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  1. Article ; Online: Fractal dimension based geographical clustering of COVID-19 time series data.

    Natalia, Yessika Adelwin / Faes, Christel / Neyens, Thomas / Chys, Pieter / Hammami, Naïma / Molenberghs, Geert

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 4322

    Abstract: Understanding the local dynamics of COVID-19 transmission calls for an approach that characterizes the incidence curve in a small geographical unit. Given that incidence curves exhibit considerable day-to-day variation, the fractal structure of the time ... ...

    Abstract Understanding the local dynamics of COVID-19 transmission calls for an approach that characterizes the incidence curve in a small geographical unit. Given that incidence curves exhibit considerable day-to-day variation, the fractal structure of the time series dynamics is investigated for the Flanders and Brussels Regions of Belgium. For each statistical sector, the smallest administrative geographical entity in Belgium, fractal dimensions of COVID-19 incidence rates, based on rolling time spans of 7, 14, and 21 days were estimated using four different estimators: box-count, Hall-Wood, variogram, and madogram. We found varying patterns of fractal dimensions across time and location. The fractal dimension is further summarized by its mean, variance, and autocorrelation over time. These summary statistics are then used to cluster regions with different incidence rate patterns using k-means clustering. Fractal dimension analysis of COVID-19 incidence thus offers important insight into the past, current, and arguably future evolution of an infectious disease outbreak.
    MeSH term(s) Humans ; Fractals ; Time Factors ; COVID-19/epidemiology ; Geography ; Belgium/epidemiology
    Language English
    Publishing date 2023-03-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-30948-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Application of geometric algebra for the description of polymer conformations.

    Chys, Pieter

    The Journal of chemical physics

    2008  Volume 128, Issue 10, Page(s) 104107

    Abstract: In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (theta), and rotation ... ...

    Abstract In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (theta), and rotation angle (phi) of each of the preceding bonds in the chain. Hence, the set of geometrical parameters {l(i),theta(i),phi(i)} yields all the position coordinates p(i) of the main chain atoms. Moreover, the method allows the calculation of side chain conformations and the computation of rotations of chain segments. With these features it is, in principle, possible to generate conformations of any type of chemical structure. This method is proposed as an alternative for the classical approach by matrix algebra. It is more straightforward and its final symbolic representation considerably simpler than that of matrix algebra. Approaches for realistic modeling by means of incorporation of energetic considerations can be combined with it. This article, however, is entirely focused at showing the suitable mathematical framework on which further developments and applications can be built.
    MeSH term(s) Algorithms ; Computational Biology/methods ; Computer Simulation ; Molecular Conformation ; Polymers/chemistry ; Thermodynamics
    Chemical Substances Polymers
    Language English
    Publishing date 2008-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.2831776
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Random Coordinate Descent with Spinor-matrices and Geometric Filters for Efficient Loop Closure.

    Chys, Pieter / Chacón, Pablo

    Journal of chemical theory and computation

    2013  Volume 9, Issue 3, Page(s) 1821–1829

    Abstract: Protein loop closure constitutes a critical step in loop and protein modeling whereby geometrically feasible loops must be found between two given anchor residues. Here, a new analytic/iterative algorithm denoted random coordinate descent (RCD) to ... ...

    Abstract Protein loop closure constitutes a critical step in loop and protein modeling whereby geometrically feasible loops must be found between two given anchor residues. Here, a new analytic/iterative algorithm denoted random coordinate descent (RCD) to perform protein loop closure is described. The algorithm solves loop closure through minimization as in cyclic coordinate descent but selects bonds for optimization randomly, updates loop conformations by spinor-matrices, performs loop closure in both chain directions, and uses a set of geometric filters to yield efficient conformational sampling. Geometric filters allow one to detect clashes and constrain dihedral angles on the fly. The RCD algorithm is at least comparable to state of the art loop closure algorithms due to an excellent balance between efficiency and intrinsic sampling capability. Furthermore, its efficiency allows one to improve conformational sampling by increasing the sampling number without much penalty. Overall, RCD turns out to be accurate, fast, robust, and applicable over a wide range of loop lengths. Because of the versatility of RCD, it is a solid alternative for integration with current loop modeling strategies.
    Language English
    Publishing date 2013-03-12
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9618
    ISSN 1549-9618
    DOI 10.1021/ct300977f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Spinor product computations for protein conformations.

    Chys, Pieter / Chacón, Pablo

    Journal of computational chemistry

    2012  Volume 33, Issue 21, Page(s) 1717–1729

    Abstract: Spinor operators in geometric algebra (GA) can efficiently describe conformational changes of proteins by ordered products that act on individual bonds and represent their net rotations. Backward propagation through the protein backbone yields all ... ...

