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Highly oriented and crystalline polyetheylene (PE) fibers have a large failure stress under rapid tensile loading but exhibit significant creep at much smaller stresses that limits applications. A possible mechanism is slip of chains due to stress-enhanced, thermally activated nucleation of dislocations at chain ends in crystalline regions. Molecular dynamics simulations are used to parameterize a Frenkel–Kontorova model that provides analytic expressions for the limiting stress and activation energy for dislocation nucleation as a function of stress. Results from four commonly used hydrocarbon potentials are compared to show that the qualitative behavior is robust and estimate quantitative uncertainties. In all cases, the results can be described by an Eyring model with values of the zero-stress activation energy E a 0 ≈ 1.5 eV and activation volume V* ≈ 45 Å3 that are consistent with the experimental results for increasingly crystalline materials. The limiting yield stress is ∼8 GPa. These results suggest that activated dislocation nucleation at chain ends is an important mechanism for creep in highly oriented PE fibers. [ABSTRACT FROM AUTHOR]

Biochars are an exciting class of environmental materials with a wide range of applications, including carbon storage and sequestration, soil enhancement, and pollution remediation. However, the limited knowledge of their molecular structures and compositions and the lack of comprehensive understanding of the relationship between these structures and biochars' diverse functionality, is hindering advancements in their development. In this work, we further advance the approach, first introduced by Wood et al. (2023), to constructing biochar molecular models; and now include control of microporosity (pores ≤ 2 nm size) within the developed models. We construct biochar models representative of woody biochars which are experimentally produced at 600–650 ° C highest heating temperatures. Our models reproduce experimental H/C and O/C atomic ratios, percentage aromatic carbon, true density, cumulative porosity, and pore size distribution. The development of microporous biochar molecular models allows us to identify the importance of chemical structures involved in the assembly of biochar materials, and describe the relationship between these structures and obtained micropores. To facilitate other researchers integrating our approach into their work, we detail the steps taken, including the tests and reasons for each decision, in the construction of the biochar models. Furthermore, we share our developed molecular models in a format that can be easily integrated into other group's work in the form of molecular dynamics simulations. • Molecular models of biochar with controlled pore volumes and pore size distribution. • Models truthful to experimental H/C, O/C, aromaticity, true density and microporosity. • Identification of structural moieties within biochar – key to supporting micropores. [ABSTRACT FROM AUTHOR]

Enterovirus-D68 (EV68) has emerged as a global health concern over the last decade with severe symptomatic infections resulting in long-lasting neurological deficits and death. Unfortunately, there are currently no FDA-approved antiviral drugs for EV68 or any other non-polio enterovirus. One particularly attractive class of potential drugs are small molecules inhibitors, which can target the conserved active site of EV68-3C protease. For other viral proteases, we have demonstrated that the emergence of drug resistance can be minimized by designing inhibitors that leverage the evolutionary constraints of substrate specificity. However, the structural characterization of EV68-3C protease bound to its substrates has been lacking. Here, we have determined the substrate specificity of EV68-3C protease through molecular modeling, molecular dynamics (MD) simulations, and co-crystal structures. Molecular models enabled us to successfully characterize the conserved hydrogen-bond networks between EV68-3C protease and the peptides corresponding to the viral cleavage sites. In addition, co-crystal structures we determined have revealed substrate-induced conformational changes of the protease which involved new interactions, primarily surrounding the S1 pocket. We calculated the substrate envelope, the three-dimensional consensus volume occupied by the substrates within the active site. With the elucidation of the EV68-3C protease substrate envelope, we evaluated how 3C protease inhibitors, AG7088 and SG-85, fit within the active site to predict potential resistance mutations. [ABSTRACT FROM AUTHOR]

[Display omitted] • Non-idealities at the solid/liquid interface obtained from molecular simulations. • Molecular dynamics simulations maintain a constant solution composition. • NaCl(aq) at graphite and at NaCl(s) surfaces displays asymmetric ion adsorption. • Asymmetric adsorption induces an electric potential at the solid/liquid interface. Solid/liquid interfaces control various processes of technological relevance in the process industry and many fundamental physicochemical phenomena. This work examines the link between the atomistic description of mass transfer at solid/liquid interfaces out of equilibrium and constitutive mass transfer equations which are typically used to model these processes at the mesoscale. In our analyses we discuss the microscopic inconsistencies apparent in simplified models of mass transfer whenever non-idealities dominate the liquid phase in the proximity of solid/liquid interfaces. Using C μ MD – a molecular simulation technique to investigate out-of-equilibrium, concentration-driven processes with pseudo open-boundary conditions – we outline a strategy to capture and quantify non-idealities induced by specific interactions between the solid surface and molecules in the fluid phase. We demonstrate our approach by studying electrolyte solutions in technologically important, multi-component systems where the introduction of a solid/liquid interface induces substantial deviations in the composition and electrochemical properties locally compared to the bulk fluid phase. To this aim, we analyse NaCl(aq) solutions in contact with (i) the graphite basal surface and (ii) {100} NaCl(s) crystalline surfaces. We uncover the tendency of the sodium cation to preferentially adsorb at the surfaces considered, which induces local violations of electroneutrality that leads to the emergence of an electric potential in the fluid phase at the solid/liquid interface. [ABSTRACT FROM AUTHOR]

