scholarly journals Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model

2019 ◽  
Vol 27 (3) ◽  
pp. 217-230
Author(s):  
Dmitry A. Tikhonov ◽  
Egor V. Sobolev ◽  
Victor D. Lakhno
Keyword(s):  
Diffusion Coefficient ◽  
Charge Distribution ◽  
Dna Sequences ◽  
Mean Square Displacement ◽  
Frequency Spectra ◽  
Velocity Autocorrelation ◽  
Holstein Model ◽  
Quantum Chemical Methods ◽  
A Chain ◽  
Charge Transfer In Dna

We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.

scholarly journals Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model

2019 ◽  
Vol 27 (3) ◽  
pp. 217-230
Author(s):  
Dmitry A Tikhonov ◽  
Egor V Sobolev ◽  
Victor D Lakhno
Keyword(s):  
Diffusion Coefficient ◽  
Charge Distribution ◽  
Dna Sequences ◽  
Mean Square Displacement ◽  
Frequency Spectra ◽  
Velocity Autocorrelation ◽  
Holstein Model ◽  
Quantum Chemical Methods ◽  
A Chain ◽  
Charge Transfer In Dna

We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.

scholarly journals Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model

2019 ◽  
Vol 27 (3) ◽  
pp. 217-230
Author(s):  
Dmitry A. Tikhonov ◽  
Egor V. Sobolev ◽  
Victor D. Lakhno
Keyword(s):  
Diffusion Coefficient ◽  
Charge Distribution ◽  
Dna Sequences ◽  
Mean Square Displacement ◽  
Frequency Spectra ◽  
Velocity Autocorrelation ◽  
Holstein Model ◽  
Quantum Chemical Methods ◽  
A Chain ◽  
Charge Transfer In Dna

We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.

Molecular dynamics study of diffusion of krypton in water at different temperatures

2016 ◽  
Vol 30 (11) ◽  
pp. 1650064 ◽  
Author(s):  
Dipendra Bhandari ◽  
N. P. Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Diffusion Coefficients ◽  
Mean Square Displacement ◽  
Mutual Diffusion ◽  
Arrhenius Behavior ◽  
Self Diffusion ◽  
Velocity Autocorrelation ◽  
Different Temperatures ◽  
Self Diffusion Coefficient

Molecular dynamics study of diffusion of two krypton atoms in 300 SPC/E water molecules at temperatures 293, 303, 313, 323 and 333 K has been carried out. Self-diffusion coefficient of krypton and water along with their mutual diffusion coefficients are estimated. Self-diffusion coefficient for krypton is calculated by using Mean Square Displacement (MSD) method and Velocity Autocorrelation (VACF) method, while that for water is calculated by using MSD method only. The mutual diffusion coefficient is estimated by using the Darken’s relation. The diffusion coefficients are found to follow the Arrhenius behavior. The structural properties of the system have been estimated by the study of solute–solute, solvent–solvent, and solute–solvent Radial Distribution Function (RDF).

scholarly journals Numerical Simulation of Small Radius Polaron in a Chain with Random Perturbations

2019 ◽  
Vol 14 (2) ◽  
pp. 406-419
Author(s):  
N.S. Fialko ◽  
V.D. Lakhno
Keyword(s):  
Computational Experiment ◽  
Center Of Mass ◽  
Small Radius ◽  
Large Radius ◽  
Zero Temperature ◽  
Time Intervals ◽  
Holstein Model ◽  
A Chain ◽  
Charge Transfer In Dna ◽  
Thermodynamic Equilibrium State

We consider the dynamics of polaron in a chain using computational experiment. The temperature, which is simulated by random Langevin-type perturbations, and influence of external electric field are taking into account. In a sufficiently long unperturbed chain, the displacement of the center of mass of the polaron and its velocity does not depend on its length. In the semiclassical Holstein model, which is applied for simulations of charge transfer in DNA, the region of polaron existence in the thermodynamic equilibrium state depends not only on temperature, but also on the chain length. Therefore, when modeling dynamics from polaron initial data, the time dependences of the average displacement of the charge mass center at the same temperature are different for chains of different lengths. According to the results of computational experiment, for polaron of large radius the time dependence of the “average polaron displacement”, which takes into account only the polaron peak and its position, for chains of different lengths behaves almost equally at time intervals until the polaron will destroyed. The same slope of the polaron displacement allows us to estimate the average polaron velocity. The results of calculations demonstrate that in Holstein model at zero temperature, the mobility value of the large radius polaron is small but non-zero.

