Search Results (258)

Magnetite (Fe₃O₄) provides a protective corrosion layer in the steam generators of nuclear power plants. The presence of monoethanolamine (MEA) in coolant water has a beneficial effect on corrosion processes. In that context, the adsorption of MEA and ethanol–ammonium cation on the {111} surface of magnetite was studied using the molecular dynamics (MD) method. A modified version of the mechanical force field (ClayFF) was used. The systems were simulated at different temperatures (423 K; 453 K; 503 K). Surface coverage data were obtained from adsorption simulations; the root-mean-square deviation (RMSD) of the target molecules were calculated, and their minimum distance to the magnetite surface was traced. The potential and adsorption energies of MEA were calculated as a function of temperature. It has been established that the interaction between MEA and magnetite is due to electrostatic phenomena and the adsorption rate increases with temperature. A comparison was made with existing experimental results and similar MD simulations. Full article

The behavior of brine solution in the porous media of the strata is of great significance for geological environment regulation. In this study, a molecular dynamics model with silicon dioxide walls was constructed to reveal the regulatory mechanism of the natural potential of the electric field on cluster aggregation. It was found that the critical electric field intensity was 7 V/m. When the electric field intensity was lower than this value, the aggregation rate was only increased by 0.73 times due to thermal motion; when it was higher than this value, the rate increased sharply by 3.2 times due to the dominant effect of electric field force. The microscopic structure analysis indicated that the strong electric field induced the transformation of clusters from fractal structure into an amorphous structure (the index of the order degree increased by 58%). The directional regulation experiments confirmed that the axial electric field led to anisotropic growth (the index of uniformity increased by 0.58 ± 0.04), and the rotational electric field could achieve a three-dimensional uniform distribution (the index of uniformity increased by 42%). This study provides theoretical support for the regulation of brine behavior and the optimization of geological energy storage. Full article

To investigate the influences of void defects of different sizes, molecular dynamics combined with ReaxFF-lg reactive force field was used to study the hot-spot formation mechanism and thermal decomposition behavior of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) crystals with different void defects at 2500 K. The results indicate that larger void defects are more conducive to the formation of hot-spots. The consistency of the trends in time evolution of the potential energy, species numbers, and small molecules amounts between the ideal and void-containing LLM-105 crystals demonstrates that the presence of the void defect does not alter the decomposition mechanism of the LLM-105 molecule. An increase in the size of the void defect significantly increases the degree of diffusion of the C, H, O, and N atoms in the crystals, which affects the effective collisions between the atoms and thus alters the occurrence frequency of relevant reactions and the production of relevant products. Full article

Understanding the adsorption mechanism is essential for developing efficient technologies to capture carbon dioxide from industrial flue gases. In this work, laboratory measurements, density functional theory calculations, and molecular dynamics simulations were employed to study CO₂ adsorption and diffusion behavior in LTA-type zeolites. The CO₂ adsorption isotherms measured in zeolite 5A are best described by the Toth model. Thermodynamic analysis indicates that the adsorption process is spontaneous and exothermic, with an enthalpy change of −44.04 kJ/mol, an entropy change of −115.23 J/(mol·K), and Gibbs free energy values ranging from −9.68 to −1.03 kJ/mol over the temperature range of 298–373 K. The isosteric heat of CO₂ adsorption decreases from 40.35 to 21.75 kJ/mol with increasing coverage, reflecting heterogeneous interactions at Ca²⁺ and Na⁺ sites. The adsorption kinetics follow a pseudo-first-order model, with an activation energy of 2.24 kJ/mol, confirming a physisorption mechanism. The intraparticle diffusion model indicates that internal diffusion is the rate-limiting step, supported by a significant reduction in the diffusion rate. The DFT calculations demonstrated that CO₂ exhibited a −35 kJ/mol more negative adsorption energy in zeolite 5A than in zeolite ITQ-29, attributable to strong interactions with Ca²⁺/Na⁺ cations in 5A that were absent in the pure silica ITQ-29 framework. The molecular dynamics simulations based on molecular force fields indicate that CO₂ diffuses more rapidly in ITQ-29, with a diffusion coefficient measuring 2.54 × 10⁻⁹ m²/s at 298 K, whereas it was 1.02 × 10⁻⁹ m²/s in zeolite 5A under identical conditions. The activation energy for molecular diffusion reaches 5.54 kJ/mol in zeolite 5A, exceeding the 4.12 kJ/mol value in ITQ-29 by 33%, which accounts for the slower diffusion kinetics in zeolite 5A. There is good agreement between experimental measurements and molecular simulation results for zeolite 5A across the studied temperature and pressure ranges. This confirms the accuracy and reliability of the selected simulation parameters and allows for the study of zeolite ITQ under similar simulation conditions. This research provides insights into CO₂ adsorption energetics and diffusion within LTA-type zeolite frameworks, supporting the rational design of high-performance adsorbents for industrial gas separation. Full article

