Phase transitions in the classical exchange-anisotropic Kitaev-Heisenberg model.

The Kitaev model on the honeycomb lattice has been receiving substantial attention due to the discovery of quantum spin liquid state associated with this model. Consequently, its classical partners such as the Kitaev-Heisenberg (KH) model and associated phase transitions become concerned. Specifically, an intermediate Kosterlitz-Thouless (KT) phase engaged in the transition from the high-temperature (T) disordered state to the low-T sixfold degenerate state is predicted in the isotropic KH model [Phys. Rev. Lett. 109, 187201 (2012)10.1103/PhysRevLett.109.187201], but so far no sufficient experimental proof has been reported. In this work, we consider an essential extension of this KH model on the honeycomb lattice by including the Kitaev exchange anisotropy that is non-negligible in realistic materials. The associated phase transitions are thus investigated using the Monte Carlo simulations. It is found that such an anisotropy will result in a degradation of the sixfold degeneracy of the ground state in the isotropic KH model down to the fourfold or twofold degenerate ground state, and the finite-T phase transitions will also be modified remarkably. Interestingly, the intermediate KT phase can be suppressed by this Kitaev exchange anisotropy. This work thus provides a more realistic description of the physics ingredient with the KH model and presents a possible explanation on absence of the intermediate phase in real materials where the Kitaev exchange anisotropy can be more or less available.

Helical and skyrmion lattice phases in three-dimensional chiral magnets: Effect of anisotropic interactions.

In this work, we study the magnetic orders of a classical spin model with anisotropic exchanges and Dzyaloshinskii-Moriya interactions in order to understand the uniaxial stress effect in chiral magnets such as MnSi. Variational zero temperature calculations demonstrate that various helical orders can be developed depending on the interaction anisotropy magnitude, consistent with experimental observations at low temperatures. Furthermore, the uniaxial stress induced creation and annihilation of skyrmions can be also qualitatively reproduced in our Monte Carlo simulations. Our work suggests that the interaction anisotropy tuned by applied uniaxial stress may play an essential role in modulating the magnetic orders in strained chiral magnets.

Magnetic impurity doping induced spin-glass state and short-range zigzag order in the honeycomb iridate Na2IrO3.

Based on the modified Heisenberg-Kitaev model, the effects of magnetic substitution on the magnetic properties of the honeycomb-lattice iridate [Formula: see text] [Formula: see text] are studied using Monte Carlo simulations. It is observed that the long-range zigzag state of the original system is rather fragile and can be replaced by a spin-glass state even for small substitution, well consistent with the experimental observation in Ru-substituted samples (Mehlawat et al 2015 Phys. Rev. B 92 134412). Both the disordered Heisenberg and Kitaev interactions caused by the magnetic ion-doping are suggested to be responsible for the magnetic phase transitions in the system. More interestingly, a short-range zigzag order is suggested to survive above the freezing temperature even at high magnetic impurity doping levels.

Ashkin-Teller criticality and weak first-order behavior of the phase transition to a fourfold degenerate state in two-dimensional frustrated Ising antiferromagnets.

We study the thermal phase transition of the fourfold degenerate phases (the plaquette and single-stripe states) in the two-dimensional frustrated Ising model on the Shastry-Sutherland lattice using Monte Carlo simulations. The critical Ashkin-Teller-like behavior is identified both in the plaquette phase region and the single-stripe phase region. The four-state Potts critical end points differentiating the continuous transitions from the first-order ones are estimated based on finite-size-scaling analyses. Furthermore, a similar behavior of the transition to the fourfold single-stripe phase is also observed in the anisotropic triangular Ising model. Thus, this work clearly demonstrates that the transitions to the fourfold degenerate states of two-dimensional Ising antiferromagnets exhibit similar transition behavior.

Understanding the multiferroicity in TmMn2O5 by a magnetically induced ferrielectric model.

