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Phase separation of polymer blends has attracted much interest in designing high-performance materials with specific mechanical and dielectric properties. To this end, three types of poly(methacrylic ester)s, including poly(methyl methacrylate) (PMMA), poly(butyl methacrylate) (PBMA), and poly(isobutyl methacrylate) [P(iBMA)], have been incorporated in the poly(vinylidene fluoride-co-hexafluoropropylene) [P(VDF-HFP)] matrix, respectively. As exemplified in P(VDF-HFP)/P(iBMA) blended films, a conspicuous phase separation is experimentally observed and the blended film presents an enhanced Young's modulus and a one-fold increment in the elongation over the pristine P(VDF-HFP). The excellent plasticity is benefited from the interfacial regions between the two phases, which could effectively pin the cracks and retard the slippage under deformation. Simultaneously, an ultra-high Weibull breakdown strength (∼774 MV/m) is obtained in the blends, benefiting from the improved Young's modulus and excellent plasticity. The blends are endowed with an excellent energy storage density (∼21 J/cm3 at 830 MV/m), along with an impressive cycling stability. In contrary, P(VDF-HFP)/PMMA and P(VDF-HFP)/PBMA blended films sacrifice the plasticity due to the scarcity of phase separation; therefore, even though Young's moduli have been improved, there is no remarkable improvement for breakdown strengths and energy storage performances. The experimental results are augmented by molecular dynamics simulations. This contribution provides a facile approach to develop high-performance polymer dielectric materials through a phase separation design and emphasize the importance of plasticity for breakdown strength. [ABSTRACT FROM AUTHOR]

Riboswitch can bind small molecules to regulate gene expression. Unlike other RNAs, riboswitch relies on its conformational switching for regulation. However, the understanding of the switching mechanism is still limited. Here, we focussed on the add A-riboswitch to illustrate the dynamical switching mechanism as an example. We performed molecular dynamics simulation, conservation and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding, whereas the switching base pairings are co-evolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design. Riboswitch can bind small molecules to regulate gene expression. However, the understanding of switching mechanism is very limited. We performed molecular dynamics simulation, conservation, and co-evolution calculations to infer the dynamical motions and evolutionary base pairings. The results suggest that the binding domain is stable for molecule recognition and binding while the switching base pairings are coevolutionary for translation. The understanding of the add A-riboswitch switching mechanism provides a potential solution for riboswitch drug design. [ABSTRACT FROM AUTHOR]

• We study the effects of randomly distributed He bubbles on the spall damage in single crystal aluminum under decaying shock loadings. • He bubble plays important role in the dynamic properties, including the spall damage mechanism and characteristics. • The mechanism of spall damage is dominated by He bubble expansion-merging-absorption, followed by void nucleation-growth-coalescence. • The spall strength of Al in solid state is reduced by He bubble, but this effect becomes negligible when the crystal is melted. The mechanism and characteristics of spall damage in single crystal Al with randomly distributed helium bubbles under decaying shock loading are studied by molecular dynamics simulations. We find that He bubble plays important role in the dynamic process. The mechanism of spall damage is dominated by He bubble expansion-merging-absorption, followed by void nucleation-growth-coalescence. During spalling process, He bubbles impede the nucleation of surrounding voids, they expand at a higher rate than that for void growth, adjacent He bubbles merge together, and small voids are absorbed by nearby large He bubble. These behaviors finally lead to a very different morphology of the damaged zone from that for the perfect crystal, whose spall damage mechanism is void nucleation-growth-coalescence. Obvious differences in temperature profile are observed between the crystal with He bubbles and the perfect crystal because the compression of surrounding atoms induced by He bubble expansion results in higher local temperature, especially in solid state. In melted state, the contribution of He bubbles becomes comparatively small since more voids are nucleated followed by faster voids growth and coalescence that lead to higher temperature rising. Additionally, He bubble significantly reduces the spall strength of Al in solid state, but this effect becomes negligible when the crystal is melted. [ABSTRACT FROM AUTHOR]

