Surface modification by substitution: Changing topology of conformational potential energy surfaces

Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.

Assessment techniques for measurement of target erosion/ redeposition in large tokamaks

The heavy ion time‐of‐flight elastic recoil detection analysis (HI‐ERDA) technique was used to investigate the possibility of measuring near‐surface elemental depth profiles of light and mid‐ Z elements in thin films of plasma‐assisted molecular beam epitaxy (PAMBE)‐grown GaN and helium‐implanted titanium. The great advantage of HI‐ERDA is the ability to measure mass‐separated elemental depth profiles simultaneously. However for some materials it is not certain whether HI‐ERDA can be used successfully because significant sputtering or other beam‐induced damage may occur. The damage to the surfaces by a 77 MeV iodine beam was assessed using RBS, AFM and profilometry. The results show that for thin PAMBE‐grown polycrystalline GaN films and for titanium that has been heavily implanted with helium a significant modification of the near‐surface region is caused by the probing heavy ion beam. For the PAMBE‐grown GaN films the most significant loss trend is observed for nitrogen. Surprisingly this was not accompanied by a change in surface topology. In contrast, an almost complete removal of the heavily helium‐implanted surface layer was measured for the titanium specimens. The investigation shows that reference measurements with additional techniques such as RBS, AFM and profilometry have to be performed to ascertain sample integrity before HI‐ERDA data can be used. Copyright © 2004 John Wiley & Sons, Ltd.

The paper is dedicated to studying of the efficiency of application of the dust control agents not only for their original aims, but also for increasing of oxidation resistance of the solid fossil fuels. The complex investigation included: studying of coals quality alteration after treatment by the selected solution, scanning electron microscopy for investigation of their surface topology changes and, finally, ozonating treatment at low ozone concentrations with kinetic modeling for evaluation of oxidation resistivity. As it was expected, application of the selected solution allows no quality loss for coals. Scanning electron microscopy allowed to visualize the mechanism of working of the dust control agent. It revealed that the studied solution forms a thin smooth film around coal particles. This film tightly binds all the fine particles that were already formed and stored at the coal surface. Also, the solution tends to cover the surface thus decreasing the accessibility of the surface to active oxygen. The latter was proved by treated and untreated coals ozonating processing at low concentrations of ozone. The applied kinetic model allowed evaluation of the total coals activity to ozone decomposition. It was found that the treated coals have twice as low total activity to ozone decomposition as compared with the untreated ones. The latter parameter is closely related to coals oxidation resistivity (the lower the coals activity, the higher the coals oxidation resistivity). Therefore, it was finally concluded that application of the studied dust control agent allows for significant increase of sought-for quality indicator.

A descriptive model of wear evolution in rolling bearings

Distance geometry and molecular dynamics simulation techniques were compared in their ability to search the conformational potential energy surface of β‐cyclodextrin. Structures generated by the DISGEO program were minimized using three different atomic point charge sets. Some of these structures were used as starting points for molecular dynamics simulation in vacuo at 298K. The distance geometry results showed that the global features of the conformational potential energy surface were generally independent of the point charge set. The distance geometry technique was able to find structures of lower energy than those obtained by direct minimization of the X‐ray or neutron diffraction structures. However, the molecular dynamics simulation technique was consistently able to find structures of lower energy than those generated by distance geometry. Root mean square fit of the trajectory structures to the starting structure showed that the simulation allowed the molecule to explore regions of the potential energy surface in the neighborhood of the starting structure. Both the distance geometry and molecular dynamics simulation techniques showed that β‐cyclodextrin can adopt a wide range of conformations in the gas phase and that these conformations are much less symmetrical than the crystalline structure.

Sevoflurane and Isoflurane induce structural changes in brain vascular endothelial cells and increase blood−brain barrier permeability: Possible link to postoperative delirium and cognitive decline

The long-term stability of plasma-sprayed hydroxyapatite coatings is influenced by the dissolution behavior of the coating in in vivo conditions. Plasma-spraying generates a mixture of phases and this study has focused on how the balance of phases affects the in vitro dissolution behavior of the coatings in double distilled-deionized water and in tris-buffer solutions. The pH changes in double distilled-deionized water were monitored, whilst the pH value was maintained at 7.25 for the tris-buffer solution at 37 degrees C with 5% CO2 atmosphere. The phosphate and calcium ions released were measured using UV-Visible Spectrophotometer and Atomic Absorption Spectroscopy respectively. Changes in crystal and surface topology were also studied. The results indicate that the dissolution behavior of the coatings depends on several factors. The rate of release of phosphate ions was found to increase significantly for the tris-buffer solution compared to the deionized water, indicating that the presence of electrolyte constituents affects the dissolution behavior of the coatings. The Ca/P ratio in the tris-buffer solution is approximately three. Increases in the level of crystallinity of the coatings significantly decreased the dissolution rate and hence, the amount of phosphate ions released. The higher the percentage of crystallinity, the higher the stability of the coating under in vitro conditions.

Morse theory shows how the topology of an implicit surface is affected by its function's critical points, whereas catastrophe theory shows how these critical points behave as the function's parameters change. Interval analysis finds the critical points, and they can also be tracked efficiently during parameter changes. Changes in the function value at these critical points cause changes in the topology. Techniques for modifying the polygonization to accommodate such changes in topology are given. These techniques are robust enough to guarantee the topology of an implicit surface polygonization, and are efficient enough to maintain this guarantee during interactive modeling. The impact of this work is a topologically-guaranteed polygonization technique, and the ability to directly and accurately manipulate polygonized implicit surfaces in real time.

