Selenium catalysis enables negative feedback organic oscillators

The construction of materials regulated by chemical reaction networks requires regulatory motifs that can be stacked together into systems with desired properties. Multiple autocatalytic reactions producing thiols are known. However, negative feedback loop motifs are unavailable for thiol chemistry. Here, we develop a negative feedback loop based on the selenocarbonates. In this system, thiols induce the release of aromatic selenols that catalyze the oxidation of thiols by organic peroxides. This negative feedback loop has two important features. First, catalytic oxidation of thiols follows Michaelis-Menten-like kinetics, thus increasing nonlinearity for the negative feedback. Second, the strength of the negative feedback can be tuned by varying substituents in selenocarbonates. When combined with the autocatalytic production of thiols in a flow reactor, this negative feedback loop induces sustained oscillations. The availability of this negative feedback motif enables the future construction of oscillatory, homeostatic, adaptive, and other regulatory circuits in life-inspired systems and materials.

Expanding Predictive Capacities in Toxicology: Insights from Hackathon-Enhanced Data and Model Aggregation

In the realm of predictive toxicology for small molecules, the applicability domain of QSAR models is often limited by the coverage of the chemical space in the training set. Consequently, classical models fail to provide reliable predictions for wide classes of molecules. However, the emergence of innovative data collection methods such as intensive hackathons have promise to quickly expand the available chemical space for model construction. Combined with algorithmic refinement methods, these tools can address the challenges of toxicity prediction, enhancing both the robustness and applicability of the corresponding models. This study aimed to investigate the roles of gradient boosting and strategic data aggregation in enhancing the predictivity ability of models for the toxicity of small organic molecules. We focused on evaluating the impact of incorporating fragment features and expanding the chemical space, facilitated by a comprehensive dataset procured in an open hackathon. We used gradient boosting techniques, accounting for critical features such as the structural fragments or functional groups often associated with manifestations of toxicity.

NeuroClick: software for mimicking click reaction to generate drug-like molecules permeating the blood-brain barrier

Background: Traditional methods for chemical library generation in virtual screening often impose limitations on the accessible chemical space or produce synthetically irrelevant structures. Incorporating common chemical reactions into generative algorithms could offer significant benefits. Materials & methods: In this study, we developed NeuroClick, a graphical user interface software designed to perform in silico azide-alkyne cycloaddition, a widely utilized synthetic approach in modern medicinal chemistry. Results & conclusion: NeuroClick facilitates the generation and filtering of large combinatorial libraries at a remarkable rate of 10,000 molecules per minute. Moreover, the generated products can be filtered to identify subsets of pharmaceutically relevant compounds based on Lipinski's rule of five and blood-brain barrier permeability prediction. We demonstrate the utility of NeuroClick by generating and filtering several thousand molecules for dopamine D3 receptor ligand screening.

Ultrasensitive Detection of PSA Using Antibodies in Crowding Polyelectrolyte Multilayers on a Silicon Nanowire Field-Effect Transistor

Immunosensors based on field-effect transistors with nanowire channels (NWFETs) provide fast and real-time detection of a variety of biomarkers without the need for additional labels. The key feature of the developed immunosensor is the coating of silicon NWs with multilayers of polyelectrolytes (polyethylenimine (PEI) and polystyrene sulfonate (PSS)). By causing a macromolecular crowding effect, it ensures the "soft fixation" of the antibodies into the 3-D matrix of the oppositely charged layers. We investigated the interaction of prostate-specific antigen (PSA), a biomarker of prostate cancer, and antibodies adsorbed in the PEI and PSS matrix. In order to visualize the formation of immune complexes between polyelectrolyte layers using SEM and AFM techniques, we employed a second clone of antibodies labeled with gold nanoparticles. PSA was able to penetrate the matrix and concentrate close to the surface layer, which is crucial for its detection on the nanowires. Additionally, this provides the optimal orientation of the antibodies' active centers for interacting with the antigen and improves their mobility. NWFETs were fabricated from SOI material using high-resolution e-beam lithography, thin film vacuum deposition, and reactive-ion etching processes. The immunosensor was characterized by a high sensitivity to pH (71 mV/pH) and an ultra-low limit of detection (LOD) of 0.04 fg/mL for PSA. The response of the immunosensor takes less than a minute, and the measurement is carried out in real time. This approach seems promising for further investigation of its applicability for early screening of prostate cancer and POC systems.

Ergodicity Breaking and Self-Destruction of Cancer Cells by Induced Genome Chaos

During the progression of some cancer cells, the degree of genome instability may increase, leading to genome chaos in populations of malignant cells. While normally chaos is associated with ergodicity, i.e., the state when the time averages of relevant parameters are equal to their phase space averages, the situation with cancer propagation is more complex. Chromothripsis, a catastrophic massive genomic rearrangement, is observed in many types of cancer, leading to increased mutation rates. We present an entropic model of genome chaos and ergodicity and experimental evidence that increasing the degree of chaos beyond the non-ergodic threshold may lead to the self-destruction of some tumor cells. We study time and population averages of chromothripsis frequency in cloned rhabdomyosarcomas from rat stem cells. Clones with frequency above 10% result in cell apoptosis, possibly due to mutations in the BCL2 gene. Potentially, this can be used for suppressing cancer cells by shifting them into a non-ergodic proliferation regime.

