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  1. Article: Structural dynamics of COVID-19 main protease.

    Shekaari, Ashkan / Jafari, Mahmoud

    Journal of molecular structure

    2020  Volume 1223, Page(s) 129235

    Abstract: Based on the importance of protease enzymes in functioning some viruses particularly coronaviridae, we have carried out an in silico investigation on the biologically important, yet unmapped phenomenon of activity and internal dynamics of COVID-19 main ... ...

    Abstract Based on the importance of protease enzymes in functioning some viruses particularly coronaviridae, we have carried out an in silico investigation on the biologically important, yet unmapped phenomenon of activity and internal dynamics of COVID-19 main protease (M
    Keywords covid19
    Language English
    Publishing date 2020-09-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 194476-9
    ISSN 0022-2860 ; 0377-046X
    ISSN 0022-2860 ; 0377-046X
    DOI 10.1016/j.molstruc.2020.129235
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1205: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Book ; Online: A concise introduction to molecular dynamics simulation

    Shekaari, Ashkan / Jafari, Mahmoud

    theory and programming

    2021  

    Abstract: We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting via the Lennard- ... ...

    Abstract We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting via the Lennard-Jones pairwise potential, was also written in Python programming language in both top-down and function-based designs.
    Keywords Condensed Matter - Materials Science ; Physics - Computational Physics
    Publishing date 2021-03-31
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Theory and Simulation of the Ising Model

    Shekaari, Ashkan / Jafari, Mahmoud

    2021  

    Abstract: We have provided a concise introduction to the Ising model as one of the most important models in statistical mechanics and in studying the phenomenon of phase transition. The required theoretical background and derivation of the Hamiltonian of the model ...

    Abstract We have provided a concise introduction to the Ising model as one of the most important models in statistical mechanics and in studying the phenomenon of phase transition. The required theoretical background and derivation of the Hamiltonian of the model have also been presented. We finally have discussed the computational method and details to numerically solve the two- and three-dimensional Ising problems using Monte Carlo simulations. The related computer codes in both Python and Fortran, as well as a simulation trick to visualize the spin lattice, have also been provided.
    Keywords Condensed Matter - Statistical Mechanics ; Condensed Matter - Materials Science
    Publishing date 2021-04-24
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Modeling the action of environment on proton tunneling in the adenine-thymine base pair.

    Shekaari, Ashkan / Jafari, Mahmoud

    Progress in biophysics and molecular biology

    2019  Volume 150, Page(s) 98–103

    Abstract: Effect of environment coupling on the quantum-biological phenomenon of proton tunneling in the hydrogen bonds of the adenine-thymine base pair in DNA was modeled within the framework of quantum statistics and perturbation theory. A number of important ... ...

    Abstract Effect of environment coupling on the quantum-biological phenomenon of proton tunneling in the hydrogen bonds of the adenine-thymine base pair in DNA was modeled within the framework of quantum statistics and perturbation theory. A number of important thermodynamic indicators including partition function, free energy, and entropy were then calculated and examined. The proton was then assumed to be subject to an attraction represented by a double-well potential energy surface with a small asymmetry, which was considered as the perturbation introduced to the system. The action of environment manifested itself in the form of a global minimum in the free energy curve, as an implicit implication of the tendency of the system toward randomness and disorder, at which no spontaneous change such as quantum tunneling will accordingly occur. Furthermore, assuming the free energy to be in a close neighborhood of its minimum truly explained the smallness of the contribution of environment coupling to the tunneling probability reported in the literature based on the fact that the closer the free energy to its minimum, the less the transition probability to this point.
    MeSH term(s) Adenine/chemistry ; Base Pairing ; DNA/chemistry ; Gene-Environment Interaction ; Hydrogen Bonding ; Models, Genetic ; Models, Molecular ; Nucleic Acid Conformation ; Protons ; Quantum Theory ; Thermodynamics ; Thymine/chemistry
    Chemical Substances Protons ; DNA (9007-49-2) ; Adenine (JAC85A2161) ; Thymine (QR26YLT7LT)
    Language English
    Publishing date 2019-07-09
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 209302-9
    ISSN 1873-1732 ; 0079-6107
    ISSN (online) 1873-1732
    ISSN 0079-6107
    DOI 10.1016/j.pbiomolbio.2019.07.002
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    Uc I Zs.281: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  5. Book ; Online: Thermodynamic equilibrium of biological macromolecules under mechanical constraints

    Shekaari, Ashkan / Jafari, Mahmoud

    2021  

    Abstract: Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic equilibrium with the ...

