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1.
Entropic cost of folding and phase diagrams of polypeptides: Why are IDPs unfolded at room temperature?
Artem Badasyan, invited lecture at foreign university

Abstract: In spin models, that are applied to describe the conformational transitions in polymers, the number of spin orientations, that correspond to the disordered conformation, can be estimated using fundamental definitions of Statistical Physics. For instance, when considering alpha-helix to coil transition in polypeptides, the role of generalized coordinates is played by pairs of torsional angle, and the repeating unit populates different regions of that 2D contour map, depending on conformation. By scanning over all possible torsional angles, that do not violate the obvious limitations due to the excluded volume, the so-called Ramachandran map can be plotted, which is actually the phase space visualization for the helix-coil transition problem. The region of phase space, corresponding to the ordered, helical conformations, is much more limited, than the one, corresponding to all other (allowed) conformations. We can calculate the areas of these regions as Γhelix and Γcoil , and construct the ratio Q = Γcoil . Naturally, it can be interpreted as log(Q) = Scoil − Shelix = ΔS, the entropic cost of helix with respect to coil. To illustrate the importance of the entropic price of ordered conformation we report our recent results, that allowed to explain the peculiarity of phase diagrams of Intrinsically Disordered Proteins (IDP) out of larger Q-values, as compared to globular counterparts. In particular, it has been shown, that due to larger Q, the phase diagram of IDP is shifted towards higher temperatures.
Found in: ključnih besedah
Keywords: IDP, protein folding, phase diagram
Published: 23.06.2016; Views: 2817; Downloads: 0
.pdf Fulltext (2,96 MB)
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2.
Agent based modelling for the 2D molecular self-organization of realistic molecules
Sara Fortuna, Alessandro Troisi, 2010, original scientific article

Abstract: We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.
Found in: ključnih besedah
Summary of found: ...part of the protocol to calculate the phase diagram with less computational effort than standard...
Keywords: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram
Published: 11.10.2016; Views: 2977; Downloads: 0
.pdf Fulltext (4,00 MB)

3.
Development and Validation of a High- Performance Liquid Chromatography– Tandem Mass Spectrometry Method for the Simultaneous Determination of Irinotecan and Its Main Metabolites in Human Plasma and Its Application in a Clinical Pharmacokinetic Study
Giuseppe Toffoli, Elena Marangon, Elisa Mazzega, Bianca Posocco, 2015, original scientific article

Abstract: Irinotecan is currently used in several cancer regimens mainly in colorectal cancer (CRC). This drug has a narrow therapeutic range and treatment can lead to side effects, mainly neutropenia and diarrhea, frequently requiring discontinuing or lowering the drug dose. A wide inter-individual variability in irinotecan pharmacokinetic parameters and pharmacodynamics has been reported and associated to patients’ genetic background. In particular, a polymorphism in the UGT1A1 gene (UGT1A1*28) has been linked to an impaired detoxification of SN-38 (irinotecan active metabolite) to SN-38 glucuronide (SN-38G) leading to increased toxicities. Therefore, therapeutic drug monitoring of irinotecan, SN-38 and SN-38G is recommended to personalize therapy. In order to quantify simultaneously irinotecan and its main metabolites in patients’ plasma, we developed and validated a new, sensitive and specific HPLC–MS/MS method applicable to all irinotecan dosages used in clinic. This method required a small plasma volume, addition of camptothecin as internal standard and simple protein precipitation. Chromatographic separation was done on a Gemini C18 column (3 μM, 100 mm x 2.0 mm) using 0.1% acetic acid/bidistilled water and 0.1% acetic acid/acetonitrile as mobile phases. The mass spectrometer worked with electrospray ionization in positive ion mode and selected reaction monitoring. The standard curves were linear (R20.9962) over the concentration ranges (10–10000 ng/mL for irinotecan, 1–500 ng/mL for SN-38 and SN-38G and 1–5000 ng/mL for APC) and had good back-calculated accuracy and precision. The intra- and inter-day precision and accuracy, determined on three quality control levels for all the analytes, were always <12.3% and between 89.4% and 113.0%, respectively. Moreover, we evaluated this bioanalytical method by re-analysis of incurred samples as an additional measure of assay reproducibility. This method wassuccessfully applied to a pharmacokinetic study in metastatic CRC patients enrolled in a genotype-guided phase Ib study of irinotecan administered in combination with 5-fluorouracil/ leucovorin and bevacizumab.
Found in: ključnih besedah
Summary of found: ...water and 0.1% acetic acid/acetonitrile as mobile phases. The mass spectrometer worked with electrospray ionization...
Keywords: Pharmacokinetic, pharmacodynamics, phase I clinical study, colorectal cancer, Mass spectrometry, pharmacogenetics
Published: 21.03.2017; Views: 2596; Downloads: 0
.pdf Fulltext (1018,06 KB)

4.
The comparison of anthocyanin and pyranoanthocyanin extraction efficiency in Pinot Noir wine using SPE
Branka Mozetič Vodopivec, Dorota Korte, Jelena Topić, 2017, published scientific conference contribution abstract

