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In order to study the importance of the diffusion mechanism of CH4 and CO2 in coal for the development of coalbed methane, the aim of this paper is to reveal the influence mechanism of pressure, temperature, water content and other factors on the molecular diffusion behavior of gas at the molecular level. In this paper, non-sticky coal in Chicheng Coal Mine is taken as the research object. Based on the molecular dynamics method (MD) and Monte Carlo (GCMC) method, the diffusion characteristics and microscopic mechanism of CH4 and CO2 in coal under different pressures (100 kPa–10 MPa), temperatures (293.15–313.15 K) and water contents (1–5%) were analyzed in order to lay a theoretical foundation for revealing the diffusion characteristics of CBM in coal, and provide technical support for further improving CBM extraction. The results show that high temperature is conducive to gas diffusion, while high pressure and water are not conducive to gas diffusion in the coal macromolecular model. [ABSTRACT FROM AUTHOR]

α-Amylase inhibitory peptides are used to treat diabetes, but few studies have statistically characterized their interaction with α-amylase. This study performed the molecular docking of α-amylase with inhibitory peptides from published papers. The key sites, side chain chargeability, and hydrogen bond distribution characteristics were analyzed. Molecular dynamics simulated the role of key sites in complex stability. Moreover, partial least squares regression (PLSR) was used to analyze the contribution of different amino acids in the peptides to inhibition. The results showed that, for the α-amylase molecule, His201 and Gln63, with the highest interaction numbers (INs, 15, 15) and hydrogen bond values (HBVs, 11.50, 10.33), are the key sites on α-amylase, and amino acids with positively charged side chains were important for inhibitory activity. For the inhibitory peptides, Asp and Arg had the highest HBVs, and amino acids with charged side chains were more likely to form hydrogen bonds and exert inhibitory activity. In molecular dynamics simulations, peptides involving key binding sites formed more stable complexes with α-amylase than α-amylase alone, suggesting enhanced inhibitory effects. Further, PLSR results showed that amino acids close to the N-terminus of the inhibitory peptide, located in the third and fifth positions, were significantly correlated with its inhibitory activity. In conclusion, this study provides a new approach to developing and screening α-amylase inhibitors. [ABSTRACT FROM AUTHOR]

Hydrogen, ammonia, and methanol are typical carbon-neutral fuels. Combustion characteristics and pollutant formation problems can be significantly improved by their blending. In this paper, reactive molecular dynamics were used to investigate the pollutant formation characteristics of hydrogen/ammonia/methanol blended fuel combustion and to analyze the mechanisms of CO, CO2, and NOX formation at different temperatures and blending ratios. It was found that heating can significantly increase blending and combustion efficiency, leading to more active oxidizing groups and thus inhibiting N2 production. Blended combustion pollutant formation was affected by coupling effects. NH3 depressed the rate of CO production when CH4O was greater than 30%, but the amount of CO and CO2 was mainly determined by CH4O. This is because CH4O provides more OH, H, and carbon atoms for CO and CO2 to collide efficiently. CH4O facilitates the combustion of NH3 by simplifying the reaction pathway, making it easier to form NOX. [ABSTRACT FROM AUTHOR]

The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we used an innovative sequence-activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this paper, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability mutants than those predicted using the existing data. We successfully improved the coefficient of determination (R2) of the model from 0.66 to 0.92. In addition, root-mean-squared deviation (RMSD), root-mean-squared fluctuation (RMSF), solvent accessible surface area (SASA), hydrogen bonds, and the radius of gyration were estimated based on molecular dynamics simulations, and the differences between the predicted mutants and the wild-type (WT) were analyzed. The successful application of the innov'SAR algorithm in improving the thermostability of AT-ATA may help in directed evolutionary screening and open up new avenues for protein engineering. [ABSTRACT FROM AUTHOR]

CO2 foam injection has been shown to be effective under reservoir conditions for enhanced oil recovery. However, its application requires a certain stability and surfactant absorbability on rock surface, and it is also associated with borehole corrosion in the presence of water. Adding surfactants to CO2 can enhance the interaction between CO2 and crude oil and control the CO2 mobility, thereby improving the performance of CO2 flooding. This paper presents a review of the research of CO2-soluble surfactants and their applications. Molecular dynamics simulation is introduced as a tool for analyzing the behavior of the surfactants in supercritical CO2 (scCO2). The applications of CO2-soluble surfactants, including CO2 thickening, reducing miscibility pressure, and generating supercritical CO2 foam, are discussed in detail. Moreover, some opportunities for the research and development of CO2-soluble surfactants are proposed. [ABSTRACT FROM AUTHOR]

Inhibition of the Embryonic Ectoderm Development (EED) subunit in Polycomb Repressive Complex 2 (PRC2) can inhibit tumor growth. In this paper, we selected six experimentally designed EED competitive Inhibitors of the triazolopyrimidine derivatives class. We investigated the difference in the binding mode of the natural substrate to the Inhibitors and the effects of differences in the parent nuclei, heads, and tails of the Inhibitors on the inhibitory capacity. The results showed that the binding free energy of this class of Inhibitors was close to or lower compared to the natural substrate, providing an energetic basis for competitive inhibition. For the Inhibitors, the presence of a strong negatively charged group at the 6-position of the parent nucleus or the 8′-position of the head would make the hydrogen atom on the head imino group prone to flip, resulting in the vertical movement of the parent nucleus, which significantly decreased the inhibitory ability. When the 6-position of the parent nucleus was a nonpolar group, the parent nucleus would move horizontally, slightly decreasing the inhibitory ability. When the 8′-position of the head was methylene, it formed an intramolecular hydrophobic interaction with the benzene ring on the tail, resulting in a significant increase in inhibition ability. [ABSTRACT FROM AUTHOR]

