Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNaseS and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model, According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Einstein Relation in n-Channel Inversion Layers of Nonlinear Optical, Optoelectronic and Related Materials: Simplified Theory, Relative Comparison and Suggestion for an Experimental Determination

In this paper, we study the Einstein relation for the diffusivity to mobility ratio (DMR) in n-channel inversion layers of non-linear optical materials on the basis of a newly formulated electron dispersion relation by considering their special properties within the frame work of k.p formalism. The results for the n-channel inversion layers of III-V, ternary and quaternary materials form a special case of our generalized analysis. The DMR for n-channel inversion layers of II-VI, IV-VI and stressed materials has been investigated by formulating the respective 2D electron dispersion laws. It has been found, taking n-channel inversion layers of CdGeAs2, Cd(3)AS(2), InAs, InSb, Hg1-xCdxTe, In1-xGaxAsyP1-y lattice matched to InP, CdS, PbTe, PbSnTe, Pb1-xSnxSe and stressed InSb as examples, that the DMR increases with the increasing surface electric field with different numerical values and the nature of the variations are totally band structure dependent. The well-known expression of the DMR for wide gap materials has been obtained as a special case under certain limiting conditions and this compatibility is an indirect test for our generalized formalism. Besides, an experimental method of determining the 2D DMR for n-channel inversion layers having arbitrary dispersion laws has been suggested.

In situ investigation of explosive crystallization in a-Ge: Experimental determination of the interface response function using dynamic transmission electron microscopy

The crystallization of amorphous semiconductors is a strongly exothermic process. Once initiated the release of latent heat can be sufficient to drive a self-sustaining crystallization front through the material in a manner that has been described as explosive. Here, we perform a quantitative in situ study of explosive crystallization in amorphous germanium using dynamic transmission electron microscopy. Direct observations of the speed of the explosive crystallization front as it evolves along a laser-imprinted temperature gradient are used to experimentally determine the complete interface response function (i.e., the temperature-dependent front propagation speed) for this process, which reaches a peak of 16 m/s. Fitting to the Frenkel-Wilson kinetic law demonstrates that the diffusivity of the material locally/immediately in advance of the explosive crystallization front is inconsistent with those of a liquid phase. This result suggests a modification to the liquid-mediated mechanism commonly used to describe this process that replaces the phase change at the leading amorphous-liquid interface with a change in bonding character (from covalent to metallic) occurring in the hot amorphous material.

A combined experimental and theoretical study of the charge-transfer compound between C60Br8 and tetrathiafulvalene

C60Br8, unlike C60Br6 and C60Cl6, forms a solid charge-transfer compound with tetrathiafulvalene (TTF), the composition being C60Br8(TTF)(8). The unique complex-forming property of C60Br8 can be understood on the basis of the electronic structures of the halogenated derivatives of C-60. Molecular orbital calculations show that the low LUMO energy of C60Br8 compared with the other halogen derivatives renders the formation of the complex with TTF favourable, the four virtual LUMOs being able to accept 8 electrons. The Raman spectrum of C60Br8(TTF)(8) shows a marked softening of the bands (-46 cm(-1) on average) with respect to C60Br8 suggesting that indeed 8 electrons are transferred per C60Br8 molecule, one from each TTF molecule. The complex is weakly paramagnetic and shows a magnetic transition around 80 K.

Experimental people

From Kurt Vonnegut to Stephen King, many novelists use metanarrative techniques to insert fictional versions of themselves in the stories they tell. The function of deploying such techniques is often to draw attention to the liminal space between the fictional constructs inherent in the novel as a form, and the real world from which the constructs draw inspiration, and indeed, are read by an audience. For emerging writers working in short form narratives, however, the structural demands of the short story or flash fiction make the use of similar techniques problematic in the level of depth to which they can be deployed. Experimental People, the third in series of short stories, works to overcome the structural limitations of a succinct form by developing a fractured fictional version of the author over a number of pieces and published across a range of sites. The accumulative affect is a richer metanarrative textual arrangement that also allows for the individual short stories to function independently.