Found in: ključnih besedah
Summary of found: ...Anthocyanins, wine , Pinot Noir, HPLC, solid- phase extraction...
Keywords: Anthocyanins, wine, Pinot Noir, HPLC, solid-phase extraction
Published: 05.07.2017; Views: 3436; Downloads: 0
.pdf Fulltext (109,24 KB)

5.
Unusual magnetodielectric effects in La2CuMnO6 induced by a dynamic crossover in dielectric relaxation at TC
Jasnamol Pezhumkattil Palakkal, Cheriyedath Raj Sankar, Ajeesh Parayancheri Paulose, Matjaž Valant, Artem Badasyan, Manoj Raama Varma, 2018, original scientific article

Abstract: A series of fixed frequency dielectric measurements shows dielectric relaxation in La2CuMnO6, with a dynamic (Arrhenius to Arrhenius) crossover at TC. The external magnetic field alters the relaxation parameters in the vicinity of crossover and induces an unusual trend in the magnetodielectric coupling around TC. A large magnetodielectric coupling of 55% (at 68 K, 4 kHz) and 61% (at 105 K, 285.8 kHz) under a small magnetic field of 5 kOe is discovered. Presence of ferromagnetic short-range correlations above TC and a sign reversal of magnetoresistance around TC are observed. Specific heat analysis revealed the presence of ferromagnetic, variable range hopping active charge localized state. The presence of ferromagnetic short-range correlations and the influence of a core-grain dominated magnetoresistance on the Maxwell-Wagner interfacial polarization are responsible for the observed large magnetodielectric effect. Both the magnetic ordering and external magnetic field control the electric dipole relaxation in the material.
Found in: ključnih besedah
Keywords: Double perovskite Griffiths-like phase Dielectric Magnetoresistance Magnetodielectric
Published: 03.01.2018; Views: 2007; Downloads: 0
.pdf Fulltext (1,24 MB)

6.
7.
CONTRIBUTION TO DEVELOPMENT OF MESHLESS METHODS FOR FREE AND MOVING BOUNDARY PROBLEMS
NAZIA TALAT, 2018, doctoral dissertation

Found in: ključnih besedah
Summary of found: ...Two- phase flow, free and moving boundaries, computational fluid...
Keywords: Two-phase flow, free and moving boundaries, computational fluid dynamics, phasefield formulation, 2D problems, axisymmetric problems, diffuse approximate meshless method, Rayleigh-Taylor instability, Boussinesq approximation, variable density and viscosity, flow focusing, dripping, jetting
Published: 11.09.2018; Views: 2313; Downloads: 109 
(1 vote)
.pdf Fulltext (4,24 MB)

8.
Gypsum under pressure: A first-principles study
Sandro Scandolo, Luigi Giacomazzi, 2010, original scientific article

Found in: ključnih besedah
Keywords: Gypsum, Hydrous minerals, ab initio, high-pressure phase
Published: 15.10.2018; Views: 1518; Downloads: 0
.pdf Fulltext (372,22 KB)

9.
Crystal habit modification of Cu(II) isonicotinate-N-oxide complexes using gel phase crystallisation
Jonathan Steed, Žygimantas Drabavičius, Katja Ferfolja, Dipankar Ghosh, Krishna Kumar Damodaran, 20, original scientific article

Abstract: We report the crystallisation of three forms of copper(II) isonicotinate-N-oxide complex and their phase interconversion via solvent-mediated crystal to crystal transformation. The different forms of copper complex have been isolated and characterised by single crystal X-ray diffraction. Gel phase crystallisation performed in hydrogels, low molecular weight gels and gels of tailored gelator showed crystal habit modification. Crystallisation in aqueous ethanol resulted in concomitant formation of blue (form-I) and green (form-II/IV) crystals while use of low molecular weight gel results in selective crystallization of the blue form-I under identical conditions. Comparison of gel phase and the solution state crystallisation in various solvent compositions reveals that the blue form-I is the thermodynamically stable form under ambient conditions.
Found in: ključnih besedah
Keywords: copper(II) complex, gel phase crystallisation, crystal habit modification, isonicotinate-N-oxide, X-ray diffraction
Published: 08.11.2018; Views: 1614; Downloads: 0
.pdf Fulltext (968,24 KB)

10.
Complete Characterization of Phase and Amplitude of Bichromatic Extreme Ultraviolet Light
Primož Rebernik Ribič, Giovanni De Ninno, 2019, original scientific article

Abstract: Intense, mutually coherent beams of multiharmonic extreme ultraviolet light can now be created using seeded free-electron lasers, and the phase difference between harmonics can be tuned with attosecond accuracy. However, the absolute value of the phase is generally not determined. We present a method for determining precisely the absolute phase relationship of a fundamental wavelength and its second harmonic, as well as the amplitude ratio. Only a few easily calculated theoretical parameters are required in addition to the experimental data.
Found in: ključnih besedah
Keywords: free-electron lasers, coherence, phase, attosecond
Published: 12.01.2020; Views: 1266; Downloads: 0
.pdf Fulltext (293,60 KB)

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