Parameterizing elastic network models to capture the dynamics of proteins
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26701
Abstract: Coarse‐grained normal mode analyses of protein dynamics rely on the idea that the geometry of a protein structure contains enough information for computing its fluctuations around its equilibrium conformation. This geometry is captured in the… read more here.
Keywords: network; network models; geometry; parameterizing elastic ... See more keywords
Quasi-normal modes and microscopic description of 2D black holes
Sign Up to like & getrecommendations! Published in 2022 at "Journal of High Energy Physics"
DOI: 10.1007/jhep01(2022)087
Abstract: We investigate the possibility of using quasi-normal modes (QNMs) to probe the microscopic structure of two-dimensional (2D) anti-de Sitter (AdS 2 ) dilatonic black holes. We first extend previous results on the QNMs spectrum, found… read more here.
Keywords: quasi normal; black holes; normal modes; microscopic description ... See more keywords
Normal modes of a double pendulum at low energy levels
Sign Up to like & getrecommendations! Published in 2020 at "Nonlinear Dynamics"
DOI: 10.1007/s11071-019-05424-5
Abstract: This study is concerned with a double pendulum and its regular behaviour associated with low energy levels and the influence of the associated initial conditions on the frequency of normal modes. The case of nonlinear… read more here.
Keywords: energy; low energy; double pendulum; normal modes ... See more keywords
Nonlinear normal modes, resonances and energy exchange in single-walled carbon nanotubes
Sign Up to like & getrecommendations! Published in 2020 at "International Journal of Non-linear Mechanics"
DOI: 10.1016/j.ijnonlinmec.2019.103398
Abstract: Abstract The nonlinear resonance interaction and energy exchange between bending and circumferential flexure modes in single-walled carbon nanotubes is studied. First, the results of an analytical model of the resonance interaction between the considered nonlinear… read more here.
Keywords: nonlinear normal; carbon; energy; model ... See more keywords
Pyridine’s ring normal modes as footprints for its derivatives: The impact of perfluorination
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Fluorine Chemistry"
DOI: 10.1016/j.jfluchem.2020.109716
Abstract: Abstract The effects of full fluorination of pyridine, quinoline, 1,8-naphthyridine and 1,10-phenathroline were investigated through quantum mechanical calculations using pyridine as a reference. Among their vibrational normal modes, 6 out of 7 ring related normal… read more here.
Keywords: pyridine ring; modes footprints; ring normal; perfluorination ... See more keywords
Experimentally measuring an isolated branch of Nonlinear normal modes
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Sound and Vibration"
DOI: 10.1016/j.jsv.2019.06.006
Abstract: Abstract Nonlinear normal modes (NNMs) are a key tool for investigating the behaviour of nonlinear dynamic systems. Previous work has shown that branches of NNMs can be isolated from other NNM responses, in a similar… read more here.
Keywords: experimentally measuring; normal modes; isolated branch; nnm branches ... See more keywords
Analysis of scattering by finite sonic crystals in free field with infinite elements and normal modes
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Sound and Vibration"
DOI: 10.1016/j.jsv.2020.115291
Abstract: Abstract Acoustic exterior problems are in this paper solved numerically using the Astley-Leis infinite element method (IFEM). Normal modes can be determined thanks to the frequency independence of the system matrices. Convergence properties of the… read more here.
Keywords: acoustics; free field; finite sonic; sonic crystals ... See more keywords
MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00599
Abstract: Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions.… read more here.
Keywords: enhanced sampling; molecular dynamics; normal modes; excited normal ... See more keywords
Selectively exciting quasi-normal modes in open disordered systems
Sign Up to like & getrecommendations! Published in 2018 at "Nature Communications"
DOI: 10.1038/s41467-018-07180-3
Abstract: Transmission through disordered samples can be controlled by illuminating a sample with waveforms corresponding to the eigenchannels of the transmission matrix (TM). But can the TM be exploited to selectively excite quasi-normal modes and so… read more here.
Keywords: quasi; selectively exciting; transmission; quasi normal ... See more keywords
Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations
Sign Up to like & getrecommendations! Published in 2021 at "Scientific Reports"
DOI: 10.1038/s41598-021-92480-w
Abstract: Sulfotransferases (SULTs) are phase II drug-metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to a substrate. It has been previously suggested that a considerable shift of SULT structure caused by PAPS binding… read more here.
Keywords: insights substrate; paps bound; molecular dynamics; excited normal ... See more keywords
Morphology-sensitive infrared absorption bands of polymers derived from surface polaritons
Sign Up to like & getrecommendations! Published in 2019 at "AIP Advances"
DOI: 10.1063/1.5116280
Abstract: Infrared (IR) spectroscopy is mostly used for analysis of normal modes, which provides rich chemical information of molecular structure at each chemical group. In practice, however, we sometimes encounter an unusually broad peak that cannot… read more here.
Keywords: normal modes; spectra polymer; polariton; polymer thin ... See more keywords