Composite solid propellants, which serve as the core energetic materials in aerospace and military propulsion systems, necessitate tailored enhancement of their mechanical properties to ensure operational safety and stability. A critical challenge involves elucidating the interfacial interactions among the multiple propellant components (≥6 components, including the polymer binder HTPB, curing agent IPDI, oxidizer particles AP/Al, bonding agents MAPO/T313, plasticizer DOS, etc.) and their influence on crosslinked network formation. In this study, we propose an integrated computational framework that combines coarse-grained simulations with reactive force fields to investigate these complex interactions at the molecular level. Our approach successfully elucidates the two-step reaction mechanism propagating along the AP interface in multicomponent propellants, comprising interfacial self-polymerization of bonding agents followed by the participation of curing agents in crosslinked network formation. Furthermore, we assess the mechanical performance through tensile simulations, systematically investigating both defect formation near the interface and the influence of key parameters, including the self-polymerization time, HTPB chain length, and IPDI content. Our results indicate that the rational selection of parameters enables the optimization of mechanical properties (e.g., ~20% synchronous improvement in tensile modulus and strength, achieved by selecting a side-chain ratio of 20%, a DOS molar ratio of 2.5%, a MAPO:T313 ratio of 1:2, a self-polymerization MAPO time of 260 ns, etc.). Overall, this study provides molecular-level insights into the structure–property relationships of composite propellants and offers a valuable computational framework for guided formulation optimization in propellant manufacturing. Full article

Cyclohexane-containing semi-aromatic polyamides (c-SaPA) exhibit excellent comprehensive properties. Existing studies predominantly focus on synthesis and modification, while fundamental investigations into pyrolysis mechanisms remain limited, which restricts the development of advanced materials for high-performance applications such as automotive and energy systems. This study employs Reactive Force Field Molecular Dynamics (ReaxFF-MD) simulations to establish a pyrolysis model for poly(terephthaloyl-hexahydro-m-xylylenediamine) (PHXDT), systematically probing its pyrolysis kinetics and evolutionary pathways under elevated temperatures. The simulation results reveal an activation energy of 107.55 kJ/mol and a pre-exponential factor of 9.64 × 10¹³ s⁻¹ for the pyrolysis process. The primary decomposition pathway involves three distinct stages. The first is initial backbone scission generating macromolecular fragments, followed by secondary fragmentation that preferentially occurs at short-chain hydrocarbon formation sites alongside radical recombination. Ultimately, the process progresses to deep dehydrogenation, carbonization, and heteroatom elimination through sequential reaction steps. Mechanistic analysis identifies multi-pathway pyrolysis involving carboxyl/amide bond cleavage and radical-mediated transformations (N-C-O, C-C-O, OH· and H·), yielding primary products including H₂, CO, H₂O, CH₃N, C₂H₂, and C₂H₄. Crucially, the cyclohexane structure demonstrates preferential participation in dehydrogenation and hydrogen transfer reactions due to its conformational dynamic instability and low bond dissociation energy, significantly accelerating the rapid generation of small molecules like H₂. Full article