This work evaluates four popular 3-site water models, TIP3P, SPC/E, SPC, and F3C, in predicting temperature-dependent O2 diffusion and dissolution and self-diffusion in liquid water for electrochemical devices, such as fuel cells, electrolyzers and metal-air batteries, using molecular dynamics simulations. We report that the TIP3P and SPC models overestimate O2 diffusivity, though qualitatively describe its temperature dependence, while the SPC/E and F3C models show a good prediction of O2 diffusivity with the former accurately predicting its activation energy. The TIP3P, SPC, and F3C models overestimate the O2 solubility with the TIP3P even incorrectly predicting its temperature dependence. The SPC/E model shows the best performance in predicting both the O2 diffusivity (<15% error) and solubility (<16% error) in the temperature range. The radial distribution functions of O atoms are present and show that lower peaks, i.e. more intermolecular space among water molecules for the random walks, leads to higher prediction of diffusivities. Comparison with literature experimental data is summarized. [ABSTRACT FROM AUTHOR]

A set of molecular models for the alkali nitrates (LiNO3, NaNO3, KNO3, RbNO3, and CsNO3) in aqueous solutions is presented and used for predicting the thermophysical properties of these solutions with molecular dynamics simulations. The set of models is obtained from a combination of a model for the nitrate anion from the literature with a set of models for the alkali cations developed in previous works of our group. The water model is SPC/E and the Lorentz–Berthelot combining rules are used for describing the unlike interactions. This combination is shown to yield fair predictions of thermophysical and structural properties of the studied aqueous solutions, namely the density, the water activity and the mean ionic activity coefficient, the self-diffusion coefficients of the ions, and radial distribution functions, which were studied at 298 K and 1 bar; except for the density of the solutions of all five nitrates and the activity properties of solutions of NaNO3, which were also studied at 333 K. For calculating the water the activity and the mean ionic activity coefficient, the OPAS (osmotic pressure for the activity of selvents) method was applied. The new models extend an ion model family for the alkali halides developed in previous works of our group in a consistent way. [ABSTRACT FROM AUTHOR]

In this study, we constructed molecular friction models for polytetrafluoroethylene (PTFE)/graphene composites with various defect ratios to represent their different wear stages and simulated their friction processes under different load conditions. The friction and wear mechanisms were revealed by analyzing the variations in their molecular architectures and energies during friction. The results indicate that the friction coefficient decreased with increasing load. When the load was constant, the friction coefficients of the composites containing defections were resemble, indicating that they remained unchanged in the different wear stages. The composite wear continued to increase during friction. However, the wear increment decreased gradually. In addition, by analyzing the changes in MSD, wear can be divided into initial, stable, and accelerated wear stages. Highlights: Construct PTFE/Gr molecular models to represent their different wear stages.Simulate the dynamic changes of PTFE/Gr molecular structure during friction.The influence of PTFE/Gr dynamic structural changes was revealed.Reveal the normal force variation from an energy perspective. [ABSTRACT FROM AUTHOR]

This study employed molecular dynamics simulation to investigate the mechanism of action of graphene-modified asphalt. A series of molecular models of graphene-modified asphalt were constructed and validated using thermodynamic parameters. The impact of the graphene (PGR) size and number of layers on its interaction with asphalt components were examined, and the self-healing process and mechanism of action of PGR-modified asphalt were analyzed. The results demonstrated that the size and number of layers of PGR significantly influenced its interaction with asphalt components, with polar components demonstrating a stronger affinity for PGR. When the size and number of layers of PGR were held constant, the interfacial binding energy between it and ACR-modified asphalt was the highest, followed by SBS-modified asphalt, and 70# matrix asphalt exhibited the lowest interfacial binding strength. This interfacial binding strength is primarily attributed to intermolecular van der Waals interactions. Furthermore, the incorporation of multi-layer PGR can markedly enhance the mechanical properties of matrix asphalt, whereas small-sized PGR is more efficacious in improving the low-temperature performance of polymer-modified asphalt. PGR can act as a bridge between asphalt molecules through rapid heat transfer and π-π stacking with aromatic ring-containing substances, which markedly increases the free diffusion ability of asphalt molecules, shortens the healing time of asphalt, and enhances the collective self-healing performance of asphalt. This study provides an essential theoretical basis for understanding the mechanism and application of PGR in asphalt modification. [ABSTRACT FROM AUTHOR]

Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an important role in the stabilization of complex. Interestingly, it was observed from the equilibrated structures of dendrimer-drug complexes at low pH that encapsulated drug molecules in the G4 PAMAM(NH2) formed cluster, while in the case of nontoxic G4 PAMAM(Ac) they were uniformly distributed inside the dendritic cavities. Thus, the latter dendrimer is suggested to be suitable nanovehicle for the delivery of Ntg. This computational analysis highlighted the importance of realistic molecular models of dendrimer-drug complexes (1:n) in order to obtain reliable results. [ABSTRACT FROM AUTHOR]

In this work, the solid–liquid coexistence curves of classical fully flexible atomistic models of α‐RDX and β‐HMX were calculated using thermodynamically rigorous methodologies that identify where the free energy difference between the phases is zero. The free energy difference between each phase at a given state point was computed using the pseudosupercritical path (PSCP) method, and Gibbs–Helmholtz integration was used to evaluate the solid–liquid free energy difference as a function of temperature. This procedure was repeated for several pressures to determine points along the coexistence curve, which were then fit to the Simon–Glatzel functional form. While effective, this method is computationally expensive. An alternative approach is to compute the melting point at a single pressure via the PSCP method, and then use the Gibbs–Duhem integration technique to trace out the coexistence curve in a more computationally economical manner. Both approaches were used to determine the coexistence curve of α‐RDX. The Gibbs–Duhem integration method was shown to generate a melt curve that is in good agreement with the PSCP‐derived melt curve, while only costing ∼10 % of the computational resources used for the PSCP method. For α‐RDX, the predicted melting temperature increases significantly more for a given increase in pressure when compared to available experimental data. [ABSTRACT FROM AUTHOR]

Investigation of new active therapeutic drugs against the emerging drug‐resistant Mycobacterium tuberculosis is a current medical and health challenge. Based on previously reported isoxazole‐based molecules that have a potent effect against Mycobacterium tuberculosis, computational methods were used in the current study to investigate the effect of isoxazole‐based molecules as a potential active drug‐resistant drug Mycobacterium tuberculosis H37Rv. Molecular models of isoxazole‐based molecules were established by 3D‐QSAR study, and different results were interpreted to propose 6 candidate agents more active than the previously reported compounds in the literature. Also, the candidate structures are more active than the therapeutic drug agent Isoniazid (NIH) against Mycobacterium Tuberculosis. Evaluation of the synthetic accessibility coefficient and the Lipinski properties of newly designed agent candidates indicate that these agents meet the criteria of a drug according to the Lipinski and Veber rules because they can be synthesized. In‐silico evaluation of ADMETox properties shows satisfactory results for most newly designed agent candidates. According to molecular docking, the drug candidates have a high score with a stable docked pose in the receptor (PDB code: 5v3y) compared to Isoniazid (NIH). The DFT and molecular dynamics study confirmed the previous results of 3D‐QSAR and molecular docking models. [ABSTRACT FROM AUTHOR]

We derive a systematic and general method for parameterizing coarse-grained molecular models consisting of anisotropic particles from fine-grained (e.g., all-atom) models for condensed-phase molecular dynamics simulations. The method, which we call anisotropic force-matching coarse-graining (AFM-CG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarse-grained and fine-grained phase-space distributions to derive equations for the coarse-grained forces, torques, masses, and moments of inertia in terms of properties of a condensed-phase fine-grained system. We verify the accuracy and efficiency of the method by coarse-graining liquid-state systems of two different anisotropic organic molecules, benzene and perylene, and show that the parameterized coarse-grained models more accurately describe properties of these systems than previous anisotropic coarse-grained models parameterized using other methods that do not account for finite-temperature and many-body effects on the condensed-phase coarse-grained interactions. The AFM-CG method will be useful for developing accurate and efficient dynamical simulation models of condensed-phase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids. [ABSTRACT FROM AUTHOR]

