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Background Sequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesting depletions. Current alternatives that try to highlight depletion often produce visually cluttered logos. Results We introduce a new sequence logo plot, the EDLogo plot, that highlights both enrichment and depletion, while minimizing visual clutter. We provide an easy-to-use and highly customizable R package Logolas to produce a range of logo plots, including EDLogo plots. This software also allows elements in the logo plot to be strings of characters, rather than a single character, extending the range of applications beyond the usual DNA, RNA or protein sequences. And the software includes new Empirical Bayes methods to stabilize estimates of enrichment and depletion, and thus better highlight the most significant patterns in data. We illustrate our methods and software on applications to transcription factor binding site motifs, protein sequence alignments and cancer mutation signature profiles. Conclusions Our new EDLogo plots and flexible software implementation can help data analysts visualize both enrichment and depletion of characters (DNA sequence bases, amino acids, etc.) across a wide range of applications.

A dislocation-density based crystalline plasticity (DCP) and nonlinear finite element (FE) analysis were used to predict, and fundamentally understand how and why fracture nucleation and propagation are related to the interrelated microstructural mechanisms of dislocation-density pileups, GB structure, orientation, and total and partial dislocation density interactions within and adjacent for a random low angle grain boundary (LAGB) and a random high angle GB (HAGB). The GB orientations and structures were obtained from micropillar experiments, such that LAGBs and the HAGBs can be accurately represented and used for the modeling predictions. The normal stress, density of pileups, and dislocation-density accumulation along and within the GB were higher for the low angle GB bicrystal. These interrelated phenomena delineate how fracture for high angle GBs nucleate and propagate at lower nominal strains than the lower angle GB bicrystal case. These predictions underscore how fundamental mechanisms can be identified and used to understand how failure nucleates and propagates for different GB structures and orientations.

Iron-chromium-aluminum (FeCrAl) alloys are used in automobile exhaust gas purifying systems and nuclear reactors due to its superior high-temperature oxidation and excellent corrosion resistance. Single-phase FeCrAl alloys with a body centered cubic structure plastically deform through dislocation slips at room temperature. Here, we investigated the orientation dependence of mechanical responses of FeCrAl alloy through testing single-crystal and bi-crystal micropillars in a scanning electron microscopy at room temperature. Single-crystal micropillars were fabricated with specific orientations which favor the activity of single slip system or two slip systems or multiple slip systems. The strain hardening rate and flow strength increase with increasing the number of activated slip system in micropillars. Bi-crystal micropillars with respect to the continuity of slip systems across grain boundary were fabricated to study the effect of grain boundary on slip transmission. The high geometrical compatibility factor corresponds to a high flow strength and strain hardening rate. Experimental results provide insight into understanding mechanical response of FeCrAl alloy and developing the mechanisms-based constitutive laws for FeCrAl polycrystalline aggregates.

Due to the coexistence of Al3+ and RE3+ and their similar properties, the separation of aluminum from rare earths is difficult. In this study, selective precipitation was used to separate aluminum from rare earth chloride solution via electrochemical regulated hydrolysis. By controlling the current density and electrolytic time, the rate of hydroxyl ion production was regulated, and the selective separation of rare earth and aluminum was realized according to the different precipitation sequences. By altering the temperature, current density, pH value, and other parameters, the separation performance of aluminum from rare earth in mixed rare earth chloride systems was systematically investigated. The removal rate of aluminum reached 88.35%, and the loss rate of rare earth was only 5.99% under optimized conditions. Compared with traditional neutralization hydrolysis, the new process showed higher efficiency and lower rare earth loss rate. Furthermore, a kinetic analysis of aluminum precipitation revealed that the reaction adhered to pseudo-first order kinetics. Additionally, the precipitate obtained via separation and filtration was amorphous alumina hydroxide with a small amount of rare earth attached. No reagent was consumed for the new process, which was more efficient and cleaner, providing a new idea for removing aluminum impurities from rare earth solutions.

The mechanical behavior and microstructural evolution of a BCC‐phase NbTaTiV refractory multi‐principal element alloy (RMPEA) is studied over a wide range of strain rates (10−3 to 103 s−1) and temperatures (room temperature to 850 °C). The mechanical property of present RMPEA shows less strain‐rate dependence and strong resistance to softening at high temperatures. Under high strain‐rate loading, the formation of thin type‐I twins is observed, which could lead to an increase in strain‐hardening rates. However, this hardening mechanism competes with adiabatic heating effects, resulting in the deterrence of strain‐hardening behaviors. In contrast, substantial strain‐hardening occurs at cryogenic temperatures due to the formation of twins, which act as stronger barriers to dislocation motion and interact with each other. To further understand the different strain‐hardening behaviors, density functional theory (DFT) calculations predict relatively low stacking fault energies and high twinning stress for the NbTaTiV RMPEA. Exceptional mechanical stability of refractory multi‐principal element alloy (RMPEA) across various strain‐rates and temperature is studied through multiscale experiments coupled with theoretical calculations. This stability originates from competition between twinning and adiabatic heating during dynamic deformation, contributed from severe lattice distortion and edge dislocation strengthening. However, cryogenic testing still shows pronounced strain hardening from abundant twins.

Chemical vapor deposition (CVD) is one of the most versatile techniques for the controlled synthesis of functional nanomaterials. When multiple precursors are induced, the CVD process often gives rise to the growth of doped or alloy compounds. In this work, we demonstrate the self-assembly of a variety of ‘phase-separated’ functional nanostructures from a single CVD in the presence of various precursors. In specific, with silicon substrate and powder of Mn and SnTe as precursors, we achieved self-organized nanostructures including Si/SiO x core-shell nanowire heterostructures both with and without embedded manganese silicide particles, Mn 11 Si 19 nanowires, and SnTe nanoplates. The Si/SiO x core-shell nanowires embedded with manganese silicide particles were grown along the direction of the crystalline Si via an Au-catalyzed vapor-liquid-solid process, in which the Si and Mn vapors were supplied from the heated silicon substrates and Mn powder, respectively. In contrast, direct vapor-solid deposition led to particle-free -oriented Si/SiO x core-shell nanowires and -oriented Mn 11 Si 19 nanowires, a promising thermoelectric material. No Sn or Te impurities were detected in these nanostructures down to the experimental limit. Topological crystalline insulator SnTe nanoplates with dominant {100} and {111} facets were found to be free of Mn (and Si) impurities, although nanoparticles and nanowires containing Mn were found in the vicinity of the nanoplates. While multiple-channel transport was observed in the SnTe nanoplates, it may not be related to the topological surface states due to surface oxidation. Finally, we carried out thermodynamic analysis and density functional theory calculations to understand the ‘phase-separation’ phenomenon and further discuss general approaches to grow phase-pure samples when the precursors contain residual impurities.

H-H binding energies in tetragonal and octahedral sites (TS & OS) of α -Fe lattice were calculated by density functional theory (DFT) under correction of elastic energy. Strong attractive interactions were identified as H atoms were incorporated in 3rd and 4th nearest OS neighbors. OS-type H-aggregated clusters with binding energies exceeding 200 meV were identified. Monte Carlo simulation of H-loading indicates abnormal H-aggregation behavior around a 1/2[111] ( 10 1 ¯ ) edge dislocation in relation with the enhanced H-H binding specifically in OS of α -Fe lattice.

The proton irradiation-induced hardening effect of dislocations in C35M FeCrAl alloy on glide resistance was quantified by in-situ micropillar compression testing in a scanning electron microscope (SEM). Irradiation tests with a proton energy of 2 MeV were conducted at room temperature, producing plateau damage of 0.01 and 0.1 displacement per atom (dpa), respectively, and generating high density of dislocation loops with fine size (<10 nm). Single-crystal micropillars were prepared with maximizing Schmid factor for a specific slip system while minimizing the others and then compressed to active one specific slip system to measure the critical resolve shear stress (CRSS) of {110} and {112} slip systems, respectively. The CRSS for these two slip systems increases with increasing irradiation dose. {112} slip system shows larger hardening than {110} slip system. Microstructure characterization after deformation indicates that the hardening effect originates from the pinning effect of irradiation-induced defects on moving dislocations.

Type II and IV twins with irrational twin boundaries are studied by high-resolution transmission electron microscopy in two plagioclase crystals. The twin boundaries in these and in NiTi are found to relax to form rational facets separated by disconnections. The topological model (TM), amending the classical model, is required for a precise theoretical prediction of the orientation of the Type II/IV twin plane. Theoretical predictions also are presented for types I, III, V, and VI twins. The relaxation process that forms a faceted structure entails a separate prediction from the TM. Hence, faceting provides a difficult test for the TM. Analysis of the faceting by the TM is in excellent agreement with the observations.

Al-Cu eutectic composites are composed of α -Al and θ -Al 2 Cu phases. Al-Al 2 Cu interfaces play a crucial role in determining the deformation modes and mechanical properties of nanoscale Al-Cu composites. In this work, we studied the structures and properties of the 110 Al 2 Cu 111 Al interface and elucidated corresponding plastic deformation mechanisms by using atomistic simulations. The 110 Al 2 Cu 111 Al interface comprises three sets of Shockley partial dislocations that divide the interface into three types of coherent structures. The interface exhibits isotropic, low shear resistance corresponding to the easy gliding and threefold symmetry of interface dislocations. Under mechanical straining parallel to the interface, unusual slips occur on 011 Al 2 Cu planes. Such an unexpected shear mode in Al 2 Cu phase is ascribed to the slip continuity across the Al-Al 2 Cu interface and the dislocations deposited at Al-Al 2 Cu interfaces.