Radius Of Gyration Research Articles

Experimental Investigation and Computational Insights of Enhanced Rheological Stability of Water-Based Drilling Fluids by Microspherical Polymers

Summary 3D bulk polymer, as an alternative to linear polymer, has exhibited large potential in formulating high-performance water-based drilling fluids. Understanding the mechanism behind the enhanced rheological stability of drilling fluids by microspherical polymers is critical for designing and developing new high-performance drilling fluids. In this work, we conducted a pioneering investigation that integrated experimental techniques with computational modeling, to explore the enhancement mechanism involved in the targeted drilling fluids. Inverse emulsion polymerization experiments were first carried out to fabricate the microspherical polymer acrylic acid (AA), acrylamide (AM), and 2-acryloylamino-2-methyl-1-propanesulfonic acid [P(AA-AM-AMPS)], and then physicochemical properties of microspherical polymer were characterized. Subsequently, the performance of drilling fluids with microspherical polymer as an additive was systematically evaluated. Finally, molecular simulations were used to investigate the characteristics of chemical active sites, molecular conformation, and structural variation at various temperatures. The results showed that the final microspherical polymer has a core-shell structure, with an average size of 198.3 nm and a molecular weight of 6.2×106 g/mol. The 3D structure exhibits good thermal stability, and thermal decomposition occurs above 220°C. The drilling fluids formulated with the microspherical polymer showed better rheological stability in the medium-low (4–65°C) and medium-ultrahigh (40–240°C) temperature ranges, compared with the relevant drilling fluids with the parallel linear polymer. Analyses on electrostatic potentials (ESPs) and frontier molecular orbital (FMO) revealed that active groups within the confined sphere domain mainly include carbonyl C = O and amide -CO(NH2). Additionally, these active groups exhibit a hierarchical distribution in the outer molecular region. Analyses on the radius of gyration (Rg) and the radial distribution function g(r) further validated the core-shell structure of microspherical polymer and its temperature-resistant stability. Moreover, a new self-consistent structural compensation model was proposed to rationalize the structure-activity relationship of microspherical polymer in drilling fluids. The computational results align well with the experimental findings. This pioneering work will provide valuable information for both the synthesis of new functional additives and the formulation of tailored-performance drilling fluids.

Understanding scholar-trajectories across scientific periodicals

Despite the rapid growth in the number of scientific publications, our understanding of author publication trajectories remains limited. Here we propose an embedding-based framework for tracking author trajectories in a geometric space that leverages the information encoded in the publication sequences, namely the list of the consecutive publication venues for each scholar. Using the publication histories of approximately 30,000 social media researchers, we obtain a knowledge space that broadly captures essential information about periodicals as well as complex (inter-)disciplinary structures of science. Based on this space, we study academic success through the prism of movement across scientific periodicals. We use a measure from human mobility, the radius of gyration, to characterize individual scholars' trajectories. Results show that author mobility across periodicals negatively correlates with citations, suggesting that successful scholars tend to publish in a relatively proximal range of periodicals. Overall, our framework discovers intricate structures in large-scale sequential data and provides new ways to explore mobility and trajectory patterns.

D-Glucosamine is a Potential Urease Inhibitor from Middle Eastern Medicinal Plants for Combatting Helicobacter Pylori Infections; a Molecular Docking and Simulation Approach.

Helicobacter pylori stands as a significant risk factor for both peptic and stomach ulcers. Their resistance to the highly acidic host environment primarily stems from their capability to produce urease, an enzyme that rapidly converts urea into NH3 and CO2. These byproducts are crucial for the bacterium's survival under such harsh conditions. Given the pivotal role of medicinal plants in treating various ailments with minimal side effects, there is an urgent need for a natural drug that can effectively eliminate H. pylori by inhibiting urease. Hence, the current study aims to identify the most potent urease inhibitor among the natural compounds found in Middle Eastern medicinal plants, taking into consideration factors such as optimal affinity, drug-like properties, pharmacokinetic characteristics, and thermodynamic attributes. In total, 5599 ligand conformers from 151 medicinal plants were subjected to docking against the urease's active site. The top-ranking natural compounds, as determined by their high docking scores, were selected for further analysis. Among these compounds, D-glucosamine (PubChem code 439,213) exhibited the most interactions with the crucial amino acid residues in the urease's active site. Furthermore, D-glucosamine demonstrated superior absorption, distribution, metabolism, excretion, and toxicity properties compared to other top-ranked candidates. Molecular dynamics simulations conducted over 100 nanoseconds revealed stable root mean square deviations and fluctuations of the protein upon complexation with D-glucosamine. Additionally, the radius of gyration and solvent-accessible surface area values for the D-glucosamine-urease complex were notably lower than those observed in other typical urease-inhibitor complexes. In conclusion, this study provides valuable insights into the potential development of D-glucosamine as a novel urease inhibitor. This promising compound holds the potential to serve as an effective drug for combating H. pylori infections in the near future.