The microstructural evolution of ferritic/martensitic steels SIMP and T91 in oxygen-saturated liquid LBE at different temperatures (400, 470, 550 and 620 °C) has been studied by experiments and molecular dynamics simulations. It is shown that the SIMP steel offers better oxidation resistance at 400–550 °C due to the formation of protective SiO 2 particles and bands. At 620 °C, both the SIMP and T91 steels undergo dissolution corrosion with similar dissolved layer thicknesses. Molecular dynamics simulations reveal that the number of Fe-O pairs decreases with increasing temperatures and the enhanced dissolution of Fe makes the surfaces of the steel difficult to oxidize at 620 °C. • SIMP steel has better oxidation resistance than T91 steel at 400–550 ℃. • SiO 2 particles and bands appear at the oxide front of SIMP steel. • At 620 °C, dissolution corrosion occurs on both steels. • At 620 °C, the dissolved layer thickness on both steels is comparable. • The oxides can't nucleate at 620 ℃ due to the violent dissolution of Fe atoms. [ABSTRACT FROM AUTHOR]

• Strain rate effect of tensile damage of liquid Cu containing He bubbles is studied. • The strain rate-dependent damage mechanism of Cu-He system is first discovered. • He bubbles only reduce the tensile strength of liquid Cu when ε ˙ < 3.0×1010 /s. • The first mechanical model of dynamic tensile damage of Cu-He system is developed. The dynamic tensile fracture process of liquid copper containing helium bubbles system is systematically investigated by molecular dynamics simulations and theoretical modeling. A strain rate-dependent damage mechanism that transforms from a co-growth of voids and helium bubbles to a sole expansion of helium bubbles as the strain rate decreases is firstly found, and a corresponding physical explanation is proposed. Meanwhile, it is found that the dynamic tensile strength of the material is significant affected by the transition of the damage mechanism. Based on the revealed damage mechanism and the basic properties of helium bubbles such as internal pressure and surface tension obtained with the help of molecular dynamics simulations, a mechanical model is constructed to describe the dynamic damage process of the system. The volume evolution of each helium bubble as well as stress evolution of the system obtained from molecular dynamics simulations is well reproduced by the mechanical model in a wide range of strain rate. The strain rate-dependent damage mechanism and the proposed theoretical damage model will provide insights into understanding the dynamic responses of metals containing initial bubbles under extreme conditions. [Display omitted] [ABSTRACT FROM AUTHOR]

Micro-spall is a large-area of liquid cavitation debris cloud formed near the free surface when metal melts during shocking or releasing process. We performed a molecular dynamics simulation to investigate the evolution of micro-spall and the related physical mechanism during the re-compaction process of a single crystal Pb by the second shock wave loading. The temperature and pressure obviously increase during re-compaction process. The ultra-high temperature-rise and local high pressure in the damage area is due to the collision between atoms and the collapse of voids. There is also one more pressure-rise and temperature-rise in the damage region, which is originated from the formation of high-speed internal micro jet and its striking on the back wall of large voids. Due to the uneven distribution of pressure and temperature after the 2nd shock wave passing through the micro spall damage region, the microstructures are also unevenly distributed. Besides, the damage region will swell due to the high temperature-rise during re-compaction process. Therefore, the micro-spall damaged region closed to the free surface is difficult to be compacted to dense state. Because that the voids in the damage region near the free surface are larger for the longer time interval, the temperature-rise originated from the collapse of voids is more severe. The wavefront plane is gradually broadened in the process of re-compaction. [ABSTRACT FROM AUTHOR]

