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Nitrogen vacancy (NV) color centers in diamond have useful applications in quantum sensing and fluorescent marking. They can be generated experimentally by ion implantation, femtosecond lasers, and chemical vapor deposition. However, there is a lack of studies of the yield of NV color centers at the atomic scale. In the molecular dynamics simulations described in this paper, NV color centers are prepared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing. The differences between the yields of NV color centers produced by implantation of carbon (C) and nitrogen (N) ions, respectively, are investigated. It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy. The effects of different pre-doping concentrations (400–1500 ppm) and implantation energies (1.0–3.0 keV) on the NV color center yield are analyzed, and it is shown that a pre-doping concentration of 1000 ppm with 2 keV C-ion implantation can produce a 13% yield of NV color centers after 1600 K annealing for 7.4 ns. Finally, a brief comparison of the NV color center identification methods is presented, and it is found that the error rate of an analysis utilizing the identify diamond structure + coordination analysis method is reduced by about 7% compared with conventional identification methods. HIGHLIGHTS: • Homologous ion implantation can produce excellent nitrogen vacancy (NV) color centers. • Appropriate implantation parameters determine the quality of NV color centers. • A 13% yield of NV color centers can be realized at 2 keV C implantation. • Enhanced quality of NV color centers benefits quantum applications. [ABSTRACT FROM AUTHOR]

Clostridioides difficile (C. difficile), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for Clostridioides difficile infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against C. difficile is of paramount importance. In our study, the complete proteome sequences of 118 strains of C. difficile were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.

Microscopic tests, molecular dynamics (MD) simulation, and two-piece healing (TPH) approaches were employed to investigate the interfacial intrinsic healing behavior and mechanisms of graphene-modified asphalt (GMA) binders at different aging levels. A vacuum layer 10-Å thick was injected between two molecules of asphalt binder to resemble a pattern of cracks. The mean squared displacement (MSD), molecular diffusion coefficient (D), and surface free energy (SFE) of asphalt molecules were utilized to evaluate the micro intrinsic healing behavior of asphalt binders. The macro intrinsic healing capacity of asphalt binders was determined using the intrinsic healing function [Rh(t)] developed from the TPH test. The GMA binder had a higher healing efficiency than the base binder in the short-term healing condition according to the density of the MD simulations, the SFE of the sessile drop method, and the initial healing rate (R0) of the TPH experiment. GMA binder had higher potential for instantaneous healing than the base binder because of its greater SFE in general. According to an analysis of parameters MSD, D , and Rh(t) quantified by MD simulations and TPH tests, the GMA binder had a greater capacity for long-term healing than the base binder after a long-term aging process. An R2 of 0.87 was obtained from the regression analysis of R0 against SFE, and an R2 of 0.93 was obtained from the regression analysis of Rh(3,600)−R0 against D. The experimental findings at the macroscopic scale and the simulation outcomes at the microscopic level were mutually supportive. [ABSTRACT FROM AUTHOR]

Abstract Acinetobacter baumannii is a gram-negative bacillus prevalent in nature, capable of thriving under various environmental conditions. As an opportunistic pathogen, it frequently causes nosocomial infections such as urinary tract infections, bacteremia, and pneumonia, contributing to increased morbidity and mortality in clinical settings. Consequently, developing novel vaccines against Acinetobacter baumannii is of utmost importance. In our study, we identified 10 highly conserved antigenic proteins from the NCBI and UniProt databases for epitope mapping. We subsequently screened and selected 8 CTL, HTL, and LBL epitopes, integrating them into three distinct vaccines constructed with adjuvants. Following comprehensive evaluations of immunological and physicochemical parameters, we conducted molecular docking and molecular dynamics simulations to assess the efficacy and stability of these vaccines. Our findings indicate that all three multi-epitope mRNA vaccines designed against Acinetobacter baumannii are promising; however, further animal studies are required to confirm their reliability and effectiveness.

Acinetobacter baumannii is a gram-negative bacillus prevalent in nature, capable of thriving under various environmental conditions. As an opportunistic pathogen, it frequently causes nosocomial infections such as urinary tract infections, bacteremia, and pneumonia, contributing to increased morbidity and mortality in clinical settings. Consequently, developing novel vaccines against Acinetobacter baumannii is of utmost importance. In our study, we identified 10 highly conserved antigenic proteins from the NCBI and UniProt databases for epitope mapping. We subsequently screened and selected 8 CTL, HTL, and LBL epitopes, integrating them into three distinct vaccines constructed with adjuvants. Following comprehensive evaluations of immunological and physicochemical parameters, we conducted molecular docking and molecular dynamics simulations to assess the efficacy and stability of these vaccines. Our findings indicate that all three multi-epitope mRNA vaccines designed against Acinetobacter baumannii are promising; however, further animal studies are required to confirm their reliability and effectiveness. [ABSTRACT FROM AUTHOR]

Nucleation is a fundamental and general process at the initial stage of first-order phase transition. Although various models based on the classical nucleation theory (CNT) have been proposed to explain the energetics and kinetics of nucleation, detailed understanding at nanoscale is still required. Here, in view of the homogeneous bubble nucleation, we focus on cavity formation, in which evaluation of the size dependence of free energy change is the key issue. We propose the application of a formula in stochastic thermodynamics, the Jarzynski equality, for data analysis of molecular dynamics (MD) simulation to evaluate the free energy of cavity formation. As a test case, we performed a series of MD simulations with a Lennard-Jones (LJ) fluid system. By applying an external spherical force field to equilibrated LJ liquid, we evaluated the free energy change during cavity growth as the Jarzynski's ensemble average of required works. A fairly smooth free energy curve was obtained as a function of bubble radius in metastable liquid of mildly negative pressure conditions. [ABSTRACT FROM AUTHOR]

Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 (and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines. [ABSTRACT FROM AUTHOR]

The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics (MD) simulations and experiments. The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms, which has laser-induced high stress. However, under high fluence and short pulse width laser irradiation, the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film. In addition, Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg [ 10 1 ¯ 0 ] . The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments. The results show that, under multiple pulsed laser irradiation, not only does the crater depth increase linearly with the pulse number, but also the quadratic term and constant term of the fitted crater profile curve increase linearly. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, is a highly contagious respiratory disease with widespread societal impact. The symptoms range from cough, fever, and pneumonia to complications affecting various organs, including the heart, kidneys, and nervous system. Despite various ongoing efforts, no effective drug has been developed to stop the spread of the virus. Although various types of medications used to treat bacterial and viral diseases have previously been employed to treat COVID-19 patients, their side effects have also been observed. The way SARS-CoV-2 infects the human body is very specific, as its spike protein plays an important role. The S subunit of virus spike protein cleaved by human proteases, such as furin protein, is an initial and important step for its internalization into a human host. Keeping this context, we attempted to inhibit the furin using phytochemicals that could produce minimal side effects. For this, we screened 408 natural phytochemicals from various plants having antiviral properties, against furin protein, and molecular docking and dynamics simulations were performed. Based on the binding score, the top three compounds (robustaflavone, withanolide, and amentoflavone) were selected for further validation. MM/GBSA energy calculations revealed that withanolide has the lowest binding energy of -57.2 kcal/mol followed by robustaflavone and amentoflavone with a binding energy of -45.2 kcal/mol and -39.68 kcal/mol, respectively. Additionally, ADME analysis showed druglike properties for these three lead compounds. Hence, these natural compounds robustaflavone, withanolide, and amentoflavone, may have therapeutic potential for the management of SARS-CoV-2 by targeting furin. [ABSTRACT FROM AUTHOR]