    Abstract Spinor operators in geometric algebra (GA) can efficiently describe conformational changes of proteins by ordered products that act on individual bonds and represent their net rotations. Backward propagation through the protein backbone yields all rotational spinor axes in advance allowing the efficient computation of atomic coordinates from internal coordinates. The introduced mathematical framework enables to efficiently manipulate and generate protein conformations to any arbitrary degree. Moreover, several new formulations in the context of rigid body motions are added. Emphasis is placed on the intimate relationship between spinors and quaternions, which can be recovered from within the GA approach. The spinor methodology is implemented and tested versus the state of the art algorithms for both protein construction and coordinate updating. Spinor calculations have a smaller computational cost and turn out to be slightly faster than current alternatives.
    MeSH term(s) Algorithms ; Computational Biology ; Computer Simulation ; Protein Conformation ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2012-08-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-x
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.23002
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  5. Article: FTIR 2D correlation spectroscopy of α₁ and α₂ fractions of an alkali-pretreated gelatin

    Chys, Pieter / Gielens, Constant / Meersman, Filip

    BBA - Proteins and Proteomics. 2011 Feb., v. 1814, no. 2

    2011  

    Abstract: An alkali-pretreated gelatin (pI~4.9) was fractionated by means of alcohol coacervation and semi-preparative gel chromatography. The thermal responses of the isolated α fractions, the coacervate and the total gelatin were investigated by 2D-correlation ... ...

    Abstract An alkali-pretreated gelatin (pI~4.9) was fractionated by means of alcohol coacervation and semi-preparative gel chromatography. The thermal responses of the isolated α fractions, the coacervate and the total gelatin were investigated by 2D-correlation FTIR spectroscopy in the amide I band region (1600–1700cm⁻¹). The gelation temperature was the same for all examined samples (24.5°C) while the melting temperature of the α₂ fraction was lower (30°C) than that of the other samples (32.5°C). The 2D COS plots indicate that on cooling (gelation) the core sequence of conformational changes is the same for all samples. On heating, however, the α₂ fraction deviates from the α₁-containing samples and shows an earlier disappearance of the triple helix signal in the event sequence. The lower melting temperature (less thermostable gelatin gel) of the α₂ fraction thus results from a different conformational cascade of the α₂ chains upon melting. In all samples the initial conformational changes take place in the β-turns, providing further evidence for the models proposed previously.
    Keywords Fourier transform infrared spectroscopy ; alcohols ; cooling ; gel chromatography ; gelatin ; gelatinization temperature ; gelation ; heat ; melting ; melting point ; models ; sampling ; thermal stability
    Language English
    Dates of publication 2011-02
    Size p. 318-325.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2209540-8
    ISSN 1878-1454 ; 1570-9639
    ISSN (online) 1878-1454
    ISSN 1570-9639
    DOI 10.1016/j.bbapap.2010.10.003
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: FTIR 2D correlation spectroscopy of α₁ and α₂ fractions of an alkali-pretreated gelatin.

    Chys, Pieter / Gielens, Constant / Meersman, Filip

    Biochimica et biophysica acta

    2011  Volume 1814, Issue 2, Page(s) 318–325

    Abstract: An alkali-pretreated gelatin (pI~4.9) was fractionated by means of alcohol coacervation and semi-preparative gel chromatography. The thermal responses of the isolated α fractions, the coacervate and the total gelatin were investigated by 2D-correlation ... ...

    Abstract An alkali-pretreated gelatin (pI~4.9) was fractionated by means of alcohol coacervation and semi-preparative gel chromatography. The thermal responses of the isolated α fractions, the coacervate and the total gelatin were investigated by 2D-correlation FTIR spectroscopy in the amide I band region (1600-1700 cm⁻¹). The gelation temperature was the same for all examined samples (24.5°C) while the melting temperature of the α₂ fraction was lower (30°C) than that of the other samples (32.5°C). The 2D COS plots indicate that on cooling (gelation) the core sequence of conformational changes is the same for all samples. On heating, however, the α₂ fraction deviates from the α₁-containing samples and shows an earlier disappearance of the triple helix signal in the event sequence. The lower melting temperature (less thermostable gelatin gel) of the α₂ fraction thus results from a different conformational cascade of the α₂ chains upon melting. In all samples the initial conformational changes take place in the β-turns, providing further evidence for the models proposed previously.
    MeSH term(s) Alkalies ; Animals ; Cattle ; Chromatography, Gel ; Electrophoresis, Gel, Two-Dimensional ; Gelatin/chemistry ; Gelatin/isolation & purification ; In Vitro Techniques ; Multiprotein Complexes/chemistry ; Phase Transition ; Protein Conformation ; Spectroscopy, Fourier Transform Infrared/methods ; Thermodynamics
    Chemical Substances Alkalies ; Multiprotein Complexes ; Gelatin (9000-70-8)
    Language English
    Publishing date 2011-02
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 60-7
    ISSN 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbapap.2010.10.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.247: Show issues Location:
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