The structural transition of a single polymer chain with chain length of 100, 200 and 300 beads was investigated by parallel tempering MD simulation. Our simulation results can capture the structural change from random coil to orientationally ordered structure with decreasing temperature. The clear transition was observed on the curves of radius of gyration and global orientational order parameter P as the function of temperature, which demonstrated structural formation of a single polymer chain. The linear relationships between three components of square radius of gyration R, R, R and global orientational order P can be obtained under the structurally transformational process. The slope of the linear relationship between x (or y-axis) component R (or R) and P is negative, while that of R as the function of P is positive. The absolute value of slope is proportional to the chain length. Once the single polymer chain takes the random coil or ordered configuration, the linear relationship is invalid. The conformational change was also analyzed on microscopic scale. The polymer chain can be treated as the construction of rigid stems connecting by flexible loops. The deviation from exponentially decreased behavior of stem length distribution becomes prominent, indicating a stiffening of the chain arises leading to more and more segments ending up in the trans state with decreasing temperature. The stem length N is about 21 bonds indicating the polymer chain is ordered with the specific fold length. So, the simulation results, which show the prototype of a liquid-crystalline polymer chain, are helpful to understand the crystallization process of crystalline polymers. [ABSTRACT FROM AUTHOR]

Effects of molecular vacancies on the decomposition mechanisms and reaction dynamics of condensed-phase β-HMX at various temperatures were studied using ReaxFF molecular dynamics simulations. Results show that three primary initial decomposition mechanisms, namely, N−NO2 bond dissociation, HONO elimination, and concerted ring fission, exist at both high and lower temperatures. The contribution of the three mechanisms to the initial decomposition of HMX is influenced by molecular vacancies, and the effects vary with temperature. At high temperature (2500 K), molecular vacancies remarkably promote N−N bond cleavage and concerted ring breaking but hinder HONO formation. N−N bond dissociation and HONO elimination are two primary competing reaction mechanisms, and the former is dominant in the initial decomposition. Concerted ring breaking of condensed-phase HMX is not favored at high temperature. At lower temperature (1500 K), the most preferential initial decomposition pathway is N−N bond dissociation followed by the formation of NO3 (O migration), although all three mechanisms are promoted by molecular vacancies. The promotion effect on concerted ring breaking is considerable at lower temperature. Products resulting from concerted ring breaking appear in the defective system but not in the perfect crystal. The mechanism of HONO elimination is less important at lower temperature. We also estimated the reaction rate constant and activation barriers of initial decomposition with different vacancy concentrations. Molecular vacancies accelerate the decomposition of condensed-phase HMX by increasing the reaction rate constant and reducing activation barriers. [ABSTRACT FROM AUTHOR]

Abstract: We introduce the mixed product of three vectors spanning four molecular locations as a descriptor of optical isomerism. This descriptor is very efficient as it does not require molecular superposition, and is very robust in discriminating between a given isomer and its mirror image. In particular, conformational isomers that are mirror images of each other, as well as optical isomers have opposite sign of the descriptor value. For efficient database searches, the optical isomerism descriptor can be used to complement an available ultrafast shape recognition (USR) method based solely on distances, which is not able to distinguish enantiomers. By an extensive comparison of the USR-based similarity score with an approach based on Gaussian molecular volume overlap, the accuracy and completeness of the former are discussed. [ABSTRACT FROM AUTHOR]

Behaviors of body centered cubic (bcc) Fe(100)-liquid lead-bismuth eutectic (LBE) solid-liquid interface have been studied by classical molecular dynamics simulation (MD) with embedded-atom model potential under anaerobic conditions. Both static and dynamic simulation results indicate that Fe atoms prefer to bind with Bi atoms rather than Pb atoms. Trajectories of Bi and Pb perpendicular to the interface show obvious thermal vibrations of both liquid components at the time scale of about 0.9 ns for atoms Bi, and about 0.3 ns for atoms Pb, respectively. Temperature effect on penetration of liquid atoms into bulk Fe and dissolution of Fe into liquid in the solid-liquid interface system show that interactions between the bcc Fe(100) and liquid LBE mount perceptibly in the temperature range of 823 to 873 K. This result indicates that the critical temperature of the interaction between the bcc Fe(100) and liquid LBE is between 823 K and 873 K, which is consistent with the designed operating temperature for LBE coolant. [ABSTRACT FROM AUTHOR]

• The expansion and merging of He bubble play a leading role in spall mechanisms of Al, instead of void nucleation-growth-coalescence. • The dynamic evolution process of He bubble involves four stages: slow and independent expansion, rapid and independent expansion, deceleration expansion due to inter-bubble interaction and merging, and fast expansion after merging. • The mechanism for bubble expansion (growth) in solid metal includes plastic deformation and local temperature rising; the overlap of plastic deformation regions of adjacent bubbles and local melting promote the flow of inter-bubble atoms, leading to the thinning and breaking of inter-bubble ligament and thus bubble coalescence (merging). • He bubble impedes the nucleation and growth of nearby voids and the expanded bubble absorbs grown voids when they contact. Such suppression enhances with the increase of bubble size or density while attenuates with the increase of shock strength. Using molecular dynamics simulation, we investigate the dynamic evolution characteristics of He bubble and its effects on void nucleation-growth and thermomechanical properties in single crystal Al during spallation. The evolution process of bubble includes four stages: slow and independent expansion, rapid and independent expansion, deceleration expansion due to inter-bubble interaction and merging, and fast expansion after merging. The bubble radius-time relation is approximately linear both before and after merging and the corresponding expansion rates are obtained. The mechanism of bubble expansion (growth) in solid metal under dynamic tension involves plastic deformation via dislocation nucleation and movement and temperature rising around the bubble. The growth toward neighboring bubble leads to the overlap of plastic deformation regions that promotes local melting. The flows of melted atoms along both normal and tangential directions of the two bubbles result in the thinning and breaking of the inter-bubble ligament, and thus bubble merging occurs. In melted metal, the tension deformation under velocity gradient leads to bubble growth and coalescence. He bubble impedes the nucleation and growth of nearby voids and the expanded bubble absorbs grown voids when they contact. Such suppression enhances with the increase of bubble size or density while attenuates with the increase of shock strength. The number of nucleated voids is much lower and the average radius of voids is smaller for the sample with He bubbles in solid state. After melting, the reduction in quantity gets smaller and the radius becomes a little higher due to the suppression on continuing nucleation of voids. The bubble behavior and its influence on void evolution result in the variation of spall mechanism: the expansion and merging of He bubble play the leading role, independent on shock strength, bubble density, or bubble size. The effects of He bubble on temperature and stress are also addressed. [ABSTRACT FROM AUTHOR]

Four categories of globular proteins, including all-α, all-β, α + β, and α/β types, are simplified as the off-lattice HNP model involving the secondary-structural information of each protein. The propensity of three types of residues, i.e., H, N, and P to form a secondary structure is investigated based on 146 protein samples. We find that P residues are easy to form α-helices, whereas H residues have a higher tendency to construct β-sheets. The statistical analysis also indicates that the occurrence of P residues is invariably higher than that of H residues, which is independent of protein category. Changes in bond- and non-bonded potential energies of all protein samples under a wide temperature range are presented by coarse-grained molecular dynamics (MD) simulation. The simulation results clearly show a linear relationship between the bond-stretching/bending potential energy and the reduced temperature. The bond-torsional and non-bonded potential energies show distinct transitions with temperature. The bond-torsional energy increases to the maximum and then decreases with the increase of temperature, which is opposite to the change in non-bonded potential energy. The transition temperature of non-bonded potential energy is independent of the protein category, while that of bond-torsional energy is closely related to the protein secondary structure, i.e., α-helix or β-sheet. The quantitatively bonded- and semi-quantitatively non-bonded potential energy of 24 α + β and 23 α/β protein samples are successfully predicted according to the statistical results obtained from MD simulations. [ABSTRACT FROM AUTHOR]