Electrochemical Sensor to Detect Antibiotics in Milk Based on Machine Learning Algorithms

The present study is dedicated to the problem of electrochemical analysis of multicomponent mixtures, such as milk. A combination of cyclic voltammetry facilities and machine learning techniques made it possible to create a pattern recognition system for the detection of antibiotic residues in skimmed milk. A multielectrode sensor including copper, nickel, and carbon fiber was fabricated for the collection of electrochemical data. Processes occurring at the electrode surface were discussed and simulated with the help of molecular docking and density functional theory modeling. It was assumed that the antibiotic fingerprint reveals a potential drift of electrodes, owing to complexation with metal ions present in milk. The gradient boosting algorithm showed the best efficiency in training the machine learning model. High accuracy was achieved for the recognition of antibiotics in milk. The elaborated method may be incorporated into existing milking systems at dairy farms for monitoring the residue concentrations of antibiotics.

Calix[4]arene-pyrazole conjugates as potential cancer therapeutics

Tumor selectivity is yet a challenge in chemotherapy-based cancer treatment. A series of calixarenes derivatized at the lower rim with 3-phenyl-1H-pyrazole units with variable upper-rim substituent and conformations of macrocyclic core, alkyl chain length between heterocycle and core, as well as phenolic monomer (5-(4-tert-butylphenyloxy)methoxy-3-phenyl-1H-pyrazole) have been synthesized and characterized in a range of therapeutically relevant cellular models (M-HeLa, MCF7, A-549, PC3, Chang liver, and Wi38) from different target organs/systems. Specific cytotoxicity for M-HeLa cells has been observed in tert-butylcalix[4]arene pyrazoles in 1,3-alternate (compound 7b) and partial cone (compound 7c) conformations with low mutagenicity and haemotoxicity and in vivo toxicity in mice. Compounds 7b,c have induced mitochondrial pathway of apoptosis of M-HeLa cells through caspase-9 activation preceded by the cell cycle arrest at G0/G1 phase. A concomitant overexpression of DNA damage markers in pyrazole-treated M-HeLa cells suggests that calixarene pyrazoles target DNA, which was supported by the presence of interactions between calixarenes and ctDNA at the air-water interface.

Deposition of Nanostructured Tungsten Oxide Layers by a New Method: Periodic Modulation of the Deposition Angle

Periodic modulation of the deposition angle (PMDA) is a new method to deposit nanostructured and continuous layers with controllable periodic density fluctuation. The method is used for the magnetron sputtering of a WO3 layer for an electrochromic device (ECD). An experimental study indicates that the electrochromic coloration-bleaching rate nearly doubles and the electrochromic efficiency grows by about 25% in comparison with the traditional method. The ECD efficiency rises with the increasing degree of nanostructure ordering, surface roughness, and homogeneity of the WO3 layer. The method is promising for coating deposition techniques needed to produce versatile devices with specific requirements for ion transport in surface layers, coatings, and interfaces, such as fuel cells, batteries, and supercapacitors.

Memristive Effect in Ti3 C2 Tx (MXene) Polyelectrolyte Multilayers

The emerging novel class of two-dimensional materials - MХenes - have attracted significant research attention. However, there are only few reports on using the most prominent member of the MXene family, Ti3 C2 Tx , as an active material for memristive devices within a polyelectrolyte matrix and its deposition on inert electrodes like ITO and Pt. In this study, we systematically investigate Ti3 C2 Tx MXenes synthesized with two classical delamination agents, such as lithium chloride and tetramethylammonium hydroxide, to identify the most suitable candidate for memristive device applications. The characteristics of memristors based on the hybrid structures consisting of MXene-polyelectrolyte multilayers, specifically polyethyleneimine (PEI) and poly(sodium 4-styrenesulfonate) (PSS) are explored. The PEI(MXene)/PSS memristor exhibits a voltage threshold (VSET/RESET ) range of 1.5-2.0 V, enabling the transition from a high-resistive state (HRS) to a low-resistive state (LRS), along with a significant current switching ratio of approximately two orders of magnitude. The observed VSET/RESET difference of approximately 4 V is further supported by density functional theory (DFT) calculated redox potential. These findings underscore the potential of polyelectrolyte-based memristors, such as the in PEI-Ti3 C2 Tx -PSS system, in facilitating the development of highly functional, self-assembled memristive devices with diverse applications.

Universal Method Based on Layer-by-Layer Assembly for Aptamer-Based Sensors for Small-Molecule Detection

Development of a fast and accurate pesticide analysis system is a challenging task, as a large amount of commonly used pesticide has negative effects on humans' health. Detection of pesticide residues is crucial for food safety management and environmental protection. Aptamers─short single-stranded oligonucleotides (RNA or DNA) selected by aptamer selection method SELEX─can selectively bind to their target pesticide molecules with high affinity. Thus, in the present study, we developed an electrochemical biosensor based on aptamers to detect the commonly used pesticide, glyphosate. Carbon fibers were used as the platform to assemble polyelectrolyte layers with the incorporated aptamers selectively binding with glyphosate molecules for electrochemical detection. The best limit of detection of 0.3 μM was achieved at open-circuit potential measurements, which is comparable to the current need in detection of glyphosate. The developed method can be implemented into existing systems for the determination of pesticides on farms to control residual concentrations of glyphosate in soil and water.

Diffusion-Limited Processes in Hydrogels with Chosen Applications from Drug Delivery to Electronic Components

Diffusion is one of the key nature processes which plays an important role in respiration, digestion, and nutrient transport in cells. In this regard, the present article aims to review various diffusion approaches used to fabricate different functional materials based on hydrogels, unique examples of materials that control diffusion. They have found applications in fields such as drug encapsulation and delivery, nutrient delivery in agriculture, developing materials for regenerative medicine, and creating stimuli-responsive materials in soft robotics and microrobotics. In addition, mechanisms of release and drug diffusion kinetics as key tools for material design are discussed.

