The stretching of single poly-ubiquitin molecules: Static versus dynamic disorder in the non-exponential kinetics of chain unfolding

Static disorder has recently been implicated in the non-exponential kinetics of the unfolding of single molecules of poly-ubiquitin under a constant force Kuo, Garcia-Manyes, Li, Barel, Lu, Berne, Urbakh, Klafter, and Fernandez, Proc. Natl. Acad. Sci. U. S. A. 107, 11336 (2010)]. In the present paper, it is suggested that dynamic disorder may provide a plausible, alternative description of the experimental observations. This suggestion is made on the basis of a model in which the barrier to chain unfolding is assumed to be modulated by a control parameter r that evolves in a parabolic potential under the action of fractional Gaussian noise according to a generalized Langevin equation. The treatment of dynamic disorder within this model is pursued using Zwanzig's indirect approach to noise averaging Acc. Chem. Res. 23, 148 (1990)]. In conjunction with a self-consistent closure scheme developed by Wilemski and Fixman J. Chem. Phys. 58, 4009 (1973); ibid. 60, 866 (1974)], this approach eventually leads to an expression for the chain unfolding probability that can be made to fit the corresponding experimental data very closely. (C) 2011 American Institute of Physics.

Orientational disorder and other aspects of C70 and C60-C70 films deposited on single-crystal substrates

C-70 films deposited on highly oriented pyrolytic graphite (HOPG), Ag(110), Ag(111) and Pt(110) substrates have been investigated by scanning tunnelling microscopy. Interesting observations on novel molecular arrangements, as well as orientational disorder, are presented. Solid solutions of C-60 and C-70 show interesting packing of these molecules when deposited on HOPG.

Metamorphic-metasomatic fluids and Al, Si order/disorder of K-rich alkali feldspars from southern Indian high grade terrain

The structural state of K-feldspars in the quartzofeldspathic gneisses, charnockites, metapelites and pegmatites from the southern Kamataka, northern Tamil Nadu and southern Kerala high-grade regions of southern India has been characterized using petrographic and powder X-ray diffraction methods. The observed distribution pattern of structural state with a preponderance of disordered K-feldspar polymorphs in granulites compared to the ordered microclines in the amphibolite facies rocks is interpreted to reflect principally the varying H2O contents in the metamorphic-metasomatic fluids across metamorphic grade. The K-feldspars in the pegmatites of granitic derivation and in a pegmatite of inferred metamorphic origin also point to the important role of aqueous fluids in their structural state.

Non-exponentiality in electron transfer kinetics: Static versus dynamic disorder models

Non-exponential electron transfer kinetics in complex systems are often analyzed in terms of a quenched, static disorder model. In this work we present an alternative analysis in terms of a simple dynamic disorder model where the solvent is characterized by highly non-exponential dynamics. We consider both low and high barrier reactions. For the former, the main result is a simple analytical expression for the survival probability of the reactant. In this case, electron transfer, in the long time, is controlled by the solvent polarization relaxation-in agreement with the analyses of Rips and Jortner and of Nadler and Marcus. The short time dynamics is also non-exponential, but for different reasons. The high barrier reactions, on the other hand, show an interesting dynamic dependence on the electronic coupling element, V-el.

Temperature dependence of non-Debye disorder in doped manganites

Ca-doped manganite La1-xCaxMnO3 samples with x=0.2 and 0.4 were investigated by extended x-ray absorption fine structure (EXAFS) as a function of temperature and preparation method. The samples exhibit characteristic resistivity change across the metal-insulator (MI) transition temperature whose shape and position depend on Ca-doping concentration and sample thermal treatment. EXAFS results evidenced an increase of nonthermal disorder at the MI transition temperature which is significantly correlated with the resistivity behavior.

Muon-spin rotation spectra in the mixed phase of high-T-c superconductors: Thermal fluctuations and disorder effects

We study muon-spin rotation (mu SR) spectra in the mixed phase of highly anisotropic layered superconductors, specifically Bi2+xSr2-xCaCu2O8+delta (BSCCO), by modeling the fluid and solid phases of pancake Vortices using liquid-state and density functional methods. The role of thermal fluctuations in causing motional narrowing of mu SR line shapes is quantified in terms of a first-principles theory of the flux-lattice melting transition. The effects of random point pinning are investigated using a replica treatment of liquid-state correlations and a replicated density functional theory. Our results indicate that motional narrowing in the pure system, although substantial, cannot account for the remarkably small linewidths obtained experimentally at relatively high fields and low temperatures. We find that satisfactory agreement with the mu SR data for BSCCO in this regime can be obtained through the ansatz that this ''phase'' is characterized by frozen short-range positional correlations reflecting the structure of the liquid just above the melting transition. This proposal is consistent with recent suggestions of a ''pinned liquid'' or ''glassy'' state of pancake Vortices in the presence of pinning disorder. Our results for the high-temperature liquid phase indicate that measurable linewidths may be obtained in this phase as a consequence of density inhomogeneities induced by the pinning disorder. The results presented here comprise a unified, first-principles theoretical treatment of mu SR spectra in highly anisotropic layered superconductors in terms of a controlled set of approximations. [S0163-1829(99)08033-9].

