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  1. Book ; Online: Modified Theories of Gravity and Cosmological Applications

    Stavrinos, Panayiotis / Saridakis, Emmanuel N

    2023  

    Keywords Research & information: general ; Physics ; Gauss-Bonnet ; innermost stable circular orbits ; spinning test particle ; Einstein-Maxwell-scalar black holes ; modified gravity theory ; Hawking-Page phase transition ; regular black hole ; Minkowski core ; Lambert W function ; black hole mimic ; modified and massive gravity ; two measure theories ; Einstein and Finsler gravity ; off-diagonal cosmological solutions ; nonholonomic dynamical Weyl-scale symmetry breaking ; (anisotropic) inflation ; dark energy ; reconstructing procedure ; Einstein-Gauss-Bonnet gravity ; nonlinear electrodynamics ; hawking temperature ; entropy ; heat capacity ; black hole shadow ; energy emission rate ; quasinormal modes ; cosmology ; torsion ; multifield cosmology ; anisotropic spacetimes ; Kantowski-Sachs ; anisotropic inflation ; galactic rotation ; nonspherical gravitational sources ; modified gravity ; cosmology:theory ; large-scale structure of universe ; gravitation ; fractional-dimension gravity ; dark matter ; cosmological dynamics ; Weyl integrable theory ; scalar field ; interaction ; Painlevé-Gullstrand metrics ; Lense-Thirring metric ; Killing tensor ; Killing-Yano tensor ; separability ; Carter constant ; geodesic integrability ; isometric embeddings ; symmetrical surfaces ; free embedding ; unfolded embedding ; Regge-Teitelboim gravity ; embedding theory ; black hole ; magnetic field ; chaos ; symplectic integrator ; non-linear symmetry realization ; conformal symmetry ; Ricci-based gravity ; Palatini gravity ; exoplanets ; planet's interior ; electromagnetic ; covariant ; field ; constraints ; curved space ; alternative theories of gravity ; supermassive black hole ; stellar dynamics ; variation of constants ; inflation ; f(R)-gravity ; k-inflation ; n/a
    Language English
    Size 1 electronic resource (318 pages)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Publishing place Basel
    Document type Book ; Online
    Note English
    HBZ-ID HT030379069
    ISBN 9783036558301 ; 3036558306
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: The genetic informational network: how DNA conveys semantic information.

    Saridakis, Emmanuel

    History and philosophy of the life sciences

    2021  Volume 43, Issue 4, Page(s) 112

    Abstract: The question of whether "genetic information" is a merely causal factor in development or can be made sense of semantically, in a way analogous to a language or other type of representation, has generated a long debate in the philosophy of biology. It is ...

    Abstract The question of whether "genetic information" is a merely causal factor in development or can be made sense of semantically, in a way analogous to a language or other type of representation, has generated a long debate in the philosophy of biology. It is intimately connected with another intense debate, concerning the limits of genetic determinism. In this paper I argue that widespread attempts to draw analogies between genetic information and information contained in books, blueprints or computer programs, are fundamentally inadequate. In development, gene exons are the central part of an intricate and densely ramified semantic Genetic Informational Network. DNA in the entire genome is in a state of continuous positive and negative feedback with itself and with its 'environment', and is 'read' and acted upon by the cell in various alternative and complementary ways. The linear combinatorial coding relation between codons and amino acids is but one aspect of semantic genetic information, which is, when considered in its entirety, a far wider and richer concept.
    MeSH term(s) DNA ; Language ; Philosophy ; Semantics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2021-11-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2094240-0
    ISSN 1742-6316 ; 0391-9714
    ISSN (online) 1742-6316
    ISSN 0391-9714
    DOI 10.1007/s40656-021-00470-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Protein Thermodynamic Properties, Crystallisation, and the Hofmeister Series.

    Saridakis, Emmanuel / Donta, Katerina

    ChemPlusChem

    2024  , Page(s) e202300733

    Abstract: The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of ... ...

    Abstract The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive. A correlation, based on published data and crystallisation conditions for several proteins, is proposed here between some thermodynamic properties of proteins and the position in the Hofmeister series of the salts from which they preferentially crystallise. Namely, a high ratio between the entropic or enthalpic protein-solvent interactions contribution to thermodynamic stability and the total thermodynamic stability of a given protein, indicate the protein's high propensity to crystallise in solutions of highly kosmotropic salts. Low such ratios on the other hand, indicate that chaotropic salts can be equally successful, i.e. that the protein in question is rather indifferent to the Hofmeister character of the salt. Testing various model proteins for crystallisation against screens containing salts found at different points on the Hofmeister series, as well as further bibliographic analysis, have yielded results that appear to largely corroborate this hypothesis. These conclusions may conceivably be used as a crystallisation predictive tool.
    Language English
    Publishing date 2024-05-03
    Publishing country Germany
    Document type Journal Article
    ISSN 2192-6506
    ISSN (online) 2192-6506
    DOI 10.1002/cplu.202300733
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Growing Crystals for X-ray Free-Electron Laser Structural Studies of Biomolecules and Their Complexes.

