Length Dependence Research Articles

Prediction of State of Charge for Lead-acid Batteries Based on GRU Network and Isolated Forest

Accurate prediction of the state of charge (SOC) of lead-acid batteries is the key to ensuring battery life. In this paper, a new combined SOC prediction model IF-GRU (Isolation Forest, Gated Recurrent Unit) is proposed. The model combines the Isolation Forest anomaly detection algorithm and the Gated Recurrent Network. The Isolation Forest algorithm is used to detect anomalous and missing values in the raw data. Length dependence of the GRU network can be further utilized to perform high-accuracy SOC estimation by implementing a sliding window that takes into account the data's charging and discharging details. In addition, the conventional Adam optimizer is utilized to improve the convergence speed of model training. The experimental data demonstrate that the IF-GRU model proposed in this paper has higher prediction accuracy and convergence speed with a RMSE of 1.59% compared with traditional LSTM network, GRU network, and BP network.

Passivating Blunt‐Ended Helices to Control Monodispersity and Multi‐Subunit Assembly of DNA Origami Structures

Deoxyribonucleic acid (DNA) origami enables the synthesis of bespoke nanoscale structures suitable for diverse applications. Effective design requires preventing uncontrolled aggregation, while still facilitating directed multi‐subunit assembly. Uncontrolled aggregation is often caused by base‐stacking interactions between arrays of blunt‐ended helices, a problem which is typically mitigated by incorporating disordered single‐stranded DNA (ssDNA) (like scaffold loops or poly‐thymine brushes) at the end of double‐stranded DNA (dsDNA) helices. Such disordered regions are ubiquitous in DNA origami structures yet their optimal design requirements in various chemical environments remains unclear. This study systematically investigates scaffold loops and poly‐nucleotide brushes for aggregation prevention and control of multi‐subunit assembly, examining length, sequence, and MgCl2 concentration dependencies. Additionally, a novel strategy is introduced using orthogonal double‐stranded DNA helices to create a steric shield against base stacking. The results reveal key considerations. Poly‐thymine brushes excel in achieving monodispersity across diverse conditions whereas scaffold loops aid directed multi‐subunit assembly. Orthogonal DNA helices remove the need for disordered regions altogether, preventing aggregation over a broad range of MgCl2 concentrations and facilitating controlled multi‐subunit assembly. This study expands the toolbox for DNA origami design and enables a more informed approach for achieving control of monodispersity and multi‐subunit assembly in DNA origami structures.

Seebeck Effect in Molecular Wires Facilitating Long-Range Transport.

The study of molecular wires facilitating long-range charge transport is of fundamental interest for the development of various technologies in (bio)organic and molecular electronics. Defining the nature of long-range charge transport is challenging as electrical characterization does not offer the ability to distinguish a tunneling mechanism from the other. Here, we show that investigation of the Seebeck effect provides the ability. We examine the length dependence of the Seebeck coefficient in electrografted bis-terpyridine Ru(II) complex films. The Seebeck coefficient ranges from 307 to 1027 μV/K, with an increasing rate of 95.7 μV/(K nm) as the film thickness increases to 10 nm. Quantum-chemical calculations unveil that the nearly overlapped molecular-orbital energy level of the Ru complex with the Fermi level accounts for the giant thermopower. Landauer-Büttiker probe simulations indicate that the significant length dependence evinces the Seebeck effect dominated by coherent near-resonant tunneling rather than thermal hopping. This study enhances our comprehension of long-range charge transport, paving the way for efficient electronic and thermoelectric materials.

Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003–0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

Molecular Graphene Nanoribbon Junctions.

