Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (T-m's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At T-m Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at T-m with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a P-fold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for both the thermodynamics and kinetics of folding are not only in agreement with experiments but also provide missing details not resolvable in standard experiments. The key prediction that folding mechanism varies dramatically with pH is amenable to experimental tests.

A novel acoustic-vibratory multimodal duet

The communication strategy of most crickets and bushcrickets typically consists of males broadcasting loud acoustic calling songs, while females perform phonotaxis, moving towards the source of the call. Males of the pseudophylline bushcricket species Onomarchus uninotatus produce an unusually low-pitched call, and we found that the immediate and most robust response of females to the male acoustic call was a bodily vibration, or tremulation, following each syllable of the call. We hypothesized that these bodily oscillations might send out a vibrational signal along the substrate on which the female stands, which males could use to localize her position. We quantified these vibrational signals using a laser vibrometer and found a clear phase relationship of alternation between the chirps of the male acoustic call and the female vibrational response. This system therefore constitutes a novel multimodal duet with a reliable temporal structure. We also found that males could localize the source of vibration but only if both the acoustic and vibratory components of the duet were played back. This unique multimodal duetting system may have evolved in response to higher levels of bat predation on searching bushcricket females than calling males, shifting part of the risk associated with partner localization onto the male. This is the first known example of bushcricket female tremulation in response to a long-range male acoustic signal and the first known example of a multimodal duet among animals.

Role of different scattering mechanisms on the temperature dependence of transport in graphene

Detailed experimental and theoretical studies of the temperature dependence of the effect of different scattering mechanisms on electrical transport properties of graphene devices are presented. We find that for high mobility devices the transport properties are mainly governed by completely screened short range impurity scattering. On the other hand, for the low mobility devices transport properties are determined by both types of scattering potentials - long range due to ionized impurities and short range due to completely screened charged impurities. The results could be explained in the framework of Boltzmann transport equations involving the two independent scattering mechanisms.

Neutron powder diffraction study of Ba3ZnRu2-xIrxO9 (x=0, 1, 2) with 6H-type perovskite structure

The triple perovskites Ba3ZnRu2-xIrxO9 with x = 0, 1, and 2 are insulating compounds in which Ru(Ir) cations form a dimer state. Polycrystalline samples of these materials were studied using neutron powder diffraction (NPD) at 10 and 295 K. No structural transition nor evidence of long range magnetic order was observed within the investigated temperature range. The results from structural refinements of the NPD data and its polyhedral analysis are presented, and discussed as a function of Ru/Ir content. (C) 2015 Elsevier Masson SAS. All rights reserved.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.

Anomalous re-entrant glassy magnetic phase in LaMn0.5Co0.5O3 single crystals

We report an anomalous re-entrant glassy magnetic phase in (l00) oriented ferromagnetic LaMn0.5Co0.5O3 single crystals. The characterization is fortified with conventional magnetometry, like linear as-well-as non-linear ac susceptibility and specific heat. As the sample is cooled below the ferromagnetic transition temperature, it reenters a glassy magnetic phase whose dynamics have little resemblance with the conventional response. The glassy transition shifts to a higher temperature with increasing frequency of the applied ac field. But it does not respond to the dc biasing or memory experiment. Specific heat as well as non-linear ac susceptibility data also do not relate to the conventional glassy response. Unusually low magnetic entropy indicates the lack of long range magnetic ordering. The results demonstrate that the glassy phase in LaMn0.5Co0.5O3 is not due to any of the known conventional origins. We infer that the competing ferromagnetic and antiferromagnetic interaction due to high B-site disorder is responsible for this anomalous re-entrant glassy phase. (C) 2016 AIP Publishing LLC.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.