Accurate determination of intermolecular non-covalent-bonded or non-bonded interactions is the key to potentially useful molecular dynamics simulations of polymer systems. However, it is challenging to balance both the accuracy and computational cost in force field modelling. One of the main difficulties is properly representing the calculated energy data as a continuous force function. In this paper, we employ well-developed machine learning techniques to construct a general purpose intermolecular non-bonded interaction force field for organic polymers. The original ab initio dataset SOFG-31 was calculated by us and has been well documented, and here we use it as our training set. The CLIFF kernel type machine learning scheme is used for predicting the interaction energies of heterodimers selected from the SOFG-31 dataset. Our test results show that the overall errors are well below the chemical accuracy of about 1 kcal/mol, thus demonstrating the promising feasibility of machine learning techniques in force field modelling. [ABSTRACT FROM AUTHOR]

The assumption that nuclear motion is classical explains many phenomena. The problems of Schrödinger's cat and the EPR paradoxon do not exist in a perfectly deterministic theory. All it needs is to describe nuclear motion classically right from the beginning. To establish this simple idea, it must be tested for as many examples as possible. In the present paper, we use ab initio molecular dynamics to investigate the infrared spectrum of a 'magic' protonated water cluster H 3 O + (H 2 O) 20 which exhibits some features that were believed to afford a quantum treatment of nuclear motion. The role of the temperature in contrast to a quantum mechanical description is discussed. [ABSTRACT FROM AUTHOR]

Organic acid is an important factor that accelerates the aging of cellulosic insulation materials. In this study, the interactions between cellulose and five acids, representative of what may be found in an aging transformer, were studied using molecular dynamics. The adsorption process of the five acids onto the surface of crystalline cellulose shows that the three low molecular acids are more readily adsorbed onto cellulose than the two high molecular acids. The deformation and adsorption energies of the acids all increase with an increase in molecular weight when they are stably interacting with cellulose. However, the differences between adsorption energies and deformation energies are positive for the three low molecular acids, whereas they are negative for the two high molecular acids. This indicates that the attachments onto cellulose of low molecular acids are considerably more stabilized than those of the high molecular acids. This is consistent with the experimental results. Furthermore, based on the calculated solubility parameters of acids, the experimental result that the three low molecular acids are to a large degree absorbed onto the cellulose, whereas the two high molecular acids remain in the oil, was theoretically elucidated using the theory of similarity and intermiscibility. [ABSTRACT FROM AUTHOR]

This paper studies the mechanism of electrochemically induced carbon–bromine dissociation in 1-Br-2-methylnaphalene in the reduction regime. In particular, the bond dissociation of the relevant radical anion is disassembled at a molecular level, exploiting quantum mechanical calculations including steady-state, equilibrium and dissociation dynamics via dynamic reaction coordinate (DRC) calculations. DRC is a molecular-dynamic-based calculation relying on an ab initio potential surface. This is to achieve a detailed picture of the dissociation process in an elementary molecular detail. From a thermodynamic point of view, all the reaction paths examined are energetically feasible. The obtained results suggest that the carbon halogen bond dissociates following the first electron uptake follow a stepwise mechanism. Indeed, the formation of the bromide anion and an organic radical occurs. The latter reacts to form a binaphthalene intrinsically chiral dimer. This paper is respectfully dedicated to Professors Anny Jutand and Christian Amatore for their outstanding contribution in the field of electrochemical catalysis and electrosynthesis. [ABSTRACT FROM AUTHOR]

Recently calcium alginate has been successfully applied to encapsulate asphalt rejuvenator, which can protect asphalt rejuvenator from early leakage and release asphalt rejuvenator when triggered by specific factors such as cracks. The interfacial adhesion property of asphalt binder with calcium alginate carrier is of great importance to its actual performance. In this paper, the molecular model of the interface region between asphalt binder and calcium alginate was established, and molecular dynamics simulations were performed on it to investigate the molecular interaction at the interface region. By extracting and processing the data during the simulation process, the interfacial adhesion behavior was expounded using the spreading coefficient (S), permeation depth and permeation degree. Furthermore, the interfacial adhesion strength was evaluated by adopting the interfacial adhesion work. Results showed that the value of S was greater than 0, implying that asphalt binder could wet the surface of calcium alginate. Saturate had the highest value of permeation degree, followed by resin, aromatic and asphaltene. However, asphalt binder could not infiltrate into the interior of TiO2, only accumulating and spreading on the surface of TiO2. The interfacial adhesion work of unaged and aged asphalt binder to calcium alginate was −114.18 mJ/m2 and −186.37 mJ/m2, respectively, similar to that of asphalt–aggregate interface. The van der Waals interactions contributed the most to the formation of the interfacial adhesion strength. In addition, a certain degree aging of asphalt binder and addition of titanium dioxide in the calcium alginate carrier were helpful to enhance the interfacial adhesion strength. [ABSTRACT FROM AUTHOR]

The aggregation structure of Triton X (TX) amphiphilic molecules in aqueous solution plays an important role in determining the various properties and applications of surfactant solutions. In this paper, the properties of micelles formed by TX-5, TX-114, and TX-100 molecules with different poly(ethylene oxide) (PEO) chain lengths in TX series of nonionic surfactants were studied via molecular dynamics (MD) simulation. The structural characteristics of three micelles were analyzed at the molecular level, including the shape and size of micelles, the solvent accessible surface area, the radial distribution function, the micelle configuration, and the hydration numbers. With the increase of PEO chain length, the micelle size and solvent accessible surface area also increase. The distribution probability of the polar head oxygen atoms on the surface of the TX-100 micelle is higher than that in the TX-5 or TX-114 micelle. In particular, the tail quaternary carbon atoms in the hydrophobic region are mainly located at the micelle exterior. For TX-5, TX-114, and TX-100 micelles, the interactions between micelles and water molecules are also quite different. These structures and comparisons at the molecular level contribute to the further understanding of the aggregation and applications of TX series surfactants. [ABSTRACT FROM AUTHOR]