One of the challenges for the realization of molecular electronics is the design of nanoscale molecular wires displaying long-range charge transport. Graphene nanoribbons are an attractive platform for the development of molecular wires with long-range conductance owing to their unique electrical properties. Despite their potential, the charge transport properties of single nanoribbons remain underexplored. Herein, we report a synthetic approach to prepare N-doped pyrene-pyrazinoquinoxaline molecular graphene nanoribbons terminated with diamino anchoring groups at each end. These terminal groups allow for the formation of stable molecular graphene nanoribbon junctions between two metal electrodes that were investigated by scanning tunneling microscope-based break-junction measurements. The experimental and computational results provide evidence of long-range tunneling charge transport in these systems characterized by a shallow conductance length dependence and electron tunneling through >6 nm molecular backbone.

Impact of the Hydrocarbon Chain Length of Biodegradable Ester-Bonded Cationic Gemini Surfactants on Self-Assembly, In Vitro Gene Transfection, Cytotoxicity, and Antimicrobial Activity.

Gemini surfactants, due to their unique structural features and enhanced properties compared to conventional surfactants, are becoming more popular in the domain of colloid and interface science, drug delivery, and gene delivery science. This distinct class of surfactants forms a wide range of self-assembled aggregates depending on their chemical structure and environmental conditions. The present work aims to develop Gemini with three distinct chain lengths linked through the ester group and quaternary nitrogen head groups that can bind DNA molecules and ultimately serve as vectors for DNA transfection. Thus, we synthesized three distinct cationic Gemini with 12, 14, and 16 carbons in their tails and studied the effect of the hydrocarbon chain length on their physicochemical properties and biological applications. The self-assembly of these Geminis in aqueous solution was investigated by a number of techniques, including surface tension, electrical conductivity, fluorescence probe, calorimetry, dynamic light scattering, and atomic force microscopy. All three Gemini were extremely surface active and self-assembled above a very low critical micelle concentration. Calorimetric studies suggested the formation of thermodynamically favorable aggregates in an aqueous medium. Chain length dependence was observed in the size as well as the morphology of the aggregates. These Gemini ions were found to bind DNA strongly, as indicated by the high binding constant values. In vitro gene transfection studies using the RAW 264.7 cell line suggested that all three cationic Gemini had transfection efficiencies comparable to that of commercial standard turbofectamine. MTT assay was also performed for concentration selection while using these Gemini as transfection vectors. Overall, it was observed that Gemini had very little cytotoxicity within the investigated concentration range, highlighting the significance of the ester link within the structure. When compared with known antimicrobials such as kanamycin and ampicillin, all three Gemini furnished excellent antimicrobial activity in both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) microorganisms.

Stop Blaming Hopping Conduction in Nanocrystal Arrays, Use it for Active Photonics!

AbstractNanocrystals (NCs) are now established building blocks for photonic applications. However, their integration for optoelectronics has not yet reached the same level of maturity, in part due to the perceived bottleneck that is the inherent limited mobility resulting from hopping conduction. Significant efforts are made to improve this mobility, notably by tuning the particle surface chemistry to enable larger interparticle electronic coupling, and values of mobility of ≈10 cm2 V−1 s−1 have been achieved. It is acknowledged that this value remains significantly lower than those obtained in 2D electron gases but is on par with the mobility reported for vertical transport in epitaxially grown heterostructures with similar confinement energies. Since there appears to be limited perspectives for further increasing mobility values, a suggestion is made that efforts should instead be directed toward exploring the potential benefits offered by hopping conduction. One of these benefits is the bias dependence of the diffusion length, which plays a key role in designing bias‐reconfigurable optical responses for NC‐based devices. Some recent achievements in building bias‐activated devices will be reviewed and the essential criteria for designing future structures will be discussed. Ultimately, hopping conduction is an opportunity to generate new functionalities that low‐disorder materials would be unable to provide.

Chain Length Dependence of Electron Transport in an n-Type Conjugated Polymer with a Rigid-Rod Chain Topology.

