Modeling and simulations of strain-induced phase transformations in materials under compression and compression-torsion in traditional and rotational diamond anvil cells

Phase transformations (PTs) under high pressure and plastic shear are widespread in nature, physical experiments, and modern technologies. In order to study the effect of plastic deformations on PTs, a rotational diamond anvil cell (RDAC) and diamond anvil cell (DAC) without hydrostatic media are utilized, in which large plastic shear is superposed in the sample under high pressure. Such PTs are classified as strain-induced ones and they occur by nucleation at defects that continuously appear during the plastic deformation. By applying finite element approach, plastic strain-induced PTs in a sample in DAC and RDAC are investigated in detail. A large-strain model for coupled PTs and plastic flow is developed, which includes micromechanically based strain-controlled kinetics. First, detailed analyses of the coupled plastic flow and PTs are studied during loading, unloading, and reloading. Second, an extended version of the Coulomb and plastic friction model for multiphase material with evolving concentration of phases is developed to model contact interaction on the contact surface. Third, cases without and with deformable gasket are compared and effects of gasket\u27s size and strength are discussed. A new sliding mechanism at the contact line between the sample, gasket, and anvil called extrusion-based pseudoslip is revealed. Various experimentally observed effects are reproduced and interpreted. Possible misinterpretation of experimental PT pressure is found. The obtained results will allow one optimal design of experiments and conditions for synthesis of new high pressure phases

Quantum Computing by Cooling

Interesting problems in quantum computation take the form of finding low-energy states of spin systems with engineered Hamiltonians that encode the problem data. Motivated by the practical possibility of producing very low-temperature spin systems, we propose and exemplify the possibility to compute by coupling the computational spins to a non-Markovian bath of spins that serve as a heat sink. We demonstrate both analytically and numerically that this strategy can achieve quantum advantage in the Grover search problem.Comment: 6 figure

Strong Strand Composition Bias in the Genome of Ehrlichia canis Revealed by Multiple Methods

Genes located on the two replicating strands are found to have two separate base/codon usages in Ehrlichia canis genome. Although strand-specific codon usage is not the first observation, for the first time we have applied multiple methods to the analysis of strand composition bias. By combining multiple methods, comprehensive and interesting results are obtained. Among three types of correspondence analysis (COA), absolute codon usages between genes on the two replicating strands are more distinct than relative synonymous codon usage (RSCU) and base usages are more sensitive than both types of codon usages. PR2-plots show that replication-induced bias is much higher than transcription/translation associated bias in the genome. By using the Z curve method, two common genomic characters, i.e., stronger strand composition bias and lower rearrangement frequency are found to exist in 11 obligate intracellular bacteria with separate base/codon usages. We hope more and more researchers will use the multiple methods to analyze strand composition bias in sequenced microbes, particularly obligate intracellular bacteria

ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes

BACKGROUND: It necessary to use highly accurate and statistics-based systems for viral and phage genome annotations. The GeneMark systems for gene-finding in virus and phage genomes suffer from some basic drawbacks. This paper puts forward an alternative approach for viral and phage gene-finding to improve the quality of annotations, particularly for newly sequenced genomes. RESULTS: The new system ZCURVE_V has been run for 979 viral and 212 phage genomes, respectively, and satisfactory results are obtained. To have a fair comparison with the currently available software of similar function, GeneMark, a total of 30 viral genomes that have not been annotated by GeneMark are selected to be tested. Consequently, the average specificity of both systems is well matched, however the average sensitivity of ZCURVE_V for smaller viral genomes (< 100 kb), which constitute the main parts of viral genomes sequenced so far, is higher than that of GeneMark. Additionally, for the genome of Amsacta moorei entomopoxvirus, probably with the lowest genomic GC content among the sequenced organisms, the accuracy of ZCURVE_V is much better than that of GeneMark, because the later predicts hundreds of false-positive genes. ZCURVE_V is also used to analyze well-studied genomes, such as HIV-1, HBV and SARS-CoV. Accordingly, the performance of ZCURVE_V is generally better than that of GeneMark. Finally, ZCURVE_V may be downloaded and run locally, particularly facilitating its utilization, whereas GeneMark is not downloadable. Based on the above comparison, it is suggested that ZCURVE_V may serve as a preferred gene-finding tool for viral and phage genomes newly sequenced. However, it is also shown that the joint application of both systems, ZCURVE_V and GeneMark, leads to better gene-finding results. The system ZCURVE_V is freely available at: . CONCLUSION: ZCURVE_V may serve as a preferred gene-finding tool used for viral and phage genomes, especially for anonymous viral and phage genomes newly sequenced