A coupled DEM-CFD analysis of asphaltene particles agglomeration in turbulent pipe flow

We performed numerical investigations of the agglomeration behaviour of asphaltene particles in a turbulent pipe flow by using a commercial discrete element modelling (DEM) software, EDEM, coupled with a computational fluid dynamics (CFD) software package, FLUENT, in four-way coupling. We describe the particle–particle and particle–wall interactions to the Hertz–Mindlin approach extended with the Johnson–Kendall–Roberts contact force model. The very small size of asphaltene particles, however, requires minor time steps resulting in excessively long computing times. To reduce the latter, we developed a novel scaling method in which (a) the value of the shear modulus is reduced while the non-dimensional Cohesion number is kept constant by also reducing the value of the interfacial energy, and (b) the values of the friction parameters are adapted. We calibrated our scaling method by means of two tests, viz. the stop distance of a single particle sliding and rolling over a flat surface, and a common angle of repose test, both for particles 100 and 60 µm in size. As a result, we were able to increase both the Rayleigh time step and the DEM time step by a factor of 25. The eventual DEM/CFD simulations for 5 µm particles in a turbulent pipe flow still took almost 4 months on a 48 cores workstation. They resulted in visualisations and in quantitative data on, among other things, number and size (gyration radius) of agglomerates, their fractal dimension, and a coordination number, all as a function of time.

Predicting Ion Sequestration in Charged Polymers with the Steepest-Entropy-Ascent Quantum Thermodynamic Framework.

The steepest-entropy-ascent quantum thermodynamic framework is used to investigate the effectiveness of multi-chain polyethyleneimine-methylenephosphonic acid in sequestering rare-earth ions (Eu3+) from aqueous solutions. The framework applies a thermodynamic equation of motion to a discrete energy eigenstructure to model the binding kinetics of europium ions to reactive sites of the polymer chains. The energy eigenstructure is generated using a non-Markovian Monte Carlo model that estimates energy level degeneracies. The equation of motion is used to determine the occupation probability of each energy level, describing the unique path through thermodynamic state space by which the polymer system sequesters rare-earth ions from solution. A second Monte Carlo simulation is conducted to relate the kinetic path in state space to physical descriptors associated with the polymer, including the radius of gyration, tortuosity, and Eu-neighbor distribution functions. These descriptors are used to visualize the evolution of the polymer during the sequestration process. The fraction of sequestered Eu3+ ions depends upon the total energy of the system, with lower energy resulting in greater sequestration. The kinetics of the overall sequestration are dependent on the steepest-entropy-ascent principle used by the equation of motion to generate a unique kinetic path from an initial non-equilibrium state.

Dimensions of Cellulose Nanocrystals from Cotton and Bacterial Cellulose: Comparison of Microscopy and Scattering Techniques.