Using novel click chemistry algorithm to design D3R inhibitors as blood-brain barrier permeants

Dopamine receptor D3 (D3R) has gained attention as a promising therapeutic target for neurological disorders. In this study, an innovative in silico click reaction strategy was employed to identify potential D3R binders. The ligand template, 1-phenyl-4-[4-(1H-1,2,3-triazol-5-yl)butyl]piperazine, with substitution at the 1,2,3-triazole ring, served as the starting point. Generated compounds underwent filtration based on their brain-to-blood concentration ratio (logBB), leading to the identification of 1-{4-[1-(decahydronaphthalen-1-yl)-1H-1,2,3-triazol-5-yl]butyl}-4-phenylpiperazine as the most promising candidate, displaying superior D3R affinity and blood-brain barrier (BBB) permeability compared to the reference ligand, eticlopride. Molecular dynamics simulations further supported these findings. This study presents a novel hit for designing D3R ligands and establishes a workflow utilizing in silico click chemistry to screen compounds with BBB permeability. The proposed click reaction-based algorithm holds significant potential as a valuable tool in the development of effective antipsychotic compounds.

Folding-unfolding asymmetry and a RetroFold computational algorithm

We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process as the driving force is opposed by damping. Protein folding takes two orders of magnitude longer than unfolding. We suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modelling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns, while unfolding (denaturation) takes only about 5.0 ns and, therefore, fewer computational resources are needed for its simulation. This RetroFold approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.

Functionalization of chitosan with poly aromatic hydroxyl molecules for improving its antibacterial and antioxidant properties: Practical and theoretical studies

In this study, the chitosan backbone was functionalized with 2,2',4,4'-tetrahydroxybenzophenone by Schiff base, bonding the molecules into the repeating amine groups. The use of ¹H NMR, FT-IR, and UV-Vis analyses provided compelling evidence of the structure of the newly developed derivatives. The deacetylation degree was calculated to be 75.35 %, and the degree of substitution was 5.53 % according to elemental analysis. The thermal analysis of samples using TGA demonstrated that CS-THB derivatives are more stable than chitosan itself. SEM was used to investigate the change in surface morphology. The improvement of the biological properties of chitosan was investigated in terms of its antibacterial activity against pathogenic antibiotic-resistant bacteria. The antioxidant properties showed an improvement in activity compared to chitosan by two times against ABTS radicals and four times against DPPH radicals. Furthermore, the cytotoxicity and anti-inflammatory properties were investigated using normal skin cells (HBF4) and WBCs. Quantum chemistry calculations revealed that combining polyphenol with chitosan makes it more effective as an antioxidant than either chitosan or polyphenol alone. Our findings suggest that the new chitosan Schiff base derivative could be utilized for tissue regeneration applications.

Melamine Barbiturate as a Light-Induced Nanostructured Supramolecular Material for a Bioinspired Oxygen and Organic Radical Trap and Stabilization

Use of coantioxidant systems is a prospective way to increase the effectiveness of antioxidant species in tissue repair and regeneration. In this paper, we introduce a novel scheme of a reactive oxygen species (ROS) trap and neutralization during self-assembly of supramolecular melamine barbiturate material. The performed reaction chain mimics the biological process of ROS generation in key stages and enables one to obtain stable hydroperoxyl and organic radicals in a melamine barbiturate structure. Melamine barbiturate also neutralizes hydroxyl radicals, and the effectiveness of the radical trap is controlled with ROS scavenger incorporation. The number of radicals dramatically increases during light-inducing and depends on pH. The proposed scheme of the ROS trap and neutralization opens a way to the use of supramolecular assemblies as a component of coantioxidant systems and a source of organic radicals.

Periodic Self-Assembly of Poly(ethyleneimine)-poly(4-styrenesulfonate) Complex Coacervate Membranes

Coacervation is a self-assembly strategy based on the complexation of polyelectrolytes, which is utilized in biomedicine and agriculture, as well as automotive and textile industries. In this paper, we developed a new approach to the on-demand periodic formation of polyelectrolyte complexes through a Liesegang-type hierarchical organization. Adjustment of reaction conditions allows us to assemble materials with a tunable spatiotemporal geometry and establish materials' production cycles with a regulated periodicity. The proposed methodology allows the membrane to self-assemble when striving to reach balance and self-heal after exposure to external stimuli, such as potential difference and high pH. Using chronopotentiometry, K⁺ ion permeability behavior of the PEI-PSS coacervate membranes was demonstrated. The periodically self-assembled polyelectrolyte nanomembranes could further be integrated into novel energy storage devices and intelligent biocompatible membranes for bionics, soft nanorobotics, biosensing, and biocomputing.

Reaction-Diffusion Pathways for a Programmable Nanoscale Texture of the Diamond-SiC Composite

The diamond-SiC composite has a low density and the highest possible speed of sound among existing materials except for diamond. The composite is synthesized by a complex exothermic chemical reaction between diamond powder and liquid Si. This makes it an ideal material for protection against impact loading. Experiments show that a system of patterns is formed at the diamond-SiC interface. Modeling of reaction-diffusion processes of composite synthesis proves a formation of ceramic materials with a regular (periodic) interconnected microstructure in a given system. The composite material with interconnected structures at the interface has very high mechanical properties and resistance to impact since its fractioning is intercrystallite.

