed with short cervix ≤ 25mm, with the mean time to diagnosis of 18.0 ± 8.0 days. The f/u intervals with the greatest yield was 15 – 21 days and 22 – 28 days, with 6 (30.0%) and 5 (41.7%) patients respectively diagnosed with short cervix (Figure 1). Compared to a 14 day f/u interval, significantly more patients with a short cervix were identified within 28 days [7 (36.84%) vs. 18 (94.7%), p < .001] (Figure 2). The mean delta CL was -2.4mm. Two patients progressed to a severely short cervix ( < 10mm). Of those diagnosed with short cervix, 12 (63.2%) started VP and 7 (36.8%) did not. No patients with VP delivered < 37 weeks gestation, and 1 patient without VP delivered at 36 5/7 weeks gestation. In patients with no history of sPTB and an intermediate CL, 31% will progress to short cervix and may be VP candidates. Given that 94.7% of those patients with a short cervix were identified within a 28 day f/u interval, a single f/u TVUS 3-4 weeks after the initial study will allow for identification of these patients and for appropriate intervention.View Large Image Figure ViewerDownload Hi-res image Download (PPT)

Order of Intermittent Rock Fractured Surfaces

According to chaos theory, some underlying patterns can disclose the order of disordered systems. Here, it has been discussed that intermittency of rough rock fractured surfaces is an orderable disorder at intermediate length scales. However, this kind of disorder is more complicated than simple fractal or even multi-scaling behaviours. It is planned to deal with some multifractal spectra that systematically change as a function of the analysed domain. Accordingly, some parameters are introduced that can perfectly take into account such systematic behaviour and quantify the intermittency of the studied surfaces. This framework can be used to quantify and model the roughness of fractured surfaces as a prerequisite factor for the analysis of fluid flow in rock media as well as the shear strength of rock joints. Ultimately, the presented framework can be used for analysing the intermittency of time series and developing new models for predicting, for instance, seismic or flood events in a short time with higher accuracy.

Phase imaging in scanning transmission electron microscopy using bright-field balanced divergency method

We introduce a phase imaging mechanism for scanning transmission electron microscopy that exploits the complementary intensity changes of transmitted disks at different scattering angles. For scanning transmission electron microscopy, this method provides a straightforward, dose-efficient, and noise-robust phase imaging, from atomic resolution to intermediate length scales, as a function of scattering angles and probe defocus. At atomic resolution, we demonstrate that the phase imaging using the method can detect both light and heavy atomic columns. Furthermore, we experimentally apply the method to the imaging of nanoscale magnetic phases in FeGe samples. Compared with conventional methods, phase retrieval using the new method has higher effective spatial resolution and robustness to non-phase background contrast. Our method complements traditional phase imaging modalities in electron microscopy and has the potential to be extended to other scanning transmission techniques and to characterize many emerging material systems.

Effect of oligothiophene spacer length on photogenerated charge transfer from perylene diimide to boron-doped diamond electrodes

Organic-based photovoltaic devices emerged as a complementary technology to silicon solar cells with specific advantages in terms of cost, ease of deployment, semi-transparency, and performance under low and diffuse light conditions. In this work, thin-film boron-doped diamond (B:NCD) electrodes are employed for their useful optical, electronic, and chemical properties, as well as stability and environmental safety. A set of oligothiophene perylene diimide (nT-PDI) donor-acceptor chromophores is designed and synthesized in order to investigate the influence of the oligothiophene spacer length when the nT-PDI molecule is attached to a B:NCD electrode. The chromophores are anchored to the diamond surface via diazonium grafting followed by Sonogashira cross-coupling. X-ray photoelectron spectroscopy shows that the surface coverage decreases with increasing oligothiophene length. Density functional theory (DFT/TDDFT) calculations reveal the upright nT-PDI orientation and the most efficient photogenerated charge separation and injection to diamond for elongated oligothiophene chains (8T-PDI). Yet, the maximum photovoltage is obtained for an intermediate oligothiophene length (3T-PDI), providing an optimum between decreasing transport efficiency and increasing efficiency of charge separation and reduced recombination with increasing oligothiophene length. Holes transferred from nT-PDI to diamond persist there even after the illumination is switched off. Such features may be beneficial for application in solar cells. • Variable donor-acceptor chromophore/diamond system designed in-silico and fabricated. • Oligothiophene donor length adjusts valence band and charge transport with diamond. • Intermediate oligothiophene length (3 units) yields the maximum photovoltage. • Up to 0.87 electron per molecule transferred to diamond across 44 Å under excitation.