Different microscopy and scattering methods used in the literature to determine the dimensions of cellulose nanocrystals derived from cotton and bacterial cellulose were compared to investigate potential bias and discrepancies. Atomic force microscopy (AFM), small-angle X-ray scattering (SAXS), depolarized dynamic light scattering (DDLS), and static light scattering (SLS) were compared. The lengths, widths, and heights of the particles and their respective distributions were determined by AFM. In agreement with previous work, the CNCs were found to have a ribbon-like shape, regardless of the source of cellulose or the surface functional groups. Tip broadening and agglomeration of the particles during deposition cause AFM-derived lateral dimensions to be systematically larger those obtained from SAXS measurements. The radius of gyration determined by SLS showed a good correlation with the dimensions obtained by AFM. The hydrodynamic lateral dimensions determined by DDLS were found to have the same magnitude as either the width or height obtained from the other techniques; however, the precision of DDLS was limited due to the mismatch between the cylindrical model and the actual shape of the CNCs, and to constraints in the fitting procedure. Therefore, the combination of AFM and SAXS, or microscopy and small-angle scattering, is recommended for the most accurate determination of CNC dimensions.

Nanoparticles insertion and dimerization in polymer brushes.

Molecular dynamics simulations are conducted to systematically investigate the insertion of spherical nanoparticles (NPs) in polymer brushes as a function of their size, strength of their interaction with the polymers, polymer grafting density, and polymer chain length. For attractive interactions between the NPs and the polymers, the depth of NPs' penetration in the brush results from a competition between the enthalpic gain due to the favorable polymer-NP interaction and the effect of osmotic pressure resulting from displaced polymers by the NP's volume. A large number of simulations show that the average depth of the NPs increases by increasing the strength of the interaction strength. However, it decreases by increasing the NPs' diameter or increasing the polymer grafting density. While the NPs' effect on the polymer density is local, their effect on their conformations is long-ranged and extends laterally over length scales larger than the NP's size. This effect is manifested by the emergence of laterally damped oscillations in the normal component of the chains' radius of gyration. Interestingly, we found that for high enough interaction strength, two NPs dimerize in the polymer brush. The dimer is parallel to the substrate if the NPs' depth in the brush is shallow. However, the dimer is perpendicular to the substrate if the NPs' are deep in the brush. These results imply that polymer brushes can be used as a tool to localize and self-assemble NPs in polymer brushes.

Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers

A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known.

Fractional Extended Diffusion Theory to capture anomalous relaxation from biased/accelerated molecular simulations.

Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586-599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head-tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes.

Structural insights into non-hotspot KRAS mutations and their potential as targets for effective cancer therapies

Kirsten rat sarcoma virus protein (KRAS) is a protein that plays a central role in signal transduction using extracellular signal regulated kinase (ERK) and mitogen activated protein kinase (MAPK) cellular signaling pathway. KRAS is a frequently mutated oncogene and plays a pivotal role in tumor initiation and progression. Hotspot mutations on codon 12, 13 and 61 in KRAS are well-known for their role in drug resistance and non-hotspot mutations also play a significant part in contributing to resistance mechanisms. The understanding of how these non-hotspot mutations might affect the signal transduction of KRAS and their contribution towards drug resistance is understudied. Here we provide structural insights into the interaction of non-hotspot KRAS mutants with GTP (the native ligand) using a molecular docking and molecular dynamics simulation approach. Extensive molecular docking and simulation studies suggest that non-hotspot mutations (E31D and E63K) show stable interaction with native ligand using all five trajectories, as evidenced by root mean square of distance (RMSD), root mean square of fluctuation (RMSF), radius of gyration (RoG), coulomb short-range energy and MMGBSA analysis. These results suggest that non-hotspot mutations do not undermine the oncogenic nature of KRAS. This observation is consistent with previous findings where overexpressing E31D and E63K mutations share phenotypic features with G12D and G13D transfected cells, including increased proliferative capacity, actin cytoskeleton organization, and migration rates. We further test whether FDA-approved KRAS inhibitors sotorasib and adagrasib successfully inhibit the E31D and E63K mutants. Results suggest that these two non-hotspot mutants can be inhibited by both drugs with following trend of structural stability (E31D > E63K > wild-KRAS > Q61H > G12C). Based on sharp coherence in trajectories between wild KRAS and non-hotspot mutants, it is suggested that these novel mutants do not contribute to drug resistance mechanism. Overall, we provide a comprehensive understanding of the impact of non-hotspot mutations on KRAS and their potential as targets for effective cancer therapies. Communicated by Ramaswamy H. Sarma

In-silico analysis of potential anticancer drug for NEK7 and PPP1CA proteins overexpressed in pancreatic ductal adenocarcinoma