In silico investigation of nonsynonymous single nucleotide polymorphisms in BCL2 apoptosis regulator gene to design novel protein-based drugs against cancer

BCL2 apoptosis regulator gene encodes Bcl-2 pro-survival protein, which plays an important role to evade apoptosis in various cancers. Moreover, single nucleotide polymorphisms (SNPs) in the BCL2 gene can be nonsynonymous (nsSNPs), which might affect the protein stability and probably its function. Therefore, we implement cutting-edge computational techniques based on the Spherical Polar Fourier and Monte-Carlo algorithms to investigate the impact of these SNPs on the B cell lymphoma-2 (Bcl-2) stability and therapeutic potential of protein-based molecules to inhibit this protein. As a result, we identified two nsSNPs (Q118R and R129C) to be deleterious and highly conserved, having a negative effect on protein stability. Additionally, molecular docking and molecular dynamics simulations confirmed the decreased binding affinity of mutated Bcl-2 variants to bind three-helix bundle protein inhibitor as these mutations occurred in the protein-protein binding site. Overall, this computational approach investigating nsSNPs provides a useful basis for designing novel molecules to inhibit Bcl-2 pro-survival pathway in malignant cells.

Uricase Crowding via Polyelectrolyte Layers Coacervation for Carbon Fiber-Based Electrochemical Detection of Uric Acid

Urate oxidase (UOx) surrounded by synthetic macromolecules, such as polyethyleneimine (PEI), poly(allylamine hydrochloride) (PAH), and poly(sodium 4-styrenesulfonate) (PSS) is a convenient model of redox-active biomacromolecules in a crowded environment and could display high enzymatic activity towards uric acid, an important marker of COVID-19 patients. In this work, the carbon fiber electrode was modified with Prussian blue (PB) redox mediator, UOx layer, and a layer-by-layer assembled polyelectrolyte film, which forms a complex coacervate consisting of a weakly charged polyelectrolyte (PEI or PAH) and a highly charged one (PSS). The film deposition process was controlled by cyclic voltammetry and scanning electron microscopy coupled with energy-dispersive X-ray analysis (at the stage of PB deposition) and through quartz crystal microbalance technique (at latter stages) revealed uniform distribution of the polyelectrolyte layers. Variation of the polyelectrolyte film composition derived the following statements. (1) There is a linear correlation between electrochemical signal and concentration of uric acid in the range of 10^-4-10^-6 M. (2) An increase in the number of polyelectrolyte layers provides more reproducible values for uric acid concentration in real urine samples of SARS-CoV-2 patients measured by electrochemical enzyme assay, which are comparable to those of spectrophotometric assay. (3) The PAH/UOx/PSS/(PAH/PSS)₂-coated carbon fiber electrode displays the highest sensitivity towards uric acid. (4) There is a high enzyme activity of UOx immobilized into the hydrogel nanolayer (values of the Michaelis-Menten constant are up to 2 μM) and, consequently, high affinity to uric acid.

Piezo-Responsive Hydrogen-Bonded Frameworks Based on Vanillin-Barbiturate Conjugates

A concept of piezo-responsive hydrogen-bonded π-π-stacked organic frameworks made from Knoevenagel-condensed vanillin–barbiturate conjugates was proposed. Replacement of the substituent at the ether oxygen atom of the vanillin moiety from methyl (compound 3a) to ethyl (compound 3b) changed the appearance of the products from rigid rods to porous structures according to optical microscopy and scanning electron microscopy (SEM), and led to a decrease in the degree of crystallinity of corresponding powders according to X-ray diffractometry (XRD). Quantum chemical calculations of possible dimer models of vanillin–barbiturate conjugates using density functional theory (DFT) revealed that π-π stacking between aryl rings of the vanillin moiety stabilized the dimer to a greater extent than hydrogen bonding between carbonyl oxygen atoms and amide hydrogen atoms. According to piezoresponse force microscopy (PFM), there was a notable decrease in the vertical piezo-coefficient upon transition from rigid rods of compound 3a to irregular-shaped aggregates of compound 3b (average values of d₃₃ coefficient corresponded to 2.74 ± 0.54 pm/V and 0.57 ± 0.11 pm/V), which is comparable to that of lithium niobate (d₃₃ coefficient was 7 pm/V).

Topological bio-scaling analysis as a universal measure of protein folding

Scaling relationships for polymeric molecules establish power law dependencies between the number of molecular segments and linear dimensions, such as the radius of gyration. They also establish spatial topological properties of the chains, such as their dimensionality. In the spatial domain, power exponents α = 1 (linear stretched molecule), α = 0.5 (the ideal chain) and α = 0.333 (compact globule) are significant. During folding, the molecule undergoes the transition from the one-dimensional linear to the three-dimensional globular state within a very short time. However, intermediate states with fractional dimensions can be stabilized by modifying the solubility (e.g. by changing the solution temperature). Topological properties, such as dimension, correlate with the interaction energy, and thus by tuning the solubility one can control molecular interaction. We investigate these correlations using the example of a well-studied short model of Trp-cage protein. The radius of gyration is used to estimate the fractal dimension of the chain at different stages of folding. It is expected that the same principle is applicable to much larger molecules and that topological (dimensional) characteristics can provide insights into molecular folding and interactions.