Metal Nanocatalyst Sintering Interrogated at Complementary Length Scales.

Metal nanoparticle (NP) sintering is a prime cause of catalyst degradation, limiting its economic lifetime and viability. To date, sintering phenomena are interrogated either at the bulk scale to probe averaged NP properties or at the level of individual NPs to visualize atomic motion. Yet, "mesoscale" strategies which bridge these worlds can chart NP populations at intermediate length scales but remain elusive due to characterization challenges. Here, a multi-pronged approach is developed to provide complementary information on Pt NP sintering covering multiple length scales. High-resolution scanning electron microscopy (HRSEM) and Monte Carlo simulation show that the size evolution of individual NPs depends on the number of coalescence events they undergo during their lifetime. In its turn, the probability of coalescence is strongly dependent on the NP's mesoscale environment, where local population heterogeneities generate NP-rich "hotspots" and NP-free zones during sintering. Surprisingly, advanced in situ synchrotron X-ray diffraction shows that not all NPs within the small NP sub-population are equally prone to sintering, depending on their crystallographic orientation on the support surface. The demonstrated approach shows that mesoscale heterogeneities in the NP population drive sintering and mitigation strategies demand their maximal elimination via advanced catalyst synthesis strategies.

Microwave spectroscopy of Andreev states in InAs nanowire-based hybrid junctions using a flip-chip layout

Josephson junctions based on semiconductor nanowires are potential building blocks for electrically tunable qubit structures, e.g., the gatemon or the Andreev qubit. However, an actual realization requires the thorough investigation of the intrinsic excitation spectrum. Here, we demonstrate the fabrication of low-loss superconducting microwave circuits that combine high quality factors with a well-controlled gate architecture by utilizing a flip-chip approach. This platform is then used to perform single-tone and two-tone experiments on Andreev states in in-situ grown InAs/Al core/half-shell nanowires with shadow mask defined Josephson junctions. In gate-controlled and flux-biased spectroscopic measurements we find clear signatures of single quasiparticle as well as quasiparticle pair transitions between discrete Andreev bound states mediated by photon-absorption. Our experimental findings are supported by simulations that show that the junction resides in the intermediate channel length regime.

Influence of the Width of Launch Beam Distribution on the Transmission Performance of Seven-Core Polymer-Clad Silica Fibers

We propose a space division multiplexing (SDM) in a newly constructed multicore polymer-clad silica fiber (PCSF) with seven cores arrayed in a hexagonal array, each carrying a centrally launched beam. This enables a higher SDM capacity at longer fiber lengths in the proposed seven-core PCSF if compared with previously proposed angular division multiplexing (ADM) in single-core (SC) PCSF. As a result, the SDM is not limited to short fiber lengths in the proposed seven-core PCSF, as it is in the case of the ADM channels due to mode coupling in the SC PCSF. In addition, the time-independent power flow equation (TI PFE) is used to analyze the effect of the width of the launch beam distribution on the equilibrium mode distribution (EMD) and steady state distribution (SSD) in each of the seven cores of the investigated PCSF. The width of the launch beam distribution has a considerable impact on the fiber length at which the EMD and SSD are attained, according to our numerical results. Thus, by decreasing the full width at half maximum (FWHM) of the launch beam distribution from 20 to 2°, the length at which EMD is established increases from Lc = 1020 to 1250 m, and the length at which SSD is attained increases from zs = 2650 to 3250 m. A narrow launch beam distribution leads to higher bandwidth at small and intermediate fiber lengths. On the other hand, at shorter fiber lengths, a wider launch beam distribution induces a bandwidth change from 1/z proportional to 1/z1/2 proportional curve, e.g., a slower bandwidth reduction. When building a multicore optical fiber transmission system for SDM, such characterization of multicore PCSFs under various launch conditions should be taken into account.

