Massively-Parallel Dislocation Dynamics Simulations

Abstract. Prediction of the plastic strength of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of the existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, in order to be statistically representative and to reproduce experimentally observed microstructures. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We dis-cuss the general aspects of this code that make such large scale simulations possible, as well as a few initial simulation results

Enabling Strain Hardening Simulations with Dislocation Dynamics

Numerical algorithms for discrete dislocation dynamics simulations are investigated for the purpose of enabling strain hardening simulations of single crystals on massively parallel computers. The algorithms investigated include the /(N) calculation of forces, the equations of motion, time integration, adaptive mesh refinement, the treatment of dislocation core reactions, and the dynamic distribution of work on parallel computers. A simulation integrating all of these algorithmic elements using the Parallel Dislocation Simulator (ParaDiS) code is performed to understand their behavior in concert, and evaluate the overall numerical performance of dislocation dynamics simulations and their ability to accumulate percents of plastic strain

ParaDiS on Blue Gene/L: stepping up to the challenge

This paper reports on the efforts to enable fully scalable simulations of Dislocation Line Dynamics (DLD) for direct calculations of strength of crystalline materials. DLD simulations are challenging and do not lend themselves naturally to parallel computing. Through a combinations of novel physical approaches, mathematical algorithms and computational science developments, a new DLD code ParaDiS is shown to take meaningful advantage of BG/L and, by doing so, to enable discovery class science by computation

Dislocation multi-junctions and strain hardening

At the microscopic scale, the strength of a crystal derives from the motion, multiplication and interaction of distinctive line defects--dislocations. First theorized in 1934 to explain low magnitudes of crystal strength observed experimentally, the existence of dislocations was confirmed only two decades later. Much of the research in dislocation physics has since focused on dislocation interactions and their role in strain hardening: a common phenomenon in which continued deformation increases a crystal's strength. The existing theory relates strain hardening to pair-wise dislocation reactions in which two intersecting dislocations form junctions tying dislocations together. Here we report that interactions among three dislocations result in the formation of unusual elements of dislocation network topology, termed hereafter multi-junctions. The existence of multi-junctions is first predicted by Dislocation Dynamics (DD) and atomistic simulations and then confirmed by the transmission electron microscopy (TEM) experiments in single crystal molybdenum. In large-scale Dislocation Dynamics simulations, multi-junctions present very strong, nearly indestructible, obstacles to dislocation motion and furnish new sources for dislocation multiplication thereby playing an essential role in the evolution of dislocation microstructure and strength of deforming crystals. Simulation analyses conclude that multi-junctions are responsible for the strong orientation dependence of strain hardening in BCC crystals

Elastic instabilities and structural responses of β-SiC under stress

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1995.Includes bibliographical references (leaves 202-210).by Meijie Tang.Ph.D

Genome Features and AntiSMASH Analysis of an Endophytic Strain Fusarium sp. R1

Endophytic fungi are one of the most prolific sources of functional biomolecules with therapeutic potential. Besides playing an important role in serious plant diseases, Fusarium strains possess the powerful capability to produce a diverse array of bioactive secondary metabolites (SMs). In order to in-depth mine gene clusters for SM biosynthesis of the genus Fusarium, an endophytic strain Fusarium sp. R1 isolated from Rumex madaio Makino was extensively investigated by whole-genome sequencing and in-depth bioinformatic analysis, as well as antiSMASH annotation. The results displayed that strain R1 harbors a total of 51.8 Mb genome, which consists of 542 contigs with an N50 scaffold length of 3.21 Mb and 50.4% GC content. Meanwhile, 19,333 functional protein-coding genes, 338 tRNA and 111 rRNA were comprehensively predicted and highly annotated using various BLAST databases including non-redundant (Nr) protein sequence, nucleotide (Nt) sequence, Swiss-Prot, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), as well as Pathogen Host Interactions (PHI) and Carbohydrate-Active enzymes (CAZy) databases. Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) results showed that strain R1 has 37 SM biosynthetic gene clusters (BGCs), including 17 nonribosomal peptide synthetases (NRPSs), 13 polyketide synthetases (PKSs), 3 terpene synthases (Ts), 3 hybrid NRPS + PKS and 1 hybrid indole + NRPS. These findings improve our knowledge of the molecular biology of the genus Fusarium and would promote the discovery of new bioactive SMs from strain R1 using gene mining strategies including gene knockout and heteroexpression