As a member of the class I PI3K family, phosphoinositide 3-kinase δ (PI3Kδ) is an important signaling biomolecule that controls immune cell differentiation, proliferation, migration, and survival. It also represents a potential and promising therapeutic approach for the management of numerous inflammatory and autoimmune diseases. We designed and assessed the biological activity of new fluorinated analogues of CPL302415, taking into account the therapeutic potential of our selective PI3K inhibitor and fluorine introduction as one of the most frequently used modifications of a lead compound to further improve its biological activity. In this paper, we compare and evaluate the accuracy of our previously described and validated in silico workflow with that of the standard (rigid) molecular docking approach. The findings demonstrated that a properly fitted catalytic (binding) pocket for our chemical cores at the induced-fit docking (IFD) and molecular dynamics (MD) stages, along with QM-derived atomic charges, can be used for activity prediction to better distinguish between active and inactive molecules. Moreover, the standard approach seems to be insufficient to score the halogenated derivatives due to the fixed atomic charges, which do not consider the response and indictive effects caused by fluorine. The proposed computational workflow provides a computational tool for the rational design of novel halogenated drugs. [ABSTRACT FROM AUTHOR]

In order to investigate the type IV hydrogen storage bottle with better hydrogen storage capacity, the polymer lining of the hydrogen storage bottle was further developed. In this paper, the molecular dynamics method was used to simulate the helium adsorption and diffusion processes within a modified montmorillonite (OMMT)-filled polyamide 6 (PA6) system. The effects of the barrier properties of the composites were investigated at different filler contents (3%, 4%, 5%, 6% and 7%), different temperatures (288 K and 328 K) and different pressures (0.1 MPa, 41.6 MPa, 52 MPa and 60 MPa) for certain contents. It was found that when the filler content was 5%, the permeability coefficient of the material was lower than 2 × 10−13 cm3∙cm/(cm2∙s∙Pa) and the barrier performance was the best. The modified filler with 5% OMMT/PA6 at 328 K still had the strongest barrier performance. When the pressure increased, the permeability coefficient of the modified material first decreased and then increased. In addition to this, the effect of the fractional free volume on the barrier properties of the materials was also investigated. This study provides a basis and reference for the selection and preparation of polymer linings for high-barrier hydrogen storage cylinders. [ABSTRACT FROM AUTHOR]

The solid particles in the produced fluids from the oil wells treated by compound flooding can greatly stabilize the strength of the interfacial film and enhance the stability of the emulsion, increasing the difficulty of processing these produced fluids on the ground. In this paper, the oil phase and the water phase were separated from the SPAN series emulsions by electrical dehydration technology and adding demulsifier agents. The changing trends of the current at both ends of the electrodes were recorded during the process. The efficient demulsification of the emulsion containing solid particles was studied from the perspective of oil-water separation mechanisms. Combined with the method of molecular dynamics simulation, the effect of the addition of a demulsifier on the free movement characteristics of crude oil molecules at the position of the liquid film of the emulsion were further analyzed. The results indicated that the presence of solid particles greatly increased the emulsifying ability of the emulsion and reduced its size. Under the synergistic effect of demulsifier and electric dehydration, the demulsification effect of the emulsion increased significantly, and the demulsification rate could reach more than 82%. The addition of demulsifiers changed the stable surface state of the solid particles. The free movement ability of the surrounding crude oil molecules was enhanced, which led to a decrease in the strength of the emulsion film so that the water droplets in the emulsions were more likely to coalesce and break. These results are of great significance for the efficient treatment of wastewater from oilfields, promoting the sustainability of environment-friendly oilfield development. [ABSTRACT FROM AUTHOR]

Water must be separated from water-in-oil (W/O) emulsion because of the corrosion it brings to the relative equipment in the process of transportation and storage. It is an effective method to apply external electric field to achieve high performance of separating small, dispersed water droplets from W/O emulsion; however, the coalescing micromechanism of such small salty droplets under AC electric field is unclear. In this paper, molecular dynamics simulation was adopted to investigate the coalescence and separation process of two NaCl-aqueous droplets under AC electric field and discuss the effect of AC electric field frequency, as well as the time required for contacting, the critical electric field strength, the dynamic coalescence process and the stability of the final merged droplet. The results show that the critical electric field strength of the droplet coalescence increases with the increase of frequency, while the time required for droplet contacting becomes shorter. The shrinkage function curve was applied to characterize the droplet coalescence effect and it was found that the droplets coalescence and form a nearly spherical droplet under the AC electric field with a frequency of 1.25 GHz and strength of 0.5 V/nm. When the electric field frequency is 10 GHZ, the merged droplet presents a periodic fluctuation with the same period as the AC electric field, which mainly depends on the periodic movement of cations and anions under the AC electric field. The results can provide theoretical basis for the practical application of electrostatic demulsification technology in the petroleum or chemical industry from the microscopic perspective. [ABSTRACT FROM AUTHOR]