Xinjiang’s representative asphalt binders, such as Karamay and Tahe asphalt, lack sufficient research on warm-mix additive modification effects. Given their unique microstructure and molecular composition differences, comprehensive investigations are essential for a nuanced understanding of these binders. This study added Sasobit and Evotherm warm mix additives to Karamay 90# asphalt and Tahe 90# asphalt, respectively. The evaluation of diverse warm mix additives’ impact on diverse asphalt binders involved viscosity, softening point, penetration tests, Fourier transform infrared (FTIR) and analysis of saturate, aromatic, resin, and asphaltene (SARA) fractions. Additionally, molecular models of asphalt were constructed using Materials Studio software, based on the SARA test data. Molecular models of Sasobit and Evotherm were also developed, representing organic wax and a cationic quaternary ammonium surfactant, respectively. Conducting molecular dynamics simulations of warm mix additives and two asphalt molecules yielded valuable insights into solubility parameters and the radial distribution function (RDF). This approach enabled a thorough and comparative exploration of the modification mechanisms employed by various warm mix additives on different asphalt types at a molecular scale. The results indicate that, Evotherm excelled in enhancing high-temperature asphalt performance, while Sasobit surpassed it in low-temperature. The viscosity reduction by Sasobit proved more effective for K90, while for T90 asphalt, the trend was reversed with Evotherm exhibiting superior performance. The solubility parameter in MD simulations consistently correlates with asphalt viscosity results. Sasobit showed enhanced compatibility with K90 asphalt, while T90 asphalt demonstrated greater suitability for modification with Evotherm. [ABSTRACT FROM AUTHOR]

Nicotinic acetylcholine receptors (nAChRs) are drug targets for neurological diseases and disorders, but selective targeting of the large number of nAChR subtypes is challenging. Marine cone snail α‐conotoxins are potent blockers of nAChRs and some have been engineered to achieve subtype selectivity. This engineering effort would benefit from rapid computational methods able to predict mutational energies, but current approaches typically require high‐resolution experimental structures, which are not widely available for α‐conotoxin complexes. Herein, five mutational energy prediction methods were benchmarked using crystallographic and mutational data on two acetylcholine binding protein/α‐conotoxin systems. Molecular models were developed for six nAChR subtypes in complex with five α‐conotoxins that were studied through 150 substitutions. The best method was a combination of FoldX and molecular dynamics simulations, resulting in a predictive Matthews Correlation Coefficient (MCC) of 0.68 (85 % accuracy). Novel α‐conotoxin mutants designed using this method were successfully validated by experimental assay with improved pharmaceutical properties. This work paves the way for the rapid design of subtype‐specific nAChR ligands and potentially accelerated drug development. [ABSTRACT FROM AUTHOR]

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The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behave correctly and consistently with, e.g., available higher-resolution simulation data and/or experimental observables. Automatic data-driven approaches are increasingly used to develop accurate models for molecular dynamics simulations. However, the parameters obtained via such automatic methods often make use of specifically designed interaction potentials and are typically poorly transferable to molecular systems or conditions other than those used for training them. Using a multi-objective approach in combination with an automatic optimization engine (SwarmCG), here, we show that it is possible to optimize CG models that are also transferable, obtaining optimized CG force fields (FFs). As a proof of concept, here, we use lipids for which we can avail reference experimental data (area per lipid and bilayer thickness) and reliable atomistic simulations to guide the optimization. Once the resolution of the CG models (mapping) is set as an input, SwarmCG optimizes the parameters of the CG lipid models iteratively and simultaneously against higher-resolution simulations (bottom-up) and experimental data (top-down references). Including different types of lipid bilayers in the training set in a parallel optimization guarantees the transferability of the optimized lipid FF parameters. We demonstrate that SwarmCG can reach satisfactory agreement with experimental data for different resolution CG FFs. We also obtain stimulating insights into the precision-resolution balance of the FFs. The approach is general and can be effectively used to develop new FFs and to improve the existing ones. [ABSTRACT FROM AUTHOR]

The voltage-gated potassium channel KCNQ1 (KV7.1) assembles with the KCNE1 accessory protein to generate the slow delayed rectifier current, IKS, which is critical for membrane repolarization as part of the cardiac action potential. Loss-of-function (LOF) mutations in KCNQ1 are the most common cause of congenital long QT syndrome (LQTS), type 1 LQTS, an inherited genetic predisposition to cardiac arrhythmia and sudden cardiac death. A detailed structural understanding of KCNQ1 is needed to elucidate the molecular basis for KCNQ1 LOF in disease and to enable structure-guided design of new anti-arrhythmic drugs. In this work, advanced structural models of human KCNQ1 in the resting/closed and activated/open states were developed by Rosetta homology modeling guided by newly available experimentally-based templates: X. leavis KCNQ1 and various resting voltage sensor structures. Using molecular dynamics (MD) simulations, the capacity of the models to describe experimentally established channel properties including state-dependent voltage sensor gating charge interactions and pore conformations, PIP2 binding sites, and voltage sensor–pore domain interactions were validated. Rosetta energy calculations were applied to assess the utility of each model in interpreting mutation-evoked KCNQ1 dysfunction by predicting the change in protein thermodynamic stability for 50 experimentally characterized KCNQ1 variants with mutations located in the voltage-sensing domain. Energetic destabilization was successfully predicted for folding-defective KCNQ1 LOF mutants whereas wild type-like mutants exhibited no significant energetic frustrations, which supports growing evidence that mutation-induced protein destabilization is an especially common cause of KCNQ1 dysfunction. The new KCNQ1 Rosetta models provide helpful tools in the study of the structural basis for KCNQ1 function and can be used to generate hypotheses to explain KCNQ1 dysfunction. [ABSTRACT FROM AUTHOR]

