Single-Molecule DNA Analysis Reveals That Yeast Hop1 Protein Promotes DNA Folding and Synapsis: Implications for Condensation of Meiotic Chromosomes

During meiosis, long-range interaction between homologous chromosomes is thought to be crucial for homology recognition, exchange of DNA strands, and production of normal haploid gametes. However, little is known about the identity of the proteins involved and the actual molecular mechanism(s) by which chromosomes recognize and recombine with their appropriate homologous partners. Single-molecule analyses have the potential to provide insights into our understanding of this fascinating and long-standing question. Using atomic force microscopy and magnetic tweezers techniques, we discovered that Hop1 protein, a key structural component of Saccharomyces cerevisiae synaptonemal complex, exhibits the ability to bridge noncontiguous DNA segments into intramolecular stem-loop structures in which the DNA segments appear to be fully synapsed within the filamentous protein stems. Additional evidence suggests that Hop1 folds DNA into rigid protein DNA filaments and higher-order nucleoprotein structures. Importantly, Hop1 promotes robust intra- and intermolecular synapsis between double-stranded DNA molecules, suggesting that juxtaposition of DNA sequences may assist in strand exchange between homologues by recombination-associated proteins. Finally, the evidence from ensemble experiments is consistent with the notion that Hop1 causes rigidification of DNA molecules. These results provide the first direct evidence for long-range protein-mediated DNA DNA synapsis, independent of crossover recombination, which is presumed to occur during meiotic recombination.

Effect of substrate surface roughness on electric current induced flow of liquid metals

Electric current can induce long-range flow of liquid metals over a conducting substrate. This work reports on the effect of the substrate surface roughness on the liquid metal-front velocity during such a flow. Experiments were conducted by passing electric current through liquid gallium placed over similar to 170 nm thick, 500 mu m wide gold and platinum films of varying roughness. The ensuing flow, thus, resembles micro-fluidics behavior in an open-channel. The liquid-front velocity decreased linearly with the substrate surface roughness; this is attributed to the reduction in the effective electric field along the liquid metal-substrate interface with the substrate surface roughness. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4790182]

Exploiting coherence for the simultaneous discovery of latent facets and associated sentiments

Facet-based sentiment analysis involves discovering the latent facets, sentiments and their associations. Traditional facet-based sentiment analysis algorithms typically perform the various tasks in sequence, and fail to take advantage of the mutual reinforcement of the tasks. Additionally,inferring sentiment levels typically requires domain knowledge or human intervention. In this paper, we propose aseries of probabilistic models that jointly discover latent facets and sentiment topics, and also order the sentiment topics with respect to a multi-point scale, in a language and domain independent manner. This is achieved by simultaneously capturing both short-range syntactic structure and long range semantic dependencies between the sentiment and facet words. The models further incorporate coherence in reviews, where reviewers dwell on one facet or sentiment level before moving on, for more accurate facet and sentiment discovery. For reviews which are supplemented with ratings, our models automatically order the latent sentiment topics, without requiring seed-words or domain-knowledge. To the best of our knowledge, our work is the first attempt to combine the notions of syntactic and semantic dependencies in the domain of review mining. Further, the concept of facet and sentiment coherence has not been explored earlier either. Extensive experimental results on real world review data show that the proposed models outperform various state of the art baselines for facet-based sentiment analysis.

Low-pass filters and differential tympanal tuning in a paleotropical bushcricket with an unusually low frequency call

Low-frequency sounds are advantageous for long-range acoustic signal transmission, but for small animals they constitute a challenge for signal detection and localization. The efficient detection of sound in insects is enhanced by mechanical resonance either in the tracheal or tympanal system before subsequent neuronal amplification. Making small structures resonant at low sound frequencies poses challenges for insects and has not been adequately studied. Similarly, detecting the direction of long-wavelength sound using interaural signal amplitude and/or phase differences is difficult for small animals. Pseudophylline bushcrickets predominantly call at high, often ultrasonic frequencies, but a few paleotropical species use lower frequencies. We investigated the mechanical frequency tuning of the tympana of one such species, Onomarchus uninotatus, a large bushcricket that produces a narrow bandwidth call at an unusually low carrier frequency of 3.2. kHz. Onomarchus uninotatus, like most bushcrickets, has two large tympanal membranes on each fore-tibia. We found that both these membranes vibrate like hinged flaps anchored at the dorsal wall and do not show higher modes of vibration in the frequency range investigated (1.5-20. kHz). The anterior tympanal membrane acts as a low-pass filter, attenuating sounds at frequencies above 3.5. kHz, in contrast to the high-pass filter characteristic of other bushcricket tympana. Responses to higher frequencies are partitioned to the posterior tympanal membrane, which shows maximal sensitivity at several broad frequency ranges, peaking at 3.1, 7.4 and 14.4. kHz. This partitioning between the two tympanal membranes constitutes an unusual feature of peripheral auditory processing in insects. The complex tracheal shape of O. uninotatus also deviates from the known tube or horn shapes associated with simple band-pass or high-pass amplification of tracheal input to the tympana. Interestingly, while the anterior tympanal membrane shows directional sensitivity at conspecific call frequencies, the posterior tympanal membrane is not directional at conspecific frequencies and instead shows directionality at higher frequencies.