NIMA-related kinase 7 (NEK7) and phosphoprotein phosphatase-1 catalytic subunit alpha (PPP1CA) are the most common proteins overexpressed in pancreatic ductal adenocarcinoma, which is the most common type of pancreatic cancer. The goal of the current study was to identify a possible NEK7 and PPP1CA therapeutic inhibitor. For this investigation, 5000 compounds were retrieved from the IMPPAT library of phytochemicals, which were docked with our respective target proteins. Also, a reference compound, gemcitabine, which is a Food and Drug Administration (FDA) approved drug, was docked with the target proteins. The binding energy of the reference compound for both the targeted proteins was −6.5 kcal/mol. The common ligand with the lowest binding energy for both targets is boeravinone B (PubChem ID: 14018348) with −9.2 kcal/mol of NEK7 and −7.6 kcal/mol for PPP1CA. The compound was further investigated through density function theory (DFT) and molecular dynamic simulation analysis. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and hydrogen bonding analysis indicated the stability of the boeravinone B with the target proteins (NEK7 and PPP1CA). Communicated by Ramaswamy H. Sarma

Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CLPro and PLPro) by Molecular Docking and Dynamic Simulation Studies.

We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.

Comparison of Polypentenamer and Polynorbornene Bottlebrushes in Dilute Solution.

Bottlebrush (BB) polymers were synthesized via grafting-from-atom transfer radical polymerization (ATRP) of styrene on polypentenamer and polynorbornene macroinitiators with matched grafting density (n g = 4) and backbone degrees of polymerization (122 ≥ N bb ≥ 61) to produce a comparative study on their respective dilute solution properties as a function of increasing side chain degree of polymerization (116 ≥ N sc ≥ 5). The grafting-from technique produced near quantitative grafting efficiency and narrow dispersity N sc as evidenced by spectroscopic analysis and ring closing metathesis depolymerization of the polypentenamer BBs. The versatility of this synthetic approach permitted a comprehensive survey of power law expressions that arise from monitoring intrinsic viscosity, hydrodynamic radius, and radius of gyration as a function of increasing the molar mass of the BBs by increasing N sc. These values were compared to a series of linear (nongrafted, N sc = 0) macroinitiators in addition to linear grafts. This unique study allowed elucidation of the onset of bottlebrush behavior for two different types of bottlebrush backbones with identical grafting density but inherently different flexibility. In addition, grafting-from ATRP of methyl acrylate on a polypentenamer macroinitiator allowed the observation of the effects of graft chemistry in comparison to polystyrene. Differences in the observed scaling relationships in dilute solution as a function of each of these synthetic variants are discussed.

Investigation on the structural and dynamical properties of cationic, anionic, and catanionic niosomes as multifunctional controlled drug delivery system for cabozantinib

BackgroundNiosomes are versatile nanocarriers for therapeutic compounds, and optimizing their structures via ionic surfactants can enhance their functionality considerably. Catanionic niosomes, which have the capability of both cationic and anionic niosomes, are attractive vehicles for drug delivery objectives. Here, we aim to design and evaluate catanionic niosome as a vehicle for anticancer agents. MethodsA molecular modeling pipeline was performed to model the physicochemical properties of cationic, anionic, and catanionic niosomes as a multifunctional drug delivery system for Cabozantinib. SPAN60 was used as the nonionic surfactant, cholesterol was the stabilizer, DOTAP and DCP were used as the cationic and anionic surfactants, respectively, and cabozantinib, an FDA-approved c-Met inhibitor was chosen as the drug compound. Some meaningful parameters relevant to the cabozantinib molecule and its characteristics in the bilayer, such as hydrogen bonding, total energy, the radius of gyration (Rgyr), mean square displacements (MSD), diffusion coefficient, and the radial distribution function (RDF) were evaluated and compared between the formulations. ResultsThe outcomes revealed that hydrogen bonding of cabozantinib is more probable with DOTAP, and the total energy of the drug is lower in anionic formulation (-180 kcal/mol). The MSD showed that cationic niosome restricts the movement of cabozantinib, while the drug could be efficiently released from the anionic niosome, and catanionic niosome can equilibrate the movement of the drug with a diffusion coefficient of 5.73 × 10−12 (m2/s). ConclusionsThis technique could effectively describe the behavior of drugs in various bilayer compositions, and the catanionic niosomes are potential multifunctional carriers for anticancer agents.