An experimental study on anisotropic mechanical properties of porcine thoracic aorta

Objective: To study the anisotropic mechanical properties of the thoracic aorta in porcine. Methods: Twenty-one porcine thoracic aortas were collected and categorized into three groups. The aortas were then cut through in their axial directions and expanded into two-dimensional planes. Then, by setting the length direction of the planar aortas (i.e., axial directions of the aortas) as 0°, each planar aorta was counterclockwisely cut into 8 samples with orientation of 30°, 45°, 60°, 90°, 120°, 135°, 150° and 180°, respectively. Finally, the uniaxial tensile tests were applied on three groups of samples at the loading rates of 1, 5 and 10 mm/min, respectively, to obtain the elastic modulus and ultimate stress of the aorta in different directions and at different loading rates. Results: The stress-strain curves exhibited different viscoelastic behaviors. With the increase of sample orientations, the elastic modulus gradually increased from 30°, reached the maximum value at 90°, and then gradually decreased till 180°. The variation trend of ultimate stress was similar to that of elastic modulus. Moreover, different loading rates showed a significant influence on the results of elastic modulus and ultimate stress, but a weak influence on the anisotropic degree. Conclusions: The porcine thoracic aorta is highly anisotropic. This research finding provides parameter references for assignment of material properties in finite element modeling, and is significant for understanding biomechanical properties of the arteries.

Experimental measurement of the mechanical properties of carotid atherothrombotic plaque fibrous cap

Eleven carotid atherothrombotic plaque samples were harvested from patients. Three samples that were highly calcified were discarded, while eight yielded results. The elastic properties of the material were estimated by fitting the measured indentation response to finite element simulations. The methodology was refined and its accuracy quantified using a synthetic rubber. The neo-Hookean form of the material model gave a good fit to the measured response of the tissue. The inferred shear modulus μ was found to be in the range 7-100 kPa, with a median value of 11 kPa. A review of published materials data showed a wide range of material properties for human atherothrombotic tissue. The effects of anisotropy and time dependency in these published results were highlighted. The present measurements were comparable to the static radial compression tests of Lee et al, 1991 [Structure-dependent dynamic behaviour of fibrous caps from human atherosclerotic plaques. Circulation 83, 1764-1770].

Nonlinear mechanical property of tracheal cartilage: A theoretical and experimental study

Background: Despite being the stiffest airway of the bronchial tree, the trachea undergoes significant deformation due to intrathoracic pressure during breathing. The mechanical properties of the trachea affect the flow in the airway and may contribute to the biological function of the lung. Method: A Fung-type strain energy density function was used to investigate the nonlinear mechanical behavior of tracheal cartilage. A bending test on pig tracheal cartilage was performed and a mathematical model for analyzing the deformation of tracheal cartilage was developed. The constants included in the strain energy density function were determined by fitting the experimental data. Result: The experimental data show that tracheal cartilage is a nonlinear material displaying higher strength in compression than in tension. When the compression forces varied from -0.02 to -0.03 N and from -0.03 to -0.04 N, the deformation ratios were 11.03±2.18% and 7.27±1.59%, respectively. Both were much smaller than the deformation ratios (20.01±4.49%) under tension forces of 0.02 to 0.01 N. The Fung-type strain energy density function can capture this nonlinear behavior very well, whilst the linear stress-strain relation cannot. It underestimates the stability of trachea by exaggerating the displacement in compression. This study may improve our understanding of the nonlinear behavior of tracheal cartilage and it may be useful for the future study on tracheal collapse behavior under physiological and pathological conditions.

Pulse-echo ultrasound transit time spectroscopy: A comparison of experimental measurements and simulation prediction

Considering ultrasound propagation through complex composite media as an array of parallel sonic rays, a comparison of computer simulated prediction with experimental data has previously been reported for transmission mode (where one transducer serves as transmitter, the other as receiver) in a series of ten acrylic step-wedge samples, immersed in water, exhibiting varying degrees of transit time inhomogeneity. In this study, the same samples were used but in pulse-echo mode, where the same ultrasound transducer served as both transmitter and receiver, detecting both ‘primary’ (internal sample interface) and ‘secondary’ (external sample interface) echoes. A transit time spectrum (TTS) was derived, describing the proportion of sonic rays with a particular transit time. A computer simulation was performed to predict the transit time and amplitude of various echoes created, and compared with experimental data. Applying an amplitude-tolerance analysis, 91.7±3.7% of the simulated data was within ±1 standard deviation (STD) of the experimentally measured amplitude-time data. Correlation of predicted and experimental transit time spectra provided coefficients of determination (R2) ranging from 100.0% to 96.8% for the various samples tested. The results acquired from this study provide good evidence for the concept of parallel sonic rays. Further, deconvolution of experimental input and output signals has been shown to provide an effective method to identify echoes otherwise lost due to phase cancellation. Potential applications of pulse-echo ultrasound transit time spectroscopy (PE-UTTS) include improvement of ultrasound image fidelity by improving spatial resolution and reducing phase interference artefacts.