The magnetically induced electric polarization behaviors in multiferroic TmMn2O5 in response to varying temperature and magnetic field are carefully investigated by means of a series of characterizations including the high precision pyroelectric current technique. Here polycrystalline rather than single crystal samples are used for avoiding the strong electrically self-polarized effect in single crystals, and various parallel experiments on excluding the thermally excited current contributions are performed. The temperature-dependent electric polarization flop as a major character is identified for different measuring paths. The magneto-current measurements indicate that the electric polarization in the low temperature magnetic phase region has different origin from that in the high temperature magnetic phase. It is suggested that the electric polarization does have multiple components which align along different orientations, including the Mn3+-Mn4+-Mn3+ exchange striction induced polarization PMM, the Tm3+-Mn4+-Tm3+ exchange striction induced polarization PTM, and the low temperature polarization PLT probably associated with the Tm3+ commensurate phase. The observed electric polarization flop can be reasonably explained by the ferrielectric model proposed earlier for DyMn2O5, where PMM and PTM are the two antiparallel components both along the b-axis and PLT may align along the a-axis. Finally, several issues on the unusual temperature dependence of ferroelectric polarizations are discussed.

Effect of further-neighbor interactions on the magnetization behaviors of the Ising model on a triangular lattice.

In this work, we study the magnetization behaviors of the classical Ising model on the triangular lattice using Monte Carlo simulations, and pay particular attention to the effect of further-neighbor interactions. Several fascinating spin states are identified to be stabilized in certain magnetic field regions, respectively, resulting in the magnetization plateaus at 2/3, 5/7, 7/9 and 5/6 of the saturation magnetization M S, in addition to the well-known plateaus at 0, 1/3 and 1/2 of M S. The stabilization of these interesting orders can be understood as the consequence of the competition between Zeeman energy and exchange energy.

Role of further-neighbor interactions in modulating the critical behavior of the Ising model with frustration.

In this work, we investigate the phase transitions and critical behaviors of the frustrated J(1)-J(2)-J(3) Ising model on the square lattice using Monte Carlo simulations, and particular attention goes to the effect of the second-next-nearest-neighbor interaction J(3) on the phase transition from a disordered state to the single stripe antiferromagnetic state. A continuous Ashkin-Teller-like transition behavior in a certain range of J(3) is identified, while the four-state Potts-critical end point [J(3)/J(1)](C) is estimated based on the analytic method reported in earlier work [Jin, Sen, and Sandvik, Phys. Rev. Lett. 108, 045702 (2012)]. It is suggested that the interaction J(3) can tune the transition temperature and in turn modulate the critical behaviors of the frustrated model. Furthermore, it is revealed that an antiferromagnetic J(3) can stabilize the staggered dimer state via a phase transition of strong first-order character.

Multi-step magnetization of the Ising model on a Shastry-Sutherland lattice: a Monte Carlo simulation.

The magnetization behaviors and spin configurations of the classical Ising model on a Shastry-Sutherland lattice are investigated using Monte Carlo simulations, in order to understand the fascinating magnetization plateaus observed in TmB(4) and other rare-earth tetraborides. The simulations reproduce the 1/2 magnetization plateau by taking into account the dipole-dipole interaction. In addition, a narrow 2/3 magnetization step at low temperature is predicted in our simulation. The multi-step magnetization can be understood as the consequence of the competitions among the spin-exchange interaction, the dipole-dipole interaction, and the static magnetic energy.

Fiber surface characterization of old newsprint pulp deinked by combining hemicellulase with laccase-mediator system.

Deinking of old newsprint (ONP) by combining hemicellulase with laccase-mediator system (LMS) was investigated, and surface chemical composition and fiber morphology changes during the deinking process were studied by electron spectroscopy for chemical analysis (ESCA), contact angle (CA), attenuated total reflectance fourier transform infrared spectrometry (ATR-FTIR), fiber quality analyzer (FQA), and environmental scanning electronic microscopy (ESEM). Results showed that, compared to the pulp deinked with hemicellulase or LMS individually, effective residual ink concentration (ERIC) was lower for the hemicellulase/LMS-deinked pulp. This indicated that there is a synergistic deinking effect between hemicellulase and LMS. It was found that O/C ratio of the fiber surface increased and the surface coverage of lignin decreased during the hemicellulase/LMS deinking process. The contact angle of the hemicellulase/LMS-deinked pulp was lower than that of pulps deinked with each individual enzyme. ESEM observations showed that more fibrils appeared on the fiber surface due to synergistic treatment.

Effect of bio-treatment on the lipophilic and hydrophilic extractives of wheat straw.