In the global scenario, wind turbines and their aerodynamics are always subjected to constant research for increasing their efficiency which converts the abundant wind energy into usable electrical energy. In this research, an attempt is made to increase the efficiency through the changes in surface topology of wind turbines through computational fluid dynamics. Dimples on the other hand are very efficient in reducing air drag as is it evident from the reduction of drag and increase in lift in golf balls. The predominant factors influencing the efficiency of the wind turbines are lift and drag which are to be maximized and minimized respectively. In this research, surface of turbine blades are integrated with dimples of various sizes and arrangements and are analyzed using computational fluid dynamics to obtain an optimum combination. The analysis result shows that there is an increase in power with about 15% increase in efficiency. Hence, integration of dimples on the surface of wind turbine blades has helped in increasing the overall efficiency of the wind turbine.

Dynamic chirality in selected diaryl methane containing drugs. An exploratory ab initio conformational study

Control over minivalley polarization and interlayer coupling is demonstrated in double bilayer graphene twisted with an angle of 2.37°. This intermediate angle is small enough for the minibands to form and large enough such that the charge carrier gases in the layers can be tuned independently. Using a dual-gated geometry we identify and control all possible combinations of minivalley polarization via the population of the two bilayers. An applied displacement field opens a band gap in either of the two bilayers, allowing us to even obtain full minivalley polarization. In addition, the carriers, formerly separated by their minivalley character, are mixed by tuning through a Lifshitz transition, where the Fermi surface topology changes. The high degree of control over the minivalley character of the bulk charge transport in twisted double bilayer graphene offers new opportunities for realizing valleytronics devices such as valley valves, filters, and logic gates.

We describe the state of development of a white light interferometer to characterize the cryogenic mirrors for GW detector on operation. We include the first experimental results from the proof of concept of the metrology instrument. The instrument will characterize the topology as well as the vibration of the mirrors. This development takes place in the frame of the E-TEST project. E-TEST is one of the technology demonstrators for the future Einstein Telescope (ET). ET is dedicated to the measure and characterization of gravitational waves. The prototype built by E-TEST includes a large silicon mirror of 40 cm diameter suspended by innovative vibration isolation hanging modules. To reach the detection specification, the mirror is cooled down at cryogenic temperatures around 20 K. Nevertheless, even after the isolation, the mirror may not reach perfect stability once at cryogenic temperatures. Furthermore, the mirror may experience surface topology changes and wavefront deformation due to the extreme variations in temperature and gradient. With our metrology instrument, we can obtain on a single camera frame a set of interferogram maps of the area observed on the mirror at different optical path differences. To do this, we design an innovative phase mask for a white light low-coherence interferometer. In addition, we implement new algorithms for the white light interferogram analysis, avoiding the limitations of the conventional Phase Shifting Interferometry algorithms.

SecA, the ATPase of Sec translocase, mediates the post-translational translocation of preprotein through the protein-conducting channel SecYEG in the bacterial inner membrane. Here we report the structures of Escherichia coli Sec intermediates during preprotein translocation as visualized by electron microscopy to probe the oligomeric states of SecA during this process. We found that the translocase holoenzyme is symmetrically assembled by SecA and SecYEG on proteoliposomes, whereas the translocation intermediate 31 (I(31)) becomes asymmetric because of the presence of preprotein. Moreover, SecA is a dimer in these two translocation complexes. This work also shows surface topological changes in the components of translocation intermediates by immunogold labeling. The channel entry for preprotein translocation was found at the center of the I(31) structures. Our results indicate that the presence of preprotein introduces asymmetry into translocation intermediates, while SecA remains dimeric during the translocation process.

Peptidomimetics are molecules of particular interest in the context of drug design and development. They are proteolytically and metabolically more stable than their natural peptide counterparts but still offer high specificity toward their biological targets. In recent years, 1,4- and 1,5-disubstituted 1,2,3-triazole-based peptidomimetics have emerged as promising lead compounds for the design of various inhibitory and tumor-targeting molecules as well as for the synthesis of peptide analogues. The growing popularity of triazole-based peptidomimetics and a constantly broadening range of their application generated a demand for elaborate theoretical investigations by classical molecular dynamics simulations and molecular docking. Despite this rising interest, accurate and coherent force field parameters for triazole-based peptidomimetics are still lacking. Here, we report the first complete set of parameters dedicated to this group of compounds, named TZLff. This parametrization is compatible with the latest version of the AMBER force field (ff14SB) and can be readily applied for the modeling of pure triazole-based peptidomimetics as well as natural peptide sequences containing one or more triazole-based modifications in their backbone. The parameters were optimized to reproduce HF/6-31G* electrostatic potentials as well as MP2/cc-pVTZ equilibrium Hessian matrices and conformational potential energy surfaces through the use of a genetic algorithm-based search and least-squares fitting. Following the standards of AMBER, we introduce residue building units, thus allowing the user to define any given sequence of triazole-based peptidomimetics. Validation of the parameter set against ab initio- and NMR-based reference systems shows that we obtain fairly accurate results, which properly capture the conformational features of triazole-based peptidomimetics. The successful and efficient parametrization strategy developed in this work is general enough to be applied in a straightforward manner for parametrization of other peptidomimetics and, potentially, any polymeric assemblies.