Abstract: For years, conventional drug design at G-protein coupled receptors (GPCRs) has mainly focused on the inhibition of a single receptor at a usually well-defined ligand-binding site. The recent discovery of more and more physiologically relevant GPCR dimers/oligomers suggests that selectively targeting these complexes or designing small molecules that inhibit receptor–receptor interactions might provide new opportunities for novel drug discovery. To uncover the fundamental mechanisms and dynamics governing GPCR dimerization/oligomerization, it is crucial to understand the dynamic process of receptor–receptor association, and to identify regions that are suitable for selective drug binding. This minireview highlights current progress in the development of increasingly accurate dynamic molecular models of GPCR oligomers based on structural, biochemical, and biophysical information that has recently appeared in the literature. In view of this new information, there has never been a more exciting time for computational research into GPCRs than at present. Information-driven modern molecular models of GPCR complexes are expected to efficiently guide the rational design of GPCR oligomer-specific drugs, possibly allowing researchers to reach for the high-hanging fruits in GPCR drug discovery, i.e. more potent and selective drugs for efficient therapeutic interventions. [Copyright &y& Elsevier]

Molecular dynamics simulations were performed to determine two-phase configurations of model propane molecules below the critical point and in the near-critical, two-phase region. A postprocessor that uses a Monte Carlo method for determination of volumes attributable to each molecule was used to obtain density histograms of the particles from which the bulk coexisting equilibrium vapor and liquid densities were determined. This method of analyzing coexisting densities in a two-phase simulation is straightforward and can be easily implemented for complex, multisite models. Various degrees of internal flexibility in the propane models have little effect on the coexisting densities at temperatures 40 K or more below the critical point, but internal flexibility (angle bending and bond vibrations) does affect the saturated liquid densities in the near-critical region, changing the critical temperature by approximately 20 K. Shorter cutoffs were also found to affect the phase dome and the location of the critical point. [ABSTRACT FROM AUTHOR]

Molecular simulations are currently receiving significant attention for their ability to offer a microscopic perspective that explains macroscopic phenomena. An essential aspect is the accurate characterization of molecular structural parameters and the development of realistic numerical models. This study investigates the surface morphology and elemental distribution of silicon nitride fibers through TEM and EDS, and SEM and EDS analyses. Utilizing a customized molecular dynamics approach, molecular models of amorphous and multi-interface silicon nitride fibers with complex structures were constructed. Tensile simulations were conducted to explore correlations between performance and molecular structural composition. The results demonstrate successful construction of molecular models with amorphous, amorphous–crystalline interface, and mixed crystalline structures. Mechanical property characterization reveal the following findings: (1) The nonuniform and irregular amorphous structure causes stress concentration and crack formation under applied stress. Increased density enhances material strength but leads to higher crack sensitivity. (2) Incorporating a crystalline reinforcement phase without interfacial crosslinking increases free volume and relative tensile strength, improving toughness and reducing crack susceptibility. (3) Crosslinked interfaces effectively enhance load transfer in transitional regions, strengthening the material's tensile strength, while increased density simultaneously reduces crack propagation. [ABSTRACT FROM AUTHOR]

The goal of this work was to use molecular dynamics (MD) simulations to build amorphous surface layers of polypropylene (PP) and cellulose and to inspect their physical and interfacial properties. A new method to produce molecular models for these surfaces was developed, which involved the use of a “soft” confining layer comprised of a xenon crystal. This method compacts the polymers into a density distribution and a degree of molecular surface roughness that corresponds well to experimental values. In addition, calculated properties such as density, cohesive energy density, coefficient of thermal expansion, and the surface energy agree with experimental values and thus validate the use of soft confining layers. The method can be applied to polymers with a linear backbone such as PP as well as those whose backbones contain rings, such as cellulose. The developed PP and cellulose surfaces were characterized by their interactions with water. It was found that a water nanodroplet spreads on the amorphous cellulose surfaces, but there was no significant change in the dimension of the droplet on the PP surface; the resulting MD water contact angles on PP and amorphous cellulose surfaces were determined to be 106 and 33°, respectively. [ABSTRACT FROM AUTHOR]