The pharmacology of antimicrobial agents comprises pharmacodynamics and pharmacokinetics. Pharmacodynamics refers to studying drugs’ mode of action on their molecular targets at various concentrations and the resulting effect(s). Pharmacokinetics refers to studying the way(s) in which drugs enter the body and are distributed to their targets in various compartments (such as tissues) and how local drug concentrations are modified in time, such as by metabolism or excretion. Pharmacodynamics and pharmacokinetics constitute pivotal knowledge for establishing the breakpoints used to identify the appropriate antimicrobial agents for infection therapy. Antibiotic resistance is the biological force opposing antimicrobials’ pharmacological effects. However, we do not have a term similar to pharmacology for microbial antibiotic resistance reactions. Here, we propose the new scientific field of antechology (from the classic Greek antechó, resistance), studying the dynamics and kinetics of antibiotic resistance molecules which oppose the effect of antimicrobial drugs. Antechodynamics refers to the study of the molecular mechanisms through which antibiotic molecules are chemically modified or degraded by particular bacterial resistance enzymes (primary effectors) or drive the modification of an antibiotic’s target inhibition sites through molecules released by antibiotic action on the microorganism (secondary effectors). Antechokinetics refers to the study of the processes leading to bacterial spatial cellular (subcellular, pericellular, extracellular) localizations of the molecules involved in antibiotic detoxifying mechanisms. Molecules’ local concentrations change over time due to their production, their degradation, and ultimately their excretion rates. We will examine the antechodynamics and antechokinetics for various antimicrobial classes and the relation between pharmacodynamics/pharmacokinetics and antechodynamics/antechokinetics. Full article

β-glucuronidase is an important hydrolase, which plays an important role in drug metabolism, clinical diagnostics, and biotransformation. This study focuses on the heterologous expression, isolation, purification, and its enzymatic properties of β-glucuronidase CpGUS from Clostridium perfringens, as well as its application in the whole-cell transformation of unconjugated bilirubin from pig bile. A recombinant E. coli BL21(DE3)/pET-28a-CpGUS was constructed for the heterologous expression of CpGUS, with the majority of the expressed enzyme being soluble. Enzymatic analysis showed that CpGUS displayed optimal activity at pH 5.0 and 45 °C, and it rapidly lost activity at pH < 4.5. Metal ions, such as Mg²⁺ and Fe²⁺, enhanced CpGUS catalysis, while Zn²⁺, K⁺, Fe³⁺, Mn²⁺, Cu²⁺, and Na⁺ inhibited it. Notably, Cu²⁺ and Fe³⁺ can significantly inhibit β-glucuronidase, resulting in the complete loss of its activity. The results of the whole-cell transformation experiment show that when E.coli BL21(DE3)/ pET-28a-CpGUS at an OD₆₀₀ of 10 was incubated at pH 5.0, a temperature of 45 °C, and a rotation speed of 200 rpm for 12 h, the hydrolysis rate of the conjugated bilirubin in pig bile reached 81.1%, the yield of unconjugated bilirubin was 76.8%, and the purity of unconjugated bilirubin was 98.2%. The three-dimensional structure of CpGUS was predicted using AlphaFold2 (AlphaFold v2.0, DeepMind Technologise Limited, London, UK), and p-Nitrophenyl-β-D-Glucuronide (pNPG) and conjugated bilirubin were then docked to the CpGUS protein model using SWISSDOCK. The best docked conformations of the CpGUS–pNPG and CpGUS–conjugated bilirubin complex systems were simulated by independent 500 ns molecular dynamics (MD) runs with the RSFF2C force field, and the binding dynamic and catalytic mechanism of each system were obtained. The results indicated that π-π stacking, hydrogen bonding, and hydrophobic interactions between the key residue Tyr472 and the benzene ring of pNPG molecules are crucial for its catalytic process. Similarly, for the binding and catalysis of conjugated bilirubin by CpGUS, the π-π stacking and hydrogen bonding and hydrophobic interactions between the sidechains of residues Phe368 and Tyr472 and the benzene ring of conjugated bilirubin play a synergistic role during its catalytic process. Their total binding free energy (∆G_bind) values were calculated to be as high as −65.05 ± 12.66 and −86.70 ± 17.18 kJ/mol, respectively. These results suggest that CpGUS possesses high binding and catalytic hydrolysis properties for both pNPG and conjugated bilirubin. Full article