Wheat straw, an important papermaking raw material in China, was treated with a white-rot fungus of Phanerochaete chrysosporium ME446, and the lipophilic and hydrophilic extractives from the control and bio-treated samples were analyzed by GC and GC-MS. Bio-treatment of wheat straw could alter the chemical composition of both the lipophylic and hydrophilic extractives. Sugars and phenolic substances such as coniferyl alcohol, 4-hydroxycinnamic acid, 1-guaiacylglycerol and ferulic acid were substantially degraded or consumed by the fungus. More lipophilic substances such as wax, glycerides and steryl esters were degraded into the corresponding components, resulting in much higher concentrations of fatty acids and sterols in the bio-treated samples. Obviously, the bio-treatment of wheat straw was of benefit to pitch control in pulping and papermaking processes, in the view of degradation of the more lipophilic substances. In addition, the bio-treatment could increase the lignin concentration in hot-water extractives of wheat straw.

Succinoylation of sugarcane bagasse under ultrasound irradiation.

The chemical modification of sugarcane bagasse with succinic anhydride using pyridine as solvent after ultrasound irradiation was studied. The optimized parameters included ultrasound irradiating time 0-50 min, reaction time 30-120 min, succinic anhydride concentration by the ratio of dried sugarcane bagasse to succinic anhydride from 1:0.25 to 1:1.50, and reaction temperature 75-115 degrees C are required in the process. The extent of succinoylation was measured by the weight percent gain (WPG), which increased with increments of reaction time, succinic anhydride concentration, and reaction temperature. The ultrasound irradiation has a positive effect on bagasse succinoylation process. On the other hand, the ultrasonic pre-treatment application broke down the cell wall polymers, resulting in, therefore, a negative effect on the WPG. Evidences of succinoylation were also provided by FT-IR and CP MAS (13)C NMR and the results showed that the succinoylation at C-2 and C-3 occurred. The thermal stability of the succinylated bagasse decreased upon chemical modification.

Homogeneous modification of sugarcane bagasse cellulose with succinic anhydride using a ionic liquid as reaction medium.

The homogeneous chemical modification of sugarcane bagasse cellulose with succinic anhydride using 1-allyl-3-methylimidazolium chloride (AmimCl) ionic liquid as a reaction medium was studied. Parameters investigated included the molar ratio of succinic anhydride/anhydroglucose units in cellulose in a range from 2:1 to 14:1, reaction time (from 30 to 160min), and reaction temperature (between 60 and 110 degrees C). The succinylated cellulosic derivatives were prepared with a low degree of substitution (DS) ranging from 0.071 to 0.22. The results showed that the increase of reaction temperature, molar ratio of SA/AGU in cellulose, and reaction time led to an increase in DS of cellulose samples. The products were characterized by FT-IR and solid-state CP/MAS (13)C NMR spectroscopy, and thermal analysis. It was found that the crystallinity of the cellulose was completely disrupted in the ionic liquid system under the conditions given. The data also demonstrated that homogeneous modification of cellulose with succinic anhydride in AmimCl resulted in the production of cellulosic monoester. The thermal stability of the succinylated cellulose decreased upon chemical modification.

Development of simple and efficient protocol for isolation of plasmids from mycobacteria using zirconia beads.

A two-step protocol has been developed for isolation of plasmids from recombinant mycobacteria via Escherichia coli. First either mycobacterial primary transformants or propagated cultures were lysed in a mini-bead beater using zirconia beads and the lysate thus obtained was used to transform E. coli recA mutant cells. Secondly, plasmid DNA was isolated from recombinant E. coli cells and analysed. Bead beating times of 2 min for Mycobacterium smegmatis, a rapid grower, and 4 min for M. bovis BCG, a slow grower, were found to be optimal for recovery of plasmid DNA. This protocol was also amenable to other mycobacterial species such as M. avium, M. fortuitum and M. tuberculosis H37Ra. Plasmid recovery from the recombinant M. bovis BCG using this protocol is approximately 300-fold higher than that reported for the electroduction method.

The dnaA gene region of Mycobacterium avium and the autonomous replication activities of its 5' and 3' flanking regions.

A 3.9 kb DNA fragment containing the dnaA gene region of Mycobacterium avium was cloned and its nucleotide sequence was determined. Nucleotide sequence analyses indicated that this region encodes three genes in the order rpmH (ribosomal protein L34), dnaA (the putative initiator protein) and dnaN (the beta subunit of DNA polymerase III). The intergenic regions between the rpmH-dnaA and dnaA-dnaN genes were found to contain several putative DnaA boxes, 9 nt long DnaA protein recognition sequences. A DNA fragment containing the 3' but not the 5' flanking region of the M. avium dnaA gene when cloned in Escherichia coli plasmids, which are otherwise non-replicative in mycobacteria, exhibited autonomous replication activity in M. avium but not in Mycobacterium bovis BCG and Mycobacterium smegmatis. The 5' flanking region of dnaA, on the other hand, exhibited autonomous replication activity in M. bovis BCG but not in M. avium and M. smegmatis. The implications of these results for the understanding of the M. avium oriC replication initiation process are discussed.