When Bubbles Are Not Spherical: Artificial Intelligence Analysis of Ultrasonic Cavitation Bubbles in Solutions of Varying Concentrations

Ultrasonic irradiation of liquids, such as water-alcohol solutions, results in cavitation or the formation of small bubbles. Cavitation bubbles are generated in real solutions without the use of optical traps making our system as close to real conditions as possible. Under the action of the ultrasound, bubbles can grow, oscillate, and eventually collapse or decompose. We apply the mathematical method of separation of motions to interpret the acoustic effect on the bubbles. While in most situations, the spherical shape of a bubble is the most energetically profitable as it minimizes the surface energy, when the acoustic frequency is in resonance with the natural frequency of the bubble, shapes with the dihedral symmetry emerge. Some of these resonance shapes turn unstable, so the bubble decomposes. It turns out that bubbles in the solutions of different concentrations (with different surface energies and densities) attain different evolution paths. While it is difficult to obtain a deterministic description of how the solution concentration affects bubble dynamics, it is possible to separate images with different concentrations by applying the artificial neural network (ANN) algorithm. An ANN was trained to detect the concentration of alcohol in a water solution based on the bubble images. This indicates that artificial intelligence (AI) methods can complement deterministic analysis in nonequilibrium, near-unstable situations.

Spatiotemporal Regulation of Hydrogel Actuators by Autocatalytic Reaction Networks

Regulating hydrogel actuators with chemical reaction networks is instrumental for constructing life-inspired smart materials. Herein, hydrogel actuators are engineered that are regulated by the autocatalytic front of thiols. The actuators consist of two layers. The first layer, which is regular polyacrylamide hydrogel, is in a strained conformation. The second layer, which is polyacrylamide hydrogel with disulfide crosslinks, maintains strain in the first layer. When thiols released by the autocatalytic front reduce disulfide crosslinks, the hydrogel actuates by releasing the mechanical strain in the first layer. The autocatalytic front is sustained by the reaction network, which uses thiouronium salts, disulfides of β-aminothiols, and maleimide as starting components. The gradual actuation by the autocatalytic front enables movements such as gradual unrolling, screwing, and sequential closing of "fingers." This actuation also allows the transmission of chemical signals in a relay fashion and the conversion of a chemical signal to an electrical signal. Locations and times of spontaneous initiation of autocatalytic fronts can be preprogrammed in the spatial distribution of the reactants in the hydrogel. To approach the functionality of living matter, the actuators triggered by an autocatalytic front can be integrated into smart materials regulated by chemical circuits.

Soft Hydrogel Actuator for Fast Machine-Learning-Assisted Bacteria Detection

We demonstrate that our bio-electrochemical platform facilitates the reduction of detection time from the 3-day period of the existing tests to 15 min. Machine learning and robotized bioanalytical platforms require the principles such as hydrogel-based actuators for fast and easy analysis of bioactive analytes. Bacteria are fragile and environmentally sensitive microorganisms that require a special environment to support their lifecycles during analytical tests. Here, we develop a bio-electrochemical platform based on the soft hydrogel/eutectic gallium-indium alloy interface for the detection of Streptococcus thermophilus and Bacillus coagulans bacteria in various mediums. The soft hydrogel-based device is capable to support bacteria' viability during detection time. Current-voltage data are used for multilayer perceptron algorithm training. The multilayer perceptron model is capable of detecting bacterial concentrations in the 10⁴ to 10⁸ cfu/mL range of the culture medium or in the dairy products with high accuracy (94%). Such a fast and easy biodetection is extremely important for food and agriculture industries and biomedical and environmental science.

Topological Data Analysis of Nanoscale Roughness in Brass Samples

Rough surfaces possess complex topographies, which cannot be characterized by a single parameter. The selection of appropriate roughness parameters depends on a particular application. Large datasets representing surface topography possess orderliness, which can be expressed in terms of topological features in high-dimensional dataspaces reflecting properties such as anisotropy and the number of lay directions. The features are scale-dependent because both sampling length and resolution affect them. We study nanoscale surface roughness using 3 × 3, 4 × 4, and 5 × 5 pixel patches obtained from atomic force microscopy (AFM) images of brass (Cu Zn alloy) samples roughened by a sonochemical treatment. We calculate roughness parameters, correlation length, extremum point distribution, persistence diagrams, and barcodes. These parameters of interest are discussed and compared.

Separation of motions and vibrational separation of fractions for biocide brass

The mathematical method of separation of motions represents the effect of fast high-frequency oscillations by an effective averaged force or potential. Ultrasound acoustic vibrations are an example of such rapid oscillations leading to cavitation in water due to the gas phase formation (bubbles). Ultrasound cavitation is used to treat the surface of brass microparticles submerged in water. The formation of bubbles and their collapse triggers the modification of surface roughness and chemical composition. Consequently, the suspension separates into various fractions related to demonstrating biocide properties. While the exact mechanism of this process is complex, it can be explained phenomenologically by using the Onsager reciprocal relations for coupling the copper ion diffusion with the gas phase separation in water as a result of the action of the effective average vibrational force.

Scaffold Searching of FDA and EMA-Approved Drugs Identifies Lead Candidates for Drug Repurposing in Alzheimer's Disease

Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a significant amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA), European Medicines Agency (EMA), or Worldwide for another indication is a more rapid and less expensive option. Therefore, we apply the scaffold searching approach based on known amyloid-beta (Aβ) inhibitor tramiprosate to screen the DrugCentral database (n = 4,642) of clinically tested drugs. As a result, menadione bisulfite and camphotamide substances with protrombogenic and neurostimulation/cardioprotection effects were identified as promising Aβ inhibitors with an improved binding affinity (ΔGbind) and blood-brain barrier permeation (logBB). Finally, the data was also confirmed by molecular dynamics simulations using implicit solvation, in particular as Molecular Mechanics Generalized Born Surface Area (MM-GBSA) model. Overall, the proposed in silico pipeline can be implemented through the early stage rational drug design to nominate some lead candidates for AD, which will be further validated in vitro and in vivo, and, finally, in a clinical trial.

