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[HTML][HTML] RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Metal ion modeling using classical mechanics
Metal ions play significant roles in numerous fields including chemistry, geochemistry,
biochemistry, and materials science. With computational tools increasingly becoming …
biochemistry, and materials science. With computational tools increasingly becoming …
RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Parameterization of monovalent ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models
Monovalent ions play significant roles in various biological and material systems. Recently,
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …
Systematic parameterization of monovalent ions employing the nonbonded model
Monovalent ions play fundamental roles in many biological processes in organisms.
Modeling these ions in molecular simulations continues to be a challenging problem. The 12 …
Modeling these ions in molecular simulations continues to be a challenging problem. The 12 …
Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water
Highly charged metal ions act as catalytic centers and structural elements in a broad range
of chemical complexes. The nonbonded model for metal ions is extensively used in …
of chemical complexes. The nonbonded model for metal ions is extensively used in …
A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization
Molecular simulations can elucidate atomistic-level mechanisms of key biological
processes, which are often hardly accessible to experiment. However, the results of the …
processes, which are often hardly accessible to experiment. However, the results of the …
Systematic parametrization of divalent metal ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models
Divalent metal ions play important roles in biological and materials systems. Molecular
dynamics simulation is an efficient tool to investigate these systems at the microscopic level …
dynamics simulation is an efficient tool to investigate these systems at the microscopic level …
Unlocking the computational design of metal–organic cages
Metal–organic cages are macrocyclic structures that can possess an intrinsic void that can
hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal …
hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal …
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications
We report the parametrization of the approximate density functional theory, DFTB3, for
magnesium and zinc for chemical and biological applications. The parametrization strategy …
magnesium and zinc for chemical and biological applications. The parametrization strategy …