Despite the significant outcomes attained by scientific research, breast cancer (BC) still represents the second leading cause of death in women. Estrogen receptor-positive (ER+) BC accounts for the majority of diagnosed BCs, highlighting the disruption of estrogenic signalling as target for first-line treatment. This goal is presently pursued by inhibiting aromatase (AR) enzyme or by modulating Estrogen Receptor (ER) α. An appealing strategy for fighting BC and reducing side effects and resistance issues may lie in the design of multifunctional compounds able to simultaneously target AR and ER. In this paper, previously reported flavonoid-related potent AR inhibitors were suitably modified with the aim of also targeting ERα. As a result, homoisoflavone derivatives 3b and 4a emerged as well-balanced submicromolar dual acting compounds. An extensive computational study was then performed to gain insights into the interactions the best compounds established with the two targets. This study highlighted the feasibility of switching from single-target compounds to balanced dual-acting agents, confirming that a multi-target approach may represent a valid therapeutic option to counteract ER+ BC. The homoisoflavone core emerged as a valuable natural-inspired scaffold for the design of multifunctional compounds. [ABSTRACT FROM AUTHOR]

This paper reviews graph-theory-based methods that were recently developed in our group for post-processing molecular dynamics trajectories. We show that the use of algorithmic graph theory not only provides a direct and fast methodology to identify conformers sampled over time but also allows to follow the interconversions between the conformers through graphs of transitions in time. Examples of gas phase molecules and inhomogeneous aqueous solid interfaces are presented to demonstrate the power of topological 2D graphs and their versatility for post-processing molecular dynamics trajectories. An even more complex challenge is to predict 3D structures from topological 2D graphs. Our first attempts to tackle such a challenge are presented with the development of game theory and reinforcement learning methods for predicting the 3D structure of a gas-phase peptide. [ABSTRACT FROM AUTHOR]

In order to investigate the self-healing behavior of asphalt binder at the molecule scale, the self-healing models of neat and aged asphalt binder with different damage degrees were established by introducing a vacuum pad between two layers filled with asphalt molecules. With this model, the self-healing process was simulated at various healing conditions to reveal the effects of oxidative aging, damage degree and healing temperature on the self-healing property. In addition, self-healing efficiency was evaluated using the indexes representative of the characteristics of different self-healing stages. Our results show that the oxidative aging weakened the stacked structure of the asphalt binder and increased the healing activation energy barrier. The increasing damage degree extended the distance for particles to travel, thus prolonging the time required for the crack interfaces contacting with each other. The elevated temperature improved the molecular mobility by supplying more energy to the molecular system. Furthermore, the self-healing process was evaluated quantitatively by the density variation at the crack closing stage and the diffusion coefficient at the intrinsic healing stage. The duration of each stage was influenced by the oxidative aging, damage degree and healing temperature. The findings in this paper are helpful to reveal and evaluate the self-healing property of asphalt binder. [ABSTRACT FROM AUTHOR]

Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds. [ABSTRACT FROM AUTHOR]

Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out to be promising rational drug design tools. In this paper, we report the first application of SMD to evaluate the binding properties of small molecules toward FABP4, considering our recent interest in inhibiting fatty acid binding protein 4 (FABP4). FABP4 inhibitors (FABP4is) are small molecules of therapeutic interest, and ongoing clinical studies indicate that they are promising for treating cancer and other diseases such as metabolic syndrome and diabetes. [ABSTRACT FROM AUTHOR]

Aqueous zinc-ion batteries (AZIBs), the favorite of next-generation energy storage devices, are popular among researchers owing to their environmental friendliness, low cost, and safety. However, AZIBs still face problems of low cathode capacity, fast attenuation, slow ion migration rate, and irregular dendrite growth on anodes. In recent years, many researchers have focused on Zn anode modification to restrain dendrite growth. This review introduces the energy storage mechanism and current challenges of AZIBs, and then some modifying strategies for zinc anodes are elucidated from the perspectives of experiments and theoretical calculations. From the experimental point of view, the modification strategy is mainly to construct a dense artificial interface layer or porous framework on the anode surface, with some research teams directly using zinc alloys as anodes. On the other hand, theoretical research is mainly based on adsorption energy, differential charge density, and molecular dynamics. Finally, this paper summarizes the research progress on AZIBs and puts forward some prospects. [ABSTRACT FROM AUTHOR]

Rutin is a natural flavonoid that carries out a variety of biological activities, but its application in medicine and food is limited by its water solubility. One of the classical methods used to enhance drug solubility is encapsulation with cyclodextrins. In this paper, the encapsulation of different cyclodextrins with rutin was investigated using a combination of experimental and simulation methods. Three inclusions of rutin/beta-cyclodextrin (β-CD), rutin/2-hydroxypropyl beta-cyclodextrin (HP-β-CD) and rutin/2,6-dimethyl beta-cyclodextrin (DM-β-CD) were prepared by the freeze-drying method, and the inclusions were analyzed using Fourier infrared spectroscopy (FTIR), X-ray diffraction analysis (XRD), differential scanning calorimetry (DSC) and ultraviolet–visible spectroscopy (UV) to characterize and demonstrate the formation of the inclusion complexes. Phase solubility studies showed that rutin formed a 1:1 stoichiometric inclusion complex and significantly increased its solubility. β-CD, HP-β-CD, DM-β-CD, rutin and the three inclusion complexes were modeled by using MS2018 and AutoDock 4.0, and molecular dynamics simulations were performed to calculate the solubility parameters, binding energies, mean square displacement (MSD), hydrogen bonding and radial distribution functions (RDF) after the equilibration of the systems. The results of simulation and experiment showed that rutin/DM-β-CD had the best encapsulation effect among the three cyclodextrin inclusion complexes. [ABSTRACT FROM AUTHOR]