Pressure-volume-temperature-composition (PVTX) properties of gas mixtures are important to model and predict flow and compression performance in a range of industrial processes. It is time consuming and sometimes impractical to obtain these properties from experiments. Here, molecular dynamics (MD) simulations were conducted to compute the thermodynamic volumetric properties of pure H 2 , CH 4 , CO 2 , and binary mixtures of H 2 /CH 4 and H 2 /CO 2 at temperatures of 310.9–470 K, pressures up to 172 MPa. MD simulation results were used to develop five analytical equations explicit in pressure as a function of density or volume, temperature, and composition, for the pure gases and mixtures. Our simulated results matched very well with the predictions from the established GERG-2008 equation and data published by NIST. The simplified equations of state (EOS) developed in this work will be more computationally efficient than other EOS for mixed systems. This can be significant in reservoir simulations. • Develop analytical PVT/PρT models for supercritical pure H 2 , CH 4 , CO 2. • Develop analytical PVTX/PρTX models for supercritical H 2 /CH 4 and H 2 /CO 2 mixtures. • The models developed by this work were validated by simulated and experimental data. • The models developed can be more computationally efficient than other models. [ABSTRACT FROM AUTHOR]

The aging process of asphalt materials encompasses varying levels of oxidation reactions within its components. This process increases the polarity of the molecules, prompting aggregation among asphaltenes. Thus, a thorough examination of asphaltene molecule aggregation and disaggregation patterns holds vital implications for the performance restoration of aged asphalt. According to the density functional theory (DFT), the interaction form between oxidized asphaltene dimers was inferred by electrostatic potential (ESP) and confirmed through the charge density difference. This study identified asphaltene dimers optimal configurations via energy minimization principles and determined the factors influencing aggregation based on interaction energy. On the basis of the molecular structure design theory, the basic structures of three different rejuvenators—chain alkanes, aromatic hydrocarbons, and cycloalkanes—were constructed. Functional groups such as hydroxyl, carboxyl, ether, ester, and amide were incorporated to explore the disaggregation patterns of oxidized asphaltene dimers induced by varying rejuvenator structures. Our results revealed that asphaltene molecules form dimers through the π-π stacking interaction of aromatic rings and the electrostatic interaction between positive-negative ESP regions. Dimer disaggregation predominantly follows two rejuvenation mechanisms: T-shaped and parallel. Parallel rejuvenation is the primary mechanism for chain alkanes, aromatic hydrocarbons, cycloalkanes ether, and ester groups. Here, methyl decyl ether exhibited the most potent disaggregation effect, reducing interaction energy between asphaltene dimers by 61.7%. The conclusions could offer a theoretical foundation for understanding asphaltene molecule aggregation and disaggregation and suggest strategies for high-performance rejuvenator design. [ABSTRACT FROM AUTHOR]

The enzyme protein kinase G1 (PRKG1) plays a crucial role in cellular signaling pathways such as smooth muscle relaxation, neuronal signaling, and platelet aggregation. The dysregulation of PRKG1 leads to different diseases, making it a promising drug target. In this study, we employed a comprehensive in silico strategy to explore potential inhibitors of PRKG1 by using the crystal structure of the PRKG1 protein. The active site of PRKG1 protein was parameterized within a three-dimensional grid box. The 100 hit compounds identified during virtual screening were docked to the prepared PRKG1 receptor to predict binding affinities. The top ten compounds were chosen, and their binding affinities ranged from −10.734 to −10.398 kcal/mol. Finally, a 200 ns long simulation was run to confirm the stability of the protein–ligand complexes at the binding sites of the two top compounds against the PRKG1 receptor. All these findings suggest that the selected compounds can serve as potential compounds to inhibit the PRKG1 function in biological assays.

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The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, is a highly contagious respiratory disease with widespread societal impact. The symptoms range from cough, fever, and pneumonia to complications affecting various organs, including the heart, kidneys, and nervous system. Despite various ongoing efforts, no effective drug has been developed to stop the spread of the virus. Although various types of medications used to treat bacterial and viral diseases have previously been employed to treat COVID-19 patients, their side effects have also been observed. The way SARS-CoV-2 infects the human body is very specific, as its spike protein plays an important role. The S subunit of virus spike protein cleaved by human proteases, such as furin protein, is an initial and important step for its internalization into a human host. Keeping this context, we attempted to inhibit the furin using phytochemicals that could produce minimal side effects. For this, we screened 408 natural phytochemicals from various plants having antiviral properties, against furin protein, and molecular docking and dynamics simulations were performed. Based on the binding score, the top three compounds (robustaflavone, withanolide, and amentoflavone) were selected for further validation. MM/GBSA energy calculations revealed that withanolide has the lowest binding energy of −57.2 kcal/mol followed by robustaflavone and amentoflavone with a binding energy of −45.2 kcal/mol and −39.68 kcal/mol, respectively. Additionally, ADME analysis showed drug-like properties for these three lead compounds. Hence, these natural compounds robustaflavone, withanolide, and amentoflavone, may have therapeutic potential for the management of SARS-CoV-2 by targeting furin.

Activated blood coagulation factor X (FXa) plays a critical initiation step of the blood-coagulation pathway and is considered a desirable target for anticoagulant drug development. It is reversibly inhibited by nonvitamin K antagonist oral anticoagulants (NOACs) such as apixaban, betrixaban, edoxaban, and rivaroxaban. Thrombosis is extremely common and is one of the leading causes of death in developed countries. In previous studies, novel thiourea and oxime ether isosteviol derivatives as FXa inhibitors were designed through a combination of QSAR studies and molecular docking. In the present contribution, molecular dynamics (MD) simulations were performed for 100 ns to assess binding structures previously predicted by docking and furnish additional information. Moreover, three thiourea- and six oxime ether-designed isosteviol analogs were then examined for their drug-like and ADMET properties. MD simulations demonstrated that four out of the nine investigated isosteviol derivatives, i.e., one thiourea and three oxime ether ISV analogs, form stable complexes with FXa. These derivatives interact with FXa in a manner similar to Food and Drug Administration (FDA)-approved drugs like edoxaban and betrixaban, indicating their potential to inhibit factor Xa activity. One of these derivatives, E24, displays favorable pharmacokinetic properties, positioning it as the most promising drug candidate. This, along with the other three derivatives, can undergo further chemical synthesis and bioassessment. [ABSTRACT FROM AUTHOR]

