Efficient Coarse-Grained Superplasticity of a Gigapascal Lightweight Refractory Medium Entropy Alloy

Superplastic metals that exhibit exceptional ductility (>300%) are appealing for use in high-quality engineering components with complex shapes. However, the wide application of most superplastic alloys has been constrained due to their poor strength, the relatively long superplastic deformation period, and the complex and high-cost grain refinement processes. Here these issues are addressed by the coarse-grained superplasticity of high-strength lightweight medium entropy alloy (Ti_43.3 V₂₈ Zr₁₄ Nb₁₄ Mo_0.7 , at.%) with a microstructure of ultrafine particles embedded in the body-centered-cubic matrix. The results demonstrate that the alloy reached a high coarse-grained superplasticity greater than ≈440% at a high strain rate of 10^-2 s^-1 at 1173 K and with a gigapascal residual strength. A consecutively triggered deformation mechanism that sequences of dislocation slip, dynamic recrystallization, and grain boundary sliding in such alloy differs from conventional grain-boundary sliding in fine-grained materials. The present results open a pathway for highly efficient superplastic forming, broaden superplastic materials to the high-strength field, and guide the development of new alloys.

Design and simulation of a caprylic acid enzymatically modified phosphatidylcholine micelle using a coarse-grained molecular dynamics simulations approach

Computationally simulated micelle models provide useful structural information on the molecular and biological sciences. One strategy to study the self-aggregation process of surfactant molecules that make up a micelle is through molecular dynamics (MD) simulations. In this study, a theoretical approach with a coarse-grained MD simulation (CG-MD) was employed to evaluate the critical micellar concentration (CMC), the micellization process, building a tridimensional (3D) model system of a micelle using data from the experimentally enzymatically modified phospholipids (PL) by phospholipase A1 (PA1). This required enzymatic interesterification of soybean phosphatidylcholine (PC) with caprylic acid, along with purification and characterization by chromatographic techniques to measure the esterified fatty acids and the corresponding PL composition. The number of molecules used in the CG-MD simulation system was determined from the experimental CMC data which was 0.025%. The molecular composition of the system is: 1 C 18:2, 2 C 8:0/8:0, 3 C 8:0/18:3n-9, 4 C 8:0/18:0, 5 C8:0/18:2n-6, 6 C8:0/18:1n-9, and 7 C 8:0/16:0. According to our theoretical results, the micelle model is structurally stable with an average Rg of 3.64 ± 0.10 Å, and might have an elliptical form with a radius of 24.6 Å. Regarding CMC value there was a relationship between the experimental data of the modified PLs and the theoretical analysis by GC-MD, which suggest that the enzymatic modification of PLs does not affect their self-aggregation properties. Finally, the micellar system obtained in the current research can be used as a simple and useful model to design optimal biocompatible nanoemulsions as possible vehicles for bioactive small molecules.Communicated by Ramaswamy H. Sarma.

Molecular dynamics simulation of an entire cell

The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell's spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future.

The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X3-small transmembrane motifs

Fibronectin Leucine-rich Repeat Transmembrane (FLRT 1-3) proteins are a family of broadly expressed single-spanning transmembrane receptors that play key roles in development. Their extracellular domains mediate homotypic cell-cell adhesion and heterotypic protein interactions with other receptors to regulate cell adhesion and guidance. These in trans FLRT interactions determine the formation of signaling complexes of varying complexity and function. Whether FLRTs also interact at the surface of the same cell, in cis, remains unknown. Here, molecular dynamics simulations reveal two dimerization motifs in the FLRT2 transmembrane helix. Single particle tracking experiments show that these Small-X₃-Small motifs synergize with a third dimerization motif encoded in the extracellular domain to permit the cis association and co-diffusion patterns of FLRT2 receptors on cells. These results may point to a competitive switching mechanism between in cis and in trans interactions, which suggests that homotypic FLRT interaction mirrors the functionalities of classic adhesion molecules.

Effect of Thermal Treatment on the Physicochemical, Ultrastructural, and Antioxidant Characteristics of Euryale ferox Seeds and Flour

Euryale ferox seeds (EFS) were less gelatinized, preventing the release of nutrients and functional compounds, resulting in limited applications in meals and the food industry. Nutraceutical importance of EFS includes starch, protein, lipids, 20 amino acids, minerals, and vitamins (C, E, and beta carotene). This study aimed to evaluate the effect of three different thermal treatments on EFS’s physicochemical and nutritional properties and expected to improve its applicability. The results showed that the bulk density, thousand-grain weight, and hardness of thermal treated EFS were significantly decreased (p < 0.05), whereas the maximum decrease was observed in the industrial infrared heating-assisted fluidized bed (IHFH) treatment. Meanwhile, there were more crevices, fissures, and heightened porous structures in EFS between the pericarp and episperm and the endosperm after heat treatment, which facilitated grinding and water absorption. Notably, EFS’s water and oil absorption capacities increased significantly (p < 0.05) with microwave and IHFH treatments. EFS ground’s solubility into powder was increased significantly with thermal treatment (p < 0.05). Furthermore, the functional properties of TPC, TFC, DPPH radical scavenging activity, and reducing power were significantly increased (p < 0.05). In general, the changes in the physicochemical properties of EFS and increased bioactivity were caused by microwave and IHFH treatments. Hence, it might improve the food value of EFS while providing valuable information to researchers and food manufacturers.

Learning to Model G-Quadruplexes: Current Methods and Perspectives

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.

Protein Unfolding and Aggregation near a Hydrophobic Interface

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we study how the presence of a hydrophobic surface affects this course of events. To this goal, we use a coarse-grained model of proteins and study by simulations their folding and aggregation near an ideal hydrophobic surface in an aqueous environment by changing parameters such as temperature and hydrophobic strength, related, e.g., to ions concentration. We show that the hydrophobic surface, as well as the other parameters, affect both the protein unfolding and aggregation. We discuss the interpretation of these results and define future lines for further analysis, with their possible implications in neurodegenerative diseases.