Most currently known n-type conjugated polymers have a semiflexible chain topology, and their charge carrier mobilities are known to peak at modest chain lengths of below 40-60 repeat units. Herein, we show that the field-effect electron mobility of a model n-type conjugated polymer that has a rigid-rod chain topology grows continuously without saturation, even at a chain length exceeding 250 repeat units. We found the mechanism underlying the novel chain length-dependent electron transport to originate from the reduced structural disorder and energetic disorder with the increasing degree of polymerization inherent to the rigid-rod chain topology. Furthermore, we demonstrate a unique chain length-dependent decay of threshold voltage, which is rationalized by decreased trap densities and trap depths with respect to the degree of polymerization. Our findings provide new insights into the role of polymer chain topology in electron transport and demonstrate the promise of rigid-rod chain architectures for the design of future high-mobility conjugated polymers.

Internal friction as a factor in the anomalous chain length dependence of DNA transcriptional dynamics.

Recent experiments by Brückner et al. [Science 380, 1357 (2023)] have observed an anomalous chain length dependence of the time of near approach of widely separated pairs of genomic elements on transcriptionally active chromosomal DNA. In this paper, I suggest that the anomaly may have its roots in internal friction between neighboring segments on the DNA backbone. The basis for this proposal is a model of chain dynamics formulated in terms of a continuum scaled Brownian walk (sBw) of polymerization index N. The sBw is an extension of the simple Brownian walk model widely used in path integral calculations of polymer properties, differing from it in containing an additional parameter H (the Hurst index) that can be tuned to produce varying degrees of correlation between adjacent monomers. A calculation using the sBw of the mean time τc for chain closure predicts-under the Wilemski-Fixman approximation for diffusion-controlled reactions-that at early times, τc varies as the 2/3 power of N, in close agreement with the findings of the Brückner et al. study. Other scaling relations of that study, including those related to the probability of loop formation and the mean square displacements of terminal monomers, are also satisfactorily accounted for by the model.

Comparative assessment of the genotypes of oats of domestic and foreign breeding to the toxic effect of aluminum ions

The purpose of the research is to identify the genetic resistance to the toxic effects of aluminum ions in oat genotypes for the targeted selection of aluminum-resistant varieties. The work was carried out on the basis of the laboratory of genomic research in crop production of the Research Institute of Agricultural Sciences, a branch of the Tyumen Scientific Research Center SB RAS in 2024. The research object were oat species: Avena sativa L., A. abyssinica L., A. strigosa L., A. byzantina L. The research is based on changes in the growth of plant roots during the phase of early ontogenesis (the first 7 days) under the action of aluminum ions. Aqueous solutions of aluminum sulfate were prepared at a concentration of 1.5; 3.0; 5.0 g/l with concomitant measurement of the acidity level (pH). Distilled water was used as a control. The most resistant to the toxic manifestation of aluminum ions at concentrations of 1.5 and 3.0 g/l in solution was the Tobolyak variety (k-15827), which belongs to the species Avena sativa L. The root length index was 57 and 20%, respectively (root length 89±1.8 and 32±0.9 mm). Aluminum-resistance in the variant with a maximum concentration (5.0 g/l) of Al3+ in solution is noted in oat genotypes Raduzhny (A. sativa L., k-15887) and Mestny (A. strigosa L., k-5200) root length index reached 10% relative to the control. The oat genotypes belonging to the species Avena abyssinica L. were unstable to the effects of aluminum ions. (Mestny k-4971 and k-5075). At an aluminum ion concentration of 3.0 g/l, the genotype of Avena byzantina L. (Haruabusa k-14873) was the least resistant to stress – the root length index was 11% relative to the control. The mathematical dependence of the root length of oat sprouts correlated (R2=1) with the concentration of Al3+ in solution was also determined, expressed by the following regression equation: y=5,32x2-48,4x+117,34 where y is the index of the root length of seven-day oat seedlings, mm; x is the concentration of aluminum ions, g/l.

Microreactor designed for efficient plasma-liquid segmented flows.