The transmission and infectivity of COVID-19 have caused a pandemic that has lasted for several years. This is due to the constantly changing variants and subvariants that have evolved rapidly from SARS-CoV-2. To discover drugs with therapeutic potential for COVID-19, we focused on the 3CL protease (3CLpro) of SARS-CoV-2, which has been proven to be an important target for COVID-19 infection. Computational prediction techniques are quick and accurate enough to facilitate the discovery of drugs against the 3CLpro of SARS-CoV-2. In this paper, we used both ligand-based virtual screening and structure-based virtual screening to screen the traditional Chinese medicine small molecules that have the potential to target the 3CLpro of SARS-CoV-2. MD simulations were used to confirm these results for future in vitro testing. MCCS was then used to calculate the normalized free energy of each ligand and the residue energy contribution. As a result, we found ZINC15676170, ZINC09033700, and ZINC12530139 to be the most promising antiviral therapies against the 3CLpro of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7H-pyrrolo[2,3-d]pyrimidine competitive inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations and binding free energy calculations. The results show that the inhibitors had strong interactions with the hinge region, the β-sheets, and the residues with charged side chains around the 4-substituent. The terminal amino group of the inhibitor 5n was different from the other three, which could cause the enhancement of hydrogen bonds or electrostatic interactions formed with the surrounding residues. Thus, inhibitor 5n had the strongest inhibition capacity. The different halogen atoms on the 2-substituents of the inhibitors 5h, 5g, and 5e caused differences in the positions of the 2-benzene rings and affected the interactions of the hinge region. It also affected to some extent the orientations of the 4-imino groups and consequently their affinities for the surrounding charged residues. The combined results lead to the weakest inhibitory capacity of inhibitor 5e. [ABSTRACT FROM AUTHOR]

Chitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence chitosan's affinity for collagen. One of the most important ones is the deacetylation degree (DD) in chitosan and the hydroxylation degree (HD) of proline (PRO) moieties in collagen. In this paper, combinations of both factors were analyzed using a very efficient molecular dynamics approach. It was found that DD and HD modifications significantly affect the structural features of the complex related to considered types of interactions, namely hydrogen bonds, hydrophobic, and ionic contacts. In the case of hydrogen bonds both direct and indirect (water bridges) contacts were examined. In case of the most collagen analogues, a very good correlation between binding free energy and DD was observed. [ABSTRACT FROM AUTHOR]

Restricted economic conditions and limited sewage treatment facilities in rural areas lead to the discharge of small-scale breeding wastewater containing higher values of residual beta-lactam antibiotics (β-lactams), which seriously threatens the aquatic environment. In this paper, molecular docking and a comprehensive method were performed to quantify and fit the source modification for the combined biodegradation of β-lactams. Using penicillin (PNC) as the target molecule, combined with contour maps for substitute modification, a three-dimensional quantitative structure–activity relationship (3D-QSAR) model was constructed for the high-performance combined biodegradation of β-lactams. The selected candidate with better environmental friendliness, functionality, and high performance was screened. By using the homology modeling algorithms, the mutant penicillin-binding proteins (PBPs) of Escherichia coli were constructed to have antibacterial resistance against β-lactams. The molecular docking was applied to obtain the target substitute by analyzing the degree of antibacterial resistance of β-lactam substitute. The combined biodegradation of β-lactams and substitute in the constructed wetland (CW) by different wetland plant root secretions was studied using molecular dynamics simulations. The result showed a 49.28% higher biodegradation of the substitutes than PNC when the combined wetland plant species of Eichhornia crassipes, Phragmites australis, and Canna indica L. were employed. [ABSTRACT FROM AUTHOR]

Previous studies have been carried out on the effect of silica nanoparticles (SNPs) on the stability of oil–water emulsions. However, the combining configuration of SNPs and oil droplets at the molecular level and the effect of SNP content on the coalescence behavior of oil droplets cannot be obtained through experiments. In this paper, molecular dynamics (MD) simulation was performed to investigate the adsorption configuration of hydrophilic SNPs in an O/W emulsion system, and the effect of adsorption of SNPs on coalescence of oil droplets. The simulation results showed: (i) SNPs adsorbed on the surface of oil droplets, and excessive SNPs self-aggregated and connected by hydrogen bonds. (ii) Partially hydrophilic asphaltene and resin molecules formed adsorption configurations with SNPs, which changed the distribution of oil droplet components. Furthermore, compared with hydrophobic asphaltene, the hydrophilic asphaltene was easier to combine with SNPs. (iii) SNPs would extend the oil droplet coalescence time, and the π–π stacking structures were formed between asphaltene and asphaltene or resin molecules to enhance the connection between oil droplets during the oil droplet contact process. (iv) Enough SNPs tightly wrapped around the oil droplet, similar to the formation of a rigid film on the surface of an oil droplet, which hindered the contact and coalescence of components between oil droplets. [ABSTRACT FROM AUTHOR]

The adhesion phenomenon of polymers occurs in nature and in human activity. In the present paper, an adhesion system of steamed bread and eggshell was observed in formation when steamed bread and eggshells were placed in close contact and cooled slightly in the ambient air. The adhesion phenomena and mechanism of the adhesion interface between the steamed bread and eggshell were investigated and systematically discussed. Strong-bond interfaces were observed by scanning electron microscope (SEM). The formation process and mechanism of the strong-bond adhesion were also analyzed molecular dynamics simulation technology, and the results are discussed. The simulation analyses showed that the starch molecules at the calcite (104) crystal face were diffused in a water vapor environment, and the formation and solidification of multiple hydrogen bonds in the starch chain and oxygen atoms in the calcium carbonate were observed in detail during cooling. The diffusion rate of hydrogen atoms in hydroxyl groups on the calcite surface decreased gradually with the decrease of the cooling temperature of the steamed bread's upper surface. The strong adhesion of the steamed bread and eggshell is attributed to the synthetic effect of the absorption, diffusion, surface chemistry, and the formation of multiple hydrogen bonds between the starch from the steamed bread and the calcium carbonate crystals in eggshell. The interesting findings are helpful for the design of strong bonds, and provide an idea for new environmentally friendly adhesive materials. [ABSTRACT FROM AUTHOR]