Anomalous re-entrant glassy magnetic phase in LaMn0.5Co0.5O3 single crystals

We report an anomalous re-entrant glassy magnetic phase in (l00) oriented ferromagnetic LaMn0.5Co0.5O3 single crystals. The characterization is fortified with conventional magnetometry, like linear as-well-as non-linear ac susceptibility and specific heat. As the sample is cooled below the ferromagnetic transition temperature, it reenters a glassy magnetic phase whose dynamics have little resemblance with the conventional response. The glassy transition shifts to a higher temperature with increasing frequency of the applied ac field. But it does not respond to the dc biasing or memory experiment. Specific heat as well as non-linear ac susceptibility data also do not relate to the conventional glassy response. Unusually low magnetic entropy indicates the lack of long range magnetic ordering. The results demonstrate that the glassy phase in LaMn0.5Co0.5O3 is not due to any of the known conventional origins. We infer that the competing ferromagnetic and antiferromagnetic interaction due to high B-site disorder is responsible for this anomalous re-entrant glassy phase. (C) 2016 AIP Publishing LLC.

Effect of morphology on the magnetic properties of Gd2O3 nanotubes

Gadolinium oxide (Gd2O3) nanotubes of micron length and average diameter 100 nm have been synthesized by a controlled template-assisted electrochemical deposition technique. Structure and morphology of the synthesized nanotubes have been well characterized by using microscopy and spectroscopy analyses. HRTEM and XRD analysis revealed the crystalline planes of Gd2O3 nanotubes. Magnetic measurements of the aligned Gd2O3 nanotubes have been performed for both parallel and perpendicular orientations of the magnetic field with respect to the axis of the Gd2O3 nanotube array. Large bifurcation in ZFC-FC over the regime of 2-320 K without any signature of long range magnetic ordering confirms the presence of SPM clusters in Gd2O3 nanotubes. Also, large magnetocaloric effect is observed in the cryogenic temperature regime. No anisotropy is seen at the low temperature region but is found to evolve with temperature and becomes significant 300 K. These nanotubes can be considered as promising candidates for magnetic refrigeration at cryogenic temperature. (C) 2016 Elsevier B.V. All rights reserved.

Spin-glass state in nanoparticulate (La0.7Sr0.3MnO3)(1-x) (BaTiO3)(x) solid solutions: Experimental and density-functional studies

We report the transition from robust ferromagnetism to a spin- glass state in nanoparticulate La0.7Sr0.3MnO3 through solid solution with BaTiO3. The field- and temperature-dependent magnetization and the frequency-dependent ac magnetic susceptibility measurements strongly indicate the existence of a spin- glass state in the system, which is further confirmed from memory effect measurements. The breaking of long-range ordering into short-range magnetic domains is further investigated using density-functional calculations. We show that Ti ions remain magnetically inactive due to insufficient electron leakage from La0.7Sr0.3MnO3 to the otherwise unoccupied Ti-d states. This results in the absence of a Mn-Ti-Mn spin exchange interaction and hence the breaking of the long-range ordering. Total-energy calculations suggest that the segregation of nonmagnetic Ti ions leads to the formation of short-range ferromagnetic Mn domains.

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

Using a molecular model for octamethylcydotetrasiloxane (OMCTS), molecular dynamics simulations are carried out to probe the phase state of OMCTS confined between two mica surfaces in equilibrium With a reservoir. Molecular dynamics simulations are carried out for elevations ranging from 5 to 35 K above the melting point for the OMCTS model used in this study. The Helmholtz free energy is, computed for a specific confinement using the :two-phase thermodynamic (2PT) method. Analysis of the in-plane pair correlation functions did not reveal signatures of freezing even under an extreme confinement of two layers. OMCTS is found to orient with a wide distribution of orientations with respect to the mica surface, with a distinct preference for the surface parallel configuration in the contact layers. The self-intermediate scattering function is found to decay with increasing relaxation times as the surface separation is decreased, and the two-step relaxation in the scattering function, a signature of glassy dynamics, distinctly evolves as the temperature is lowered. However, even at 5 K above the melting point, we did not observe a freezing transition and the self-intermediate scattering functions relax within 200 ps for the seven-layered confined system. The self diffusivity and relaxation times obtained from the Kohlrausch-Williams-Watts stretched exponential fits to the late alpha-relaxation exhibit power law scalings with the packing fraction as predicted by mode coupling theory. A distinct discontinuity in the Helmholtz free energy, potential energy, and a sharp change in the local bond order parameter, Q(4), was observed at 230 K for a five-layered system upon cooling, indicative of a first-order transition. A freezing point depression of about 30 K was observed for this five-layered confined system, and at the lower temperatures, contact layers were found to be disordered with long-range order present only in the inner layers. These dynamical signatures indicate that confined OMCTS undergoes a slowdown akin to a fluid approaching a glass transition upon increasing confinement, and freezing under confinement would require substantial subcooling below the bulk melting point of OMCTS.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.