Evidence of collective relaxation behavior in the reentrant phase of oxygen-rich LaMnO3

The reentrant low temperature phase of the perovskite manganite LaMnO3+delta (delta=0.22) has been investigated with ac susceptibility and dc magnetization studies. A critical examination of the memory effects in ac susceptibility leads us to the conclusion that the slow dynamics in the system is a consequence of collective relaxation processes resulting from interactions between ferromagnetic clusters, whose presence was indicated in earlier studies. Here, we postulate that the collective behavior is due to the existence of long-range (dipolar) interactions between the large ferromagnetic `superspins'. This is also confirmed by an abnormally large microscopic spin-flip time (similar to 10(-9) s) compared to a canonical spin glass. (C) 2013 Elsevier B.V. All rights reserved.

Anomalous optical phonons in Cs-0.9(NH4)(0.1)H2AsO4: a temperature-dependent Raman study

We determine the nature of coupled phonons in mixed crystal of Cs-0.9(NH4)(0.1)H2AsO4 using inelastic light scattering studies in the temperature range of 5 K to 300 K covering a spectral range of 60-1100 cm(-1). The phase transition in this system are marked by the splitting of phonon modes, appearance of new modes and anomalies in the frequency as well as linewidth of the phonon modes near transition temperature. In particular, we observed the splitting of symmetric (v(1)) and antisymmetric (v(3)) stretching vibrations associated with AsO4 tetrahedra below transition temperature (T-c(*) similar to 110 K) attributed to the lowering of site symmetry of AsO4 in orthorhombic phase below transition temperature. In addition, the step-up (hardening) and step-down (softening) of the AsO4 bending vibrations (v(4) (S9, S11) and v(2) (S6)) below transition temperature signals the rapid development of long range ferroelectric order and proton ordering. The lowest frequency phonon (S1) mode observed at similar to 92 cm(-1) shows anomalous blue shift (similar to 12 %) from 300 K to 5 K with no sharp transition near T-c(*) unlike other observed phonon modes signaling its potential coupling with the proton tunneling mode. (C) 2013 Author(s).

Linear and nonlinear optical properties of expanded porphyrins: a DMRG study

We study absorption spectra and two photon absorption coefficient of expanded porphyrins (EPs) by the density matrix renormalization group (DMRG) technique. We employ the Pariser-Parr-Pople (PPP) Hamiltonian which includes long-range electron-electron interactions. We find that, in the 4n+2 EPs, there are two prominent low-lying one-photon excitations, while in 4n EPs, there is only one such excitation. We also find that 4n+2 EPs have large two-photon absorption cross sections compared to 4n EPs. The charge density rearrangement in the one-photon excited state is mostly at the pyrrole nitrogen site and at the meso carbon sites. In the two-photon states, the charge density rearrangement occurs mostly at the aza-ring sites. In the one-photon state, the C-C bond length in aza rings shows a tendency to become uniform. In the two-photon state, the bond distortions are on C-N bonds of the pyrrole ring and the adjoining C-C bonds which connect the pyrrole ring to the aza or meso carbon sites.

Evolution of ferromagnetism from a frustrated state in LixNi(2-x)O2 (0.67 < x < 0.98)

Two-dimensional triangular-lattice antiferromagnetic systems continue to be an interesting area in condensed matter physics and LiNiO2 is one such among them. Here we present a detailed experimental magnetic study of the quasi-stoichiometric LixNi2-xO2 system (0.67long-range mean-field model. The values of the critical exponents are confirmed by the Widom scaling law: delta = 1 + gamma beta(-1). Furthermore, the universality class of the scaling relations is verified, where the scaled m and scaled h collapse into two branches. Finally, based on our observations, a phase diagram is constructed.

Correlated Conductance Fluctuations Close to the Berezinskii-Kosterlitz-Thouless Transition in Ultrathin NbN Films

We probe the presence of long-range correlations in phase fluctuations by analyzing the higher-order spectrum of resistance fluctuations in ultrathin NbN superconducting films. The non-Gaussian component of resistance fluctuations is found to be sensitive to film thickness close to the transition, which allows us to distinguish between mean field and Berezinskii-Kosterlitz-Thouless (BKT) type superconducting transitions. The extent of non-Gaussianity was found to be bounded by the BKT and mean field transition temperatures and depends strongly on the roughness and structural inhomogeneity of the superconducting films. Our experiment outlines a novel fluctuation-based kinetic probe in detecting the nature of superconductivity in disordered low-dimensional materials.