Water reduces the stability and safety of paving material, and this has been extensively studied in traditional asphalt pavement. However, the influence of water on emerging cold-mixed epoxy asphalt (CEA) has not yet been acknowledged. In addition, the microstructure composed of epoxy resin (ER) and asphalt determines the performance of the CEA binder, and the influence of water entering this structure should be focused on. Here, CEA interfacial water models were established based on experimental and molecular dynamics (MD) simulations. The distribution and motion of the interfacial water and their influence on the energy, compatibility, and mechanical properties of CEA were explored. The results showed that CEA had desirable water stability when the water content was less than 5%. Water moved and was rearranged at the interface of the CEA and tended to move toward the ER. The water diffusion coefficient increased proportionally to the quadratic of the water content, and the structure of the CEA changed from an ordered short-range arrangement to a disordered one. Water reduced the interaction between the ER and asphalt by a maximum of 41.7% but had little effect on the compatibility of the CEA. Water plasticized CEA because the glass transition temperature of the CEA decreased, and less than 3% of water decreased the modulus of the CEA by a maximum of 27.0%. Simultaneously, water also destroyed the isotropy of the properties of the CEA. The gyration radius of the CEA dropped to approximately half of the value without water. This study is positive for promoting the performance improvement of CEA and provides a framework for studying CEA modeling and evaluation with MD simulations. [ABSTRACT FROM AUTHOR]

In this research, due to the importance of oxygen evolution reactions (OER) in the production of hydrogen gas, the effects of the solvent on the OER steps on the magnesium oxide surface have been studied. For this purpose, the difference in free energy value in OER steps on the Magnesium oxide surface for two systems (in the presence and the absence of solvent) have been investigated using molecular dynamics (MD) simulation and thermodynamic integration (TI). These results are in perfect agreement with the results obtained from ab initio molecular dynamics simulations and quantum mechanics calculations. Our findings show that the presence of water solvent around the surface of magnesium oxide has a crucial role on OER and leads to an increase more than twofold in the free energy of all steps. Also, the presence of the solvent has the most effect on the third step of OER, and its ΔG increases by about 1.9 eV. This fact can be attributed to the approach of the water molecules to the substrate spontaneously, which increases the probability of forming hydrogen bonds and the number of contacts, leading to more favorable thermodynamic reactions. Close inspection of the calculated binding energies between the substrate and the intermediates confirms that the binding energy of OER's second step is significantly higher than the other steps and is the velocity determining step.

Molecular dynamics (MD) simulation and experiments were carried out in this work to probe the microstructure evolution in the semi-solid compression (SSC) of AZ80 magnesium alloy. The liquid phase flow, stress fluctuations, grain refinement, dislocation generation, and texture evolution were discussed. Results indicate that the liquid phase was squeezed out along the radial direction prior the solid phase at the beginning of compression. Stress-strain curve represented obvious fluctuation at lower strain rates. That resulted from stress reduction caused by more liquid evolving with a lower strain rate at an elevated temperature. Plastic deformation was detected in grains and the dislocations of 1/3 dominated the deformation, while and 1/3 just been activated at the beginning of SSC process. The results of EBSD showed the grains size was refined into about 38.8 μm from 92.3 μm after SSC process. During the process, grain refinement resulted in the increase of low-angle grain boundaries (LAGBs), and a strong (0001) basal plane texture evolved at the end. The higher the strain rates, the stronger the texture.

Nucleation is a fundamental and general process at the initial stage of first-order phase transition. Although various models based on the classical nucleation theory (CNT) have been proposed to explain the energetics and kinetics of nucleation, detailed understanding at nanoscale is still required. Here, in view of the homogeneous bubble nucleation, we focus on cavity formation, in which evaluation of the size dependence of free energy change is the key issue. We propose the application of a formula in stochastic thermodynamics, the Jarzynski equality, for data analysis of molecular dynamics (MD) simulation to evaluate the free energy of cavity formation. As a test case, we performed a series of MD simulations with a Lennard-Jones (LJ) fluid system. By applying an external spherical force field to equilibrated LJ liquid, we evaluated the free energy change during cavity growth as the Jarzynski’s ensemble average of required works. A fairly smooth free energy curve was obtained as a function of bubble radius in metastable liquid of mildly negative pressure conditions.

Nonaqueous reaction foam polyurethane (PU) grouting materials have found wide applications in civil engineering. However, degradation laws and mechanism of the strength performance of PU grouting materials in different corrosion environments are not clear yet. Here, the uniaxial compression test, scanning electron microscopy (SEM) characterization, Fourier-transform infrared (FTIR) spectroscopy test, and molecular dynamics (MD) simulations were conducted to investigate the influences of acidic and alkaline corrosion environments on the compressive strength, microstructure, molecular structures, and nanoscale mechanical properties. Results show that with the increase of corrosion time, the compressive strength of PU grouting materials decreases more and more. The deterioration effect of an acidic environment is stronger than that of an alkaline environment, and it is stronger when the acidic environment is with a lower pH value. At the microscale, the damage of carbamate esters and the breakage of ether bonds results in the fracture, hydrolysis, and dissolution of the long PU molecule chains, which is the main reason leading to the destruction of microfoams. Compared with sodium hydroxide solution, sulfuric acid solution produces more pronounced damage to molecular structures as well as microstructures, and thus more significant deterioration effect on compressive strength. At the nanoscale, the compressive strength, tensile strength, and shear strength of the amorphous PU elastomers after corrosion decreased by 26.7%–35.7%, 13.4%–27.9%, and 4.26%–12.73%, respectively, compared with the original model, illustrating the damaging effect of chemical corrosion on the nanostrength of the PU elastomer. MD simulation results also show that the length of the molecular chain has a great influence on compressive strength and tensile strength, and the absence of molecular fragments has a great influence on shear strength. [ABSTRACT FROM AUTHOR]

In cancer cells, short for sirtuin (SIRT7) stabilizes the transformed state via its nicotinamide adenine dinucleotide (NAD+)‐dependent deacetylase activity. Epigenetic factor SIRT7 plays important roles in cancer biology, reversing cancer phenotypes and suppressing tumor growth when inactive. In the present study, we got the SIRT7 protein structure from Alpha Fold2 Database and performed structure‐based virtual screening to develop specific SIRT7 inhibitors using the SIRT7 inhibitor 97,491 interaction mechanism. As candidates for specific SIRT7 inhibitors, compounds with high affinities to SIRT7 were chosen. ZINC000001910616 and ZINC000014708529, two of our leading compounds, showed strong interactions with SIRT7. Our MD simulation results also revealed that the 5‐hydroxy‐4H‐thioxen‐4‐one group and terminal carboxyl group were critical groups responsible for interaction of small molecules with SIRT7. In our study, we demonstrated that targeting SIRT7 may offer novel therapeutic options for cancer treatment. Compounds ZINC000001910616 and ZINC000014708529 can serve as chemical probes to investigate SIRT7 biological functions and provide starting points for the development of novel therapeutics against cancers. [ABSTRACT FROM AUTHOR]

