Supercritical and Subcritical Pitchfork Bifurcations in a Buckling Problem for a Graphene Sheet Between two Rigid Substrates

In this paper we study a model of the buckling of a sheet of graphene between two rigid substrates. We seek to understand the buckling of the sheet as the substrate separation is varied with a fixed load on each end of the sheet. We write down the expression for total energy of the system and from it derive a 2-point nonlinear boundary-value problem whose solutions are equilibrium configurations of the sheet. We cannot get an explicit solution. Instead, we perform a bifurcation analysis by using asymptotics to approximate solutions on the bifurcating branches near the bifurcation points. The bifurcating parameter is the separation between the rigid substrates. We find that the bifurcations are supercritical or subcritical pitchfork bifurcations. We perform a parametric study to understand how the nature of the bifurcations is influenced by other physical parameters in the problem. This leads to insight on the orientation of the buckled graphene sheet depending on substrate separation

Infrared spectra of hydrogen bond network in lamellar perfluorocarboxylic acid monohydrates.

The infrared spectra of the long-chain perfluorocarboxylic acid monohydrates differ markedly from those of the anhydrous dimers. Consequently, the structure of the solid perfluorocarboxylic acid monohydrates must differ from any known dimer-containing carboxylic acid crystals. Consideration of the significant features of the infrared spectra of the long-chain perfluorocarboxylic acid monohydrates, supplemented by their Raman spectra, and comparison with the spectra of auxiliary substances have led us to conclude that the rather strong neutral carboxyl-hydroxyl to water bonding can best explain the observations. The infrared spectra indicate the presence of fairly short hydrogen bonds connecting the water molecules to the carbonyl groups. In the construction of the hydrogen bonding pattern of the perfluorocarboxylic acid monohydrates, the oxalic acid dihydrate plays the key role. The striking similarity between the infrared spectra of the oxalic acid dihydrates and the perfluorocarboxylic acid monohydrates in the regions characteristic of water and OH⋯O vibration suggests that the structure of the hydrated carboxyl groups is the same in both crystals. These regions are characterized by the sharp doublet at 3539 cm-1 and 3464 cm-1, which is due to the H2O ν1 and ν3 stretching vibrations, respectively, and the broad absorption between 3000 cm-1 and 1500 cm-1 with the intense band at 1970 cm-1, both associated with the vibration of the OH⋯O group. The later peak consists of two band components at near 1980 cm-1 and 2020 cm-1. These band components show different behaviour when the temperature, polarization or deuteration is changed. In general, the infrared spectra of long-chain perfluorocarboxylic acids represent the system with very short hydrogen bonds connecting the water molecules to the carboxylates. This hydrogen bond pattern should be very similar to that found in the crystals of α-oxalic acid dihydrate

Utjecaj koncentracije otopljenog kisika na intracelularni pH i na brzinu rasta Aspergillus niger

With the results presented we would like to emphasize the influence of dissolved oxygen concentration in a medium on intracellular pH values and consequently on overall metabolism of microorganisms. Intracellular pH of mycelium grown under different concentrations of dissolved oxygen in the medium was determined by recently developed cryo 31P-NMR method. Sensitivity of proteins toward proton concentration was well recognised, therefore pH influences on the activities of some key regulatory enzymes of Aspergillus niger were determined at pH values similar to those detected in the cells grown under lower dissolved oxygen concentrations. The results have shown significantly reduced specific activities of hexokinase, 6 phosphofructokinase and glucose-6-phosphate dehydrogenase in more acidic environment, while pyruvate kinase was found to be relatively insensitive toward higher proton concentration. As expected, due to reduced specific activities of some key regulatory enzymes under more acidic conditions, overall metabolism should be hindered in media with lower dissolved oxygen concentration, as confirmed by detecting reduced specific growth rates.Prikazanim rezultatima istaknut je utjecaj koncentracije otopljenog kisika u mediju na intracelularne pH-vrijednosti i s tim u vezi na ukupni metabolizam mikroorganizama. Intracelularni pH micelija, uzgajanog pri različitim koncentracijama otopljenog kisika u mediju, određen je nedavno razvijenim postupkom krio-31P-NMR. Poznata je osjetljivost proteina na koncentracije protona. Stoga je određen utjecaj pH na aktivnosti nekih ključnih regulatornih enzima u A. niger pri pH-vrijednostima sličnim onima otkrivenim u stanica što su rasle pri smanjenim koncentracijama otopljenog kisika. Rezultati su pokazali bitno smanjenu specifičnu aktivnost heksokinaze, 6-fosfofruktokinaze i glukoza-6-fosfat dehidrogenaze u jače kiseloj sredini, dok je piruvat kinaza relativno neosjetljiva na ve}e koncentracije protona. Očekivalo bi se da će u medijima sa smanjenom koncentracijom otopljenog kisika cjelokupni metabolizam biti ometen zbog smanjenih specifičnih aktivnosti nekih ključnih regulatornih enzima u kiselijim uvjetima. To je i potvrđeno jer su utvrđene smanjene brzine specifičnog rasta A. niger