In this paper, we introduce specific approximations to simplify the vibronic treatment in modeling absorption and emission spectra, allowing us to include a huge number of vibronic transitions in the calculations. Implementation of such a simplified vibronic treatment within our general approach for modelling vibronic spectra, based on molecular dynamics simulations and the perturbed matrix method, provided a quantitative reproduction of the absorption and emission spectra of aqueous indole with higher accuracy than the one obtained when using the existing vibronic treatment. Such results, showing the reliability of the approximations employed, indicate that the proposed method can be a very efficient and accurate tool for computational spectroscopy. [ABSTRACT FROM AUTHOR]

Monoacylglycerol lipase (MAGL) can regulate the endocannabinoid system and thus becomes a target of antidepressant drugs. In this paper, molecular docking and molecular dynamics simulations, combined with binding free energy calculation, were employed to investigate the inhibitory mechanism and binding modes of four aryl formyl piperidine derivative inhibitors with different 1-substituents to MAGL. The results showed that in the four systems, the main four regions where the enzyme bound to the inhibitor included around the head aromatic ring, the head carbonyl oxygen, the tail amide bond, and the tail benzene ring. The significant conformational changes in the more flexible lid domain of the enzyme were caused by 1-substituted group differences of inhibitors and resulted in different degrees of flipping in the tail of the inhibitor. The flipping led to a different direction of the tail amide bond and made a greater variation in its interaction with some of the charged residues in the enzyme, which further contributed to a different swing of the tail benzene ring. If the swing is large enough, it can weaken the binding strength of the head carbonyl oxygen to its nearby residues, and even the whole inhibitor with the enzyme so that the inhibition decreases. [ABSTRACT FROM AUTHOR]

Protein arginine methyltransferase 5 (PRMT5) is a popular anticancer target that regulates histone or nonhistone methylation and is linked to the development and poor prognosis of non-small cell lung cancer. PRMT5 inhibitors have shown great promise in clinical trials as a cancer therapy. However, most inhibitors reported recently act in a SAM-competitive mode and lack structural diversity. In this paper, a novel non-SAM inhibitor, 3039-0164, was discovered by the structure-based virtual screening method. The binding mechanism of 3039-0164 to PRMT5 was revealed via molecular docking and molecular dynamics simulations. 3039-0164 inhibited PRMT5 enzymatic activity, downregulated the expression of PRMT5 downstream target genes (FGFR3 and eIF4E), and blocked the activation of the PI3K/AKT/mTOR and ERK signaling pathways. The discovery of 3039-0164 provides precise and creative hit compounds for the design optimization of PRMT5 lead compounds in non-small cell lung cancer. [ABSTRACT FROM AUTHOR]

Highlights: According to the design of the experiment (DoE), multivariate analysis models were used to optimize the critical process parameters combined with multi-objective optimization. Based on the optimized operating conditions, the MILT-HD method not only enhances the extraction efficiency from Amomi fructus but also reduces energy demands and CO2 emissions. Based on the density functional theoretical (DFT) and molecular dynamics (MD) simulations, the mechanisms for ionic liquids (ILs) to improve the extraction efficiency of essential oil was comprehensively revealed. In this paper, Amomi fructus (Latin) was used to explore the mechanism of ionic liquids (ILs) in improving the extraction efficiency of essential oils. Microwave assisted ionic liquid treatment followed by a hydro-distillation (MILT-HD) process for isolating Amomi fructus essential oil was optimized by multi-objective optimization. Under optimum operating conditions, the IL-assisted extraction method not only enhances extraction efficiency but also reduces energy demands and CO2 emissions. Since the hydrogen bond structure network of cellulose in the cell wall is an important reason for hindering diffusion of essential oils, the mechanism of ILs was explored by density functional theoretical (DFT) and molecular dynamics (MD) simulations. According to DFT calculations, ILs can facilitate the cleavage of cellulose chains and have strong non-covalent interactions with cellulose. Based on the MD simulations, the degree of destruction of the cellulose hydrogen bond structure was explored. According to the DFT and MD simulations, the ILs can significantly destroy cellulose structure, thereby promoting essential oil release from the plant. These results were confirmed by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). This work is conducive to better understand the MILT-HD process for isolating essential oil and comprehensively understand the mechanism of ILs in the extraction process. [ABSTRACT FROM AUTHOR]

Hydrocarbon vapor adsorption experiments (HVAs) are one of the most prevalent methods used to evaluate the proportion of adsorbed state oil, critical in understanding the recoverable resources of shale oil. HVAs have some limitations, which cannot be directly used to evaluate the proportion of adsorbed state oil. The proportion of adsorbed state oil from HVA is always smaller than that in shale oil reservoirs, which is caused by the difference in adsorption characteristics of liquid and gaseous hydrocarbons. The results of HVA need to be corrected. In this paper, HVA was conducted with kaolinite, an important component of shale. A new method is reported here to evaluate the proportion of adsorbed state oil. Molecular dynamics simulations (MDs) of gaseous/liquid hydrocarbons with the same temperature and pressure as the HVAs were used as a reference to reveal the errors in the HVAs evaluation from the molecular scale. We determine the amount of free state of hydrocarbons by HVAs, and then calculate the proportion of adsorbed state oil by the liquid hydrocarbon MD simulation under the same conditions. The results show that gaseous hydrocarbons adsorptions are monolayer at low relative pressures and bilayer at high relative pressures. The liquid hydrocarbons adsorption is multilayer adsorption. The adsorption capacity of liquid hydrocarbons is over 2.7 times higher than gaseous hydrocarbons. The new method will be more effective and accurate to evaluate the proportion of adsorbed state oil. [ABSTRACT FROM AUTHOR]