Associations of Coarse Grain Intake with Undiagnosed Hypertension among Chinese Adults: Results from the China Kadoorie Biobank

Whole grain intake was associated with better blood pressure control, but evidence is lacking in non-Western populations with different grain intake patterns. We aimed to determine the associations between coarse grain intake, usually considered as the best proxy of whole grain intake for Chinese diets, with blood pressure and undiagnosed hypertension using baseline data from the China Kadoorie Biobank study. After excluding participants with clinically diagnosed hypertension or use of antihypertensive dugs, 435,907 participants were included in our analysis. A self-reported questionnaire was used to measure coarse grain intake frequency. Overall, 12.8% and 29.2% of the participants reported daily consumption and never consumption, respectively. With multivariable adjustments including BMI, outdoor temperature, and physical activity, higher frequency of coarse grain intake was associated with lower systolic and diastolic blood pressure in those older than 40 years, p trend < 0.05. Compared to never consumers, the odds ratio (95% CI) of hypertension was 0.78 (0.73–0.84), 0.84 (0.77–0.91), 0.91 (0.88–0.94), and 0.97 (0.95–0.99) for daily, 4–6 days/week, 1–3 days/week, and monthly groups, P trend < 0.001. Our cross-sectional study in a nationwide sample of Chinese adults suggests that higher coarse grain intake was associated with lower blood pressure and lower hypertension risk.

Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives

Injection of nanoparticles (NP) into the bloodstream leads to the formation of a so-called "nano-bio" interface where dynamic interactions between nanoparticle surfaces and blood components take place. A common consequence is the formation of the protein corona, that is, a network of adsorbed proteins that can strongly alter the surface properties of the nanoparticle. The protein corona and the resulting structural changes experienced by adsorbed proteins can lead to substantial deviations from the expected cellular uptake as well as biological responses such as NP aggregation and NP-induced protein fibrillation, NP interference with enzymatic activity, or the exposure of new antigenic epitopes. Achieving a detailed understanding of the nano-bio interface is still challenging due to the synergistic effects of several influencing factors like pH, ionic strength, and hydrophobic effects, to name just a few. Because of the multiscale complexity of the system, modeling approaches at a molecular level represent the ideal choice for a detailed understanding of the driving forces and, in particular, the early events at the nano-bio interface. This review aims at exploring and discussing the opportunities and perspectives offered by molecular modeling in this field through selected examples from literature.

Predicting the Flory-Huggins χ Parameter for Polymers with Stiffness Mismatch from Molecular Dynamics Simulations

The Flory–Huggins χ parameter describes the excess free energy of mixing and governs phase behavior for polymer blends and block copolymers. For chemically-distinct nonpolar polymers, the value of χ is dominated by the mismatch in cohesive energy densities of the monomers. For blends of chemically-similar polymers, the entropic portion of χ, arising from non-ideal local packing, becomes more significant. Using polymer field theory, Fredrickson et al. predicted that a difference in backbone stiffness can result in a positive χ for chains consisting of chemically-identical monomers. To quantitatively investigate this phenomenon, we perform molecular dynamic (MD) simulations for bead-spring chains, which differ only in stiffness. From the simulations, we apply a novel thermodynamic integration to extract χ as low as 10-4 per monomer for blends with stiffness mismatch. To compare with experiments, we introduce a standardized effective monomer to map real polymers onto our bead-spring chains. The predicted χ agrees well with experimental values for a wide variety of pairs of chemically-similar polymers.

Charge Diffusion in Semiconducting Polymers: Analytical Relation between Polymer Rigidity and Time Scales for Intrachain and Interchain Hopping

We study the charge diffusion of semiconducting polymer bulk using simplified coarse grained models to investigate the relation between charge diffusion coefficient and the characteristics time of intrachain and interchain hopping, τ1 and τ2. We consider the process of charge diffusion in several standard models of polymer chains (rigid chain, Gaussian chain, worm-like chain), and we achieve an analytical expression for the diffusion coefficient in terms of the characteristic times and the geometric parameters defining the chain models. The diffusion depends only on the intrachain hopping for the rigid chain and on the geometric average of intrachain and interchain hopping times for the Gaussian chain (the least rigid model), with an analytical interpolation available between two limits. The model highlights the importance of large persistence lengths for improved transport properties. In all cases, it is incorrect to consider the slower interchain hopping as the rate-determining step for the charge transport.

COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS

We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the C_α coordinates of the protein backbone. Specifically, to mimic the unfolding process, i.e., to simulate the process of overcoming the local energy barrier on the free energy landscape with force loading, the noncovalent protein network bonds (i.e., hydrogen bonds, salt bridges, hydrophobic contacts, etc.) are broken one-by-one with a certain probability, while the strong covalent bonds along the backbone (i.e., peptide bonds, disulfide bonds, etc.) are kept intact. The jumping event from local energy minima (bonds breaking rate) are chosen according to Kramer's theory and the Bell model. Moreover, we exploit the self-similar structure of proteins at different scales to design an effective coarse-graining procedure for DENM with optimal parameter selection. The robustness of DENM is validated by coarse-grained molecular dynamics (MD) simulation against atomistic MD simulation of force-extension processes of the Fibrinogen and Titin Immunoglobulin proteins. We observe that the native structure of the proteins determines the total unfolding dynamics (including large deviations) and not just the fluctuations around the native state.

A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids

The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction perfoming among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parameterization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parameterized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential dataset has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys 'R' Us. The model is shown to perform very well compared to other existing prediction models for these properties.