Microreactors were designed for gas-liquid plasma chemical processes and operated under segmented flows in a high aspect ratio (8.76) rectangular microchannel. First, the hydrodynamics of the gas-liquid flows generated at a T-junction was investigated for fifteen solvents commonly used in organic synthesis. The classical literature scaling laws were revised to describe the dependence of bubble and slug lengths, and bubble residence time on the liquid nature by introducing their liquid vapour pressure. Liquid film thickness and liquid residence time were estimated from residence time distribution experiments. Secondly, plasma could be successfully generated in these segmented flows for all the liquids. Due to the plasma dissipation of thermal energy, gas phase temperature increased and induced the lengthening of bubbles and the decrease in bubble residence time. The flow pattern was also impacted by the gas temperature increase. A flow map describing the evolution of the flow pattern under plasma conditions was built, enabling prediction of the flow pattern based on the liquid boiling point and dielectric constant. These microreactors have demonstrated great potential, and by adapting the synthesis solvent or the operating plasma conditions, they could find promising applications in gas-liquid plasma chemical processes.

Detection of focused beams of surface magnetostatic waves in YIG / Pt structures

The purpose of this work is to experimentally study, using the inverse spin Hall effect (ISHE), the detection of focused beams of magnetostatic surface waves (MSSW) in integrated YIG (3.9 µm) / Pt (4 nm) thin-film microstructures, where the focusing effect was ensured by the curvilinear shape of the exciting antenna. Make a comparison with the case of detecting MSSWs excited by a rectilinear antenna. Methods. Experiments were carried out using the delay line structures based on the YIG/Pt. The amplitude-frequency characteristics of the YIG/Pt structure and the frequency dependence of the EMF (V(f)) induced in platinum were studied. Results. It was shown that at frequencies f near the long-wavelength limit of the MSSW spectrum, the magnitude of the EMF V(f) generated by a focused MSSW can be several times higher than the values of V(f) in the case of MSSW excitation by a common (straight) antenna. In this case, in the short-wavelength part of the spectrum, on the contrary, the magnitude of the EMF generated by the focused MSSW beam turns out to be noticeably smaller. This behavior is associated with chromatic aberration of the focusing antenna for the MSSW, which manifests itself in the frequency dependence of the focal length of the antenna, which is confirmed by the results of micromagnetic modeling. It is shown that the drop in the EMF signal generated by a focused MSSW beam in the short-wavelength part of the spectrum is associated with the focus reaching the area of the YIG not covered with the Pt film. In this case, the increase in V(f) in the long-wavelength region of the MSSW spectrum is explained by an increase in the linear power density of the MSSW and the formation of caustics under the Pt film. Conclusion. Obtained results can be used for the development of highly sensitive spin wave detectors and the creation of spin logic devices.

Frame Length Dependency for Fundamental Frequency Extraction in Noisy Speech

Frame Length Dependency for Fundamental Frequency Extraction in Noisy Speech

NEW DRILLING METHOD, DEVELOPMENT OF HYDROGEOLOGICAL AND OIL WELLS WITH IMPLOSIVE EFFECT

The peculiarities of the collimation zones of the productive formation are taken into account when rotary drilling of wells using drilling mud. A brief analysis of the most common and fundamentally different decollatation procedures, such as washing wells with water, pumping and gelation, is presented. A very effective and promising method of decollatation using the implosion effect has a special influence. A detailed example of a well-known device is given with an analysis of the features of its application, as well as significant disadvantages in the form of complexity and functionality, high cost. A fundamentally different new device was developed and proposed, free from all the disadvantages of the opposite device for which the invention was requested. This eliminates the use of pumping and compressor pipes and their sealing, as well as a sealant for the neck. There is also no need for a compressor and surface wiring with numerous valves. Replacing the intake valve valve with a disc valve eliminates the possibility of closing the intake valve as a result of the influx of reservoir fluid with a high content of collating materials caused by the implosion effect. The design and functioning features of the proposed device and its individual elements are taken into account both when creating a single, and with any number of repeated implosive effects. The generation limits necessary for the explosion effect of the liquid-filled space were mathematically analyzed to prevent the case from crumpling under the hydrostatic pressure of the solution remaining in the storage space. An example of the dependence of the permissible length of empty space on the thickness of the housing column and, in particular, on the thickness of the walls is illustrated using a computer program.