Biochar is a carbon-rich solid produced during the thermochemical processes of various biomass feedstocks. As a low-cost and environmentally friendly material, biochar has multiple significant advantages and potentials, and it can replace more expensive synthetic carbon materials for many applications in nanocomposites, energy storage, sensors, and biosensors. Due to biomass feedstock species, reactor types, operating conditions, and the interaction between different factors, the compositions, structure and function, and physicochemical properties of the biochar may vary greatly, traditional trial-and-error experimental approaches are time consuming, expensive, and sometimes impossible. Computer simulations, such as molecular dynamics (MD) simulations, are an alternative and powerful method for characterizing materials. Biomass pyrolysis is one of the most common processes to produce biochar. Since pyrolysis of decomposing biomass into biochar is based on the bond-order chemical reactions (the breakage and formation of bonds during carbonization reactions), an advanced reactive force field (ReaxFF)-based MD method is especially effective in simulating and/or analyzing the biomass pyrolysis process. This paper reviewed the fundamentals of the ReaxFF method and previous research on the characterization of biochar physicochemical properties and the biomass pyrolysis process via MD simulations based on ReaxFF. ReaxFF implicitly describes chemical bonds without requiring quantum mechanics calculations to disclose the complex reaction mechanisms at the nano/micro scale, thereby gaining insight into the carbonization reactions during the biomass pyrolysis process. The biomass pyrolysis and its carbonization reactions, including the reactivity of the major components of biomass, such as cellulose, lignin, and hemicellulose, were discussed. Potential applications of ReaxFF MD were also briefly discussed. MD simulations based on ReaxFF can be an effective method to understand the mechanisms of chemical reactions and to predict and/or improve the structure, functionality, and physicochemical properties of the products. [ABSTRACT FROM AUTHOR]

Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties. Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction (COF) because of the transformation in bond structure from sp3-C to sp2-C during friction processes. However, the mechanism for such a transformation during friction is not well understood. This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics (MD) simulation. Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear, resulting in a decrease in growth rate of the wear rate after the running-in stage. It is worth noting that the sp3-C atoms were increased during the running-in stage when the films contained lower sp3/sp2 ratios. However, the formed sp3-C atoms could only be short-lived and gradually transformed to sp2-C atoms with the graphitization generated on the wearing surface of the films. The radial distribution function and translational order parameter indicated that the films' high sp3/sp2 ratio led to an increased sp2-C proportion on the wear scar after friction, which caused an increased structural ordering. [ABSTRACT FROM AUTHOR]

Abstract Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties. Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction (COF) because of the transformation in bond structure from sp3-C to sp2-C during friction processes. However, the mechanism for such a transformation during friction is not well understood. This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics (MD) simulation. Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear, resulting in a decrease in growth rate of the wear rate after the running-in stage. It is worth noting that the sp3-C atoms were increased during the running-in stage when the films contained lower sp3/sp2 ratios. However, the formed sp3-C atoms could only be short-lived and gradually transformed to sp2-C atoms with the graphitization generated on the wearing surface of the films. The radial distribution function and translational order parameter indicated that the films’ high sp3/sp2 ratio led to an increased sp2-C proportion on the wear scar after friction, which caused an increased structural ordering.

Designing antiviral therapeutics is of great concern per current pandemics caused by novel coronavirus or SARS-CoV-2. The core polymerase enzyme in the viral replication/transcription machinery is generally conserved and serves well for drug target. In this work we briefly review structural biology and computational clues on representative single-subunit viral polymerases that are more or less connected with SARS-CoV-2 RNA dependent RNA polymerase (RdRp), in particular, to elucidate how nucleotide substrates and potential drug analogs are selected in the viral genome synthesis. To do that, we first survey two well studied RdRps from Polio virus and hepatitis C virus in regard to structural motifs and key residues that have been identified for the nucleotide selectivity. Then we focus on related structural and biochemical characteristics discovered for the SARS-CoV-2 RdRp. To further compare, we summarize what we have learned computationally from phage T7 RNA polymerase (RNAP) on its stepwise nucleotide selectivity, and extend discussion to a structurally similar human mitochondria RNAP, which deserves special attention as it cannot be adversely affected by antiviral treatments. We also include viral phi29 DNA polymerase for comparison, which has both helicase and proofreading activities on top of nucleotide selectivity for replication fidelity control. The helicase and proofreading functions are achieved by protein components in addition to RdRp in the coronavirus replication-transcription machine, with the proofreading strategy important for the fidelity control in synthesizing a comparatively large viral genome.

The biodegradation of anionic polyacrylamide (HPAM) mediated by manganese peroxidase (Mn P) has been experimentally discovered and reported by researchers, but the interaction mechanism of Mn P with HPAM at molecular level is still unclear. Here, the molecular mechanisms of HPAM structure models with Mn P obtained from Phanerochaete chrysosporium were investigated by docking and molecular dynamics (MD) simulations. The results indicate that both the number of H-bonds formed and key residues in MnP-HPAM-5 are the largest, leading to its maximal binding affinity. HPAM models contact with an active site of Mn P by H-bonds and hydrophobic interactions to maintain their stability. The binding of HPAM-5 results in the significant change and unfolding of enzyme structure, and the thicker hydration shell produced by a large amount of water molecule near the enzyme surface and the binding region makes HPAM-5 difficult to access the active site of enzyme. The enzyme structure is the most stable when it binds to HPAM-4, and the higher water molecules may form H-bonds with its binding region. These facilitate mass transfer, beneficial to its binding. This study provides the theoretical reference for designing the enzyme with higher activity and stability to enhance the degradation performance of HPAM.

The weak interlaminar properties severely hinder the high-property applications of carbon fiber (CF) reinforced thermoplastic composites. Here, interlaminar properties were significantly enhanced by introducing carbon nanotube (CNT) decorated polyether ether ketone (PEEK) films into the interlayer. PEEK films decorated with different CNT contents were fabricated by the spraying and thermoforming processes. Tensile test results show that the films with a CNT surface density of 45 mg/m2 exhibit superior tensile strength and Young's modulus due to the higher crystallinity and larger crystalline size. The introduction of this modified film into unidirectional CF reinforced PEEK laminates leads to an increase by 101% to 1.67 kJ/m2 in interlaminar fracture toughness, while the interlaminar shear strength is retained. Fractographic analysis reveals that the increase in interlayer resin content and crack path deflection are primary factors contributing to interlaminar toughening. Molecular dynamics simulation demonstrates that incorporating CNT in the interlayer resin significantly improved the interfacial bonding strength between fiber and resin, thus resulting in crack path deflection.