Three molecular models, commonly used in the simulation of polymeric solutions and melts were employed to describe the rheological behaviour of dilute, elastic and constant viscosity solution formed by bead-and-bond chain molecules immersed into a soft-sphere solvent. The intermolecular interactions for the three models were calculated by the Lennard-Jones potential. The differences amongst the models proceeded from the intramolecular restrictions: the simplest one is a Freely-Joined-Chain (FJC) model with harmonic bond potentials, in the second model bonds are restricted by a finite extensible non-linear elastic (FENE) potential plus a repulsive WCA potential, and the third model is conformed by the United Atom (UA) approach which includes bond, flexion and torsion potentials. Both Couette and Poiseuille flows were simulated using Non-Equilibrium Molecular Dynamics. Deformation displayed by the three chain models; defined in terms of their radius of gyration was calculated and according to results it was found that for Couette flow, the three chains exhibit similar response to deformation. In Poiseulle flow, the FJC and FENE models behave similarly but the UA model presents a larger resistance to deformation. For both flow regimes, the forces involved to deform the chains were estimated in terms of the first normal stress differences. From these estimations it was found that the UA model depicted the stiffest chain, followed by the FENE model, and last the FJC model. [ABSTRACT FROM PUBLISHER]

In the molecular dynamics study of short-pulsed laser processing of semiconductors, potential models capable of describing the atomistic behavior during high electronic excitations is the most critical issue at the current stage. This study of the molecular dynamics adopts the Tersoff-potential model to analyze the ultrafast laser processing of silicon. The model was modified to include electronic excitation effects by reducing the attraction of the antibonding state by half. It offers an excellent description of the experimental behavior during nonthermal melting. Subpicosecond melting is achieved above certain threshold levels of superheating and carrier density as required in experiments. Energy conservation is demonstrated with a bandgap energy of the order obtained in experiments. The modification of the potential mimics an absorption of bandgap energy and a subsequent lattice heating on a time scale within 0.3 ps. The melting kinetics establishes a correlation between nonthermal melting and thermal bulk melting. For superheating of less than two, the electronic melting of bond softening proceeds via homogeneous nucleation. The associated thermal theory, corrected with a limit on the nucleus radius to bond length, is still valid for the higher superheating regime. The original Tersoff model shows that this superheating by a factor of two is isothermal for spallation—the lowest-energy ablative mechanism. Its proximity to the evaporating point suggests the role of thermal boiling during spallation. [ABSTRACT FROM AUTHOR]

In the previous work of Cotton and Miller [J. Chem. Phys. 145, 144108 (2016)], an improved symmetrical quasi-classical (SQC) windowing model for the molecular dynamics treatment of electronically non-adiabatic processes was developed in order to extend the original SQC approach to the regime of weak-coupling between the electronic states. The improved SQC model—based on triangular-shaped window functions—handled the weak-coupling limit as intended and, as a bonus, was shown to be universally superior to the original square/histogram SQC windowing model over all coupling regimes, but only for treating systems of two electronic states, as no higher-dimensional generalization was evident. This paper, therefore, provides a generalized version for treating an arbitrary number of electronic states. By construction, the benefits of the two-state triangle model—seamless treatment of weak-coupling and improved accuracy in all coupling regimes—carry over to the generalized version. Far more significant, however, is that the new model provides vastly improved windowing statistics in higher dimensions, enabling the SQC simulation of electronically non-adiabatic processes involving many more relevant electronic states than was previously practical. Capabilities are demonstrated with respect to a 24 pigment trimer model of the Fenna-Matthews-Olson light-harvesting complex, as well as treating similar 48- and 96-electronic state model problems, illustrating the scaling properties of the new method. [ABSTRACT FROM AUTHOR]

Explores possible molecular models of voltage sensor structure and motion to understand how voltage-sensor rearrangements drive the pore domain gates to open and close. Voltage-gated ion channels; Rotation of the S4 transmembrane segment during activation; Axial translation of S4 relative to the gating canal. [ABSTRACT FROM AUTHOR]