Advancing Edge Speeds of Epithelial Monolayers Depend on Their Initial Confining Geometry

Collective cell migrations are essential in several physiological processes and are driven by both chemical and mechanical cues. The roles of substrate stiffness and confinement on collective migrations have been investigated in recent years, however few studies have addressed how geometric shapes influence collective cell migrations. Here, we address the hypothesis that the relative position of a cell within the confinement influences its motility. Monolayers of two types of epithelial cells-MCF7, a breast epithelial cancer cell line, and MDCK, a control epithelial cell line-were confined within circular, square, and cross-shaped stencils and their migration velocities were quantified upon release of the constraint using particle image velocimetry. The choice of stencil geometry allowed us to investigate individual cell motility within convex, straight and concave boundaries. Cells located in sharp, convex boundaries migrated at slower rates than those in concave or straight edges in both cell types. The overall cluster migration occurred in three phases: an initial linear increase with time, followed by a plateau region and a subsequent decrease in cluster speeds. An acto-myosin contractile ring, present in the MDCK but absent in MCF7 monolayer, was a prominent feature in the emergence of leader cells from the MDCK clusters which occurred every similar to 125 mu m from the vertex of the cross. Further, coordinated cell movements displayed vorticity patterns in MDCK which were absent in MCF7 clusters. We also used cytoskeletal inhibitors to show the importance of acto-myosin bounding cables in collective migrations through translation of local movements to create long range coordinated movements and the creation of leader cells within ensembles. To our knowledge, this is the first demonstration of how bounding shapes influence long-term migratory behaviours of epithelial cell monolayers. These results are important for tissue engineering and may also enhance our understanding of cell movements during developmental patterning and cancer metastasis.

Weak Zone Related Seismic Cycles in Progressive Failure Leading to Collapse in Brittle Crust

Until quite recently our understanding of the basic mechanical process responsible for earthquakes and faulting was not well known. It can be argued that this was partly a consequence of the complex nature of fracture in crust and in part because evidence of brittle phenomena in the natural laboratory of the earth is often obliterated or obscured by other geological processes. While it is well understood that the spatial and temporal complexity of earthquakes and the fault structures emerge from geometrical and material built-in heterogeneities, one important open question is how the shearing becomes localized into a band of intense fractures. Here the authors address these questions through a numerical approach of a tectonic plate by considering rockmass heterogeneity both in microscopic scale and in mesoscopic scale. Numerical simulations of the progressive failure leading to collapse under long-range slow driving forces in the far-field show earthquake-like rupture behavior. $En Echelon$ crack-arrays are reproduced in the numerical simulation. It is demonstrated that the underlying fracturing induced acoustic emissions (or seismic events) display self-organized criticality------from disorder to order. The seismic cycles and the geometric structures of the fracture faces, which are found greatly depending on the material heterogeneity (especially on the macroscopic scale), agree with that observed experimentally in real brittle materials. It is concluded that in order to predict a main shock, one must have extremely detailed knowledge on very minor features of the earth's crust far from the place where the earthquake originated. If correct, the model proposed here seemingly provides an explanation as to why earthquakes to date are not predicted so successfully. The reason is not that the authors do not understand earthquake mechanisms very well but that they still know little about our earth's crust.