A Theoretical Study To Understand the Impact of Mpro of nCoV on the Hormones

AbstractAmidst the unprecedented 2019 coronavirus outbreak and the substantial loss of lives due to the scarcity of information about the virus and lack of viable drugs, understanding the impact of the nCoV Main Protease (Mpro) on the endocrine system has emerged as a critical topic to pursue. This study explores the potential interactions between four key hormones (cortisol, cortisone, estradiol, and estrone) and the Mpro of nCoV using various in‐silico methodologies. Density Functional Theory (DFT) calculations scrutinized the electron density delocalization of these hormones. Through molecular docking, the molecular‐level binding of Mpro of nCoV with these hormones was studied, revealing cortisol as the hormone exhibiting the most promising binding affinity (−100.05 kcal/mol). Furthermore, molecular dynamics (MD) simulations, emulating human body conditions at distinct temperatures, were employed to study the implications of these interactions. The study analysed the various trajectories such as root mean square deviation (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg), and H‐bond trajectories to understand the potential impact on biological systems. The findings demonstrate the binding potential of the Mpro of nCoV with these hormones, raising plausible concerns regarding consequential physiological changes within the human body.

Dimension and Flexibility of Polystyrenesulfonate Chains in Methanol-Water.

The influence of the relative permittivity of the solvent medium on the single-chain dimension and flexibility of sodium polystyrenesulfonate chains has been investigated in mixed solvent media of methanol and water using viscosity experiments. Particular attention has been paid to explore the effect of the added low-molar-mass electrolyte. The root-mean-square (rms) radii of gyration of the chains in the unperturbed state have been calculated by applying the Flory model, while the intrinsic persistence lengths by the Benoit-Doty equation on the basis of the Kratky-Porod worm-like chain model. Estimation of the expansion factors for the rms radius of gyration, and the electrostatic persistence length helps evaluate the rms radii of gyration and the total persistence length of polystyrenesulfonate chains in the presence of varying amount of the supporting electrolyte. The polyion chains are highly extended at low ionic strengths but exhibit coil-like behavior with small persistence lengths when an excess of the supporting electrolyte is added in all the methanol-water mixtures investigated. Specifically, in the investigated solvent media, the polystyrenesulfonate chains have been found to shrink by ∼63-65% in the θ-state from their expanded conformation in the presence of 0.0001 mol L-1 NaCl. The chain dimensions pass through a maximum as the medium becomes richer in methanol, which could be explained by the formation and breakup of internal rings involving the polyion chain and water and/or methanol molecules. The intrinsic persistence length of sodium polystyrenesulfonate in a methanol-water mixture containing 0.1 mole fraction of methanol is ca. 1.3 times that in a medium with 0.3 mole fraction of methanol, indicating that flexibility of the polyion depends appreciably on the relative permittivity of the medium.

Unpacking urban scaling and socio-spatial inequalities in mobility: Evidence from England

Prior research on the scaling of city size and inequality has a primary focus on economic factors such as income. Limited research has addressed socio-spatial disparities in mobility, involving physical activities and social interactions among individuals and population groups. Utilising mobile phone app data, this study measured inequalities using multiple mobility-related indicators (i.e. the number of activity points, the radius of gyration, self-containment, and social interaction indices) and related to population size by scaling models. In England’s context, these indicators unfolding mobility patterns and social issues display different scaling regimes, varying from sublinear to super-linear. It was observed that larger cities are associated with greater social interactions, particularly among socioeconomically advantaged groups; however, they also exhibit exacerbated self-segregation. Due to the radiation effect of big cities, the performances (e.g. travel radius) of small surrounding towns deviate from the predicted values of scaling models. Within cities, the evenness of indicators is independent of population size and produces distinct spatial patterns. The findings expand upon previous research and provide a more nuanced understanding of the complex relationship between city size, urban inequality, and human mobility.