Abstract: This report presents evidence that ibuprofen interacts with red cell membranes as follows: a) in scanning electron microscopy (SEM) studies on human erythrocytes induced shape changes at a concentration as low as 10μM; b) in isolated unsealed human erythrocyte membranes (IUM) induced mild increase in the water content or in their molecular dynamics at the hydrophobic–hydrophilic interphase, while a corresponding ordering decrease at the deep phospholipids acyl chain level; c) at physiological temperature (37°C), 300μM ibuprofen induced a significant increase in the generalized polarization (GP) of dimyristoylphosphatidylcholine (DMPC) large unilamellar vesicles (LUV), an indication that ibuprofen molecules locate in the head polar group region of DMPC; d) X-ray diffraction studies showed that ibuprofen concentrations≥300μM induced increasing structural perturbation to DMPC bilayers; e) differential scanning calorimetry (DSC) data showed that ibuprofen was able to alter the cooperativity of DMPC phase transition in a concentration-dependent manner, to destabilize the gel phase and that ibuprofen did not significantly perturb the organization of the lipid hydrocarbon chains. Additionally, the effect on the viability of both human promyelocytic leukemia HL-60 and human cervical carcinoma HeLa cells was studied. [Copyright &y& Elsevier]

In the present study, coarse‐grained (CG) molecular models of carbon nanotubes (CNTs) strengthened vulcanized natural rubber (VNR) composites are constructed to systematically investigate the effects of length, inter‐tube cross‐linking, and polymer‐grafting of CNTs on the stress–strain behavior of VNR composites under uniaxial tension. The interfacial CG force field between CNTs and VNR is derived via the energy matching approach. The results demonstrate that increasing the length of CNTs is able to effectively enhance the mechanical performance of VNR composites, and the reinforcing efficiency increases gradually and tends to stabilize with increasing CNT length. Moreover, the cross‐linking and polymer‐grafting of CNTs are also effective approaches to significantly enhance the mechanical performance of VNR composites. The enhancement mechanism of CNTs is interpreted from the perspective of CNT networks, VNR networks, CNT‐VNR interface networks, and the interfacial load‐transfer behavior. Specifically, the dispersion of CNTs, the orientation of CNTs and VNR molecular chains, and the wrapping and interlocking behaviors between CNTs and the VNR matrix reveal a detailed structure‐mechanics relationship of CNTs‐reinforced VNR composites at the molecular level. These findings present theoretical instruction for the structural design of high‐performance rubber composites. Highlights: A coarse‐grained model of carbon nanotube‐natural rubber composites is built.The composite network structures are quantitatively characterized.The length, cross‐linking, and grafting effects of carbon nanotubes are studied.The reinforcement mechanisms of carbon nanotubes are revealed. [ABSTRACT FROM AUTHOR]

Herewith, an overview of the group's collaborative research efforts on the development and deployment of computational approaches to understand materials and tools at different length and time scales is presented. The techniques employed range from quantum mechanical approaches based on the density functional theory to classical atomistic and coarse‐grained force field methods, targeting molecular systems composed of a few to several million atoms at different levels of detail. These new tools and molecular models are presented to the computational materials science community so they can be used in more realistic molecular modelling studies of the properties of materials and their dependence on subtle modifications of their structures. The review concludes by presenting a selection of recent computational case‐studies oriented toward the understanding of the synthesis of materials, the interpretation of unexpected experimental results, the prediction of material properties, and the materials selection based on their characteristics for applications in areas such as gas adsorption/separation, corrosion protection, and catalysis. [ABSTRACT FROM AUTHOR]

Recently published molecular models of two-centre Lennard­Jones plus pointquadrupole type for pure fluids are used for the quantitative description of vapour-liquid equilibria of 28 binary mixtures. The unlike interactions are described with a modified Lorentz­Berthetol combining rule that contains one binary interaction parameter in the energetic term. A recently published simple and efficient procedure is used to adjust the binary interaction parameter to a single experimental vapour pressure of the binary mixture. Vapour-liquid equilibria from these molecular models for binary mixtures are in good agreement with experimental data also at state points faraway from those used for the parameter fit. Vapour-liquid equilibria of ternary mixtures are predicted reliably on that basis. [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 In this work two Sodium Dodecyl Sulphate (SDS) molecular models are proposed; one based on the Explicit-Atom (EA) approach while the other on the United-Atom (UA) approach. A SDS aqueous solution was simulated using the TIP4P/ ε potential for water. With the EA model the micellar aggregate spent less than 1 ns of simulation time to be formed. This is a quite low simulation time compared to the 23 ns spent by existing SDS models to attain the same micellar formation. When both proposed models are compared, micellar formation from EA model is 10 times faster than the UA model. The time reduction is due to the implementation of two repulsive sites in the carbon atoms on the hydrophobic tails. To validate the models, density, radial distribution functions, radius of gyration and shear viscosity were calculated; results were in good agreement with those reported in literature. Graphical Abstract Highlights • Two molecular models of the SDS surfactant in aqueous solutions are proposed. • A 95% in the micelle time formation by using molecular simulation is attained. • The structure of the micelle formed agrees with reported works. • The flow curve exhibits a well-defined Newtonian and a viscous thinning area. [ABSTRACT FROM AUTHOR]