Length-Dependent Photocatalytic Activity of Hybrid Ag-CdS Nanorods

Hybrid metal–semiconductor nanostructures are promising photocatalysts for a wide span of reactions. Determining the relationship of their geometry with catalytic efficiency is critical for optimization of the catalysts. In this work, Ag-CdS nanorods with five different lengths (from 25.0 to 106.5 nm) have been synthesized using a seed-mediated growth method. High-resolution transmission electron microscopy (HRTEM) and energy dispersive X-ray spectroscopy (EDS) studies confirmed that the formation of a metal tip and semiconductor body part and they absorb strongly and broadly in the UV and visible wavelength range. The nanorods have been employed as photocatalysts for methyl orange degradation and their catalytic efficiency exhibited length-dependence. Specifically, the highest efficiency was observed in the rods of intermediate length (72.1 nm). Time-dependent photoluminescence decay revealed that the Ag-CdS rods with high catalytic efficiency have a higher probability to go through charge-separation-recombination pathway than the rods with low catalytic efficiency. Understanding the physical process in these hybrid structures provides insight into fine-tuning their geometry to improve the charge transfer efficiency from the metal to the semiconductor domain. Thus, better hybrid nanomaterials can be designed and fabricated for photocatalytic and other applications.

On the Choice of Eigenmode Shapes for Interactive Cases of Local and Global Buckling of RHS/SHS and I‐Shaped Sections

AbstractBetter and simpler possibilities of structural optimization due to increasing computational power but also for reasons of environmental sustainability, the use of materials and their reusability lead to greater acceptance towards more advanced numerically intensive, so‐called “design by analysis” methods like geometrically and materially nonlinear analyses with imperfections (GMNIA). The general choice of imperfections and their combination in such models, especially for slender cross‐sections of intermediate length prone to an interaction between a global and local plate‐buckling, is crucial in terms of the reached load‐bearing capacity. Annex C of EN 1993‐1‐5 make use of the “70%‐rule” for the combination of imperfection modes and amplitudes. This rule postulates that two GMNIA calculations should be carried out when local and global interactive buckling may be dominant; one with 100% + 70% of the maximum specified amplitude in either case. In addition, extended information is provided on the choice and combination of imperfections in the newly introduced and currently available draft of the prEN1993‐1‐14:2020 (Design assisted by finite element analysis). Although information is provided how the local and global imperfections should be combined, it is not stated when it is relevant to consider those. Based on carried out GMNIA simulations on SHS/RHS and I‐shaped sections, this paper presents a general decision support on the choice of equivalent imperfections. Based on numerical analysis, the developed flowchart and design routine allows for the decision whether the consideration of the interaction of local and global imperfections is required or not.

Design, Construction, and Testing of 0.5-m, 18-mm Period Nb3Sn Superconducting Undulator Magnets

Design and fabrication of a new Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Sn-based superconducting undulator (SCU) are underway at the Advanced Photon Source (APS) of Argonne National Laboratory in collaboration with Fermilab and Lawrence Berkeley National Laboratory. To develop a robust and reliable fabrication process, the magnet development consists of several steps. First, magnetic and mechanical simulations were performed to optimize the magnet design; then, the design matured further by fabricating and testing a series of very short prototypes, ∼8 cm long with a period length of 18 mm. These short prototype studies were previously reported. Second, the design was scaled to an intermediate length of ∼0.5 m. These two steps led to the final design of ∼1.1–m-long magnets, which are currently being fabricated. The quench behavior of each 0.5-m-long undulator magnet, as well as undulator assemblies from these magnets, was studied. The first SCU magnet assembly did not meet the design specifications due to the breakdown of the insulation. With an improved design and fabrication process based on lessons learned, the second SCU assembly achieved the design undulator field of 1.2 T. The design was further optimized, and the third set of magnets was fabricated and successfully tested.

Effect of Particle Size and Coke Formation on n‐Octane Dehydrogenation

AbstractThe effect of particle size as well as of coke formation on conversion of intermediate chain length paraffins (C6–C9) to the corresponding olefins was investigated on a promoted Pt catalyst with the model substance n‐octane. Increasing the particle size leads to pore diffusion limitations and thus to a reduction of the activity for paraffin conversion and of the octene selectivity caused by more pronounced formation of consecutive products (aromatics, octadienes). Both effects are adequately predicted by the developed kinetic model. The activity of dehydrogenation declines with the content of coke, but to a lesser extent than the rate of coke formation, which is beneficial regarding the catalyst lifetime. The initial activity is fully recovered by mild coke burn‐off (T &lt; 470 °C).