Cis-1,4-polyisoprene is a widely used elastomer that demonstrates particular thermal and mechanical characteristics, in which the latter is influenced by temperature and strain rate. Molecular dynamic simulations were used to obtain thermal conductivities, glass transition temperatures (T_g), and tensile deformation. Thermal conductivities were calculated by applying the Green–Kubo method, and a decrease in thermal conductivity was observed with increasing temperature. Density–temperature relations were used to calculate T_g, which indicates the transition from the glassy to the rubbery state of the material, and this temperature influences mechanical properties. Investigation of the mechanical properties under uniaxial tensile deformation for constant strain rates indicates an increase in the stiffness and strength of the material at lower temperatures, while increasing molecular mobility at higher temperatures results in reducing these properties. The influence of strain rates at constant temperature highlighted the viscoelastic nature of the structure; increasing strain rates resulted in increases in stiffness, strength, elongation at maximum strength, and elongation at break because of restricted molecular relaxation time. The united-atom force field contributes to higher computational efficiency, which is suitable for large-scale simulations. These results provide important information on the thermo-mechanical properties and tunability of cis-1,4-polyisoprene, which supports applications in the production of interactive fiber rubber composites. Full article

The Second Law of Thermodynamics states that entropy S increases in a spontaneous process in an ideal isothermal and isolated system. Real systems are influenced by external forces and fields, including the temperature field. In this case, only entropy is not enough, and we suggest using a new function, $L_s$, which is analogous to the Lagrangian in classical mechanics. It includes total potential energy but instead of mechanical kinetic energy, $L_s$ includes the product ST, and the system always evolves towards increasing this modified Lagrangian. It reaches an equilibrium when total potential force is balanced by both entropic and thermal forces. All forces have the same units, Newton/mol, and may be added or subtracted. For condensed systems with friction forces, it is a molecular transport velocity, and not acceleration, which is proportional to the acting force. Our approach has several advantages compared to Onsager’s non-equilibrium thermodynamics with its thermodynamic forces, which may have different units, including 1/T for energy transport. For isolated systems, the description is reduced to Second Law and Clausius inequality. It easily explains diffusion, Dufour effect, and Soret thermodiffusion. The combination of electric, thermal, and entropic forces explains thermoelectric phenomena, including Peltier–Seebeck and Thomson (Lord Kelvin) effects. Gravitational and entropic forces together inside a black hole may lead to a steady state or the black hole evaporation. They are also involved in and influenced by solar atmospheric processes. Full article

Background/Objectives: The purpose of this research was to investigate the effects of bisphenol A (BPA) exposure on neurobehavioral testing in young Wistar rats and to evaluate the therapeutic potential of Thymus ciliatus (TEO) essential oil to attenuate the damage induced by this chemical toxin. Methods: The essential oil was extracted by hydro-distillation (yield of 2.26%), and the characterization by GC-MS indicates that the major components of Thymus ciliatus oil are thymol (63.33%), p-cymene (13.4%), and σ-terpinene (6.69%). Acute BPA intoxication was induced with a dose of 50 mg/kg orally for 60 days. The neurobehavioral evaluation, performed using a comprehensive set of tests including the forced swim test, dark/light box, Morris water maze, open field test, and sucrose preference test, clearly demonstrated that bisphenol A (BPA) exposure induced significant neurobehavioral impairments. Results: These impairments included reduced exploratory behavior indicative of heightened stress, anxiety, and depressive-like states, as well as deficits in memory and learning. Furthermore, BPA intoxication was associated with metabolic disturbances such as hyperglycemia along with histopathological evidence of brain tissue damage. However, TEO treatment attenuated these adverse effects by restoring neurobehavioral function. Molecular docking analysis revealed an affinity between the major essential oils identified in T. ciliatus, BPA, and the 5HT2C receptor and the MAO, AChE, and BChE enzymes, suggesting a potential mechanism underlying BPA’s effects on behavior and memory. In addition, TEO also showed an interaction with these molecules, suggesting a therapeutic potential against BPA. These findings underscore the promising role of TEO in mitigating the poisonous effects of BPA and pave the way for additional research into the molecular mechanisms and therapeutic uses of natural bioactive compounds for the prevention and treatment of toxic diseases. Thymol, the major compound in TEO, exhibited activity related to the dopamine and serotonin pathways, so it could have potential antidepressant properties. Conclusions: Thymol might be a promising candidate for the treatment of neurodegenerative and neurological disorders such as depression, Parkinson’s disease, and Alzheimer’s disease while also preventing histological damage in the brain. Full article