This study investigated the modification mechanism of polyurethane (PU) on the high- and low-temperature properties of asphalt based on experimental and molecular dynamics (MD) simulations. PU-modified asphalt was prepared using an in situ polymerization method. The high- and low-temperature properties of asphalt containing various PU contents were investigated via a series of laboratory tests. The asphalt molecular model, the PU molecular model, and the PU–asphalt mixes system were modeled using software. Based on reasonable models, the influence of PU content on the physical modulus and molecular motion of asphalt at high temperatures was researched using MD simulations. The glass transition temperature of PU-modified asphalt with different contents was obtained using software, and the free volume theory and molecular diffusion movement were used to interpret the improvement mechanism of PU content on the low-temperature performance of asphalt. The results indicate that PU effectively can improve the high- and low-temperature properties of asphalt. PU has a significant positive effect on the physical modulus of asphalt, and the effect becomes more significant with the increase of PU content. In addition, PU can form a tight structure with asphalt and increase the stability of the asphalt system. The free volume ensures the free movement of PU molecules in the asphalt, allowing PU to be dispersed homogeneously in the asphalt. However, the free volume decreases when the PU content exceeds 15% by weight, which limits the improvement of the low-temperature performance of asphalt. The results of molecular simulation can explain the enhancement mechanism of PU, providing a reference for the performance enhancement of PU-modified asphalt. [ABSTRACT FROM AUTHOR]

Engineering in vacuum or under a protective atmosphere permits the production of materials, wherever the absence of oxygen is an essential demand for a successful processing. However, very few studies have provided quantitative evidence of the effect of oxidized surfaces to tribological properties. In the current study on 99.99% pure copper, it is revealed that tribo-oxidation and the resulting increased abrasive wear can be suppressed by processing in an extreme high vacuum (XHV) adequate environment. The XHV adequate atmosphere was realized by using a silane-doped shielding gas (1.5 vol% SiH4 in argon). To analyse the influence of the ambient atmosphere on the tribological and mechanical properties, a ball—disk tribometer and a nanoindenter were used in air, argon, and silane-doped argon atmosphere for temperatures up to 800 °C. Resistance measurements of the resulting coatings were carried out. To characterize the microstructures and the chemical compositions of the samples, the scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD) were used. The investigations have revealed a formation of η-Cu3Si in silane-doped atmosphere at 300 °C, as well as various intermediate stages of copper silicides. At temperatures above 300 °C, the formation of γ-Cu5Si were detected. The formation was linked to an increase in hardness from 1.95 to 5.44 GPa, while the Young's modulus increased by 46% to 178 GPa, with the significant reduction of the wear volume by a factor of 4.5 and the suppression of further oxidation and susceptibility of chemical wear. In addition, the relevant diffusion processes were identified using molecular dynamics (MD) simulations. [ABSTRACT FROM AUTHOR]

Context: CL-20/DNDAP cocrystal is a promising new type of explosive with exceptional energy density and detonation parameters. However, compared to TATB, FOX-7 and other insensitive explosives, it still has higher sensitivity. In order to decrease the sensitivity of CL20/DNDAP cocrystal explosive, in this article, a CL20/DNDAP cocrystal model was established, and six different types of polymers, including butadiene rubber (BR), ethylene-vinyl acetate copolymer (EVA), polyethylene glycol (PEG), hydroxyl-terminated polybutadiene (HTPB), fluoropolymer (F2603), and polyvinylidene difluoride (PVDF), were added to the three cleaved surfaces of (1 0 0), (0 1 0) and (0 0 1) to obtain polymer-bonded explosives (PBXs). Predict the effects of different polymers on the stability, trigger bond length, mechanical properties, and detonation performance of PBXs. Among the six PBX models, CL-20/DNDAP/PEG model exhibited the highest binding energy and the lowest trigger bond length, indicating that CL-20/DNDAP/PEG model had the best stability, compatibility, and the least sensitivity. Furthermore, although the CL-20/DNDAP/F2603 model demonstrated superior detonation capabilities, it should be noted that this model displayed low levels of compatibility. Overall, CL-20/DNDAP/PEG model exhibited the superior comprehensive properties, thereby demonstrating that PEG is a more suitable binder option for PBXs based on the CL20/DNDAP cocrystal. Methods: The properties of CL-20/DNDAP cocrystal-based PBXs were predicted by molecular dynamics (MD) method under Materials Studio software. The MD simulation time step was set at 1fs and the total MD simulation time was 2ns. The Isothermal-isobaric (NPT) ensemble was used for the 2ns of MD simulation. The COMPASS force field was used, and the temperature was set at 295K. [ABSTRACT FROM AUTHOR]

Hydrophilic polymer coatings on artificial implants generate excellent tribological properties. The friction properties of polymer coatings are affected by salt ion factors. Herein, the atomic force microscopy (AFM) was used to show that the superlubricity was achieved between poly(vinylphosphonic acid) (PVPA)-modified Ti6Al4V and polystyrene (PS) microsphere probe lubricated with monovalent salt solutions (LiCl, NaCl, KCl, and CsCl). Considering that adhesion is an important cause of friction changes, the AFM was further utilized to obtain adhesion between friction pairs in different salt solutions. The results indicated that the larger the cation radius in the lubricant, the smaller the adhesion, and the lower the friction coefficient of the PVPA coating. The electrostatic interaction between the PVPA and one-valence cations in lubricants was analyzed by the molecular dynamics (MD) simulation as it was found to be the main influencing factor of the adhesion. Combined analysis results of friction and adhesion indicated that by adjusting the size of cation radius in lubricant, the adhesion between the tribo-pairs can be changed, and eventually the magnitude of friction can be affected. This study opens up a new avenue for analyzing the friction characteristics of hydrophilic polymer coatings from the perspective of intermolecular forces. [ABSTRACT FROM AUTHOR]

Ideal mixing between the asphalt and rejuvenator is the key to ensure the performance of the recycled asphalt mixture in hot in-place recycling. In this paper, the undetermined temperature and thermal parameters in the finite-element (FE) model of pavement were back calculated by the backward method of regression. The temperature field of the recycled asphalt layer after paving was obtained by FE simulation, and was applied to set the temperature in the subsequent molecular dynamics (MD) simulation. Molecular models of virgin asphalt, aged asphalt, and the representative rejuvenator components were applied to establish a three-layer model. New indicators were defined to analyze the interdiffusion between the virgin asphalt, aged asphalt, and rejuvenator, and the microstructure, interdiffusion, and interaction states between the asphalt and rejuvenator in the asphalt miscibility zone were analyzed. Results show that the parameter transferring from the macro FE simulated temperature field to the micro temperature setting of MD model is feasible. There is an obvious difference between the temperature fields on the surface and the inside hot in-place recycled asphalt layer during the cooling process, which causes different interaction and interdiffusion states between the asphalt and rejuvenator as well as the uneven performance of the recycled asphalt mixture. The effects of chain and aromatic rejuvenator on different interdiffusion and interaction indicators are different, so the combination of the two could have a better rejuvenation effect. The results can offer reference in aspects including prescreening the recycling temperature, the proportion of rejuvenator, virgin asphalt and aged asphalt, the rejuvenator component composition, and other parameters in hot in-place recycling. [ABSTRACT FROM AUTHOR]

The interface between asphalt and aggregate directly determines the performance of asphalt mixtures but unavoidable weaknesses can be easily found at the interfacial bonding region. In order to evaluate the interfacial adhesion behavior between asphalt and aggregate at the atomic scale, asphalt binders and two mineral aggregates (quartz and calcite) were selected to build molecular models and molecular dynamics (MD) simulations were conducted. The interfacial energy between asphalt and aggregate was calculated and the mineral aggregate has a more significant influence on the energy compared to the binder types. Also, the simulation result indicates that saturate, aromatic, resin, and asphaltene (SARA) components have different interfacial energies with respect to the aggregates. This result can also be derived from the relative concentration of SARA components on the aggregate surface. Additionally, oxidation of the asphalt binder results in increased interfacial energy due to the enhanced intermolecular bonding generated by oxidized functional groups. The intrusion of water greatly reduces the interfacial energy, but the energy increases under the coupling effect of oxidation and moisture, especially for calcite. The grey relational grade theory was conducted to evaluate the factors affecting the adhesive energy, and the results show that the energy of the asphalt-aggregate is more sensitive to the asphaltene index than other factors. [ABSTRACT FROM AUTHOR]

