scholarly journals First-principles interpretation of electron transport though single-molecule junctions using molecular dynamics of electron attached states

2021 ◽  
Author(s):  
Dávid P. Jelenfi ◽  
Attila Tajti ◽  
Péter G. Szalay
Keyword(s):  
Molecular Dynamics ◽  
Electron Transport ◽  
Single Molecule ◽  
Transition Probabilities ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Bending Vibrations ◽  
Time Resolved ◽  
State Models

The electron transport through the single-molecule junction of 1,4-Diaminobenzene (BDA) is modeled using ab initio quantum-classical molecular dynamics of electron attached states. Observations on the nature of the process are made by time-resolved analysis of energy differences, non-adiabatic transition probabilities and the spatial distribution of the excess electron. The role of molecular vibrations that facilitate the transport by being responsible for the periodic behaviour of these quantities is shown using normal mode analysis. The results support a mechanism involving the electron's direct hopping between the electrodes, without its presence on the molecule, with the prime importance of the bending vibrations that periodically alter the molecule{electrode interactions. No relevant differences are found between results provided by the ADC(2) and SOS-ADC(2) excited state models. Our approach provides an alternative insight into the role of nuclear motions in the electron transport process, one which is more expressive from the chemical perspective.

THEORETICAL INVESTIGATIONS ON ELUCIDATING FUNDAMENTAL MECHANISMS OF CATALYSIS AND DYNAMICS INVOLVED IN TRANSCRIPTION BY RNA POLYMERASE

2013 ◽  
Vol 12 (08) ◽  
pp. 1341005 ◽  
Author(s):  
FÁTIMA PARDO-AVILA ◽  
LIN-TAI DA ◽  
YING WANG ◽  
XUHUI HUANG
Keyword(s):  
Rna Polymerase ◽  
Conformational Changes ◽  
Normal Mode Analysis ◽  
Md Simulations ◽  
Mode Analysis ◽  
Transcription Process ◽  
Nucleotide Addition ◽  
Theoretical Investigations ◽  
State Models ◽  
Elongation Process

RNA polymerase is the enzyme that synthesizes RNA during the transcription process. To understand its mechanism, structural studies have provided us pictures of the series of steps necessary to add a new nucleotide to the nascent RNA chain, the steps altogether known as the nucleotide addition cycle (NAC). However, these static snapshots do not provide dynamic information of these processes involved in NAC, such as the conformational changes of the protein and the atomistic details of the catalysis. Computational studies have made efforts to fill these knowledge gaps. In this review, we provide examples of different computational approaches that have improved our understanding of the transcription elongation process for RNA polymerase, such as normal mode analysis, molecular dynamic (MD) simulations, Markov state models (MSMs). We also point out some unsolved questions that could be addressed using computational tools in the future.

scholarly journals Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

2015 ◽  
Vol 7 (17) ◽  
pp. 2317-2331 ◽  
Author(s):  
Gautier Moroy ◽  
Olivier Sperandio ◽  
Shakti Rielland ◽  
Saurabh Khemka ◽  
Karen Druart ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Conformational Ensemble ◽  
Dynamics Simulations

NO in Kr and Xe solids: Molecular dynamics and normal mode analysis

2005 ◽  
Vol 730 (1-3) ◽  
pp. 255-261 ◽  
Author(s):  
J.C. Castro Palacio ◽  
L. Velazquez Abad ◽  
G. Rojas-Lorenzo ◽  
J. Rubayo-Soneira
Keyword(s):  
Molecular Dynamics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis

Mechanical Properties of α-Helices Estimated Using Molecular Dynamics and Finite Element Simulations

2008 ◽  
Author(s):  
Peyman Honarmandi ◽  
Philip Bransford ◽  
Roger D. Kamm
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Finite Element ◽  
Solid Mechanics ◽  
Normal Mode Analysis ◽  
Computational Cost ◽  
Md Simulations ◽  
Elastic Stiffness ◽  
Mode Analysis ◽  
Molecular Volume

Mechanical properties of biomolecules and their response to mechanical forces may be studied using Molecular Dynamics (MD) simulations. However, high computational cost is a primary drawback of MD simulations. This paper presents a computational framework based on the integration of the Finite Element Method (FEM) with MD simulations to calculate the mechanical properties of polyalanine α-helix proteins. In this method, proteins are treated as continuum elastic solids with molecular volume defined exclusively by their atomic surface. Therefore, all solid mechanics theories would be applicable for the presumed elastic media. All-atom normal mode analysis is used to calculate protein’s elastic stiffness as input to the FEM. In addition, constant force molecular dynamics (CFMD) simulations can be used to predict other effective mechanical properties, such as the Poisson’s Ratio. Force versus strain data help elucidate the mechanical behavior of α-helices upon application of constant load. The proposed method may be useful in identifying the mechanical properties of any protein or protein assembly with known atomic structure.

scholarly journals Role of Beam Foil Spectroscopy in Understanding Basic Plasma Processes on the Sun

1990 ◽  
Vol 142 ◽  
pp. 439-440
Author(s):  
G. Krishnamurty ◽  
P. Meenakshi Raja Rao ◽  
P. Sarswathy ◽  
B.N. Raja Sekhar
Keyword(s):  
Quantitative Analysis ◽  
Spectral Line ◽  
Transition Probabilities ◽  
Radiative Transition ◽  
Decay Process ◽  
The Sun ◽  
Time Resolved ◽  
Beam Foil

Beam-Foil spectroscopy(BFS) has proved to be a valuable technique for the determination of radiative lifetimes of excited atomic levels leading to the evaluation of the transition probabilities. The time- resolved nature of the decay process in a collisionless environment is a unique characterstic of the beam-foil light source. The relevance of BFS to astrophysics comes from the importance of radiative transition probabilities in the quantitative analysis of optical spectra. Stellar abundances are obtained from the intensity of a spectral line which essentially is a product of the abundance of the element in the source and the probability of the transition. Thus the evaluation of accurate values of transition probabilities contribute significantly to stellar abundance analysis.

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