Using molecular dynamics methods, we investigated the spall damage in single crystal tin under different shock pressures. The results show that release melting and shock melting occur when the shock velocities increase in the metallic tin. The spall strengths in the molten tin are ~1.5–2.0 GPa lower than that in solid. When release melting occurs, the spall strength drops rapidly, whereas the downtrend of the spall strength becomes gentle during shock melting. The results also show that the spall strength is affected by not only the shock pressure and phase state, but also the temperature and strain rate. By visualizing the development of spall damage, we find that it forms a spall layer in the solid. In molten tin, a cavitation region with a large volume is formed. The maximum number of voids increases with an increase in the shock pressure. The growth rate of the void volume fraction slows down after reaching the initial time of void growth at different impact pressures. We elucidated the variation trend of spall strength between solid and molten tin under different shock pressures. The relevant results can provide a reference for future studies on spall damage investigations. • The spall strengths in the molten tin are ~1.5–2.0 GPa lower than that in solid. • The spall strength drops rapidly when release melting occurs, whereas the downtrend becomes gentle during shock melting. • The spall strength is affected by the shock pressure and phase state. [ABSTRACT FROM AUTHOR]

Displacement cascades in bcc Fe-Pb solid solution are studied by molecular dynamics (MD) simulations. The Fe-Pb alloy model with different Pb concentrations was set as the Pb penetration structure of iron-based materials in actual working conditions. The results show that Pb atom penetration enhances the radiation damage of displacement cascades in Fe. The number of stable point defects in Fe-Pb alloy increases significantly, varies with Pb concentration and PKA energy. The differences of defect recombination rate are obvious under different Pb concentrations. Point defect analysis results indicate that there are rules in the relation between the interstitial and vacancy of two elements. Besides, unconnected cascade collision is found in Fe-Pb model under 10 keV, and the size of the subcascade affects the formation of cluster. The cluster results show that the interstitial form clusters easier and larger than vacancy, the PKA energy and Pb concentration can influence the size of clusters. [ABSTRACT FROM AUTHOR]

Armadillo repeat proteins (ArmRPs) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. Thus, they may form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library. Stacked armadillo repeats, each consisting of 42 aa arranged in three α-helices, build an elongated superhelical structure. Here, we analyzed the curvature variations in natural ArmRPs and identified a repeat pair from yeast importin-α as having the optimal curvature geometry that is complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry. Computationally designed ArmRPs (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series. [ABSTRACT FROM AUTHOR]

The specific recognition of peptide sequences by proteins plays an important role both in biology and in diagnostic applications. Here we characterize the relatively weak binding of the peptide neurotensin (NT) to the previously developed Armadillo repeat protein VG_328 by a multidisciplinary approach based on solution NMR spectroscopy, mutational studies, and molecular dynamics (MD) simulations, totaling 20 μs for all MD runs. We describe assignment challenges arising from the repetitive nature of the protein sequence, and we present novel approaches to address them. Partial assignments obtained for VG_328 in combination with chemical shift perturbations allowed us to identify the repeats not involved in binding. Their subsequent elimination resulted in a reduced-size binder with very similar affinity for NT, for which near-complete backbone assignments were achieved. A binding mode suggested by automatic docking and further validated by explicit solvent MD simulations is consistent with paramagnetic relaxation enhancement data collected using spin-labeled NT. Favorable intermolecular interactions are observed in the MD simulations for the residues that were previously shown to contribute to binding in an Ala scan of NT. We further characterized the role of residues within the N-cap for protein stability and peptide binding. Our multidisciplinary approach demonstrates that an initial low-resolution picture for a low-micromolar-peptide binder can be refined through the combination of NMR, protein design, docking, and MD simulations to establish its binding mode, even in the absence of crystallographic data, thereby providing valuable information for further design. [ABSTRACT FROM AUTHOR]