Abstract Engineering in vacuum or under a protective atmosphere permits the production of materials, wherever the absence of oxygen is an essential demand for a successful processing. However, very few studies have provided quantitative evidence of the effect of oxidized surfaces to tribological properties. In the current study on 99.99% pure copper, it is revealed that tribo-oxidation and the resulting increased abrasive wear can be suppressed by processing in an extreme high vacuum (XHV) adequate environment. The XHV adequate atmosphere was realized by using a silane-doped shielding gas (1.5 vol% SiH4 in argon). To analyse the influence of the ambient atmosphere on the tribological and mechanical properties, a ball—disk tribometer and a nanoindenter were used in air, argon, and silane-doped argon atmosphere for temperatures up to 800 °C. Resistance measurements of the resulting coatings were carried out. To characterize the microstructures and the chemical compositions of the samples, the scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD) were used. The investigations have revealed a formation of η-Cu3Si in silane-doped atmosphere at 300 °C, as well as various intermediate stages of copper silicides. At temperatures above 300 °C, the formation of γ-Cu5Si were detected. The formation was linked to an increase in hardness from 1.95 to 5.44 GPa, while the Young’s modulus increased by 46% to 178 GPa, with the significant reduction of the wear volume by a factor of 4.5 and the suppression of further oxidation and susceptibility of chemical wear. In addition, the relevant diffusion processes were identified using molecular dynamics (MD) simulations.

Copyright of Rare Metals is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Due to the unique properties of carbon nanotubes (CNTs), the electrical and thermal conductivity of CNT-modified polymeric composites (CNTMPCs) can be manipulated and depend on several factors. There are many factors that affect the thermal and electrical conductivity of CNTs and CNTMPCs, such as chirality, length, type of CNTs, fabrication, surface treatment, matrix and interfacial interaction between the matrix and reinforcement (CNTs). This paper reviews the research on molecular dynamics (MD) simulations of the effects of some factors affecting the thermal and electrical conductivity of CNTs and CNTMPCs. First, the chirality dependence of the thermal and electrical conductivity of single-walled carbon nanotubes (SWNTs) was analyzed. The effect of chirality on the conductivity of short-length CNTs is greater than that of long-length CNTs, and the larger the chiral angle, the greater the conductivity of the CNTs. Furthermore, the thermal and electrical conductivity of the zigzag CNTs is smaller than that of the armchair one. Therefore, as the tube aspect ratio becomes longer and conductivity increases, while the effect of chirality on the conductivity decreases. In addition, hydrogen bonding affects the electrical and thermal conductivity of the CNTMPCs. The modeling of SWNTs shows that the thermal and electrical conductivity increases significantly with increasing overlap length. MD simulations can be effectively used to design highly conductive CNTMPCs with appropriated thermal and electrical properties. Since there are too many factors affecting the thermal and electrical conductivity of CNTMPCs, this paper only reviews the effects of limited factors on the thermal and electrical conductivity of CNTs and CNTMPCs based on MD simulations, and further detailed studies are required. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Shanghai University / Shanghai Daxue Xuebao is the property of Journal of Shanghai University (Natural Sciences) Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Since May 2022, cases of monkeypox, a zoonotic disease caused by the monkeypox virus (MPXV), have been increasingly reported worldwide. There are, however, no proven therapies or vaccines available for monkeypox. In this study, several multi-epitope vaccines were designed against the MPXV using immunoinformatics approaches. Methods: Three target proteins, A35R and B6R, enveloped virion (EV) formderived antigens, and H3L, expressed on the mature virion (MV) form, were selected for epitope identification. The shortlisted epitopes were fused with appropriate adjuvants and linkers to vaccine candidates. The biophysical andbiochemical features of vaccine candidates were evaluated. The Molecular docking and molecular dynamics(MD) simulation were run to understand the binding mode and binding stability between the vaccines and Toll-like receptors (TLRs) and major histocompatibility complexes (MHCs). The immunogenicity of the designed vaccines was evaluated via immune simulation. Results: Five vaccine constructs (MPXV-1-5) were formed. After the evaluation of various immunological and physicochemical parameters, MPXV-2 and MPXV-5 were selected for further analysis. The results of molecular docking showed that the MPXV-2 and MPXV-5 had a stronger affinity to TLRs (TLR2 and TLR4) and MHC (HLA-A*02:01 and HLA-DRB1*02:01) molecules, and the analyses of molecular dynamics (MD) simulation have further confirmed the strong binding stability of MPXV-2 and MPXV-5 with TLRs and MHC molecules. The results of the immune simulation indicated that both MPXV-2 and MPXV-5 could effectively induce robust protective immune responses in the human body. Conclusion: The MPXV-2 and MPXV-5 have good efficacy against the MPXV in theory, but further studies are required to validate their safety and efficacy. [ABSTRACT FROM AUTHOR]

Protein fluorescence signals essential information about the conformational dynamics of proteins. Different types of intrinsic fluorophores reflect different protein local or global structural changes. Bovine Serum Albumin (BSA) is a transport protein that contains two intrinsic fluorophores: Tryptophan134 (Trp134) and Tryptophan213 (Trp213). This protein displays an interesting temperature dependence of the tryptophan fluorescence. However, the molecular mechanism of the temperature dependence is still unclear. In this work, we propose a generic rotamer model to explain this phenomenon. The model assumes the presence of rotamer‐specific fluorescence lifetimes. The fluorescence temperature dependence is caused by the population shifts between different rotamers due to thermal effects. As a proof of concept, we show that the tryptophan's two fluorescence lifetimes (휏1 = 0.4–0.5 ns and 휏2 = 2‐4 ns) are sufficient to qualitatively explain the fluorescence intensity change at different temperatures, both in buffer solution (water) and in the protein. To computationally verify our rotamer hypothesis, we use an all‐atom molecular dynamics simulation to study the effects of temperature on the two tryptophans' rotamer dynamics. The simulations show that Trp134 is more sensitive to temperature, consistent with experimental observations. Overall, the results support that the temperature dependence of fluorescence in the protein BSA is due to local conformational changes at the residue level. This work sheds light on the relationship between tryptophan's rotamer dynamics and its ability to fluorescence. [ABSTRACT FROM AUTHOR]

