Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis

A new method is presented for extracting statistical potentials dependent on the relative side chain and backbone orientations in proteins. Coarse-grained, anisotropic potentials are constructed for short-, medium-, and long-range interactions using the Boltzmann method and a database of non-homologous protein structures. The new orientation-dependent potentials are analyzed using a spherical harmonics decomposition method with real eigenfunctions. This method permits a more realistic, continuous angular representation of the coarse-grained potentials. Results of tests for discriminating the native protein conformations from large sets of decoy proteins, show that the new continuous distance- and orientation-dependent potentials present significantly improved performance. Novel graphical representations are developed and used to depict the orientational dependence of the interaction potentials. These new continuous anisotropic statistical potentials could be instrumental in developing new computational methods for structure prediction, threading and coarse-grained simulations.     

Die Bestimmung des Wärmeinhalts und der spezifischen Wärme von Schmelzkalkkristallen zwischen 0 und 1720 °C

Entwicklung verschiedener Kalorimeteranordnungen zur Bestimmung des Wärmeinhalts zwischen 0 und 25, 25 und 65, 25 und 1400 und zwischen 25 und 1720 °C. Die mittlere und wahre spezifische Wärme von Schmelzkalk (Kristallkalk). Vergleich der Ergebnisse mit Angaben des Schrifttums über gebrannten Kalk.     

Parameter pe′ der Elektronenteilleitfähigkeit in ZrO2(CaO)- und ThO2(Y2O3)-Festelektrolyten bei 1200 bis 1650 °C

Bestimmung des Parameters p_e′ (t_ion = 0,5) zur Kennzeichnung der Elektronenteilleitfähigkeit in festen Elektrolyten. Anwendung einer abgewandelten Polarisationsmethode mit EMK-Messung. Angabe der Parameter p_e′ für Festelektrolyte aus ZrO₂ mit einem Molenbruch x_CaO = 0,14 und aus ThO₂ mit einem Molenbruch bei Temperaturen zwischen 1200 und 1650 °C. Berechnung korrigierter Eichkurven für die elektrochemische Messung der Sauerstoffaktivitäten in Stahlschmelzen. Empfehlung einer bevorzugten Anwendung von ThO₂(Y₂O₃)-Elektrolyten zur Messung kleinster Sauerstoffaktivitäten.     

Calibration and quantification of fast intracellular motion (FIM) in living cells using correlation analysis

Video rate confocal laser scanning microscopy at the highest spatial and temporal resolution of backscattered light (BSL) imaging allowed for regular observation of fast intracellular motion (FIM) first revealed in living neoplastic cells. However, the absence of an objective evaluation has hampered further study of the mechanisms and biological significance of FIM. Particularly, a quantification of apparent differences in velocities that would complement and improve the current demonstration of FIM by color coding using the combination of red-green-blue (RGB) images had been missing. Standard methods of tracking or pattern recognition could not be applied because of the fuzzy nature of images of FIM. A search for a suitable method led to correlation analysis. It was calibrated on Brownian motion and a known type of motion, such as cell marginal ruffling, compared with FIM. Results approved its explanatory potential. Therefore, several crucial incidences of FIM could be analyzed. Apart from an argument against viewing FIM as a manifestation of simple Brownian motion, the correlation analysis of FIM in the adjacent peripheries of a rat fibroblast and a K4 rat sarcoma cell confirmed the notion of higher and uneven distribution of velocity of FIM in a tumor cell so far shown in color-coded images only. This result and other yet unpublished observations indicate that the velocity and topology of FIM can also contribute to a biological distinction between neoplastic and normal cells. Regular application of the correlation analysis should further expand the study of FIM for its mechanisms and predictive value. Such an approach should be thoroughly examined for a contribution to the knowledge of cancer cells.     