In vivo urinary compatibility of Mg-Sr-Ag alloy in swine model

A biodegradable metallic ureteral stent with suitable mechanical properties and antibacterial activity remains a challenge. Here we reveal the scientific significance of a biodegradable Mg-Sr-Ag alloy with a favorable combination of balanced mechanical properties, adjustable indwelling time in urinary tract and evident antibacterial activity via in vivo experiments in a swine model. Attributed to the rheo-solidification process, equiaxial microstructure and significantly refined grains (average grain size: 27.1 μm) were achieved. Mg₁₇Sr₂ and Mg₄Ag were found as the primary precipitates in the matrix, due to which the alloy obtained ca. 111% increase in ultimate tensile strength in comparison to pure magnesium. Both the in vitro and in vivo results demonstrated the satisfactory biocompatibility of the alloy. Histological evaluation and bioindicators analysis suggested that there was no tissue damage, inflammation and lesions in the urinary system caused by the degradation process. The stent also improved the post-operative bladder functions viewed from the urodynamic results. Our findings highlight the potential of this alloy as antibacterial biodegradable urinary implant material.

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Innovative biodegradable antibacterial Mg-Sr-Ag alloy.

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In vivo study in pig ureter models.

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Enhanced mechanical properties and adjustable indwelling time.

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Outstanding urinary compatibility and evident antibacterial activity.

Recent Progress of Layer-by-layer Assembly, Free-Standing Film and Hydrogel Based on Polyelectrolytes

Nowadays, polyelectrolytes play an essential role in the development of new materials. Their use allows creating new properties of materials and surfaces and vary them in a wide range. Basically, modern methods are divided into three areas-the process of layer-by-layer deposition, free-standing films, and hydrogels based on polyelectrolytes. Layer-by-layer assembly of polyelectrolytes on various surfaces is a powerful technique. It allows giving surfaces new properties, for example, protect them from corrosion. Free-standing films are essential tools for the design of membranes and sensors. Hydrogels based on polyelectrolytes have recently shown their applicability in electrical and materials science. The creation of new materials and components with controlled properties can be achieved using polyelectrolytes. This review focuses on new technologies that have been developed with polyelectrolytes over the last five years.

Biocompatible pH-Degradable Functional Capsules Based on Melamine Cyanurate Self-Assembly

Development of adaptive self-regulating materials and chemical-biological systems-self-healing, self-regulating, etc.-is an advanced modern trend. The very sensitive pH-controlled functionality of supramolecular assemblies is a very useful tool for chemical and biochemical implementations. However, the assembly process can be tuned by various factors that can be used for both better functionality control and further functionalization such as active species, e.g., drugs and dyes, and encapsulation. Here, the effect of a dye, sodium fluorescein (uranine) (FL), on the formation of a self-assembled melamine cyanurate (M-CA) structure is investigated and calculated with density functional theory (DFT) and molecular dynamics. Interestingly, the dye greatly affects the self-assembly process at early stages from the formation of dimers, trimers, and tetramer to nucleation control. The supramolecular structure disassembly and subsequent release of trapped dye occurred under both high- and low-pH conditions. This system can be used for time-prolonged bacterial staining and development of supramolecular capsules for the system chemistry approach.

Infochemistry and the Future of Chemical Information Processing

Nowadays, information processing is based on semiconductor (e.g., silicon) devices. Unfortunately, the performance of such devices has natural limitations owing to the physics of semiconductors. Therefore, the problem of finding new strategies for storing and processing an ever-increasing amount of diverse data is very urgent. To solve this problem, scientists have found inspiration in nature, because living organisms have developed uniquely productive and efficient mechanisms for processing and storing information. We address several biological aspects of information and artificial models mimicking corresponding bioprocesses. For instance, we review the formation of synchronization patterns and the emergence of order out of chaos in model chemical systems. We also consider molecular logic and ion fluxes as information carriers. Finally, we consider recent progress in infochemistry, a new direction at the interface of chemistry, biology, and computer science, considering unconventional methods of information processing.

All-Dielectric Nanostructures with a Thermoresponsible Dynamic Polymer Shell

We suggest a new strategy for creating stimuli-responsive bio-integrated optical nanostructures based on Mie-resonant silicon nanoparticles covered by an ensemble of similarity negatively charged polyelectrolytes (heparin and sodium polystyrene sulfonate). The dynamic tuning of the nanostructures' optical response is due to light-induced heating of the nanoparticles and swelling of the polyelectrolyte shell. The resulting hydrophilic/hydrophobic transitions significantly change the shell thickness and reversible shift of the scattering spectra for individual nanoparticles up to 60 nm. Our findings bring novel opportunities for the application of smart nanomaterials in nanomedicine and bio-integrated nanophotonics.

All-Dielectric Nanostructures with a Thermoresponsible Dynamic Polymer Shell

We suggest a new strategy for creating stimuli-responsive bio-integrated optical nanostructures based on Mie-resonant silicon nanoparticles covered by an ensemble of similarity negatively charged polyelectrolytes (heparin and sodium polystyrene sulfonate). The dynamic tuning of the nanostructures' optical response is due to light-induced heating of the nanoparticles and swelling of the polyelectrolyte shell. The resulting hydrophilic/hydrophobic transitions significantly change the shell thickness and reversible shift of the scattering spectra for individual nanoparticles up to 60 nm. Our findings bring novel opportunities for the application of smart nanomaterials in nanomedicine and bio-integrated nanophotonics.