The molecular dynamics simulations based study of graphene (Gr) reinforced polymer nanocomposite (PNC) is a very intense research field due to the enormous range of possible applications involving such materials. Current review focuses on the reinforcing mechanisms behind the enhancement of the mechanical, thermal, and tribological properties of Gr-based PNC based on molecular dynamics (MD) simulations. It also reviews the capabilities of MD simulations to reproduce the experimentally measured materials properties and behaviour of Gr-based PNC. This review-based investigation summarizes the current literature of the MD simulation studies as well as comparisons for the tribo-thermo-mechanical properties of Gr-based PNC and identification of the suitable simulation protocols for model development, characterization, and mechanism analysis. The careful review of published MD simulation-based articles indicates that two important factors help to reproduce the experimentally measured materials properties and behaviour of Gr-based PNC. They are mainly (a) simulation models (material used for reinforcement, e.g. Gr and Gr derivatives) development and (b) simulation run parameters. In this review, details about those factors have been discussed keeping major consideration of Gr effect (e.g. shape or length, orientation, clustering, weight fraction, different layer, functionalization, and defective condition). Finally potential applications, current challenges and future prospects are discussed which can be useful to the research community. [ABSTRACT FROM AUTHOR]

Activated blood coagulation factor X (FXa) plays a critical initiation step of the blood-coagulation pathway and is considered a desirable target for anticoagulant drug development. It is reversibly inhibited by nonvitamin K antagonist oral anticoagulants (NOACs) such as apixaban, betrixaban, edoxaban, and rivaroxaban. Thrombosis is extremely common and is one of the leading causes of death in developed countries. In previous studies, novel thiourea and oxime ether isosteviol derivatives as FXa inhibitors were designed through a combination of QSAR studies and molecular docking. In the present contribution, molecular dynamics (MD) simulations were performed for 100 ns to assess binding structures previously predicted by docking and furnish additional information. Moreover, three thiourea- and six oxime ether-designed isosteviol analogs were then examined for their drug-like and ADMET properties. MD simulations demonstrated that four out of the nine investigated isosteviol derivatives, i.e., one thiourea and three oxime ether ISV analogs, form stable complexes with FXa. These derivatives interact with FXa in a manner similar to Food and Drug Administration (FDA)-approved drugs like edoxaban and betrixaban, indicating their potential to inhibit factor Xa activity. One of these derivatives, E24, displays favorable pharmacokinetic properties, positioning it as the most promising drug candidate. This, along with the other three derivatives, can undergo further chemical synthesis and bioassessment.

Abstract Hydrophilic polymer coatings on artificial implants generate excellent tribological properties. The friction properties of polymer coatings are affected by salt ion factors. Herein, the atomic force microscopy (AFM) was used to show that the superlubricity was achieved between poly(vinylphosphonic acid) (PVPA)-modified Ti6Al4V and polystyrene (PS) microsphere probe lubricated with monovalent salt solutions (LiCl, NaCl, KCl, and CsCl). Considering that adhesion is an important cause of friction changes, the AFM was further utilized to obtain adhesion between friction pairs in different salt solutions. The results indicated that the larger the cation radius in the lubricant, the smaller the adhesion, and the lower the friction coefficient of the PVPA coating. The electrostatic interaction between the PVPA and one-valence cations in lubricants was analyzed by the molecular dynamics (MD) simulation as it was found to be the main influencing factor of the adhesion. Combined analysis results of friction and adhesion indicated that by adjusting the size of cation radius in lubricant, the adhesion between the tribo-pairs can be changed, and eventually the magnitude of friction can be affected. This study opens up a new avenue for analyzing the friction characteristics of hydrophilic polymer coatings from the perspective of intermolecular forces.

BackgroundSince May 2022, cases of monkeypox, a zoonotic disease caused by the monkeypox virus (MPXV), have been increasingly reported worldwide. There are, however, no proven therapies or vaccines available for monkeypox. In this study, several multi-epitope vaccines were designed against the MPXV using immunoinformatics approaches.MethodsThree target proteins, A35R and B6R, enveloped virion (EV) form-derived antigens, and H3L, expressed on the mature virion (MV) form, were selected for epitope identification. The shortlisted epitopes were fused with appropriate adjuvants and linkers to vaccine candidates. The biophysical andbiochemical features of vaccine candidates were evaluated. The Molecular docking and molecular dynamics(MD) simulation were run to understand the binding mode and binding stability between the vaccines and Toll-like receptors (TLRs) and major histocompatibility complexes (MHCs). The immunogenicity of the designed vaccines was evaluated via immune simulation.ResultsFive vaccine constructs (MPXV-1-5) were formed. After the evaluation of various immunological and physicochemical parameters, MPXV-2 and MPXV-5 were selected for further analysis. The results of molecular docking showed that the MPXV-2 and MPXV-5 had a stronger affinity to TLRs (TLR2 and TLR4) and MHC (HLA-A*02:01 and HLA-DRB1*02:01) molecules, and the analyses of molecular dynamics (MD) simulation have further confirmed the strong binding stability of MPXV-2 and MPXV-5 with TLRs and MHC molecules. The results of the immune simulation indicated that both MPXV-2 and MPXV-5 could effectively induce robust protective immune responses in the human body.ConclusionThe MPXV-2 and MPXV-5 have good efficacy against the MPXV in theory, but further studies are required to validate their safety and efficacy.

Resistive random-access memory (ReRAM) consists of memristor cells which are the ideal alternative to embedded flash memory technology. The development of ReRAMs is dependent on the optimization of the memristor cells. In this research, lithium-doped barium titanate (Ba0.98Li0.02TiO2.99) as a memristor cell has been investigated via molecular dynamics simulation. The memristor characteristics of Ba0.98Li0.02TiO2.99, such as oxygen vacancies migration, the response under the DC and AC voltages, the hysteresis loop (I–V graph), and the resistance–voltage diagram (R–V graph) have been probed. The results indicate that the doped lithium ions lead to the free migration of oxygen vacancies, prevent the formation of cluster vacancies, and provide acceptable 0.54- and 0.46-eV diffusion and conductivity energy barriers, respectively, for oxygen ions. These energy barriers can decrease switching time, which helps develop memristor-based neuromorphic processors with fast switching times. The temperature in the range of 700–1600 K, and DC and AC voltages cannot cause the migration of the barium, titanium, and lithium ions. This causes only oxygen ions and their vacancies to perform the SET/RESET operations. The test of AC voltage bias indicates that the hysteresis loop area of Ba0.98Li0.02TiO2.99 is 5.8 times more than TiO(2-x). The R–V graph shows the clear SET/RESET operations by oxygen ions and their vacancies. The obtained results indicate the good potential of Ba0.98Li0.02TiO2.99 as a advanced memristor cell, and shows that it can be exploited as non-volatile resistance-switching memory and may increase the performance of ReRAMs. [ABSTRACT FROM AUTHOR]