Glasslike ordering and spatial inhomogeneity of magnetic structure in Ba3FeRu2O9: Role of Fe/Ru site disorder

Several doped 6H hexagonal ruthenates, having the general formula Ba3MRu2O9, have been studied over a significant period of time to understand the unusual magnetism of ruthenium metal. However, among them, the M = Fe compound appears different since it is observed that unlike others, the 3d Fe ions and 4d Ru ions can easily exchange their crystallographic positions, and as a result many possible magnetic interactions become realizable. The present study involving several experimental methods on this compound establishes that the magnetic structure of Ba3FeRu2O9 is indeed very different from all other 6H ruthenates. Local structural study reveals that the possible Fe/Ru site disorder further extends to create local chemical inhomogeneity, affecting the high-temperature magnetism of this material. There is a gradual decrease of Fe-57 Mossbauer spectral intensity with decreasing temperature (below 100 K), which reveals that there is a large spread in the magnetic ordering temperatures, corresponding to many spatially inhomogeneous regions. However, finally at about 25 K, the whole compound is found to take up a global glasslike magnetic ordering.

Ab initio study of disorder effects on the electronic and magnetic structure of Sr2FeMoO6

We have investigated the electronic structure of ordered and disordered Sr2FeMoO6 using ab initio bandstructure methods. The effect of disorder was simulated within supercell calculations to realize several configurations with mis-site disorders. It is found that such disorder effects destroy the half-metallic ferromagnetic state of the ordered compound. It also leads to a substantial reduction of the magnetic moments at the Fe sites in the disordered configurations. Most interestingly, it is found for the disordered configurations that the magnetic coupling within the Fe sublattice as well as that within the Mo sublattice always remain ferromagnetic, while the two sublattices couple antiferromagnetically, in close analogy to the magnetic structure of the ordered compound, but,in contrast to recent suggestions.

Nonlinear measures of respiration: Respiratory irregularity and increased chaos of respiration in patients with panic disorder

Background. Respiratory irregularity has been previously reported in patients with panic disorder using time domain measures. However, the respiratory signal is not entirely linear and a few previous studies used approximate entropy (APEN), a measure of regularity of time series. We have been studying APEN and other nonlinear measures including a measure of chaos, the largest Lyapunov exponent (LLE) of heart rate time series, in some detail. In this study, we used these measures of respiration to compare normal controls (n = 18) and patients with panic disorder (n = 22) in addition to the traditional time domain measures of respiratory rate and tidal volume. Methods: Respiratory signal was obtained by the Respitrace system using a thoracic and an abdominal belt, which was digitized at 500 Hz. Later, the time series were constructed at 4 Hz, as the highest frequency in this signal is limited to 0.5 Hz. We used 256 s of data (1,024 points) during supine and standing postures under normal breathing and controlled breathing at 12 breaths/min. Results: APEN was significantly higher in patients in standing posture during normal as well as controlled breathing (p = 0.002 and 0.02, respectively). LLE was also significantly higher in standing posture during normal breathing (p = 0.009). Similarly, the time domain measures of standard deviations and the coefficient of variation (COV) of tidal volume (TV) were significantly higher in the patient group (p = 0.02 and 0.004, respectively). The frequency of sighs was also higher in the patient group in standing posture (p = 0.02). In standing posture, LLE (p < 0.05) as well as APEN (p < 0.01) contributed significantly toward the separation of the two groups over and beyond the linear measure, i.e. the COV of TV. Conclusion: These findings support the previously described respiratory irregularity in patients with panic disorder and also illustrate the utility of nonlinear measures such as APEN and LLE as additional measures toward a better understanding of the abnormalities of respiratory physiology in similar patient populations as the correlation between LLE, APEN and some of the time domain measures only explained up to 50-60% of the variation. Copyright (C) 2002 S. Karger AG, Basel.

