Intermediates in the protein folding process: a computational model

The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage-ES and the late stage-LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations.     

New Core-Shell Nanostructures for FRET Studies: Synthesis,Characterization, and Quantitative Analysis

This work describes the synthesis and characterization of new core-shell material designed for Förster resonance energy transfer (FRET) studies. Synthesis, structural and optical properties of core-shell nanostructures with a large number of two kinds of fluorophores bound to the shell are presented. As fluorophores, strongly fluorescent rhodamine 101 and rhodamine 110 chloride were selected. The dyes exhibit significant spectral overlap between acceptor absorption and donor emission spectra, which enables effective FRET. Core-shell nanoparticles strongly differing in the ratio of donors to acceptor numbers were prepared. This leads to two different interesting cases: typical single-step FRET or multistep energy migration preceding FRET. The single-step FRET model that was designed and presented by some of us recently for core-shell nanoparticles is herein experimentally verified. Very good agreement between the analytical expression for donor fluorescence intensity decay and experimental data was obtained, which confirmed the correctness of the model. Multistep energy migration between donors preceding the final transfer to the acceptor can also be successfully described. In this case, however, experimental data are compared with the results of Monte Carlo simulations, as there is no respective analytical expression. Excellent agreement in this more general case evidences the usefulness of this numerical method in the design and prediction of the properties of the synthesized core-shell nanoparticles labelled with multiple and chemically different fluorophores.     

Parametric finite elements, exact sequences and perfectly matched layers

The paper establishes a relation between exact sequences, parametric finite elements, and perfectly matched layer (PML) techniques. We illuminate the analogy between the Piola-like maps used to define parametric H ¹-, H(curl)-, H(div)-, and L ₂-conforming elements, and the corresponding PML complex coordinates stretching for the same energy spaces. We deliver a method for obtaining PML-stretched bilinear forms (constituting the new weak formulation for the original problem with PML absorbing boundary layers) directly from their classical counterparts.     

Application of Design of the Experiment in Preliminary Investigations on the end Milling of Low Temperature Co‐fired Ceramics

The formation of three‐dimensional shapes is one of the most important technological steps in low temperature co‐fired ceramics (LTCC) process. Channels and chambers qualities and the process speed are strongly affected by the shaping procedure. There are three main machining techniques: laser cutting, punching, and milling. This article is dedicated to end milling process of LTCC tapes. The determined PS/DK 2³ experiment design was used in the investigations and its procedure is described in this article. The used procedure is a very flexible method to achieve much useful information about the influence of the process parameters on the output. The PS/DK 2³ experiment design enables analysis of the influence of: the three input parameters on the output (minimal obtained feature) and the interaction between the input parameters on the output (minimal obtained feature). Moreover, PS/DK 2³ experiment design enables to obtain the mathematical model of the milling process and to decrease the number of measurements demanded to achieve the correct model. Hence, the design is suitable to decrease the time and costs of the experiment. The influence of the following input parameters: spindle rotational speed, spindle feed rate, vertical spindle step, and cutter diameter on minimal obtained feature of LTCC tapes is analyzed in this article.     

Application of a genetic-fuzzy system to diesel engine pressure modeling

The aim of this work was to build an empirical–analytical model for diesel engine operation and control. The engine that was used was fueled by biofuels or diesel oil and the measurements of cylinder pressure were conducted on a test bench. The engine model was built by means of a proposed genetic-fuzzy system. This model allows simulation of cylinder pressure for each allowable crankshaft speed with accuracy required in practical technical applications.     

Helium Adsorption on Alkali Metal Substrates: Comparison of Density Functional and Path Integral Monte Carlo Resugts

Low temperature energetic and structural properties of adsorbed helium films on alkali metal substrates are studied theoretically by means of Density Functional and Path Integral Monte Carlo calculations. Comparison of the resugts obtained with the two techniques shows broad quantitative agreement.     

Evolution of Metal Phase in the Course of CO Hydrogenation on Potassium Promoted Ni/Al2O3 Catalyst

The hydrogenation of carbon monoxide on Ni/Al₂O₃ catalysts was studied in a flow system by simultaneous following CO conversion and crystallographic state of supported nickel. The examination performed for potassium promoted catalyst revealed that: (1) next to methane, considerable amount of CO₂ is produced, and (2) supported nickel transforms to supersaturated solution of carbon in nickel phase, NiC _x . The analysis of the results has led to formulation of a probable scheme of the carburisation.     

Extrusion-cooking of starch protective loose-fill foams

One of the most interesting alternatives to EPS is extrusion of starch-based materials. TPS-based biocomposites can be processed, in a one-step process, via an extrusion-cooking. Wide program of the experimental works with application of extrusion-cooking for production of starchy loose-fill foams has been started in the Department of Food Process Eng., Lublin University of Life Sciences in 2012. The object of the study is to achieve commercially acceptable biodegradable products based on locally produced potato, corn and wheat starch, which can replace popular EPS. Results of the first phase of the study are presented in the paper. The measurements of glass transition temperature of TPS samples showed that with glycerol content growth in the blend, the Tg of the obtained material decreases almost linearly. In the case of potato TPS, the highest observed Tg was 187.7 ?C for 7.0% glycerol and the lowest was at 18.1 ?C for 30% glycerol. Properties of the loose-fill foams highly depend on raw materials and process parameters used in production. In addition of plasticiser or other additives, different temperature of processing is causing changes in product's properties. All starch-based foams had high open-cell content and the expansion was attributable to the escape of water as steam during processing, resulting more than 80% open cells. The foam density of starch-based products ranged between 18.7 and 30.5 kg/m³. The products were at least 2.5 times more dense than EPS-based foams. The best products achieved by us up till now are the corn TPS-based foams containing 3% plasticizer and 1% poly-vinyl alcohol. The energy consumption during extrusion-cooking depended on the material composition of the blends, temperature and the screw rotation speed used during processing. Average value of SME was about 2.52 × 10⁵ J/kg, which is equivalent to 0.07 kW h/kg.