Studying the mechanism of tissue optical clearing using the method of molecular dynamics

2017 ◽  
Author(s):  
K. V. Berezin ◽  
K. N. Dvoretskiy ◽  
M. L. Chernavina ◽  
V. V. Nechaev ◽  
A. M. Likhter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Clearing ◽  
Method Of Molecular Dynamics ◽  
Tissue Optical Clearing

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

Handbook of Tissue Optical Clearing

2021 ◽  
Author(s):  
Valery V. Tuchin ◽  
Dan Zhu ◽  
Elina A. Genina
Keyword(s):  
Optical Clearing ◽  
Tissue Optical Clearing

scholarly journals SPECTRAL FEATURES AND HYDROGEN BOND STRUCTURE OF AQUEOUS SOLUTIONS OF ETHANOL

2021 ◽  
pp. 30-33
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Aqueous Solutions ◽  
Gaseous Medium ◽  
Water Molecules ◽  
Structural Reorganization ◽  
Intermolecular Hydrogen Bonds ◽  
Method Of Molecular Dynamics ◽  
Combined Use ◽  
Structure Of Aqueous Solutions

The aim of this work is develop an approach that makes it possible to study the spectral properties and structure of intermolecular hydrogen bonds in aqueous solutions of ethanol formed in systems whose existence in a gaseous medium or an isolated state is practically impossible. This approach bases on the combined use of infrared spectroscopy and molecular dynamics (MD) methods. An analysis give the structural reorganization of water molecules depending on the concentration of ethanol alcohol. It has been shown that the method of molecular dynamics with classical force fields makes it possible to explicitly take into account the molecules of the solvent and solute, and, thus, to investigate hydrogen bonds in the system and to interpret with the experimental data obtained by vibrational spectroscopy.

scholarly journals Molecular modeling of post-diffusion stage of biotissue optical clearing under effect of iohexol aqueous solution

2021 ◽  
Vol 2103 (1) ◽  
pp. 012048
Author(s):  
I T Shagautdinova ◽  
A M Likhter ◽  
K V Berezin ◽  
K N Dvoretsky ◽  
V V Nechaev ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Modeling ◽  
Biological Tissues ◽  
Optical Clearing ◽  
X Ray ◽  
Diffusion Stage ◽  
Collagen Peptide ◽  
Main Components

Abstract Interaction of iohexol (Omnipaque), an X-Ray contrast agent, with a mimetic peptide of collagen (GPH)3 as one of the main components of biological tissues has been studied with the use of methods of classical molecular dynamics (GROMACS). Complex molecular modeling of the post-diffusion stage of optical clearing allowed to evaluate such parameters as the average number of hydrogen bonds, formed between the clearing agent and collagen per unit time, and the immersion agent’s effect on changes in the collagen peptide volume. The obtained results are compared with similar results for glycerol, a polyatomic alcohol, and with the existing experimental data on the efficiency of optical clearing of these immersion agents.

Review of Tissue Optical Clearing Methods for Imaging Whole Organs

2020 ◽  
Vol 47 (2) ◽  
pp. 0207007
Author(s):  
俞婷婷 Yu Tingting ◽  
朱丹 Zhu Dan
Keyword(s):  
Optical Clearing ◽  
Tissue Optical Clearing
Sign in / Sign up

Export Citation Format

Share Document