Right-Hemisphere Specialization for Contour Grouping

2014 ◽  
Vol 61 (5) ◽  
pp. 331-339 ◽  
Author(s):  
Gregor Volberg
Keyword(s):  
Right Hemisphere ◽  
Contour Detection ◽  
Global Processing ◽  
Detection Accuracy ◽  
Frequency Spectra ◽  
Visual Hemifield ◽  
Spatial Frequencies ◽  
A Chain ◽  
The Right ◽  
Hemisphere Specialization

Previous studies often revealed a right-hemisphere specialization for processing the global level of compound visual stimuli. Here we explore whether a similar specialization exists for the detection of intersected contours defined by a chain of local elements. Subjects were presented with arrays of randomly oriented Gabor patches that could contain a global path of collinearly arranged elements in the left or in the right visual hemifield. As expected, the detection accuracy was higher for contours presented to the left visual field/right hemisphere. This difference was absent in two control conditions where the smoothness of the contour was decreased. The results demonstrate that the contour detection, often considered to be driven by lateral coactivation in primary visual cortex, relies on higher-level visual representations that differ between the hemispheres. Furthermore, because contour and non-contour stimuli had the same spatial frequency spectra, the results challenge the view that the right-hemisphere advantage in global processing depends on a specialization for processing low spatial frequencies.

scholarly journals Anomalous Diffusion with an Apparently Negative Diffusion Coefficient in a One-Dimensional Quantum Molecular Chain Model

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 506
Author(s):  
Sho Nakade ◽  
Kazuki Kanki ◽  
Satoshi Tanaka ◽  
Tomio Petrosky
Keyword(s):  
Diffusion Coefficient ◽  
Diffusion Constant ◽  
Mean Square Displacement ◽  
Second Law Of Thermodynamics ◽  
Molecular Chain ◽  
Chain Model ◽  
Phase Mixing ◽  
One Dimensional ◽  
The One ◽  
Negative Diffusion

An interesting anomaly in the diffusion process with an apparently negative diffusion coefficient defined through the mean-square displacement in a one-dimensional quantum molecular chain model is shown. Nevertheless, the system satisfies the H-theorem so that the second law of thermodynamics is satisfied. The reason why the “diffusion constant” becomes negative is due to the effect of the phase mixing process, which is a characteristic result of the one-dimensionality of the system. We illustrate the situation where this negative “diffusion constant” appears.

scholarly journals Difference Analysis of Gas Molecules Diffusion Behavior in Natural Ester and Mineral Oil Based on Molecular Dynamic Simulation

Molecules ◽  
2019 ◽  
Vol 24 (24) ◽  
pp. 4463 ◽  
Author(s):  
Wenyu Ye ◽  
Jian Hao ◽  
Yufeng Chen ◽  
Mengzhao Zhu ◽  
Zhen Pan ◽  
...  
Keyword(s):  
Diffusion Coefficient ◽  
Interaction Energy ◽  
Free Volume ◽  
Mean Square Displacement ◽  
Mineral Oil ◽  
Relative Molecular Mass ◽  
Diffusion Behavior ◽  
Influence Of Temperature On ◽  
Gas Molecules ◽  
Natural Ester

Natural ester, as a new environmentally green insulating oil, has been widely used in transformer. In an oil-immersed transformer, the normal aging, thermal failure, and discharge failure could easily lead to the decomposition of the oil-paper insulation system and produce different kinds of gases. Studying gas dissolution in natural ester and mineral oil could provide assistance in applying criteria to make a diagnosis of different kinds of faults in the transformer. In this paper, the molecular dynamics method was used to investigate the diffusion behavior of seven fault characteristic gases (including H2, CO, CH4, C2H2, CO2, C2H4, C2H6) in natural ester and mineral oil. The simulation parameters of free volume, interaction energy, mean square displacement, and diffusion coefficient were compared between the natural ester and mineral oil. Meanwhile, the influence of temperature on the diffusion of gas molecules in two kinds of oils was also analyzed. Results showed that the free volume, the interaction energy, and the relative molecular mass of gas molecules were the factors influenced by the diffusion of gas molecules in natural ester and mineral oil. The order of the diffusion coefficients of gas molecules in natural ester was as follows: H2 > CH4 > CO > C2H2 > C2H4 > CO2 > C2H6 and that in mineral oil was as follows: H2 > CH4 > CO> C2H2 > C2 H4 > C2H6 > CO2. By comparing the diffusion behavior of gas molecules in natural ester and mineral oil, it was found that the smaller free volume and higher interaction energy of gas molecules in natural ester were the major reasons for the gas molecules to be more difficult to diffuse in natural ester. The rising temperature could enhance the free volume and reduce the interaction energy between gas molecules and oil. The diffusion coefficient of gas molecules increased exponentially with the follow of temperature. However, the temperature didn’t affect the ordering of diffusion coefficient, free volume, and interaction energy of gas molecules in natural ester and mineral oil.

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