To explore the influence of different wax components and the shear effect exerted by the pump and pipe wall in the process of crude oil pipeline transportation on the microbehavior of wax aggregation in crude oil at low temperatures, molecular dynamics models of binary and multivariate systems of crude oil with different wax components are established in this paper. The simulation results are compared with the existing experimental results and the NIST database to verify the rationality and accuracy of the models. By using the established binary model to simulate four crude oil systems containing different wax components, it can be found that the longer the wax molecular chain, the more easily the wax molecules aggregate. The influence of temperature on the aggregation process of wax molecules with different chain lengths is also studied. The lower the temperature, the greater the difference in wax molecular aggregation degree caused by the difference in molecular chain length. Nonequilibrium molecular dynamics is used to simulate the shear process of a multivariate system of crude oil, and the micromechanisms of the shear effect on the aggregation process of wax molecules are studied. Shearing can destroy the stable structure of crude oil, resulting in the orientation and conformational transformation of wax molecules, and obtaining the region of wax molecules sensitive to temperature and shear effects, the temperatures of which are below the wax precipitation point and the shear rate of which is lower than the maximum shear rate to prevent the molecular structure from being destroyed. At the same time, the sensitivity of wax components with different chain lengths to the shear effect is studied. The research results provide theoretical guidance for ensuring the safe and economic operation of waxy crude oil production. [ABSTRACT FROM AUTHOR]

Drug design is a time-consuming and cumbersome process due to the vast search space of drug-like molecules and the difficulty of investigating atomic and electronic interactions. The present paper proposes a computational drug design workflow that combines artificial intelligence (AI) methods, i.e., an evolutionary algorithm and artificial neural network model, and molecular dynamics (MD) simulations to design and evaluate potential drug candidates. For the purpose of illustration, the proposed workflow was applied to design drug candidates against the main protease of severe acute respiratory syndrome coronavirus 2. From the ∼140,000 molecules designed using AI methods, MD analysis identified two molecules as potential drug candidates. [ABSTRACT FROM AUTHOR]

A bidirectional pulsed electric field (BPEF) method is considered a simple and novel technique to demulsify O/W emulsions. In this paper, molecular dynamics simulation was used to investigate the transformation and aggregation behavior of oil droplets in O/W emulsion under BPEF. Then, the effect of surfactant (sodium dodecyl sulfate, SDS) on the demulsification of O/W emulsion was investigated. The simulation results showed that the oil droplets transformed and moved along the direction of the electric field. SDS molecules can shorten the aggregation time of oil droplets in O/W emulsion. The electrostatic potential distribution on the surface of the oil droplet, the elongation length of the oil droplets, and the mean square displacement (MSD) of SDS and asphaltene molecules under an electric field were calculated to explain the aggregation of oil droplets under the simulated pulsed electric field. The simulation also showed that the two oil droplets with opposite charges have no obvious effect on the aggregation of the oil droplets. However, van der Waals interactions between oil droplets was the main factor in the aggregation. [ABSTRACT FROM AUTHOR]

Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer's disease. The soluble, oligomeric forms of hIAPP are the most toxic to β-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions. [ABSTRACT FROM AUTHOR]

The octanol–water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values. [ABSTRACT FROM AUTHOR]

Temporin L (TempL) is a 13 residue Host Defense Peptide (HDP) isolated from the skin of frogs. It has a strong affinity for lipopolysaccharides (LPS), which is related to its high activity against Gram-negative bacteria and also to its strong tendency to neutralize the pro-inflammatory response caused by LPS release from inactivated bacteria. A designed analog with the Q3K substitution shows an enhancement in both these activities. In the present paper, Molecular Dynamics (MD) simulations have been used to investigate the origin of these improved properties. To this end, we have studied the behavior of the peptides both in water solution and in the presence of LPS lipid-A bilayers, demonstrating that the main effect through which the Q3K substitution improves the peptide activities is the destabilization of peptide aggregates in water. [ABSTRACT FROM AUTHOR]

Disulfide-rich peptides isolated from the venom of arthropods and marine animals are a rich source of potent and selective modulators of ion channels. This makes these peptides valuable lead molecules for the development of new drugs to treat neurological disorders. Consequently, much effort goes into understanding their mechanism of action. This paper presents an overview of how molecular simulations have been used to study the interactions of disulfide-rich venom peptides with ion channels and membranes. The review is focused on the use of docking, molecular dynamics simulations, and free energy calculations to (i) predict the structure of peptide-channel complexes; (ii) calculate binding free energies including the effect of peptide modifications; and (iii) study the membrane-binding properties of disulfide-rich venom peptides. The review concludes with a summary and outlook. [ABSTRACT FROM AUTHOR]

DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology [ABSTRACT FROM AUTHOR]

In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants. [ABSTRACT FROM AUTHOR]

The metabotropic glutamate subtype 1 (mGluR1), a member of the metabotropic glutamate receptors, is a therapeutic target for neurological disorders. However, due to the lower subtype selectivity of mGluR1 orthosteric compounds, a new targeted strategy, known as allosteric modulators research, is needed for the treatment of mGluR1-related diseases. Recently, the structure of the seven-transmembrane domain (7TMD) of mGluR1 has been solved, which reveals the binding site of allosteric modulators and provides an opportunity for future subtype-selectivity drug design. In this study, a series of computer-aided drug design methods were utilized to discover potential mGluR1 negative allosteric modulators (NAMs). Pharmacophore models were constructed based on three different structure types of mGluR1 NAMs. After validation using the built-in parameters and test set, the optimal pharmacophore model of each structure type was selected and utilized as a query to screen the Traditional Chinese Medicine Database (TCMD). Then, three different hit lists of compounds were obtained. Molecular docking was used based on the latest crystal structure of mGluR1-7TMD to further filter these hits. As a compound with high QFIT and LibDock Score was preferred, a total of 30 compounds were retained. MD simulation was utilized to confirm the stability of potential compounds binding. From the computational results, thesinine-4'-O-β-D-glucoside, nigrolineaxanthone-P and nodakenin might exhibit negative allosteric moderating effects on mGluR1. This paper indicates the applicability of molecular simulation technologies for discovering potential natural mGluR1 NAMs from Chinese herbs. [ABSTRACT FROM AUTHOR]

