scholarly journals Low temperature matrix-isolation and solid state vibrational spectra of 5-chlorotetrazoleElectronic supplementary information (ESI) available: Calculated molecular geometries, rotational constants, energies and dipole moments. Definition of internal symmetry coordinates used in the normal mode analysis. Experimental spectrum of polycrystalline 5-chlorotetrazole and calculated spectrum for the 1H-tautomer. See http://www.rsc.org/suppdata/cp/b1/b111329c/

2002 ◽  
Vol 4 (10) ◽  
pp. 1725-1731 ◽  
Author(s):  
Susana C. S. Bugalho ◽  
A. C. Serra ◽  
Leszek Lapinski ◽  
M. Lurdes S. Cristiano ◽  
Rui Fausto
Keyword(s):  
Dipole Moments ◽  
Normal Mode Analysis ◽  
Experimental Spectrum ◽  
Internal Symmetry ◽  
Supplementary Information ◽  
Mode Analysis ◽  
Calculated Spectrum ◽  
Symmetry Coordinates ◽  
Temperature Matrix ◽  
Definition Of

scholarly journals MODE-TASK: Large-scale protein motion tools

2017 ◽  
Author(s):  
Caroline Ross ◽  
Bilal Nizami ◽  
Michael Glenister ◽  
Olivier Sheik Amamuddy ◽  
Ali Rana Atilgan ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Md Simulations ◽  
Supplementary Information ◽  
Mode Analysis ◽  
Analysis Tool ◽  
Link Type ◽  
Supplementary Material ◽  
Anisotropic Network

AbstractSummaryMODE-TASK, a novel software suite, comprises Principle Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using molecular dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Network Model so as to provide a variety of ways to analyse and compare large-scale motions of protein complexes for which long MD simulations are prohibitive.Availability and ImplementationMODE-TASK has been open-sourced, and is available for download from https://github.com/RUBi-ZA/MODE-TASK, implemented in Python and C++.Supplementary informationDocumentation available at http://mode-task.readthedocs.io.

scholarly journals Nonlinear modes disentangle glassy and Goldstone modes in structural glasses

2016 ◽  
Vol 1 (2) ◽  
Author(s):  
Luka Gartner ◽  
Edan Lerner
Keyword(s):  
Normal Mode Analysis ◽  
Low Frequency ◽  
Low Energy ◽  
Mode Analysis ◽  
Algebraic Equations ◽  
Low Frequencies ◽  
Nonlinear Modes ◽  
Selected Subset ◽  
Definition Of ◽  
Goldstone Modes

One outstanding problem in the physics of glassy solids is understanding the statistics and properties of low-energy excitations that stem from the disorder that characterizes these systems' microstructure. In this work we introduce a family of algebraic equations whose solutions represent collective displacement directions (modes) in the multi-dimensional configuration space of a structural glass. We explain why solutions of the algebraic equations, coined nonlinear glassy modes, are quasi-localized low-energy excitations. We present an iterative method to solve the algebraic equations, and use it to study the energetic and structural properties of a selected subset of their solutions constructed by starting from a normal mode analysis of the potential energy of a model glass. Our key result is that the structure and energies associated with harmonic glassy vibrational modes and their nonlinear counterparts converge in the limit of very low frequencies. As nonlinear modes never suffer hybridizations, our result implies that the presented theoretical framework constitutes a robust alternative definition of `soft glassy modes' in the thermodynamic limit, in which Goldstone modes overwhelm and destroy the identity of low-frequency harmonic glassy modes.

scholarly journals Collective Mode Mining from Molecular Dynamics Simulations: A Comparative Approach

2018 ◽  
Vol 15 (03) ◽  
pp. 1850108 ◽  
Author(s):  
Vito Dario Camiola ◽  
Valentina Tozzini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Normal Mode Analysis ◽  
Principal Component ◽  
Mode Analysis ◽  
Comparative Approach ◽  
Atomic Systems ◽  
Equilibrium Dynamics ◽  
Definition Of ◽  
Dynamics Simulations

The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e., normal mode analysis, principal component and spectral analysis of trajectories, basically differing by the quantity considered as the nodal one (frequency, amplitude, or pattern of displacement) and leading to the definition of different kinds of collective excitations and physical spectral observables. The different views converge in the harmonic regime and/or for homo-atomic systems. However, for anharmonic and out of equilibrium dynamics, different quantities bring different information, and only their comparison can give a complete view of the system behavior. To allow such a comparative analysis, we review and compare the different approaches, applying them in diverse combinations to two examples of physical relevance: graphene and fullerene C[Formula: see text].

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

scholarly journals Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger
Keyword(s):  
Energy Transfer ◽  
Spectral Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis
Sign in / Sign up

Export Citation Format

Share Document