Ionic liquids exhibit distinctive solvation and reactive properties, making them highly relevant for applications in energy storage, catalysis, and CO₂ capture. However, their complex molecular interactions, including proton transfer and physisorption/chemisorption, necessitate advanced computational efforts to model them at the atomic scale. This review examines key molecular dynamics approaches for simulating ionic liquid reactivity, including quantum-mechanical methods, conventional reactive force fields such as ReaxFF, and fractional force fields employed in PROTEX. The strengths and limitations of each method are assessed within the context of ionic liquid simulations. While quantum-mechanical simulations provide detailed electronic insights, their high computational cost restricts system size and simulation timescales. Reactive force fields enable bond breaking and formation in larger systems but require extensive parameterization. These approaches are well suited for investigating reaction pathways influenced by the local environment, which can also be partially addressed using multiscale simulations. Fractional force fields offer an efficient alternative for simulating significantly larger reactive systems over extended timescales. Instead of resolving individual reaction mechanisms in full detail, they incorporate reaction probabilities to model complex coupled reactions. This approach enables the study of macroscopic properties, such as conductivity and viscosity, as well as proton transport mechanisms like the Grotthuß process—phenomena that remain inaccessible to other computational methods. Full article

The injection of CO₂ into coal reservoirs occurs in its supercritical state (ScCO₂), which significantly alters the pore structure and chemical composition of coal, thereby influencing the adsorption and diffusion behavior of methane (CH₄). Understanding these changes is crucial for optimizing CH₄ extraction and improving CO₂ sequestration efficiency. This study aims to investigate the effects of ScCO₂ on the pore structure, chemical bonds, and CH₄ diffusion mechanisms in bituminous coal to provide insights into coal reservoir stimulation and CO₂ storage. By utilizing high-pressure CO₂ injection adsorption, low-pressure CO₂ gas adsorption (LP-CO₂-GA), Fourier-transform infrared spectroscopy (FTIR), and reactive force field molecular dynamics (ReaxFF-MD) simulations, this study examines the multi-scale changes in coal at the nano- and molecular levels. The following results were found: Pore Structure Evolution: After ScCO₂ treatment, micropore volume increased by 19.1%, and specific surface area increased by 11.2%, while mesopore volume and specific surface area increased by 14.4% and 5.7%, respectively. Chemical Composition Changes: The content of aromatic structures, oxygen-containing functional groups, and hydroxyl groups decreased, while aliphatic structures increased. Specific molecular changes included an increase in (CH₂)_n, 2H, 1H, and secondary alcohol (-C-OH) and phenol (-C-O) groups, while Car-Car and Car-H bonds decreased. Mechanisms of Pore Volume Changes: The pore structure evolves through three distinct phases: Swelling Phase: Breakage of low-energy bonds generates new micropores. Aromatic structure expansion reduces intramolecular spacing but increases intermolecular spacing, causing a decrease in micropore volume and an increase in mesopore volume. Early Dissolution Phase: Continued bond breakage increases micropore volume, while released aliphatic and aromatic structures partially occupy these pores, converting some mesopores into micropores. Later Dissolution Phase: Minimal chemical bond alterations occur, but weakened π-π interactions and van der Waals forces between aromatic layers result in further mesopore volume expansion. Impact on CH₄ Diffusion: Changes in pore volume directly affect CH₄ migration. In the early stages of ScCO₂ interaction, pore shrinkage reduces the mean square displacement (MSD) and self-diffusion coefficient of CH₄. However, as the reaction progresses, pore expansion enhances CH₄ diffusion, ultimately improving gas extraction efficiency. This study provides a fundamental understanding of how ScCO₂ modifies coal structure and CH₄ transport properties, offering theoretical guidance for enhanced CH₄ recovery and CO₂ sequestration strategies. Full article