Silver melamine thin film as a flexible platform for SERS analysis

New SERS detection platforms are required for the quick and easy preparation of sensing devices for food, agriculture, and environmental science. For quantitative sensing, it is important that a sensing material, in addition to efficient sensing, provides extraction and concentration of the target molecules such as toxic pesticides or healthy vitamins. We design such films adopting the Liesegang rings formation process that includes the reaction-diffusion of silver nitrate and melamine followed by the precipitation of different intermediates and their reduction by light in a pectin medium. Surprisingly, we find that the presence of melamine provides an excellent substrate for the extraction of pollutants at the solid-liquid interface giving rise to a powerful but easy and fast method for the quantification of fruits' quality. The complex silver and melamine containing films show high sensitivity even at relatively low silver concentrations.

Programmable Soft-Matter Electronics

The hydrogels of the polyelectrolytes polyethylenimine and poly(acrylic acid) are used to form a thin-layer interface on the gallium-indium eutectic alloy's surface. The proposed method of gradually increasing the applied voltage reveals the possibility of formation of electronic components: diode, capacitor, resistor, and memristor. The components can be changed to each other many times. A multilayer perceptron model with one hidden layer and 12 nodes allows identifying hydrogels' composition and automatically setting the desired architecture of electronic components. The design of electronic components makes it possible to easy-to-produce new electronic parts and programmable soft-matter electronics.

The influence of the morphology of titania and hydroxyapatite on the proliferation and osteogenic differentiation of human mesenchymal stem cells

Herein, the proliferation and osteogenic potential of human mesenchymal stem cells (hMSCs) on the disordered and ordered porous morphology of the titania surface and titania surface modified by hydroxyapatite (HA) are compared for the first time. In 5 days, the MTT-assay showed that the ordered porous morphology of electrochemically fabricated titania nanotubes (TNT) and TNT with chemically deposited hydroxyapatite (TNT–HA) was favorable for stem cell proliferation. In 14 days, RT-qPCR demonstrated that the disordered porous morphology of the sonochemically produced titania mesoporous surface (TMS) and TMS modified by the chemical deposition of HA (TMS–HA) led to the differentiation of hMSCs into the osteogenic direction in the absence of osteogenic inductors. These results originate from the mechanism of mechanotransduction, which sheds a light on the interaction of mesenchymal stem cells with the porous interface through focal adhesion, regulating the expression of genes determining stem cell self-renewal and osteogenic differentiation. The strong focal adhesion of hMSCs adjusted by the disordered TMS and TMS–HA is enough to induce osteogenic differentiation with the delay of cellular self-renewal. The weak focal adhesion of hMSCs tuned by the ordered TNT and TNT–HA affects only cellular self-renewal. The present research makes a new contribution to nanomedicine and engineering of porous implant interfaces for the replacement of bone injuries.

Herein, the proliferation and osteogenic potential of human mesenchymal stem cells (hMSCs) on the disordered and ordered porous morphology of the titania surface and titania surface modified by hydroxyapatite (HA) are compared for the first time.

Determination of sodium and potassium ions in patients with SARS-Cov-2 disease by ion-selective electrodes based on polyelectrolyte complexes as a pseudo-liquid contact phase

Supramolecular assemblies based on polyelectrolyte complexes made it possible to create complex interfaces with predictable properties. Polyelectrolyte complexes serve as a pseudo-liquid contact in ion-selective electrodes.

Characterization of transient cavitation activity during sonochemical modification of magnesium particles

Investigation of the cavitation activity during ultrasonic treatment of magnesium particles during nanostructuring has been performed. Cavitation activity is recorded in the continuous mode after switching the ultrasound on with the use of ICA-5DM cavitometer. It has been demonstrated that this characteristic of the cavitation zone may be varied in a wide range of constant output parameters of the generator. The speed and nature of the cavitation activity alteration depended on the concentration of Mg particles in the suspension and the properties of the medium in which the sonochemical treatment has been performed. Three stages of the cavitation area evolution can be distinguished: 1 - the initial increase in cavitation activity, 2 - reaching a maximum with a subsequent decrease, and 3 - reaching the plateau (or the repeated cycles with feedback loops of enlargement/reduction of the cavitation activity). The ultrasonically treated magnesium particles have been characterized by scanning electron microscopy, X-ray diffraction analysis and thermal analysis. Depending on the nature of the dispersed medium the particles can be characterized by the presence of magnesium hydroxide (brucite) and magnesium hydride. It is possible to reach the incorporation of magnesium hydride in the magnesium hydroxide/magnesium matrix by varying the conditions of ultrasonic treatment (duration of treatment, amplitude, dispersed medium etc.). The influence of the magnesium reactivity is also confirmed by the measurements of cavitation activity in organic dispersed media (ethanol, ethylene glycol) and their aqueous mixtures.

Melamine-Barbiturate Supramolecular Assembly as a pH-Dependent Organic Radical Trap Material

In the last two decades, a large number of self-assembled materials were synthesized and they have already found their way into large-scale industry and science. Hydrogen-bond-based supramolecular adducts are found to have unique properties and to be perfect host structures for trapping target molecules or ions. Such chemical systems are believed to resemble living matter and can substitute a living cell in a number of cases. Herein, a report on an organic material based on supramolecular assembly of barbituric acid and melamine is presented. Surprisingly, the structure is found to host and stabilize radicals under mild conditions allowing its use for biological applications. The number of free radicals is found to be easily tuned by changing the pH of the environment and it increases when exposed to light up to a saturation level. We describe a preparation method as well as stability properties of melamine-barbiturate self-assembly, potentiometric titration, and hydrogen ions adsorption data and EPR spectra concerning the composite.