Spatially-dependent model for rods and cones in the retina

We develop a mathematical model for photoreceptors in the retina. We focus on rod and cone outer segment dynamics and interactions with a nutrient source associated with the retinal pigment epithelium cells. Rod and cone densities (number per unit area of retinal surface) are known to have significant spatial dependence in the retina with cones located primarily near the fovea and the rods located primarily away from the fovea. Our model accounts for this spatial dependence of the rod and cone photoreceptor density as well as for the possibility of nutrient diffusion. We present equilibrium and dynamic solutions, discuss their relation to existing models, and estimate model parameters through comparisons with available experimental measurements of both spatial and temporal photoreceptor characteristics. Our model compares well with existing data on spatially-dependent regrowth of photoreceptor outer segments in the macular region of Rhesus Monkeys. Our predictions are also consistent with existing data on the spatial dependence of photoreceptor outer segment length near the fovea in healthy human subjects. We focus primarily on the healthy eye but our model could be the basis for future efforts designed to explore various retinal pathologies, eye-related injuries, and treatments of these conditions.

Fault-displacement models for aggregate and principal displacements

New fault-displacement models (FDMs) are developed for the aggregate and principal net surface displacement using the database developed by the Fault Displacement Hazard Initiative Project. An FDM for the aggregate displacement is developed, which is then partitioned into principal and distributed displacements. The model for the aggregate displacement is first formulated in the wavenumber domain to incorporate seismology-based constraints for the extrapolation of the magnitude scaling of median displacements to large-magnitude events. The results from the wavenumber-domain model are then adjusted to fit the empirical moderate-magnitude scaling (M < 7) and the shape of the displacement profile at the ends of the rupture. Segments are used in the model development to better capture the complexity of the variability of the surface-displacement profile along strike, including regions with zero displacements. For applications in which segments cannot be identified, simplified FDMs without segments are developed that treat the number, lengths, and locations of the segments as aleatory variability. The principal-displacement FDM is then developed as an adjustment to the aggregate-displacement FDM. The segmentation and the magnitude dependence of the taper length of individual segments lead to non-self-similar scaling of the median profile along the entire rupture that can have a significant impact on probabilistic fault-displacement hazard analysis (PFDHA) for sites near the ends of faults. A key feature of the new FDMs is the use of a power-normal [Formula: see text] distribution for the aleatory variability, which leads to narrower distributions of the displacement for large-magnitude earthquakes compared to the commonly used lognormal distribution. For large-magnitude earthquakes, the expected maximum displacements computed using the power-normal distribution of the FDM are consistent with the observed maximum displacements along strike, supporting the narrower shape of the upper tail of the power-normal distribution for large-magnitude events.

Effect of small molecular crowders on dynamics of kinesin molecular motors

Kinesin is a motor protein that can convert chemical energy of ATP hydrolysis into mechanical energy of moving processively on microtubules. Apart from the load and ATP concentration affecting the dynamics of the motor such as velocity, run length, dissociation rate, etc., the increase of solution viscosity by supplementing crowding agents of low molecular weight into the buffer can also affect the dynamics. Here, based on our proposed model for the chemomechanical coupling of the kinesin motor, a systematically theoretical study of the motor dynamics under the variation of the viscosity and load is presented. Both the load on the motor’s stalk and that on one of the two heads are considered. The theoretical results provide a consistent explanation of the available contradictory experimental results, with some showing that increasing viscosity decreases sensitively the velocity whereas others showing that increasing viscosity has little effect on the velocity. The theoretical results reproduce quantitatively the puzzling experimental data showing that under different directions of the load on the stalk, increasing viscosity has very different effects on the change of run length or dissociation rate. The theoretical results predict that in both the pure and crowded buffers the dependence of the run length on the load acting one of the two heads has very different feature from that on the load acting on the stalk.