The misfolding and mutation of Cu/Zn superoxide dismutase (SOD1) is commonly associated with amyotrophic lateral sclerosis (ALS). SOD1 can accumulate within stress granules (SGs), a type of membraneless organelle, which is believed to form via liquid–liquid phase separation (LLPS). Using wild‐type, metal‐deficient, and different ALS disease mutants of SOD1 and computer simulations, we report here that the absence of Zn leads to structural disorder within two loop regions of SOD1, triggering SOD1 LLPS and amyloid formation. The addition of exogenous Zn to either metal‐free SOD1 or to the severe ALS mutation I113T leads to the stabilization of the loops and impairs SOD1 LLPS and aggregation. Moreover, partial Zn‐mediated inhibition of LLPS was observed for another severe ALS mutant, G85R, which shows perturbed Zn‐binding. By contrast, the ALS mutant G37R, which shows reduced Cu‐binding, does not undergo LLPS. In addition, SOD1 condensates induced by Zn‐depletion exhibit greater cellular toxicity than aggregates formed by prolonged incubation under aggregating conditions. Overall, our work establishes a role for Zn‐dependent modulation of SOD1 conformation and LLPS properties that may contribute to amyloid formation. Synopsis: The formation of membraneless organelles, such as stress granules (SGs), is believed to occur through the process of liquid–liquid phase separation (LLPS). The amyotrophic lateral sclerosis (ALS) disease‐associated protein SOD1 is known to accumulate within SGs, but if it itself undergoes LLPS, and if this affects amyloid formation, is not well‐studied. The apo form of SOD1 undergoes LLPS.SOD1 LLPS and subsequent aggregation are regulated by a conformational transition between a disordered and a relatively compact folded state.The metal cofactor Zn prevents SOD1 LLPS via a conformational transition.SOD1 condensates show greater cytotoxicity than aggregates. [ABSTRACT FROM AUTHOR]

The interfacial interaction between carbon nanomaterial and the asphalt matrix plays a key role in the capacity for load transfer and the mechanical properties of asphalt-carbon nanocomposites. In this study, molecular dynamics (MD) simulation was used to explore the interfacial interaction between carbon nanomaterials and asphalt molecules. The microscopic interface characteristics were evaluated by scanning electron microscopy and atomic force microscopy. The high temperature properties of asphalt-carbon nanocomposites were studied by a dynamic shear rheometer. The results showed that carbon nanotubes (CNT) had the best compatibility with aromatics (minimum binding energy of 11.05kcal/mol), the second compatibility with saturate (minimum binding energy of 10.05 kcal/mol), and the lowest compatibility with asphaltene (maximum binding energy of 4.19 kcal/mol). The compatibility of graphene with the four components also follows the above rule, but graphene-asphaltene compatibility is better than CNT-asphaltene because the maximum binding energy of graphene-asphaltene is 4.63kcal/mol. CNT competes with asphaltene for nonpolar components, whereas graphene is encapsulated by asphaltene, which results in different interactions between CNT-asphalt and graphene-asphalt nanocomposites. However, neither CNT nor graphene changed the colloidal structure of asphalt. [ABSTRACT FROM AUTHOR]

The recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public health and the global economy. The resolved crystal structure of the main protease of SARS-CoV-2 or SCV2 (Mpro) has led to its identification as an attractive target for designing potent antiviral drugs. Herein, we provide a comparative molecular impact of hydroxychloroquine (HCQ), remdesivir, and β-D-N4-Hydroxycytidine (NHC) binding on SCV2 Mpro using various computational approaches like molecular docking and molecular dynamics (MD) simulation. Data analyses showed that HCQ, remdesivir, and NHC binding to SARS-CoV-2 Mpro decrease the protease loop capacity to fluctuate. These binding influences the drugs' optimum orientation in the conformational space of SCV2 Mpro and produce noticeable steric effects on the interactive residues. An increased hydrogen bond formation was observed in SCV2 Mpro–NHC complex with a decreased receptor residence time during NHC binding. The binding mode of remdesivir to SCV2 Mpro differs from other drugs having van der Waals interaction as the force stabilizing protein–remdesivir complex. Electrostatic interaction dominates in the SCV2 Mpro−HCQ and SCV2 Mpro–NHC. Residue Glu166 was highly involved in the stability of remdesivir and NHC binding at the SCV2 Mpro active site, while Asp187 provides stability for HCQ binding. [ABSTRACT FROM AUTHOR]

Solid-liquid synergistic lubrication, in combination with the advantages of solid and liquid lubrication, has gained the great popularity in recent years. However, the mechanism of solid-liquid synergetic lubrication is still unclear. In this paper, graphite and poly α-olefin base oil (PAO) were used as self-lubricating additives to evaluate their synergistic effect. The results show that the composites possess good mechanical and excellent tribological properties with a nanoindentation modulus of 3.8 GPa, a coefficient of friction of 0.0998, as well as a wear rate of 1.3 × 10−14 m3/N·m. Both transfer film and lubricating oil film exist on the friction interface, and the lubricating oil film protects the counter ball from excessive oxidation. At the same time, with combination of molecular dynamics (MD) simulation and first-principles calculations, the synergistic lubrication mechanism of graphite and PAO was manifested. PAO destroyed the interlayer structure of graphite, making it easier to form a transfer film on the counter ball surface. The weak chemical bond between graphite and PAO facilitates more PAO molecules to gather at the interface while forming the transfer film, which benefits the formation of lubricating oil film. The synergistic effect of graphite and PAO molecules is critical in promoting the further reduction of COF. [Display omitted] • The composites have good mechanical properties with the elastic modulus of 3.8 GPa. • The tribological properties is COF of 0.0998 and wear rate of 1.3 × 10−14 m3/N·m. • Both transfer film and lubricating oil film are identified on friction interface. • PAO destroys interlayer structure of graphite, facilitates transfer film formation. • Weak chemical bond between graphite and PAO benefits the formation of oil film. [ABSTRACT FROM AUTHOR]

[Display omitted] • Applicability of electro-coagulation as pretreatment for nanofiltration was evaluated. • The form of ferric ions releasing from anode depended on electro-coagulation current. • Residual microplastics provided microbial habitats and enhanced metabolites secretion. • Higher dehydration energy enabled Fe3+ to weave more porous cross-linked nets with humus. • Humic-Fe network caught unlinked pollutants and facilitated their deposition on membranes. The residue of microplastic in secondary effluent was inevitable with continuous aggravation on nanofiltration membrane fouling. Thus, this study aimed to further evaluate the applicability of electro-coagulation as pretreatment for improving the performance of a nanofiltration-oriented hybrid process during the reclamation of microplastic-contaminated secondary effluent. The electro-coagulation parameters were skillfully optimized and designed for following dynamic nanofiltration experiments. The potential influence of coagulants in different forms as well as their combined effects of microplastics on membrane fouling behaviors and pollutant rejection efficiency was distinguished. Specifically, terminal membrane permeability was reduced by 19% after 0.05 A electro-coagulation, while 0.2 A electro-coagulation almost eliminated the negative effects of microplastics. Mass transfer model analysis excluded the dominance of organic accumulation in the concentration polarization layer on membrane fouling development. Molecular dynamic (MD) simulation and egg-box model demonstrated that humic-Fe network possessed stronger bridging effects and greater porosity. This structure favored the co-deposition of other unlinked bacteria metabolites, which secretion was also facilitated by microplastics as immobilized carriers, on membrane surface. Additionally, density functional theory (DFT) calculation further confirmed that the greater demand for dehydration energy for ferric ions (1124 kcal/mol) inspired the formation of stronger humic-Fe complexes. Besides, residual microplastics in electro-coagulation effluent had different impacts on membrane rejection towards organic and inorganic pollutants, and it depended on the influenced cake-enhanced concentration polarization (CECP) by microplastic affinity with different pollutants. [ABSTRACT FROM AUTHOR]