Thermal Lipid Order−Disorder Transitions in Mixtures of Cationic Cholesteryl Lipid Analogues and Dipalmitoyl Phosphatidylcholine Membranes

Two types of cationic cholesteryl amphiphiles, one where the headgroup is attached to the steroid by an ester linkage and the second by an ether linkage, were synthesized. A third type of cholesteryl lipid bearing an oligoethylene glycol segment was also prepared. Each of these synthetic lipids generated vesicle-like aggregates with closed inner aqueous compartments from their aqueous suspensions. We examined their interaction with L-α-dipalmitoyl phosphatidylcholine (DPPC) membranes using fluorescence anisotropy, transmission electron microscopy (TEM), and differential scanning calorimetry (DSC). When included in membranes, the synthetic cholesteryl lipids were found to quench the chain motion of the acyl chains of DPPC. This suggests that these cationic cholesteryl derivatives act as filler molecules despite modification at the headgroup level from the molecular structure of natural cholesterol. Careful analyses of DSC and fluorescence anisotropy data suggest that the nature of perturbation induced by each of these cationic cholesterol derivatives is dependent on the details of their molecular structure and provides significant information on the nature of interaction of these derivatives with phospholipid molecules. In general, amphiphiles that support structured water at the interfacial region tend to rigidify the fluid phase more than others. Importantly, these cholesteryl amphiphiles behave less like cholesterol in that their incorporation in DPPC not only abolishes the phase transition but also depresses the phase transition temperature.

Effect of nortriptyline and paroxetine on measures of chaos of heart rate time series in patients with panic disorder

Tricyclic antidepressants have notable cardiac side effects, and this issue has become important due to the recent reports of increased cardiovascular mortality in patients with depression and anxiety. Several previous studies indicate that serotonin reuptake inhibitors (SRIs) do not appear to have such adverse effects. Apart from the effects of these drugs on routine 12-lead ECG, the effects on beat-to-beat heart rate (HR) and QT interval time series provide more information on the side effects related to cardiac autonomic function. In this study, we evaluated the effects of two antidepressants, nortriptyline (n = 13), a tricyclic, and paroxetine (n = 16), an SRI inhibitor, on HR variability in patients with panic disorder, using a measure of chaos, the largest Lyapunov exponent (LLE) using pre- and posttreatment HR time series. Our results show that nortriptyline is associated with a decrease in LLE of high frequency (HF: 0.15-0.5 Hz) filtered series, which is most likely due to its anticholinergic effect, while paroxetine had no such effect. Paroxetine significantly decreased sympathovagal ratios as measured by a decrease in LLE of LF/HF. These results suggest that paroxetine appears to be safer in regards to cardiovascular effects compared to nortriptyline in this group of patients. (C) 2003 Elsevier Inc. All rights reserved.

Mutations in WDR62, encoding a centrosomal and nuclear protein, in Indian primary microcephaly families with cortical malformations

Primary microcephaly is an autosomal recessive disorder characterized by smaller than normal brain size and mental retardation. It is genetically heterogeneous with seven loci: MCPH1-MCPH7. We have previously reported genetic analysis of 35 families, including the identification of the MCPH7 gene STIL. Of the 35 families, three families showed linkage to the MCPH2 locus. Recent whole-exome sequencing studies have shown that the WDR62 gene, located in the MCPH2 candidate region, is mutated in patients with severe brain malformations. We therefore sequenced the WDR62 gene in our MCPH2 families and identified two novel homozygous protein truncating mutations in two families. Affected individuals in the two families had pachygyria, microlissencephaly, band heterotopias, gyral thickening, and dysplastic cortex. Using immunofluorescence study, we showed that, as with other MCPH proteins, WDR62 localizes to centrosomes in A549, HepG2, and HaCaT cells. In addition, WDR62 was also localized to nucleoli. Bioinformatics analysis predicted two overlapping nuclear localization signals and multiple WD-40 repeats in WDR62. Two other groups have also recently identified WDR62 mutations in MCPH2 families. Our results therefore add further evidence that WDR62 is the MCPH2 gene. The present findings will be helpful in genetic diagnosis of patients linked to the MCPH2 locus.

Tracing a common ``origin'' of phase transformation, polymorphism, disorder, isosterism, and isostructuralism in fluorobenzoylcarvacryl thiourea

The terms phase transformation, polymorphism, disorder, isosterism, and isostructuralism are often the keywords used in the design and engineering of molecular crystals. Three benzoylcarvacryl thiourea derivatives with -NH-C(S)-NH-C(O)-] cores generate molecular crystals, which provide the basis for exploring a common link between the structures related by aforementioned terms. The apparent ``origin'' of all these structural modifications has been traced to the formation of a planar molecular dimeric chain built with homomeric R-2(2)(12) and R-2(2)(8) synthons occurring in tandem, one formed with N-H center dot center dot center dot O and the other with N-H center dot center dot center dot S hydrogen bonds.