    Nanev, Christo N / Saridakis, Emmanuel / Chayen, Naomi E

    International journal of molecular sciences

    2023  Volume 24, Issue 22

    Abstract: Currently, X-ray crystallography, which typically uses synchrotron sources, remains the dominant method for structural determination of proteins and other biomolecules. However, small protein crystals do not provide sufficiently high-resolution ... ...

    Abstract Currently, X-ray crystallography, which typically uses synchrotron sources, remains the dominant method for structural determination of proteins and other biomolecules. However, small protein crystals do not provide sufficiently high-resolution diffraction patterns and suffer radiation damage; therefore, conventional X-ray crystallography needs larger protein crystals. The burgeoning method of serial crystallography using X-ray free-electron lasers (XFELs) avoids these challenges: it affords excellent structural data from weakly diffracting objects, including tiny crystals. An XFEL is implemented by irradiating microjets of suspensions of microcrystals with very intense X-ray beams. However, while the method for creating microcrystalline microjets is well established, little attention is given to the growth of high-quality nano/microcrystals suitable for XFEL experiments. In this study, in order to assist the growth of such crystals, we calculate the mean crystal size and the time needed to grow crystals to the desired size in batch crystallization (the predominant method for preparing the required microcrystalline slurries); this time is reckoned theoretically both for microcrystals and for crystals larger than the upper limit of the Gibbs-Thomson effect. The impact of the omnipresent impurities on the growth of microcrystals is also considered quantitatively. Experiments, performed with the model protein lysozyme, support the theoretical predictions.
    MeSH term(s) X-Rays ; Electrons ; Crystallography, X-Ray ; Synchrotrons ; Proteins ; Lasers
    Chemical Substances Proteins
    Language English
    Publishing date 2023-11-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242216336
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Modified cosmology through spacetime thermodynamics and Barrow horizon entropy

    Saridakis, Emmanuel N.

    Abstract: We present modified cosmological scenarios that arise from the application of the"gravity-thermodynamics"conjecture, using the Barrow entropy instead of the usual Bekenstein-Hawking one. The former is a modification of the black hole entropy due to ... ...

    Abstract We present modified cosmological scenarios that arise from the application of the"gravity-thermodynamics"conjecture, using the Barrow entropy instead of the usual Bekenstein-Hawking one. The former is a modification of the black hole entropy due to quantum-gravitational effects that deform the black-hole horizon by giving it an intricate, fractal structure. We extract modified cosmological equations which contain new extra terms that constitute an effective dark-energy sector, and which coincide with the usual Friedmann equations in the case where the new Barrow exponent acquires its Bekenstein-Hawking value. We present analytical expressions for the evolution of the effective dark energy density parameter, and we show that the universe undergoes through the usual matter and dark-energy epochs. Additionally, the dark-energy equation-of-state parameter is affected by the value of the Barrow deformation exponent and it can lie in the quintessence or phantom regime, or experience the phantom-divide crossing. Finally, at asymptotically large times the universe always results in the de-Sitter solution.
    Keywords covid19
    Publisher ArXiv
    Document type Article ; Online
    DOI 10.1088/1475-7516/2020/07/031
    Database COVID19

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  6. Article: Barrow holographic dark energy

    Saridakis, Emmanuel N.

    Abstract: We formulate Barrow holographic dark energy, by applying the usual holographic principle at a cosmological framework, but using the Barrow entropy instead of the standard Bekenstein-Hawking one. The former is an extended black-hole entropy that arises ... ...

    Abstract We formulate Barrow holographic dark energy, by applying the usual holographic principle at a cosmological framework, but using the Barrow entropy instead of the standard Bekenstein-Hawking one. The former is an extended black-hole entropy that arises due to quantum-gravitational effects which deform the black-hole surface by giving it an intricate, fractal form. We extract a simple differential equation for the evolution of the dark energy density parameter, which possesses standard holographic dark energy as a limiting sub-case, and we show that the scenario can describe the universe thermal history, with the sequence of matter and dark energy eras. Additionally, the new Barrow exponent $\Delta$ significantly affects the dark energy equation of state, and according to its value it can lead it to lie in the quintessence regime, in the phantom regime, or experience the phantom-divide crossing during the evolution.
    Keywords covid19
    Publisher ArXiv
    Document type Article
    Database COVID19

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  7. Article ; Online: Thermal Shift Assay for Characterizing the Stability of RNA Helicases and Their Interaction with Ligands.

    Saridakis, Emmanuel / Coste, Franck

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2209, Page(s) 73–85

    Abstract: Thermofluor or thermal shift assay is an easily implementable, high-throughput method for assessing the thermostability of proteins and the influence of various ligands on that stability. It is particularly useful for the assaying of ligands that may ... ...