Characterization of the functional replication origin of Mycobacterium tuberculosis.

The gene order in the 5kb Mycobacterium tuberculosis dnaA region is rnpA, rpmH, dnaA, dnaN and recF. We show that M. tuberculosis DNA fragment containing the dnaA-dnaN intergenic region functioned as oriC, i.e., allowed autonomous replication to otherwise nonreplicative plasmids, in M. tuberculosis H37Ra (H37Ra), avirulent strain of M. tuberculosis, and in Mycobacterium bovis BCG (BCG), a closely related, slowly growing mycobacterial strain. Removal of Escherichia coli plasmid replication origin (ColE1) from the M. tuberculosis oriC plasmids did not abolish their ability to function as oriC, confirming that the autonomous replication activity of these plasmids is due to the presence of the DNA fragment containing the dnaA-dnaN intergenic region. Deletion analyses revealed that the minimal oriC DNA fragment is 814bp. The copy number of M. tuberculosis oriC plasmids containing ColE1 ori relative to chromosomal oriC is one and the 5' flanking region of minimal oriC contains features that support stable autonomous replication. The M. tuberculosis oriC did not function in rapidly growing mycobacterial species such as M. smegmatis. M. smegmatis oriC functioned only in M. fortuitum, but not in any of the slowly growing mycobacterial species such as M. tuberculosis and BCG. Together these data suggest that the replication initiation mechanisms in the slowly growing Mycobacteria are similar and probably different from those in the rapidly growing Mycobacteria and vice versa.

Characterization of the oriC region of Mycobacterium smegmatis.

A 3.5-kb DNA fragment containing the dnaA region of Mycobacterium smegmatis has been hypothesized to be the chromosomal origin of replication or oriC (M. Rajagopalan et al., J. Bacteriol. 177:6527-6535, 1995). This region included the rpmH gene, the dnaA gene, and a major portion of the dnaN gene as well as the rpmH-dnaA and dnaA-dnaN intergenic regions. Deletion analyses of this region revealed that a 531-bp DNA fragment from the dnaA-dnaN intergenic region was sufficient to exhibit oriC activity, while a 495-bp fragment from the same region failed to exhibit oriC activity. The oriC activities of plasmids containing the 531-bp sequence was less than the activities of those containing the entire dnaA region, suggesting that the regions flanking the 531-bp sequence stimulated oriC activity. The 531-bp region contained several putative nine-nucleotide DnaA-protein recognition sequences [TT(G/C)TCCACA] and a single 11-nucleotide AT-rich cluster. Replacement of adenine with guanine at position 9 in five of the putative DnaA boxes decreased oriC activity. Mutations at other positions in two of the DnaA boxes also decreased oriC activity. Deletion of the 11-nucleotide AT-rich cluster completely abolished oriC activity. These data indicate that the designated DnaA boxes and the AT-rich cluster of the M. smegmatis dnaA-dnaN intergenic region are essential for oriC activity. We suggest that M. smegmatis oriC replication could involve interactions of the DnaA protein with the putative DnaA boxes as well as with the AT-rich cluster.

Interactions of RecF protein with RecO, RecR, and single-stranded DNA binding proteins reveal roles for the RecF-RecO-RecR complex in DNA repair and recombination.

The products of the recF, recO, and recR genes are thought to interact and assist RecA in the utilization of single-stranded DNA precomplexed with single-stranded DNA binding protein (Ssb) during synapsis. Using immunoprecipitation, size-exclusion chromatography, and Ssb protein affinity chromatography in the absence of any nucleotide cofactors, we have obtained the following results: (i) RecF interacts with RecO, (ii) RecF interacts with RecR in the presence of RecO to form a complex consisting of RecF, RecO, and RecR (RecF-RecO-RecR); (iii) RecF interacts with Ssb protein in the presence of RecO. These data suggested that RecO mediates the interactions of RecF protein with RecR and with Ssb proteins. Incubation of RecF, RecO, RecR, and Ssb proteins resulted in the formation of RecF-RecO-Ssb complexes; i.e., RecR was excluded. Preincubation of RecF, RecO, and RecR proteins prior to addition of Ssb protein resulted in the formation of complexes consisting of RecF, RecO, RecR, and Ssb proteins. These data suggest that one role of RecF is to stabilize the interaction of RecR with RecO in the presence of Ssb protein. Finally, we found that interactions of RecF with RecO are lost in the presence of ATP. We discuss these results to explain how the RecF-RecO-RecR complex functions as an anti-Ssb factor.

