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Polyethylene (PE) is susceptible to environmental stress cracking (ESC). In the presence of an amphiphilic compound and subjected to stress, ESC starts with cavitation followed by slow crack growth and ends with brittle fracture. In this study, we used molecular dynamics simulation to study how branch ends which were chemically modified with vinyl acetate groups affect free volume coalescence around an amphiphilic compound, nonyl ethoxylate (NE), dispersed in branched PE models. Branch ends modified with vinyl acetate significantly impact the free volume coalescence dynamics around NE. Compared with methyl branch ends, vinyl acetate branch ends show a much higher affinity, as quantified by the corresponding radial distribution functions, for the hydrophilic ethylene oxide-segment of NE. However, this is not the case for the hydrophobic ethylene-segment. Interestingly, vinyl acetate branch ends tend to reduce the power (amplitude) of the free volume size fluctuations around both the ethylene oxide- and ethylene-segments. Indeed, the powers of the fluctuations with different PE branching characteristics decrease with increasing vinyl acetate concentration. We believe that free volume coalescence leads to cavitation and that vinyl acetate branches could inhibit cavitation, thereby crack propagation in PE. The power results seem to be consistent with the experimental observation that the addition of copolymer ethylene vinyl acetate to low-density polyethylene improves the ESC resistance of the blend. Highlights * Vinyl acetate branches reduce free volume coalescence activities. * Vinyl acetate branches are attracted to the hydrophilic segment of NE. * Cavitation likely starts from the free volume coalescence around NE. KEYWORDS coalescence dynamics, environmental stress cracking, free volume, polyethylene, vinyl acetate branch ends, 1 | INTRODUCTION Polyethylene (PE) is a widely used polymer known for its excellent mechanical properties, chemical resistance, and durability. (1,2) However, polyethylene is susceptible to a phenomenon called environmental [...]

For catalytic reactions, temperature has a great influence on reaction rate and reaction mechanism. The oxidation processes of soot precursors (C6H6) at different temperatures are simulated using reactive force field molecular dynamics to investigate the effect of temperature on the oxidation process. The reaction products at different temperatures and the effect of temperature are discussed. The results show that the intermediate species C3 and C4 are more and existed longer at 1400 K than at 2000 K, while hardly existed at 2000 K, indicating that as the temperature increases, the oxidation reaction takes place more completely and the products formed are more stable. The effect of temperature on the oxidation mechanism is then explored; the results show that the main reaction pathway at 1400 K is basically the same as that at 2000 K, while the final product contains less hydrogen and more oxygen atoms at 2000 K. The C6 components with two, three, and four oxygen atoms are found easier to be decomposed at both 1400 and 2000 K. It shows that temperature mainly afects the catalytic reaction process by afecting the hydrogen and oxygen content of the decomposed C6 component. This may be helpful to understand the effect of temperature on the C6H6 oxidation from the perspective of basic research. Key words: temperature, soot precursors, catalytic reaction, oxidation mechanism, ReaxFF MD Dans le contexte des reactions catalytiques, la temperature a une grande influence sur la vitesse et le mecanisme de reaction. Nous avons simule les processus d'oxydation des precurseurs de suie (C6H6) a diferentes temperatures a l'aide de la dynamique moleculaire (MD pour molecular dynamics) dans le cadre de laquelle nous avons employe un potentiel de champ de force (FF pour force field) reactif (ReaxFF MD) afin d'etudier l'efet de la temperature sur le processus d'oxydation. Nous discutons des produits de reaction a diferentes temperatures et de l'efet de la temperature. Les resultats montrent que les especes intermediaires en C3 et en C4 ont ete produites en plus grande quantite et ont existe plus longtemps a 1400 K qu'a 2000 K, temperature a laquelle elles etaient pratiquement absentes. Nous pouvons conclure d'apres ces observations que lorsque la temperature augmente, la reaction d'oxydation procede de maniere plus complete et que le produit forme est plus stable. Nous avons ensuite explore l'efet de la temperature sur le mecanisme d'oxydation. Les resultats montrent que la voie de reaction principale a 1400 K est fondamentalement la meme qu'a 2000 K, mais que le produit final contient moins d'atomes d'hydrogene et plus d'atomes d'oxygene a 2000 K. On constate egalement que les composants en C6 contenant 2, 3 et 4 atomes d'oxygene sont plus faciles a decomposer tant a 1400 K qu'a 2000 K, et que la temperature influence le processus de reaction catalytique principalement en modifiant la teneur en hydrogene et en oxygene du composant en C6 decompose. Ces observations peuvent etre utiles pour comprendre l'efet de la temperature sur l'oxydation du C6H6 dans une perspective de recherche fondamentale. [Traduit par la Redaction] Mots-cles : temperature, precurseurs de suie, reaction catalytique, mecanisme d'oxydation, ReaxFF MD, 1. Introduction The oxidation mechanism of soot is an active topic in the field of combustion. Understanding the detailed oxidation process of soot not only is important from the fundamental [...]