    Abstract Thermofluor or thermal shift assay is an easily implementable, high-throughput method for assessing the thermostability of proteins and the influence of various ligands on that stability. It is particularly useful for the assaying of ligands that may stabilize oligomeric helicases, which rely on both substrates (oligonucleotides) and nucleotide cofactors (ATP analogues) for their stability in a functional state. In this chapter, we describe the rationale and present a basic protocol for the use of this technique. Multi-ligand screening is also discussed via a worked example of the stabilization of a hexameric RNA helicase, a target protein for structural studies in our laboratories.
    MeSH term(s) Bacterial Proteins/chemistry ; Fluorometry/methods ; Mycobacterium tuberculosis/enzymology ; Protein Stability ; RNA Helicases/chemistry ; Rho Factor/chemistry ; Temperature
    Chemical Substances Bacterial Proteins ; Rho Factor ; RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2020-11-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0935-4_5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Protein Crystals Nucleated and Grown by Means of Porous Materials Display Improved X-ray Diffraction Quality.

    Nanev, Christo N / Saridakis, Emmanuel / Govada, Lata / Chayen, Naomi E

    International journal of molecular sciences

    2022  Volume 23, Issue 18

    Abstract: Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation- ... ...

    Abstract Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of crystals. Although the nucleation stage is decisive, it is the subsequent growth of crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is theoretically considered. Due to the low degree of metastability, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as bioglass ("Naomi's Nucleant"), buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of bioglass and buckypaper yield significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. Our theoretical conclusion is that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.
    MeSH term(s) Crystallization/methods ; Crystallography, X-Ray ; Gold ; Porosity ; Proteins/chemistry ; Silicon/chemistry ; X-Ray Diffraction
    Chemical Substances Proteins ; Gold (7440-57-5) ; Silicon (Z4152N8IUI)
    Language English
    Publishing date 2022-09-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231810676
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A guanidino-γ-cyclodextrin superdimer generates a twin receptor for phosphate dimers assembled by anti-electrostatic hydrogen bonds.

    Saridakis, Emmanuel / Kasimati, Eleni-Marina / Yannakopoulou, Konstantina / Mavridis, Irene M

    Chemical communications (Cambridge, England)

    2022  Volume 58, Issue 34, Page(s) 5300–5303

    Abstract: Octakis-6-guadinidino-γ-cyclodextrin (gguan) hydrochloride in the presence of phosphates crystallises from aqueous solution in the unprecedented form of a superdimer (dimer-within-a-dimer). The self-assembly exposes four circular octa-guanidinium regions ...

    Abstract Octakis-6-guadinidino-γ-cyclodextrin (gguan) hydrochloride in the presence of phosphates crystallises from aqueous solution in the unprecedented form of a superdimer (dimer-within-a-dimer). The self-assembly exposes four circular octa-guanidinium regions that bind and stabilise discrete H-bonded phosphate anion dimers. The small (∼2 nm) gguan-phosphate assembly is preorganised and stable in aqueous solution, as demonstrated by DLS and NMR experiments.
    MeSH term(s) Anions ; Hydrogen Bonding ; Phosphates/chemistry ; Static Electricity ; Water/chemistry
    Chemical Substances Anions ; Phosphates ; Water (059QF0KO0R)
    Language English
    Publishing date 2022-04-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d2cc00323f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Perspectives on high-throughput technologies applied to protein crystallization.

    Saridakis, Emmanuel

    Protein and peptide letters

    2012  Volume 19, Issue 7, Page(s) 778–783

    Abstract: High-throughput crystallisation requires the rapid and accurate dispensing of protein and precipitating agent solutions at nanovolumes, but does not end there. The choice of the initial screens is very important, especially with respect to the ... ...

    Abstract High-throughput crystallisation requires the rapid and accurate dispensing of protein and precipitating agent solutions at nanovolumes, but does not end there. The choice of the initial screens is very important, especially with respect to the availability of protein material. Data from previous crystallisation experiments that are scattered in the literature and only partially available in databases have to be analysed in efficient ways that will maximise their utility for designing new screens. A larger portion of crystallisation parameter space should be made accessible to screening, through the use of nucleants and seeding. Observation, assessment and scaling up of the crystallisation trials should be efficiently performed and, finally yet importantly, optimisation of conditions must also be adapted to the high-throughput environment. The above requirements are briefly addressed in the following paper.
    MeSH term(s) Crystallization/methods ; High-Throughput Screening Assays/methods ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2012-04-07
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 1280776-x
    ISSN 1875-5305 ; 0929-8665
    ISSN (online) 1875-5305
    ISSN 0929-8665
    DOI 10.2174/092986612800793154
    Database MEDical Literature Analysis and Retrieval System OnLINE

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