    Abstract Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic equilibrium with the surrounding is attained. However, in some important cases, we have to equilibrate the system of interest in the constant presence of certain constraints, being referred to as constrained equilibration in the present work. A clear illustration of this type is a single amyloid \b{eta}-strand or RNA, when the reaction coordinate is defined as the distance between the two ends of the strand and we are interested in carrying out replica-exchange umbrella sampling to map the associated free energy profile as the dependent quantity of interest. In such cases, each sample has to be equilibrated with the two ends fixed. Here, we introduced a simulation trick to perform this so-called constrained equilibration using steered molecular dynamics. We then applied this method to equilibrate a single, stretched \b{eta}-strand of an amyloid beta dodecamer fibril with fixed ends. Examining the associated curves of the total energy and the force exerted on the practically-fixed SMD atom over the total timespan broadly supported the validity of this kind of equilibration.
    Keywords Condensed Matter - Soft Condensed Matter
    Subject code 612
    Publishing date 2021-02-09
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Book ; Online: Mechanical stretching of amyloid Abeta11-42 fibrils using steered molecular dynamics

    Shekaari, Ashkan / Jafari, Mahmoud

    2021  

    Abstract: Mechanical strength of amyloid beta fibrils has been known to be correlated with neuronal cell death. Here, we resorted to steered molecular dynamics (SMD) simulations to mechanically stretch a single S-shape amyloid beta Abeta11-42 dodecamer fibril in ... ...

    Abstract Mechanical strength of amyloid beta fibrils has been known to be correlated with neuronal cell death. Here, we resorted to steered molecular dynamics (SMD) simulations to mechanically stretch a single S-shape amyloid beta Abeta11-42 dodecamer fibril in vacuum. It was found that the weakest sites at which the fibril was ruptured due to mechanical extension were exclusively at the interfaces of alanine and glutamic acid distributed throughout the fibril. It was also revealed that the free energy required to unfold the fibril to form a long linear conformation is equivalent to ~ 210 eV, being several thousand times larger than thermal voltage at room temperature. As a consequence, within solution a larger free energy is needed for such a maximal stretching based on the fact that amyloid beta fibrils are structurally more stable in solution due to the interplay between their hydrophobic cores and solution's entropy.
    Keywords Condensed Matter - Soft Condensed Matter ; Condensed Matter - Materials Science
    Publishing date 2021-06-16
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  7. Article ; Online: Structural dynamics of COVID-19 main protease

    Shekaari, Ashkan / Jafari, Mahmoud

    Journal of Molecular Structure

    Volume 1223, Page(s) 129235

    Keywords Inorganic Chemistry ; Organic Chemistry ; Analytical Chemistry ; Spectroscopy ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 194476-9
    ISSN 0022-2860 ; 0377-046X
    ISSN 0022-2860 ; 0377-046X
    DOI 10.1016/j.molstruc.2020.129235
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1205: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

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  8. Article: Structural dynamics of COVID-19 main protease

    Shekaari, Ashkan / Jafari, Mahmoud

    Journal of Molecular Structure

    Abstract: Based on the importance of protease enzymes in functioning some viruses particularly coronaviridae, we have carried out an in silico investigation on the biologically important, yet unmapped phenomenon of activity and internal dynamics of COVID-19 main ... ...

    Abstract Based on the importance of protease enzymes in functioning some viruses particularly coronaviridae, we have carried out an in silico investigation on the biologically important, yet unmapped phenomenon of activity and internal dynamics of COVID-19 main protease (Mpro) via applying finite-temperature all-atom molecular dynamics simulations Temperature quench echoes generated by applying two successive cooling signals have therefore been analyzed in terms of the temperature-temperature correlation function of the protease within the harmonic approximation An exponentially decaying brand of behavior has been found for the calculated echo depth values with increasing time, which has accordingly led to a much small dephasing time of about 150 fs, revealing a significant anharmonicity and therefore an overall structural stiffness for the COVID-19 main protease
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #753065
    Database COVID19

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