The design of potent indoleamine 2,3-dioxygenase 1 (IDOl) enzyme inhibitors targeting immunopathic neuroinflammation has emerged as an area of interest for the treatment of Alzheimer's disease (AD); additionally, recent findings on the clinical benefits of antibodies preventing [beta]-amyloid (Aft) aggregation have renewed efforts to discover small molecule anti-aggregants targeting proteopathic protein misfolding. Exploiting an endogenous tryptophan-like scaffold, we describe the design and synthesis of small-molecule inhibitors of both immunopathic and proteopathic processes, thus presenting the possibility of single therapeutics acting simultaneously on multiple AD pathogeneses. Specifically, investigations on compounds that inhibit both IDOl (in human recombinant enzyme, transfected HEK293 cells, and interferon-[gamma] stimulated human microglia assays) and Aft aggregation (in thioflavin-T and biotinylated-A[beta] oligomeric assays) are presented. Five compounds have been identified with high potency against both targets, identifying (E)-3-styryl indoles as useful tool compounds for developing Alzheimer's therapeutics. Brain penetration of these compounds via passive diffusion or active transport was predicted using Blood-Brain Barrier Score and Brain Exposure Efficiency Score calculations, respectively; the effects of efflux (pgp, BCRP), and influx (OCT1, OCT2) transporters were similarly predicted. Structure-activity relationships were rationalised with molecular docking and molecular dynamics simulations, which also provide insights for future lead compound optimisation. Key words: Alzheimer's disease, tryptophan, IDO-1, amyloid-[beta], neuroinflammation, neuroimmunology La conception de puissants inhibiteurs de l'indoleamine 2,3 dioxygenase 1 (IDOl) ciblant la neuro-inflammation immunopathique constitue desormais un nouveau champ d'interet pour le traitement de la maladie d'Alzheimer (alzheimer). En outre, des donnees recentes sur les bienfaits cliniques des anticorps empechant l'agregation de la beta-amyloide (Aft) ont ravive les efforts visant a decouvrir de petites molecules antiagregantes qui ciblent le mauvais repliement proteopathique des proteines. En exploitant une structure endogene de type tryptophane, nous avons concu et synthetise des inhibiteurs a petite molecule qui ciblent a la fois les processus immunopathiques et proteopathiques, ouvrant ainsi la voie a des monotherapies agissant simultanement sur plusieurs processus pathogenes de l'alzheimer. En particulier, nous presentons des experiences portant sur des composes qui inhibent a la fois IDOl (dans des essais avec des enzymes recombinantes humaines, des cellules HEK293 transferees et des microglies humaines stimulees par 1'interferon [gamma]) et l'agregation de l'A[beta] (dans des essais de liaison avec la thioflavine-T et d'inhibition de l'oligomerisation de l'A[beta] biotinylee). Nous avons identifie cinq composes presentant une forte affinite pour les deux cibles, ce qui nous a permis de definir les (E) 3 styrylindoles comme des composes pouvant servir d'outils pour le developpement d'agents therapeutiques contre l'alzheimer. La penetration cerebrale de ces composes par diffusion passive ou transport actif a ete estimee a l'aide de calculs de l'indice penetration de la barriere hematoencephalique (<< Score BBB >>) et de l'indice d'efficacite de l'exposition cerebrale (<< Score BEE >>), respectivement. Les effets des transporteurs d'efflux (P gp, BCRP) et d'influx (OCT1, OCT2) ont ete egalement ete estimes par calculs. Nous avons rationalise les relations structure-activite a l'aide de simulations d'amarrage moleculaire et de dynamique moleculaire, qui fournissent egalement des informations pour roptimisation d'eventuels composes tetes de serie. [Traduit par la Redaction] Mots-cles : maladie d'Alzheimer, tryptophane, IDOl, beta-amyloide, neuro-inflammation, neuro-immunologie, Introduction The neuropathology of Alzheimer's disease (AD) involves the brain's innate and adaptive immune systems, resulting in a complex inflammatory state that involves not only aggregation of [beta]-amyloid (Aft) and [...]