Computer-controlled mechanical simulation of the artificially ventilated human respiratory system

A mechanical lung simulator can be used to simulate specific lung pathologies, to test lung-function equipment, and in instruction. A new approach to mechanical simulation of lung behavior is introduced that uses a computer-controlled active mechatronic system. The main advantage of this approach is that the static and dynamic properties of the simulator can easily be adjusted via the control software. A nonlinear single-compartment mathematical model of the artificially ventilated respiratory system has been derived and incorporated into the simulator control system. This model can capture both the static and dynamic compliance of the respiratory system as well as nonlinear flow-resistance properties. Parameters in this model can be estimated by using data from artificially ventilated patients. It is shown that the simulation model fits patient data well. This mathematical model of the respiratory system was then matched to a model of the available physical equipment (the simulator, actuators, and the interface electronics) in order to obtain the desired lung behavior. A significant time delay in the piston motion control loop has been identified, which can potentially cause oscillations or even instability for high compliance values. Therefore, a feedback controller based on the Smith-predictor scheme was developed to control the piston motion. The control system, implemented on a personal computer, also includes a user-friendly interface to allow easy parameter setting.     

Classification of rheumatoid joint inflammation based on laser imaging

We describe a classification system for a novel imaging method for arthritic finger joints. The basis of this system is a laser imaging technique which is sensitive to the optical characteristics of finger joint tissue. From the laser images acquired at baseline and follow-up, finger joints can automatically be classified according to whether the inflammatory status has improved or worsened. To perform the classification task, various linear and kernel-based systems were implemented and their performances were compared. Based on the results presented in this paper, we conclude that the laser-based imaging permits a reliable classification of pathological finger joints, making it a sensitive method for detecting arthritic changes.     

Ternary Gels of a Polymer Blend and a Recycled Oil: Their Use as Bitumen Modifiers

A blend of random ethylene‐vinyl acetate copolymer (EVA) and triblock styrene‐butadiene‐styrene copolymer (SBS) was dissolved in a recycled engine oil to obtain ternary thermoreversible gels. As the temperature was increased, first a network associated with EVA disappeared, and a second one associated with SBS dominated, maintaining the elastic response of the system. The principal advantage of these ternary systems is that their mechanical properties and thermal stability are better than that of binary gels. These gels, made from waste, can be used as bitumen modifiers to obtain binders of improved properties and good stability, which are useful for road surfacing.

Temperature sweeps of elastic modulus performed at a frequency of 1 Hz.     

Design of phononic materials/structures for surface wave devices using topology optimization

We develop a topology optimization approach to design two- and three-dimensional phononic (elastic) materials, focusing primarily on surface wave filters and waveguides. These utilize propagation modes that transmit elastic waves where the energy is contained near a free surface of a material. The design of surface wave devices is particularly attractive given recent advances in nano- and micromanufacturing processes, such as thin-film deposition, etching, and lithography, which make it possible to precisely place thin film materials on a substrate with submicron feature resolution. We apply our topology optimization approach to a series of three problems where the layout of two materials (silicon and aluminum) is sought to achieve a prescribed objective: (1) a grating to filter bulk waves of a prescribed frequency in two and three dimensions, (2) a surface wave device that uses a patterned thin film to filter waves of a single or range of frequencies, and (3) a fully three-dimensional structure to guide a wave generated by a harmonic input on a free surface to a specified output port on the surface. From the first to the third example, the resulting topologies increase in sophistication. The results demonstrate the power and promise of our computational framework to design sophisticated surface wave devices.     

AES investigation of the stainless steel surface oxidized in plasma

Auger electron spectroscopy (AES) depth profiling was used to study the oxidation phenomena of AISI316L stainless steel during treatment with oxygen plasma. Samples were exposed to low-pressure RF plasma with a high dissociation degree, so that the flux of oxygen atoms onto the sample surface exceeded 10²⁴ m⁻² s⁻¹. A set of samples was oxidized 4 min at different temperatures up to 1300 K during plasma treatment. AES measurements showed that the oxide film thickness increased with the increasing temperature. The thickness of the oxide film on the samples oxidized in plasma at 300 K was nearly the same as for the untreated sample. The thickness of the oxide film of the samples which were oxidized at 1000 K was about 170 nm and it consisted of iron oxide. The thickest oxide film of about 350 nm was found on the samples heated in oxygen plasma to 1300 K. Depth profiling showed the uppermost layer of manganese oxide, followed by a mixture of chromium oxide and iron oxide. The scanning electron microscope analyses showed a dramatic increase of the surface roughness.