Influence of volume expansion in NaCl crystallization on the physical properties and molecular structure of asphalt: A MD simulation study

The pavement damage caused by salt-induced volume expansion is becoming increasingly noticeable. Molecular dynamics (MD) method was applied to evaluate the effects of varied volumes of NaCl crystals on physical properties and structure of asphalt. The effects of NaCl crystals on the compatibility between styrene–butadiene–styrene triblock copolymer (SBS) and asphalt, as well as the influence of SBS on the diffusion coefficient of NaCl crystals in the asphalt system, were investigated alongside their effects on the physical modulus and molecular structure of asphalt. The results show that the solubility parameter of the asphalt blends decreases as the volume of NaCl crystals increases. Specifically, the solubility parameter decreases by 52.5 % for the biaxial crystalline growth of NaCl and asphalt blends compared to the matrix asphalt. The analysis of the ion diffusion coefficient reveals that the primary disruption of NaCl crystals in asphalt blends is due to early Cl- and late Na+ diffusion. Furthermore, the rise in shear modulus of the asphalt blends suggests that the salt erosion process of SBS-modified asphalt is advantageous for its high temperature and shear resistance. The changes in peak radial distribution function and radius of gyration indicate that the inclusion of NaCl and SBS into asphalt is a physical aging process. In this case, SBS incorporation acts as a reinforcement to the asphalt to retard the erosion of NaCl.

Computational assessment of marine natural products as LasR inhibitors for attenuating quorum sensing in Pseudomonas aeruginosa

The Quorum Sensing (QS) system in bacteria has become a focal point for researchers aiming to develop novel antimicrobials to combat multidrug-resistant bacteria. Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, has developed resistance against a variety of antimicrobial agents, making it a formidable pathogen responsible for nosocomial infections. QS system mainly controls the expression of genes responsible for biofilm formation and virulence of bacteria. Within the QS system of P. aeruginosa, the transcription activator LasR plays a pivotal role and is an appealing target for the development of antimicrobial agents. In this study, we employed molecular docking and molecular dynamics simulations to identify potential inhibitors of LasR by screening marine natural products (MNPs) from the CMNPD database. We identified ten MNPs with excellent docking scores (less than −11.7 kcal/mol) against LasR, surpassing the binding energy of the co-crystal 3-oxo-C12-HSL (−8.594 kcal/mol) and the reference compound cladodionen (−6.71 kcal/mol). Furthermore, we selected five of these MNPs with the highest MM/GBSA binding energies for extensive 100 ns molecular simulations to assess their stability. The molecular dynamics simulations indicated three MNPs, namely CMNPD10886, CMNPD20987, and CMNPD20960, maintained high stability throughout the 100 ns simulation period, as evidenced by their root mean square deviation, root mean square fluctuation, radius of gyration, and hydrogen bond interactions within the ligand-protein complex analysis. Furthermore, essential dynamics (PCA and DCCM) were performed to analyse the correlated motion of amino acids. These findings suggest that these compounds hold potential as inhibitors of LasR, offering promising prospects for the development of treatments against infections. Communicated by Ramaswamy H. Sarma

Advancing Molecular Weight Determination of Lignin by Multi-Angle Light Scattering.

Due to the complexity and recalcitrance of lignin, its chemical characterization is a key factor preventing the valorization of this abundant material. Multi-angle light scattering (MALS) is becoming a sought-after technique for absolute molecular weight (MW) determination of polymers and proteins. Lignin is a suitable candidate for MW determination via MALS, yet further investigation is required to confirm its absolute MW values and molecular size. Studies aiming to break down lignin into a variety of renewable products will benefit greatly from a simple and reliable determination method like MALS. Recent pioneering studies, discussed in this review, addressed several key challenges in lignin's MW characterization. Nevertheless, some lignin-specific issues still need to be considered for in-depth characterization. This study explores how MALS instrumentation manages the complexities of determining lignin's MW, e.g., with simultaneous fractionation and fluorescence interference mitigation. Additionally, we rationalize the importance of a more detailed light scattering analysis for lignin characterization, including aspects like the second virial coefficient and radius of gyration.