Partial molar volumes of amino acids in their zwitterionic and molecular forms were calculated using molecular dynamics simulations of these systems in aqueous solutions. Calculations performed with the TIP4P, SPC (rigid and flexible), SPC/E, and polarizable water models showed that the choice of water model can have a significant impact on the calculated volumes. The effect of treatment of long-range electrostatic interactions on the calculated results was also investigated. The volumes obtained in simulations with a properly chosen water model fit well the experimental data for both molecular and zwitterionic forms of amino acids. Key words: partial molar volume, amino acids, molecular dynamics, water models Nous avons calcule les volumes molaires partiels d'acides amines sous leurs formes zwitterioniques et moleculaires a l'aide de simulations de dynamique moleculaire de ces systemes en solution aqueuse. Les calculs effectues avec les modeles TIP4P, SPC (rigide et flexible) et SPC/E et le modele d'eau polarisable montrent que le choix du modele d'eau peut avoir un effet substantiel sur les volumes calcules. Nous avons egalement etudie l'effet de la prise en compte des interactions electrostatiques a longue portee sur les resultats calcules. Les volumes obtenus avec les simulations a l'aide d'un modele d'eau judicieusement choisi correspondent bien aux donnees experimentales pour les formes moleculaires et zwitterioniques des acides amines. [Traduit par la Redaction] Mots-cles : volume molaire partiel, acides amines, dynamique moleculaire, modeles d'eau, Introduction Volumetric properties of biological molecules have drawn a significant interest of researchers, (1) particularly in the context of studies of folding kinetics using the pressure jump technique. (2) However, [...]

Nuclear magnetic resonance (NMR) spectroscopy allows the determination of atomic-level information on intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ('in-cell') or those focused on characterizing molecules or events at the cell surface ('on-cell'). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution- and solid-state NMR and survey studies that have used these techniques to uncover key information. In particular, we focus on the application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs) and receptor tyrosine kinases. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Interestingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically relevant information through on-cell NMR. We also provide a brief survey of the applicability of on-cell NMR approaches to other classes of cell surface molecules. Key words: NMR spectroscopy, ligand-receptor interactions, intact cells, atomic-level characterization, biophysics. La spectroscopie par résonance magnétique nucléaire (RMN) permet d'obtenir des informations à l'échelle atomique en matière d'interactions intermoléculaires, de structure moléculaire et de dynamique moléculaire dans l'environnement cellulaire. On peut distinguer les études axées sur l'obtention d'informations moléculaires détaillées dans le contexte intracellulaire (<< dans la cellule >>) et celles axées sur la caractérisation des molécules ou des événements à la surface de la cellule (<< sur cellule >>). Dans cette synthèse, les auteurs exposent certaines des principales techniques de RMN appliquées aux études de RMN sur cellule à travers la RMN tant à l'état de solution qu'à l'état solide, et passent en revue les études qui ont utilisé ces techniques pour obtenir des informations essentielles. Ils se concentrent en particulier sur l'application de la spectroscopie RMN sur cellule pour caractériser les interactions entre les ligands et les protéines membranaires de la surface cellulaire, comme les récepteurs couplés aux protéines G (RCPG), les récepteurs à tyrosine kinase, etc. Ces techniques permettent de quantifier les affinités de liaison, de réaliser des essais de liaison compétitive, de délimiter les portions de ligands impliquées dans la liaison, de déterminer la conformation de l'état lié du ligand, d'évaluer la structuration et la dynamique des récepteurs et de déduire les contraintes de distance caractéristiques de l'état lié ligand-récepteur. Il est intéressant de noter qu'il est possible d'éviter les obstacles liés à la production et à la purification des protéines membranaires tout en obtenant des informations directement pertinentes sur le plan physiologique grâce à la RMN sur cellule. Ils présentent également une étude plus succincte de l'applicabilité des approches de RMN sur cellule à d'autres classes de molécules de la surface cellulaire. [Traduit par la Rédaction] Mots-clés : spectroscopie RMN, interactions ligand-récepteur, cellules intactes, caractérisation à l'échelle atomique, biophysique., Introduction Membrane proteins account for ~26% of the human proteome (Fagerberg et al. 2010). This class of proteins includes a wide variety of cell surface receptors that mediate communication and [...]

In this study, the mechanical performance of polyurethane (PU)-modified asphalt was investigated. To this end, the molecular dynamics method was adopted to study the influence of the PU modifier on the compatibility, mechanical properties, and structure of asphalt. Using the Materials Studio software, a four-component molecular model of asphalt, a PU molecular model, and an asphalt-PU mixed system model were constructed, and the molecular density and glass transition temperature ([T.sub.g]) were used to verify the performance of the aforementioned models. Molecular dynamics simulations of the three molecular models were conducted under different temperatures, and the solubility parameter ([delta]), interaction energy, mechanical properties, and radial distribution functions (RDFs) were obtained. The results showed that at 413.15 K (140[degrees]C), the difference between the solubility parameters of the asphalt and PU molecules ([DELTA][delta]) is the smallest, and their interaction reaches the most optimal phase state. The effects of the PU modifier on the Young's modulus, bulk modulus, and shear modulus of asphalt were studied. Finally, the RDF analysis showed that the PU modifier has a direct effect on the degree of swelling and dispersion between the aromatic-aromatic and saturate-saturate components in the asphalt, reducing the aggregation of both molecules. This verifies the PU modification effect. KEYWORDS mechanical properties, molecular dynamics, polyurethane-modified asphalt, 1 | INTRODUCTION Bridge expansion joints (PJs) are structural separation joints that are typically set between the top beam ends of piers and platforms, as well as in back walls [...]