The novel n-channel liquid crystal organic field effect transistor (LC-n-OFET): A promising technology for low-power electronics

In this study, a novel n-channel liquid crystal organic field effect transistor (LC-n-OFET) was fabricated using a mixture of E7 nematic liquid crystal (NLC) and [6,6]-phenyl C61 butyric acid methyl ester (PCBM) in an OFET cell. The LC-n-OFET performance was investigated regarding dielectric properties, UV illumination sensitivity, and channel length dependence. Output and transfer current-voltage (I–V) characteristics were measured to evaluate the electrical properties in dark and under UV illumination for varying channel lengths. Additionally, the dielectric characteristics of the LC-n-OFET were determined along with the capacitance-frequency response (Ci-f), threshold voltage (VTh), field-effect mobility (μFET), and on/off current ratio (Ion/off) as a function of UV illumination intensity and channel length changes. Electrical measurements showed the Ion/off current ratio is inversely proportional to channel length but directly proportional to UV intensity. Meanwhile, the threshold voltage (VTh) and mobility (μFET) increased with longer channel length and higher light intensity. Overall, the novel LC-n-OFET exhibited promising performance with low VTh, high μFET, and large Ion/off.

Human cystatin C induces the disaggregation process of selected amyloid beta peptides: a structural and kinetic view

Neurodegenerative diseases, such as Alzheimer’s disease (AD) and various types of amyloidosis, are incurable; therefore, understanding the mechanisms of amyloid decomposition is crucial to develop an effective drug against them for future therapies. It has been reported that one out of three people over the age of 85 are suffering from dementia as a comorbidity to AD. Amyloid beta (Aβ), the hallmark of AD, transforms structurally from monomers into β-stranded aggregates (fibrils) via multiple oligomeric states. Astrocytes in the central nervous system secrete the human cystatin C protein (HCC) in response to various proteases and cytokines. The codeposition of Aβ and HCC in the brains of patients with AD led to the hypothesis that cystatin C is implicated in the disease process. In this study, we investigate the intermolecular interactions between different atomic structures of fibrils formed by Aβ peptides and HCC to understand the pathological aggregation of these polypeptides into neurotoxic oligomers and then amyloid plaques. To characterize the interactions between Aβ and HCC, we used a complementary approach based on the combination of small-angle neutron scattering analysis, atomic force microscopy and computational modelling, allowing the exploration of the structures of multicomponent protein complexes. We report here an optimized protocol to study that interaction. The results show a dependency of the sequence length of the Aβ peptide on the ability of the associated HCC to disaggregate it.

Discovery and Visualization of the Hidden Relationships among N-Glycosylation, Disulfide Bonds, and Membrane Topology.

Membrane proteins (MPs) are functionally important but structurally complex. In particular, MPs often carry three structural features, i.e., transmembrane domains (TMs), disulfide bonds (SSs), and N-glycosylation (N-GLYCO). All three features have been intensively studied; however, how the three features potentially correlate has been less addressed in the literature. With the growing accuracy from computational prediction, we used publicly available information on SSs and N-GLYCO and analyzed the potential relationships among post-translational modifications (PTMs) and the predicted membrane topology in the human proteome. Our results suggested a very close relationship between SSs and N-GLYCO that behaved similarly, whereas a complementary relation between the TMs and the two PTMs was also revealed, in which the high SS and/or N-GLYCO presence is often accompanied by a low TM occurrence in a protein. Furthermore, the occurrence of SSs and N-GLYCO in a protein heavily relies on the protein length; however, TMs seem not to possess such length dependence. Finally, SSs exhibits larger potential dynamics than N-GLYCO, which is confined by the presence of sequons. The special classes of proteins possessing extreme or unique patterns of the three structural features are comprehensively identified, and their structural features and potential dynamics help to identify their susceptibility to different physiological and pathophysiological insults, which could help drug development and protein engineering.