Inflammatory bowel disease is a risk factor for brain dysfunction; however, the underlying mechanisms remain largely unknown. In this study, we aimed to explore the potential molecular mechanisms through which intestinal inflammation affects brain function and to verify these mechanisms. Mice were treated with multiple cycles of 1% w/v dextran sulfate sodium (DSS) in drinking water to establish a chronic colitis model. Behavioral tests were conducted using the open field test (OFT), tail suspension test (TST), forced swimming test (FST), and Morris water maze test (MWM). Brain metabolomics, transcriptomics, and proteomics analyses were performed, and key target proteins were verified using qPCR and immunofluorescence. Four cycles of DSS administration induced colitis, anxiety, depression, and spatial memory impairment. The integrated multi-omics characterization of colitis revealed decreased brain chenodeoxycholic acid (CDCA) levels as well as reduced stearoyl-CoA desaturase (Scd1) gene and protein expression. Transplantation of the colitis microbiome resulted in anxiety, depression, impaired spatial memory, reduced CDCA content, decreased Scd1 gene and protein expression, and lower concentrations of monounsaturated fatty acids (MUFAs), palmitoleate (C16:1), and oleate (C18:1) in the brain. In addition, CDCA supplementation improved DSS-induced colitis, alleviated depression and spatial memory impairment, and increased Scd1 gene and protein expression as well as MUFA levels in the brain. The gut microbiome induced by colitis contributes to neurological dysfunction, possibly through the CDCA–Scd1 signaling axis. CDCA supplementation alleviates colitis and depressive behavior, likely by increasing Scd1 expression in the brain. Full article

Silver(I) ions and organometallic complexes thereof are well-established antimicrobial agents. They have been employed in medical applications for centuries. It is also known that some bacteria can resist silver(I) treatments through an efflux mechanism. However, the exact mechanism of action remains unclear. All-atom force-field simulations can provide valuable structural and thermodynamic insights into the molecular processes of the underlying mechanism. Lennard-Jones parameters of silver(I) have been available for quite some time; their applicability to properly describing the binding properties (affinity, binding distance) between silver(I) and peptide-based binding motifs is, however, still an open question. Here, we demonstrate that the standard 12-6 Lennard-Jones parameters (previously developed to describe the hydration free energy with the TIP3P water model) significantly underestimate the interaction strength between silver(I) and both methionine and histidine. These are two key amino-acid residues in silver(I)-binding motifs of proteins involved in the efflux process. Using free-energy calculations, we calibrated non-bonded fix (NBFIX) parameters for the CHARMM36m force field to reproduce the experimental binding constant between amino acid sidechain fragments and silver(I) ions. We then successfully validated the new parameters on a set of small silver-binding peptides with experimentally known binding constants. In addition, we monitored how silver(I) ions increased the α-helical content of the LP1 oligopeptide, in agreement with previously reported Circular Dichroism (CD) experiments. Future improvements are outlined. The implementation of these new parameters is straightforward in all simulation packages that can use the CHARMM36m force field. It sets the stage for the modeling community to study more complex silver(I)-binding processes such as the interaction with silver(I)-binding-transporter proteins. Full article