Local structural disorder and its influence on the average global structure and polar properties in Na0.5Bi0.5TiO3

Na0.5Bi0.5TiO3 (NBT) and its derivatives have prompted a great surge in interest owing to their potential as lead-free piezoelectrics. In spite of five decades since its discovery, there is still a lack of clarity on crucial issues such as the origin of significant dielectric relaxation at room temperature, structural factors influencing its depoling, and the status of the recently proposed monoclinic (Cc) structure vis-a-vis the nanosized structural heterogeneities. In this work, these issues are resolved by comparative analysis of local and global structures on poled and unpoled NBT specimens using electron, x-ray, and neutron diffraction in conjunction with first-principles calculation, dielectric, ferroelectric, and piezoelectric measurements. The reported global monoclinic (Cc) distortion is shown not to correspond to the thermodynamic equilibrium state at room temperature. The global monocliniclike appearance rather owes its origin to the presence of local structural and strain heterogeneities. Poling removes the structural inhomogeneities and establishes a long-range rhombohedral distortion. In the process the system gets irreversibly transformed from a nonergodic relaxor to a normal ferroelectric state. The thermal depoling is shown to be associated with the onset of incompatible in-phase tilted octahedral regions in the field-stabilized long range rhombohedral distortion.

Magnetic Structure and Properties of the Rechargeable Battery Insertion Compound Na2FePO4F

The magnetic structure and properties of sodium iron fluorophosphate Na2FePO4F (space group Pbcn), a cathode material for rechargeable batteries, were studied using magnetometry and neutron powder diffraction. The material, which can be described as a quasi-layered structure with zigzag Fe-octahedral chains, develops a long-range antiferromagnetic order below similar to 3.4 K. The magnetic structure is rationalized as a super-exchange-driven ferromagnetic ordering of chains running along the a-axis, coupled antiferromagnetically by super-super-exchange via phosphate groups along the c-axis, with ordering along the b-axis likely due to the contribution of dipole dipole interactions.

Electric current induced flow of liquid metals: Mechanism and substrate-surface effects

Long range, continuous flow of liquid metals occurs upon application of an electric current. Here, we report experimental results elucidating the mechanism of current-induced liquid metal flow, and its dependence on substrate surface condition. It is shown that the observed flow is diffusion-controlled, with the flow-rate depending linearly on applied current density, indicating that it is driven by electromigration. The effective charge number for liquid electromigration, Z*, of several pure metals, such as Al, Bi, Ga, Sn, and Pb, were deduced from the experimental results and were found to be close to the elemental valency. With the exception of liquid Pb, Z* for all liquid metals tested in this study were positive, indicating that: (i) electron wind contributes much less to Z* in liquid metals than in solids, and (ii) with a few exceptions, liquid metals generally flow in the direction of the electric current. On smooth substrates which are wetted well by the liquid metal, flow occurs in a thin, continuous stream. On rough surfaces which are poorly wetted, on the other hand, discrete beads of liquid form, with mass transport between adjacent beads occurring by surface diffusion on the substrate. A rationale for the role of substrate roughness in fostering this observed transition in flow mechanism is presented. (C) 2014 AIP Publishing LLC.

Beyond the ``Coffee Ring'': Re-entrant Ordering in an Evaporation-Driven Self-Assembly in a Colloidal Suspension on a Substrate

We study the phenomenon of evaporation-driven self-assembly of a colloid suspension of silica microspheres in the interior region and away from the rim of the droplet on a glass plate. In view of the importance of achieving a large-area, monolayer assembly, we first realize a suitable choice of experimental conditions, minimizing the influence of many other competing phenomena that usually complicate the understanding of fundamental concepts of such self-assembly processes in the interior region of a drying droplet. Under these simplifying conditions to bring out essential aspects, our experiments unveil an interesting competition between ordering and compaction in such drying systems in analogy to an impending glass transition. We establish a re-entrant behavior in the order disorder phase diagram as a function of the particle density, such that there is an optimal range of the particle density to realize the long-range ordering. The results are explained with the help of simulations and phenomenological theory.

Supersolid in a one-dimensional model of hard-core bosons

We study a system of hard-core boson on a one-dimensional lattice with frustrated next-nearest-neighbor hopping and nearest-neighbor interaction. At half filling, for equal magnitude of nearest- and next-nearest-neighbor hopping, the ground state of this system exhibits a first-order phase transition from a bond-ordered solid to a charge-density-wave solid as a function of the nearest- neighbor interaction. Moving away from half filling we investigate the system at incommensurate densities, where we find a supersolid phase which has concurrent off-diagonal long-range order and density-wave order which is unusual in a system of hard-core bosons in one dimension. Using the finite-size density-matrix renormalization group method, we obtain the complete phase diagram for this model.

Suppression of grain boundary relaxation in Zr-doped BiFeO3 thin films

Here, we present the results of temperature dependent dielectric studies on chemical solution processed Zr-doped BiFeO3 (BFO) thin films deposited on Pt/Si substrates. We find that in contrast to the undoped BFO films, Zr doping at Fe-site suppresses the low frequency dielectric relaxation originating from the grain boundaries, attributed to the increased dipolar rigidity due to stronger Zr-O bonds. Temperature dependent dc conductivity obtained from impedance and modulus analyses shows two distinct conduction processes occurring inside the grains. At temperature below similar to 423K, conductivity is nearly temperature independent, while in the high temperature regime (above similar to 423K), conduction is governed by the long range movement of oxygen vacancies with an activation energy of similar to 1eV. (C) 2014 AIP Publishing LLC.