Abstract This study was aimed at elucidating the molecular mechanisms of the interaction of the antitumor alkylphospholipid drug miltefosine with human erythrocytes (RBC) and molecular models of its membrane. The latter consisted of bilayers of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), representative of phospholipid classes located in the outer and inner monolayers of the human erythrocyte membrane, respectively. X-ray results showed that the drug interacted with DMPC multilayers; however, no effects on DMPE were detected. The experimental findings obtained by differential scanning calorimetry (DSC) indicated that miltefosine altered the thermotropic behavior of both DMPC and DMPE vesicles. Fluorescence spectroscopy evidenced an increase in the fluidity of DMPC vesicles and human erythrocyte membranes. Scanning electron microscopy (SEM) observations on human erythrocytes showed that miltefosine induced morphological alterations to RBC from its normal biconcave to an echinocyte type of shape. These results confirm that miltefosine interacts with the outer moiety of the human erythrocyte membrane affecting the cell morphology. Graphical abstract Unlabelled Image Highlights • Miltefosine interacted with the human erythrocyte membrane. • The drug increased the fluidity of human erythrocyte ghosts. • Miltefosine changed the shape of erythrocytes forming echinocytes. • Effects on erythrocytes occurred with very low drug concentrations. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) implicit-solvent potentials are developed for tetra-polyethylene glycol (PEG) at different water concentrations using the iterative Boltzmann inversion (IBI) technique. The resulting potentials are used to study the swelling and tensile properties of tetra-PEG gels at various swelling degrees φm. Two types of network topologies are considered, one 'ideal' with a defect-free diamond connectivity and the other 'realistic' as simulated from an experimentally based cross-linking process. Equilibrium swelling results for the realistic Tetra-PEG networks are consistent with available experimental data, while those for the ideal tetra-PEG networks exhibit much larger swelling. The realistic networks have higher Young's modulus Em at the same φm than ideal networks due to the presence of trapped entanglements. Uniaxial deformation results of realistic networks show that Em increases with degree of swelling, in accord with experimental results. The Young's moduli of gels at different φm confirm that the CG potentials developed by IBI are most suited to predict swelling states commensurate with the φm values at which the potentials were calibrated. A more generic, coarser potential, based on matching the persistence length of atomistic PEG chains in water, is able to produce a similar swelling behavior of an ideal diamond network. [ABSTRACT FROM AUTHOR]

The interactions of the polar chemical bonds such as C=O and N–H with an external electric field were investigated, and a linear relationship between the QM/MM interaction energies and the electric field along the chemical bond is established in the range of weak to intermediate electrical fields. The linear relationship indicates that the electrostatic interactions of a polar group with its surroundings can be described by a simple model of a dipole with constant moment under the action of an electric field. This relationship is employed to develop a general approach to generating an electrostatic energy-based charge (EEC) model for molecules containing single or multiple polar chemical bonds. Benchmark test studies of this model were carried out for (CH3)2–CO and N-methyl acetamide in explicit water, and the result shows that the EEC model gives more accurate electrostatic energies than those given by the widely used charge model based on fitting to the electrostatic potential (ESP) in direct comparison to the energies computed by the QM/MM method. The MD simulations of the electric field at the active site of ketosteroid isomerase based on EEC demonstrated that EEC gave a better representation of the electrostatic interaction in the hydrogen-bonding environment than the Amber14SB force field by comparison with experiment. The current study suggests that EEC should be better suited for molecular dynamics study of molecular systems with polar chemical bonds such as biomolecules than the widely used ESP or RESP (restrained ESP) charge models. [ABSTRACT FROM AUTHOR]

Molecular models of pristine graphene (GN) and GN with Thrower–Stone–Wales (TSW) defect-reinforced polymethyl methacrylate (PMMA) composites were established. The pure PMMA matrix was developed as a benchmark to study the effect of TSW defective GN (TSW-GN) on the glass transition temperature (Tg) of PMMA composites based on molecular dynamics simulations. The Tg values of these composites were obtained by fitting the scatter plots of the temperature versus the specific volume of the models. The results showed that the introduction of TSW defects can effectively increase the Tg of the PMMA composites. Additionally, the Tg of the PMMA composites gradually increased with an increase in TSW defects on the GN surface. The interaction energy between the TSW-GN and PMMA matrix, the density distribution of PMMA, the mean square displacements of the PMMA chains, and the free volume of these models were analyzed to understand the internal mechanisms with respect to the variations in the Tg from an atomic perspective. It can be concluded that the appropriate introduction of TSW-GN can improve the upper limit of the applied temperature of PMMA composites. In addition, guidance for the use of TSW-GN in different application environments of polymer composites was proposed. [ABSTRACT FROM AUTHOR]