Urban one-way system road traffic management

In the city of Ljubljana, traffic regime is unsatisfied for longer period of time. On the existent road network, traffic congestions are occuring because of unsuitable or uncomplete road segments (sections). Improvements are also necessary with public transportation traffic services, because a lot of people are still deciding for personal traffic transport instead of rather deciding for public transportation traffic services. One way of handling this situation could be introduction of one-way traffic regime, where we also have to take into account variety of factors that influence on road selection type (one-way or two-way), since we could make matters even worse with the unsuitable selection. We must found out what we gain and what we lose with the transformation, and on the basis of that we decide to implement changes, since they have influence on cities economic sphere, traffic safety, pollution and further city development. Because of all this factors we must precisely study all potential changes

Engineering inclusion bodies for non denaturing extraction of functional proteins

<p>Abstract</p> <p>Background</p> <p>For a long time IBs were considered to be inactive deposits of accumulated target proteins. In our previous studies, we discovered IBs containing a high percentage of correctly folded protein that can be extracted under non-denaturing conditions in biologically active form without applying any renaturation steps. In order to widen the concept of correctly folded protein inside IBs, G-CSF (granulocyte colony stimulating factor) and three additional proteins were chosen for this study: GFP (Green fluorescent protein), His7dN6TNF-α (Truncated form of Tumor necrosis factor α with an N-terminal histidine tag) and dN19 LT-α (Truncated form of Lymphotoxin α).</p> <p>Results</p> <p>Four structurally different proteins that accumulate in the bacterial cell in the form of IBs were studied, revealing that distribution of each target protein between the soluble fraction (cytoplasm) and insoluble fraction (IBs) depends on the nature of the target protein.</p> <p>Irrespective of the folding pattern of each protein, spectroscopy studies have shown that proteins in IBs exhibit similar structural characteristics to the biologically active pure protein when produced at low temperature. In the case of the three studied proteins, G-CSF, His7ΔN6TNF-α, and GFP, a significant amount of protein could be extracted from IBs with 0.2% N-lauroyl sarcosine (NLS) and the proteins retained biological activity although no renaturation procedure was applied.</p> <p>Conclusion</p> <p>This study shows that the presence of biologically active proteins inside IBs is more general than usually believed. A large amount of properly folded protein is trapped inside IBs prepared at lower temperatures. This protein can be released from IBs with mild detergents under non-denaturing conditions. Therefore, the active protein can be obtained from such IBs without any renaturation procedure. This is of great importance for the biopharmaceutical industry. Furthermore, such IBs composed of active proteins could also be used as pure nanoparticles in diagnostics, as biocatalysts in enzymatic processes, or even as biopharmaceuticals.</p

Χρήση Φασματογραφίας Πυρηνικού Μαγνητικού Συντονισμού για την εύρεση της βιοδραστικής διαμόρφωσης νέων φαρμακευτικών μορίων

Περίληψ

Revealing the astragalin mode of anticandidal action

Due to limited arsenal of systemically available antifungal agents, infections caused by Candida albicans are difficult to treat and the emergence of drug-resistant strains present a major challenge to the clinicians worldwide. Hence further exploration of potential novel and effective antifungal drugs is required. In this study we have explored the potential of a flavonoid, astragalin, in controlling the growth of C. albicans, in both planktonic and biofilm forms by microdilution method; and in regulating the morphological switch between yeast and hyphal growth. Astragalin ability to interfere with membrane integrity, ergosterol synthesis and its role in the regulation of genes encoding for efflux pumps has been addressed. In our study, astragalin treatment produced good antimicrobial and significant antibiofilm activity. Anticandidal activity of astragalin was not related to ERG11 downregulation, neither to direct binding to CYP51 enzyme nor was linked to membrane ergosterol assembly. Instead, astragalin treatment resulted in reduced expression of CDR1 and also affected cell membrane integrity without causing cytotoxic effect on human gingival fibroblast cells. Considering that astragalin-mediated decreased expression of efflux pumps increases the concentration of antifungal drug inside the fungal cells, a combinatorial treatment with this agent could be explored as a novel therapeutic option for candidiasis

Evidence of Polaron Excitations in Low Temperature Raman Spectra of Oxalic Acid Dihydrate

Low temperature Raman spectra of oxalic acid dihydrate (8K - 300 K) both for polycrystalline and single crystal phase show strong variation with temperature in the interval from 1200 to 2000 cm-1. Previous low temperature diffraction studies all confirmed the stability of the crystal P21/n phase with no indications of any phase transition, reporting the existence of a strong hydrogen bond between the oxalic acid and a water molecule. A new group of Raman bands in the 1200 – 1300 cm-1 interval below 90 K is observed, caused by possible loss of the centre of inversion. This in turn could originate either due to disorder in hydroxyl proton positions, or due to proton transfer from carboxylic group to water molecule. The hypothesis of proton transfer is further supported by the emergence of new bands centered at 1600 cm-1 and 1813 cm-1, which can be explained with vibrations of H3O+ ions. The broad band at 1600 cm-1 looses intensity, while the band at 1813 cm-1 gains intensity on cooling. The agreement between quantum calculations of vibrational spectra and experimentally observed Raman bands of hydronium ions in oxalic acid sesquihydrate crystal corroborate this hypothesis

Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase II&alpha;

In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors