Development of interatomic potential for Al-Tb alloys using a deep neural network learning method.

An interatomic potential for the Al-Tb alloy around the composition of Al90Tb10 is developed using the deep neural network (DNN) learning method. The atomic configurations and the corresponding total potential energies and forces on each atom obtained from ab initio molecular dynamics (AIMD) simulations are collected to train a DNN model to construct the interatomic potential for the Al-Tb alloy. We show that the obtained DNN model can well reproduce the energies and forces calculated by AIMD simulations. Molecular dynamics (MD) simulations using the DNN interatomic potential also accurately describe the structural properties of the Al90Tb10 liquid, such as partial pair correlation functions (PPCFs) and bond angle distributions, in comparison with the results from AIMD simulations. Furthermore, the developed DNN interatomic potential predicts the formation energies of the crystalline phases of the Al-Tb system with an accuracy comparable to ab initio calculations. The structure factors of the Al90Tb10 metallic liquid and glass obtained by MD simulations using the developed DNN interatomic potential are also in good agreement with the experimental X-ray diffraction data. The development of short-range order (SRO) in the Al90Tb10 liquid and the undercooled liquid is also analyzed and three dominant SROs, i.e., Al-centered distorted icosahedron (DISICO) and Tb-centered '3661' and '15551' clusters, respectively, are identified.

Crystal genes in a marginal glass-forming system of Ni50Zr50.

The marginal glass-forming ability (GFA) of a binary Ni-Zr system is an issue to be explained considering numerous bulk metallic glasses (BMGs) found in a Cu-Zr system. Using molecular dynamics, the structures and dynamics of Ni50Zr50 metallic liquid and glass are investigated at the atomistic level. To achieve a well-relaxed glassy sample, a sub-Tg annealing method is applied and the final sample is closer to the experiments than the models prepared by continuous cooling. With the state-of-the-art structural analysis tools such as cluster alignment and pair-wise alignment methods, two glass-forming motifs with some mixed traits of a metastable B2 crystalline phase and a crystalline Ni-centered B33 motif are found to be dominant in the undercooled liquid and glass samples. A new chemical order characterization on each short-range order (SRO) structure is accomplished based on the cluster alignment method. The significant amount of the crystalline motif and the few icosahedra in the glassy sample deteriorate the GFA.

Transcription levels of sirtuin family in neural stem cells and brain tissues of adult mice.

Neural stem cells (NSCs) has been used as a well-known model to investigate apoptosis, differentiation, maintenance of stem cells status, and therapy of neurological disease. The C17.2 NSCs line was produced after v-myc transformation of neural progenitor from mouse cerebellar cortex. Sirtuin family plays important roles involved in neuronal differentiation, genomic stability, lifespan, cell survival. However, little is known about gene expression variation of sirtuin family in C17.2 NSCs, primary NSCs, and different brain tissues in adult mice. Here, we confirmed that the mRNA expression levels of sirt2, 3, 4, 5, and 7 in E14.5 NSCs were significantly higher than in C17.2 NSCs, whereas that sirt 6 displayed an opposing mode. Moreover, a higher mRNA level of sirtuin family was observed in the adult mouse brain compared to C17.2 NSCs. In addition, histone deacetylase (HDAC) inhibitors nicotinamide and Trichostatin A (TSA) were used to explore differential changes at the transcriptional level of sirtuins. Results indicated that the expression of sirt1, sirt5 and sirt6 was significant downregulated by nicotinamide treatment. Whereas, a significant downregulation in sirt1 and sirt3 and a significant upregulation in sirt2, sirt4, sirt6, and sirt7 were observed in the treatment of TSA. Thus our studies indicate different sirtuin mRNA expression profiles between C17.2 NSCs, E14.5 NSCs and brain tissues, suggesting the transcriptional regulation of sirtuin family could be mediated by different histone acetylation.

Effects of Si solute on the glass formation and atomic structure of Pd liquid.

Molecular dynamics simulations were performed to study the effects of Si solute on the glass formation and crystallization of Pd liquid. Pure Pd samples prepared by a quenching process with a cooling rate of 1013 K s-1 can be in an amorphous state but the structural analysis indicates there is nearly no glass-forming motif in the sample. However, doping a small amount of Si (Si concentration ~4%) the sample can be vitrified at a cooling rate of 1012 K s-1. The glass-forming motifs such as Pd-centered Z13, Si-centered Z9-like and mixed-ICO-cube clusters with five-fold local symmetry are found to be the dominant short-range orders in the glassy samples. With the increasing of the Si-doping concentration, these glass-forming motifs tend to aggregate and connect with each other forming a network structure. Our calculated results revealed that Si solutes in liquid Pd can significantly enhance the glass-forming ability.

PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature.

SUMMARY: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research. AVAILABILITY: PDQ Wizard is freely available from http://www.gti.ed.ac.uk/pdqwizard/.