This paper proposes a new mixed quantum mechanics (QM)—molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics. [ABSTRACT FROM AUTHOR]

Tyrosinase is a key enzyme in melanin synthesis and widely distributed in plants and animals tissues. In mammals, this enzyme is related to pigment production, involved in wound healing, primary immune response and it can also contribute to catecholamines synthesis in the brain. Consequently, tyrosinase enzyme represents an attractive and selective target in the field of the medicine, cosmetics and bio-insecticides. In this paper, experimental kinetics and computational analysis were used to study the inhibition of tyrosinase by analogs of Kojic acid. The main interactions occurring between inhibitors-tyrosinase complexes and the influence of divalent cation (Cu2+) in enzymatic inhibition were investigated by using molecular docking, molecular dynamic simulations and electrostatic binding free energy by using the Linear Interaction Energy (LIE) method. The results showed that the electrostatic binding free energy are correlated with values of constant inhibition (r² = 0.97).Thus, the model obtained here could contribute to future studies of this important system and, therefore, eventually facilitate development of tyrosinase inhibitors. [ABSTRACT FROM AUTHOR]

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future. [ABSTRACT FROM AUTHOR]

The spread of the Dengue virus over the world, as well as multiple outbreaks of different serotypes, has resulted in a large number of deaths and a medical emergency, as no viable medications to treat Dengue virus patients have yet been found. In this paper, we provide an in silico virtual screening and molecular dynamics-based analysis to uncover efficient Dengue infection inhibitors. Based on a Google search and literature mining, a large phytochemical library was generated and employed as ligand molecules. In this investigation, the protein target NS2B/NS3 from Dengue was employed, and around 27 compounds were evaluated in a docking study. Phellodendroside (−63 kcal/mole), quercimeritrin (−59.5 kcal/mole), and quercetin-7-O-rutinoside (−54.1 kcal/mole) were chosen based on their binding free energy in MM-GBSA. The tested compounds generated numerous interactions at Lys74, Asn152, and Gln167 residues in the active regions of NS2B/NS3, which is needed for the protein's inhibition. As a result, the stable mode of docked complexes is defined by various descriptors from molecular dynamics simulations, such as RMSD, SASA, Rg, RMSF, and hydrogen bond. The pharmacological properties of the compounds were also investigated, and no toxicity was found in computational ADMET properties calculations. As a result, this computational analysis may aid fellow researchers in developing innovative Dengue virus inhibitors. [ABSTRACT FROM AUTHOR]

In this paper, the influence of tool shape on the surface quality of monocrystalline nickel nanofabrication is studied. The research mainly adopts the method of molecular dynamics simulation, through the statistics of the atomic coordinates of the machined surface, then calculates the influence of different tool rake angles on the surface roughness of monocrystalline nickel. It is concluded that the surface roughness distribution is 'W' when the rake angle of the diamond tool changes from −45° to +45°. When analyzing the relationship between the tool shape and the processing temperature, it is found that when the clearance angle of the tool reaches a certain range, the clearance angle is further increased, and the temperature of the workpiece does not change during machining. Therefore, a large number of simulations were carried out, and it was concluded that there is a critical clearance angle, and the critical clearance angle of the tool in the research conditions is 8–10°. [ABSTRACT FROM AUTHOR]

Natural ester, as a new environmentally green insulating oil, has been widely used in transformer. In an oil-immersed transformer, the normal aging, thermal failure, and discharge failure could easily lead to the decomposition of the oil-paper insulation system and produce different kinds of gases. Studying gas dissolution in natural ester and mineral oil could provide assistance in applying criteria to make a diagnosis of different kinds of faults in the transformer. In this paper, the molecular dynamics method was used to investigate the diffusion behavior of seven fault characteristic gases (including H2, CO, CH4, C2H2, CO2, C2H4, C2H6) in natural ester and mineral oil. The simulation parameters of free volume, interaction energy, mean square displacement, and diffusion coefficient were compared between the natural ester and mineral oil. Meanwhile, the influence of temperature on the diffusion of gas molecules in two kinds of oils was also analyzed. Results showed that the free volume, the interaction energy, and the relative molecular mass of gas molecules were the factors influenced by the diffusion of gas molecules in natural ester and mineral oil. The order of the diffusion coefficients of gas molecules in natural ester was as follows: H2 > CH4 > CO > C2H2 > C2H4 > CO2 > C2H6 and that in mineral oil was as follows: H2 > CH4 > CO> C2H2 > C2 H4 > C2H6 > CO2. By comparing the diffusion behavior of gas molecules in natural ester and mineral oil, it was found that the smaller free volume and higher interaction energy of gas molecules in natural ester were the major reasons for the gas molecules to be more difficult to diffuse in natural ester. The rising temperature could enhance the free volume and reduce the interaction energy between gas molecules and oil. The diffusion coefficient of gas molecules increased exponentially with the follow of temperature. However, the temperature didn't affect the ordering of diffusion coefficient, free volume, and interaction energy of gas molecules in natural ester and mineral oil. [ABSTRACT FROM AUTHOR]