Ultrasound-assisted fabrication of gluten-free dough for automatic producing dumplings

Nowadays celiac disease is becoming more common. It is the autonomic genetic disease that is accompanied by damage to the intestines due to a reaction to eating some proteins. People who are suffering from celiac disease cannot eat food containing gluten, including dough made from gluten-containing seeds. But the gluten-free dough has commonly bad rheological properties and cannot be used for automatic molding the dumplings. In this article, we propose the ultrasonic-assisted technology to fabricate the gluten-free dough with improved rheological properties acceptable for automatic molding of the dumplings. Application of ultrasonic treatment at a frequency of 35 kHz during the dough preparation leads to the homogenization of the dough structure and changing the rheological properties of the dough. The ultrasound induces mechanical, physical and chemical/biochemical changes of the dough components through cavitation. The sonication causes a doubled dough volume increase followed by an additional mass yield of the dumplings equal 2-10% per kilogram of dough. Besides extra beneficial economic effect, our technology provides an additional sterilization effect of the fabricated dough.

ElectroSens Platform with a Polyelectrolyte-Based Carbon Fiber Sensor for Point-of-Care Analysis of Zn in Blood and Urine

In this paper, we describe an electrochemical sensing platform-ElectroSens-for the detection of Zn based on self-assembled polyelectrolyte multilayers on the carbon fiber (CF) electrode surface. The CF-extended surface facilitates the usage of a small volume electrochemical cell (1 mL) without stirring. This approach allows making a low-cost three-electrode platform. Working electrode modification with layer-by-layer assembly of polyethyleneimine (PEI), poly(sodium 4-styrenesulfonate) (PSS), and mercury nitrate layers eliminates solution toxicity and provides stable stripping voltammetry measurements. The stable, robust, sustainable, and even reusable Ag/AgCl reference electrode consists of adsorbed 32 PEI-KCl/PSS-KCl bilayers on the CF/silver paste separated from the outer solution by a polyvinyl chloride membrane. The polyelectrolyte-based sensor interface prevents adsorption of protein molecules from biological liquids on the CF surface that leads to a sensitivity increase of up to 2.2 μA/M for Zn²⁺ detection and provides a low limit of detection of 4.6 × 10^-8 M. The linear range for Zn detection is 1 × 10^-7 to 1 × 10^-5 M. A portable potentiostat connected via wireless to a smartphone with an android-based software is also provided. The ElectroSens demonstrates reproducibility and repeatability of data for the detection of Zn in blood and urine without the digestion step.

Storage of Information Using Periodic Precipitation

In the present work, transparent flexible thin polymer films with silver patterns have been created. The resulting structures made by the printing method represent a new alternative approach for recording, protecting, and transmitting information as well as for nonlinear gradient material formation. An alphabet for process automatization was created, and an automated system for recording and reading information was developed. To protect the information, we suggest the usage of a classic XOR function: the idea of scrambling is to demonstrate the simple and clear example of coding the ITMO University logo, and the code is provided. Additionally, the resulting samples are functional gradient materials with peaks of surface plasmon resonance. In the following, automated peak decoding by UV-vis spectroscopy allows an additional physicochemical method for structure decoding.

Oscillating of physicochemical and biological properties of metal particles on their sonochemical treatment

Different metal particles are increasingly used to target bacteria as an alternative to antibiotics. Despite numerous data about treating bacterial infections, the utilization of metal particles in antibacterial coatings for implantable devices and medicinal materials promoting wound healing. The antibacterial mechanisms of nanoscale and microscale particles are poorly understood, but the currently accepted mechanisms include oxidative stress induction, metal ion release, and non-oxidative mechanisms. Thus, investigation of the antibacterial mechanisms of nanostructured metal particles is very important for the development of more effective antimicrobial materials. However, it is very difficult to develop a proper model for revealing the antibacterial mechanisms due to difficulty to choose a method that allows obtaining materials of various properties under approximately the same conditions. In this paper, we propose a green and feasible technique to create critical conditions for modification of zinc particles at highly non-equilibrium states. We demonstrate that the sonication process can be useful for fabrication the materials with oscillating physical, chemical and antibacterial properties. We believe this method besides medical applications can be also used in natural science basic research as an experimental tool for modelling the physical and chemical processes. After the sonication, the zinc particles exhibit a different surface morphology and amount of leached Zn²⁺ ions compared to initial ones. It has been revealed that oscillations of the Zn²⁺ ions concentration lead to oscillation the antibacterial properties. Thus, the properties of the materials can be easily altered by adjusting the ultrasound energy dissipated via varying the sonication.

A platform for light-controlled formation of free-stranding lipid membranes

The engineering of artificial cells is one of the most significant scientific challenges. Thus, controlled fabrication and in situ monitoring of biomimetic nanoscale objects are among the central issues in current science and technology. Studies of transmembrane channels and cell mechanics often require the formation of lipid bilayers (LBs), their modification and their transfer to a particular place. We present here a novel approach for remotely controlled manipulation of LBs. Layer-by-layer deposition of polyethyleneimine and poly(sodium 4-styrenesulfonate) on a nanostructured TiO 2 photoanode was performed to obtain a surface with the desired net charge and to enhance photocatalytic performance. The LB was deposited on top of a multi-layer positive polymer cushion by the dispersion of negative vesicles. The separation distance between the electrostatically linked polyelectrolyte cushion and the LB can be adjusted by changing the environmental pH, as zwitter-ionic lipid molecules undergo pH-triggered charge-shifting. Protons were generated remotely by photoanodic water decomposition on the TiO 2 surface under 365 nm illumination. The resulting pH gradient was characterized by scanning vibrating electrode and scanning ion-selective electrode techniques. The light-induced reversible detachment of the LB from the polymer-cushioned photoactive substrate was found to correlate with suggested impedance models.