Evaluation of the morphological characteristics and culture performance of Cladosiphon okamuranus strains

This study aimed to determine whether morphological differences of Cladosiphon okamuranus strains at different aquaculture sites were inherent characteristics and to select useful forms for aquaculture production and processing. Three candidate strains with potentially excellent morphological characteristics, that is ON, SY and KT, were selected from six local strains collected from Okinawa Islands. Then, these three candidate strains were transplanted to four aquaculture sites to evaluate their characteristics. The thallus length was significantly larger (e.g. 1.6–2.1 times) in the SY strain than in the ON strain in each area and the density of the primary lateral branches of the latter was significantly (e.g. 2.4–5.9 times) higher than that of the other two strains. The SY and ON strain characteristics were also distinguished by a comprehensive evaluation of eight traits with principal component analysis. Conversely, the KT strain tended to have an intermediate length between ON and SY strains, the biomass yield of the SY and KT strains was higher than that of ON strain. These results, indicating that some morphological differences are intrinsic strain characteristics, will provide information to aquaculture producers using appropriate strains to maximize the unit yield and thalli quality.

Relationship between type II polyproline helix secondary structure and thermal hysteresis activity of short homopeptides

BackgroundAntifreezing activity is a phenomenon of great significance in food industry that affects the quality of frozen foods. As a solution, ice-binding proteins, more specifically antifreeze proteins, have been used to mitigate recrystallization. However, knowledge about the mechanism of ice recrystallization and the influence of antifreeze proteins is scarce. ResultsIn this work, model homopeptides of three amino acids (proline, arginine and lysine) were studied by means of differential scanning calorimetry through the determination of their thermal hysteresis activity, to see the influence of several factors on their secondary structure. It was found that model homopeptides formed polyproline II type secondary structure that was more stable at low temperature. In addition, thermal hysteresis activity was higher for peptides of intermediate lengths and for proline homopeptides. ConclusionsThe study of homopeptides sheds light on the mechanism of antifreeze activity and will allow the design of new molecules with antifreeze properties to be used in diverse biotechnological fields.How to cite: Rojas R, Aróstica M, Carvajal-Rondanelli P, et al. Relationship between type II polyproline helix secondary structure and thermal hysteresis activity of short homopeptides. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.08.003.

Aggregate behavior in amphiphilic coil/rod block copolymer solutions

The self-assembly in coil/rod/coil BAB amphiphilic symmetric triblock copolymer solutions was investigated using lattice self-consistent field theory. At low concentrations, some peaks emerge on the heat capacity curve, i.e., multiple rearrangements (MRs) of micelles. For short hydrophobic rod blocks (HRBs), MRs are concerned with the emergences of vesicles, stellate, rod, and lamellar micelles (LMs), and the breakup and formation of LMs. At high concentrations with HRBs of intermediate length HRBs, MRs are associated to a few (quasi-)order/disorder transitions of micelles. For long HRBs, although only one quasi-order/disorder transition emerges, MRs do occur. It is found that the aggregation behavior of high concentrations with HRBs of intermediate length is similar to that of low concentrations compared with high concentrations with long HRBs. These results are explained by the reappearing behavior and dissolution, and the cooperative growth of micelles, where the micellar cores and coronas are rearranged alternately with temperature. This work is helpful for further interpreting the cooperativity and dynamics of self-assembly.

In-Plane Interactive Buckling of High Strength Steel Welded Wide Web I-Section Beam-Columns

A numerical investigation on the overall-local interactive buckling performance of high strength steel (HSS) wide web I-section members was conducted using finite element (FE) models verified against experimental data. The effect of overall slenderness, the height-thickness ratio of the web h w / t w , and the width-thickness ratio of the flanges (bf/tf) on ultimate load was parametrically analyzed. The result demonstrated that (i) for the beam-columns with higher steel grade, the Pz-Uz curve presents a relatively obvious deformation plateau, meaning a certain degree of ductility. (ii) The ultimate load decreased essentially linearly resulting from higher h w / t w , and the trend was graphically consistent under various steel grades. (iii) bf/tf lower than 0.6 led to the failure mode of shearing buckling, and the corresponding ultimate load increased with an increase of bf/tf. In the case of bf/tf greater than 0.6, the ultimate load decreased as a result of the higher bf/tf. Based on the concept of the direct strength method, the local postbuckling strength prediction formula was fitted with stub beam-column FE results and examined with experiment data. The correlation formula of compression and bending moment was proposed to evaluate the resistance of the interactive buckling of the HSS wide web I-section underpinned by the FE results of beam-columns with intermediate length and experiment data.