Triploid plants from endosperm cultures of sandalwood by experimental embryogenesis

Embryogenesis has been induced from endosperm callus cultures of sandalwood (Santalum album L.). Viable plantlets developed from the embryoids on subculture to White's basal medium supplemented with 0.5 mg/l of indole acetic acid. Chromosomal analysis of the root tips showed the triploid number 3n = 30.

Experimental and Analytical Investigations of the actions taking place in a Synchronous machine during the starting period when the starting Is effected by means of alternating current

The literature on the subject of the present investigation is somewhat meagre. A rotary converter or synchronous motor no! provided with any special starting devices forms, when started from the alternating current side, a type of induction motor whoso Htator is provided with a polyphase winding, and whoso rotor has a single-phase (or single magnetic axis) winding.

Development of a novel experimental model to investigate the influence of mechanics on bone healing

This dissertation proposed a novel experimental model combining a defect configuration with an active instrumented fixation device to investigate the influence of mechanics on bone healing. The proposed defect configuration aimed to minimise physiological loading within an experimental fracture gap and the instrumented fixator was used for the application of controlled displacements and in vivo stiffness monitoring of the healing process. This thesis has provided a novel approach to advance current knowledge and understanding of mechanobiology, which has been limited in previous experimental models.

Recovery and succession in a multi-species tropical seagrass meadow following experimental disturbance: the role of sexual and asexual reproduction

Recolonisation and succession in a multi-species tropical seagrass meadow was examined by creating gaps (50×50 cm) in the meadow and manipulating the supply of sexual and asexual propagules. Measurements of leaf shoot density and estimates of above-ground biomass were conducted monthly to measure recovery of gaps between September 1995 and November 1997. Measurements of the seeds stored in the sediment (seed bank) and horizontal rhizome growth of colonising species were also conducted to determine their role in the recovery process. Asexual colonisation through horizontal rhizome growth from the surrounding meadow was the main mechanism for colonisation of gaps created in the meadow. The seed bank played no role in recolonisation of cleared plots. Total shoot density and above-ground biomass (all species pooled) of cleared plots recovered asexually to the level of the undisturbed controls in 10 and 7 months, respectively. There was some sexual recruitment into cleared plots where asexual colonisation was prevented but seagrass abundance (shoot density and biomass) did not reach the level of unmanipulated controls. Seagrass species did not appear to form seed banks despite some species being capable of producing long-lived seeds. The species composition of cleared plots remained different to the undisturbed controls throughout the 26-month experiment. Syringodium isoetifolium was a rapid asexual coloniser of disturbed plots and remained at higher abundances than in the control treatments for the duration of the study. S. isoetifolium had the fastest horizontal rhizome growth of species asexually colonising cleared plots (6.9 mm day−1). Halophila ovalis was the most successful sexual coloniser but was displaced by asexually colonising species. H. ovalis was the only species observed to produce fruits during the study. Small disturbances in the meadow led to long-term (>2 years) changes in community composition. This study demonstrated that succession in tropical seagrass communities was not a deterministic process. Variations in recovery observed for different tropical seagrass communities highlighted the importance of understanding life history characteristics of species within individual communities to effectively predict their response to disturbance. A reproductive strategy involving clonal growth and production of long-lived, locally dispersed seeds is suggested which may provide an evolutionary advantage to plants growing in tropical environments subject to temporally unpredictable major disturbances such as cyclones

SHAMP: An experimental shared memory multimicroprocessor system for performance evaluation of parallel algorithms

In this paper, the design and implementation of a single shared bus, shared memory multiprocessing system using Intel's single board computers is presented. The hardware configuration and the operating system developed to execute the parallel algorithms are discussed. The performance evaluation studies carried out on Image are outlined.

Australian Bat Lyssavirus: Observations of Natural and Experimental Infection in Bats

This conference abstract gives data and conclusions arising from targeted surveillance of wild bats for naturally occuring Australian bat lyssavirus (ABLV) infection and other central nervous system diseases. It also provides data and conclusions arising from experimental infection of 10 Greyheaded flying foxes (Pteropus poliocephalus).