Mycobacterium smegmatis dnaA region and autonomous replication activity.

Two key elements that are thought to be required for replication initiation in eubacteria are the DnaA protein, a trans-acting factor, and the replication origin, a cis-acting element. As a first step in studying the replication initiation process in mycobacteria, we have isolated a 4-kb chromosomal DNA fragment from Mycobacterium smegmatis that contains the dnaA gene. Nucleotide sequence analysis of this region revealed homologies with the rpmH gene, which codes for the ribosomal protein L34, the dnaA gene, which codes for the replication initiator protein DnaA, and the 5' end of the dnaN gene, which codes for the beta subunit of DNA polymerase III. Further, we provide evidence that when cloned into pUC18, a plasmid that is nonreplicative in M. smegmatis, the DNA fragment containing the dnaA gene and its flanking regions rendered the former capable of autonomous replication in M. smegmatis. We suggest that the M. smegmatis chromosomal origin of replication is located within the 4-kb DNA fragment.

Amplification and cloning of the Mycobacterium tuberculosis dnaA gene.

To identify and subsequently clone the gene encoding the DnaA protein, degenerate oligodeoxyribonucleotide (oligo) primers targeted against two highly conserved domains of the eubacterial DnaA were used to amplify a 780-bp DNA region spanning the two primers from genomic DNA preparations of Mycobacterium tuberculosis (Mt), M. bovis (Mb) and M. avium (Ma). Nucleotide (nt) sequences and deduced amino acid (aa) sequences of these fragments revealed homologies with each other and with the corresponding regions from other bacteria. Using an oligo specific to Mt dnaA as a probe, the Mt genomic DNA cosmid libraries propagated in Escherichia coli were screened and a cosmid DNA clone hybridizing with the oligo was identified. Furthermore, a 5-kb DNA fragment containing the Mt dnaA was subcloned into a pUC18 vector.

Protein profiles of Legionella pneumophila Philadelphia-1 grown in macrophages and characterization of a gene encoding a novel 24 kDa Legionella protein.

Legionella pneumophila Philadelphia-1 strain was grown in cultured macrophages of guinea pigs, hamsters, and A/J mice and the bacteria were purified by Percoll density gradient centrifugation without any detergent. Patterns of the bacterial proteins were compared by SDS-PAGE with those of organisms cultured in vitro. A 24 kDa protein was a major protein of intracellularly grown bacteria: its expression was about four times as much as a 24 kDa protein of agar-grown bacteria. At least three novel proteins (100, 65, and 16 kDa) that were not found on agar-grown bacteria were also observed. In this paper, we focused on the 24 kDa major Legionella protein expressed within macrophages. Western blot and N-terminal amino acid analysis revealed that this protein is a novel protein different from Legionella proteins previously reported, including a 24 kDa macrophage infectivity potentiator protein (Mip). On the basis of amino acid sequence (MQRIKKI and IANAQGK), two kinds of oligonucleotides were synthesized and radiolabeled. Using these oligonucleotides as DNA probes, a 7.2 kb EcoRI-digested DNA fragment encoding the 24 kDa protein was cloned into lambda ZAP II phage vector in Escherichia coli XL1-Blue. A 0.9 kb DNA fragment from the 7.2 kb fragment was further subcloned into pUC118 in E. coli CSR603 for maxicell analysis or XL1-Blue for DNA sequencing. Maxicells which carry recombinant plasmids consisting of the 0.9 kb DNA fragment and vector plasmid pUC118 expressed the 24 kDa protein. When the DNA fragment encoding the protein was sequenced, an open reading frame of 555 base pairs was identified. The inferred polypeptide had a molecular weight of 20 kDa and an estimated isoelectric point of 8.14. Both the nucleotide sequence and the deduced amino acid sequence were distinct from those of bacterial proteins reported previously, suggesting that the protein is a novel Legionella protein.