Membrane shape deformation induced by curvature-inducing proteins consisting of chiral crescent binding and intrinsically disordered domains.

Curvature-inducing proteins containing a bin/amphiphysin/Rvs domain often have intrinsically disordered domains. Recent experiments have shown that these disordered chains enhance curvature sensing and generation. Here, we report on the modification of protein-membrane interactions by disordered chains using meshless membrane simulations. The protein and bound membrane are modeled together as a chiral crescent protein rod with two excluded-volume chains. As the chain length increases, the repulsion between them reduces the cluster size of the proteins. It induces spindle-shaped vesicles and a transition between arc-shaped and circular protein assemblies in a disk-shaped vesicle. For flat membranes, an intermediate chain length induces many tubules owing to the repulsion between the protein assemblies, whereas longer chains promote perpendicular elongation of tubules. Moreover, protein rods with zero rod curvature and sufficiently long chains stabilize the spherical buds. For proteins with a negative rod curvature, an intermediate chain length induces a rugged membrane with branched protein assemblies, whereas longer chains induce the formation of tubules with periodic concave-ring structures.

Thermodynamic analysis of nucleation of alcohol molecules with the varied alkyl chain length in nanoconfined solution

Combining the molecular dynamics (MD) simulations and the free-energy-based thermodynamic analysis, we analyze the role of alkyl chain length on the nucleation of alcohol molecules with the mono-hydroxyl in nanoconfined solution. The free energy formulae and thermodynamic equilibrium equation are parameterized by fitting the theoretical equilibrium equation to MD simulation results. We find that alcohol molecules with the varied alkyl chain length show different nucleation states, i.e., dispersion, reversible and aggregation states, corresponding to the total free energy Gconfine(n, N) with a single minimum at n∼ 1, two minima at n∼ 1 and N separated by a maximum, and a local minimum at n∼N, respectively. The alcohol molecule with a longer alkyl chain tends to aggregate into a cluster at a lower solute number in nanoconfined solution. Besides, the free energy of cluster formation in nanoconfined solution Gcluster(n) also depends on the alkyl chain length, and three regions can be identified: For the shorter alkyl chain, such as ethanol, there is no local maximum on Gcluster(n), indicating that alcohol molecules tend to be dispersed in water; For the intermediate alkyl chain length, such as 1-propanol, 1-butanol, 1-pentanol, and 1-hexanol, the critical nucleation number nc and nucleation barrier Gb monotonically decrease with the increase of alkyl chain length; For the longer alkyl chain, nc∼ 1 and Gb∼0kBT suggest that alcohol molecules, such as 1-heptanol, can aggregate into clusters easily. Our work deepens the understanding of the alkyl chain length effect on the nucleation behavior of alcohol molecules in nanoconfined solution.

Experimental and numerical study of press-braked S690 high strength steel slender channel section columns prone to local–flexural interactive buckling

This paper reports an experimental and numerical investigation into the local–flexural interactive buckling behaviour and resistance of press-braked S690 high strength steel slender channel section columns. An experimental programme was firstly conducted and included initial geometric imperfection measurements and twelve pin-ended column tests. Interaction between local buckling and flexural buckling was observed for all specimens upon testing and discussed in detail. The experimental programme was accompanied by a numerical modelling programme, where finite element models were developed and validated against the test results and then employed to perform parametric studies to generate further numerical data over a wide range of cross-section dimensions and member effective lengths. The obtained test and numerical data were used to assess the accuracy of the codified design rules for press-braked S690 high strength steel slender channel section columns failing by local–flexural interactive buckling, as set out in the European code, North American specification and Australian/New Zealand standard. The assessment results revealed that the European code leads to excessively conservative and scattered resistance predictions, while the North American specification and Australian/New Zealand standard result in a higher level of design accuracy and consistency, but still with many conservative resistance predictions for columns with short to intermediate lengths. Finally, a new design approach was proposed and shown to yield substantially more accurate and consistent resistance predictions for press-braked S690 high strength steel slender channel section columns over the design codes.