Interactions of Ozone-Functionalized Activated Charcoal with SARS-Cov-2 Proteases Using Molecular Docking and Dynamics

2021 ◽  
Vol 21 (12) ◽  
pp. 6060-6072
Author(s):  
Hérica Daniele Costa Araújo ◽  
Tiago da Silva Arouche ◽  
Raul Nunes de Carvalho Junior ◽  
Teodorico Castro Ramalho ◽  
Rosivaldo dos Santos Borges ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Activated Carbon ◽  
Activated Charcoal ◽  
Hydrophobic Interactions ◽  
Low Cost ◽  
Mean Square ◽  
Autodock Vina ◽  
The Mean ◽  
Protein Components ◽  
Molecular Docking And Dynamics

The high contamination by the SARS-Cov-2 virus has led to the search for ways to minimize contagion. Masks are used as part of a strategy of measures to suppress transmission and save lives. However, they are not sufficient to provide an adequate level of protection against COVID-19. Activated charcoal has an efficient antibacterial action, adsorption and low cost. Here, the interaction between two molecules of activated carbon was analyzed, interacting with two structures of the SARS-Cov-2, through docking and molecular dynamics using the platforms Autodock Vina 4.2.6, Gaussian 09 and Amber 16. As a result, the complexes from ozone-functionalized coal to viral structures happen mainly through hydrophobic interactions at the binding site of each receptor. The values of the mean square deviations of the two systems formed by ligands/receptors and showed better stability. The results of Gibbs free energy showed a better interaction between proteins and functionalized charcoal, with △Gtotal values of −48.530 and −38.882 kcal/mol. Thus, the set formed by combinations of proteins with functionalized activated carbon tends to more efficiently adsorb the protein components of the coronavirus to the pores of the activated carbon with ozone during filtration.

Molecular Dynamics Study of Microscopic Mechanism of Diffusion in Li2SiO3 System

1991 ◽  
Vol 46 (7) ◽  
pp. 616-620 ◽  
Author(s):  
Junko Habasaki
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Md Simulation ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Lithium Ions ◽  
Microscopic Mechanism ◽  
Trapping Model ◽  
The Mean

MD simulation has been performed to learn the microscopic mechanism of diffusion of ions in the Li2SiO3 system. The motion of lithium ions can be explained by the trapping model, where lithium is trapped in the polyhedron and moves with fluctuation of the coordination number. The mean square displacement of lithium was found to correlate well with the net changes in coordination number.

scholarly journals Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Entropy ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 405
Author(s):  
Piotr Weber ◽  
Piotr Bełdowski ◽  
Krzysztof Domino ◽  
Damian Ledziński ◽  
Adam Gadomski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
Mean Square Displacement ◽  
Conformational Space ◽  
Global Dynamics ◽  
Mean Square ◽  
Conformational Entropy ◽  
The Mean ◽  
Dynamics Simulations

This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes type exponent of 0 . 4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher’s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal–Wallis test, we also analyze differences between the mean root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306 K – 309 K are different than in another temperature. Using the Kullback–Leibler theory, we investigate differences between the distribution of the mean root mean square displacement for each temperature and time window.

scholarly journals Rheological Behavior of Polymer Nanocomposites Filled with Spherical Nanoparticles: Insights from Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Haoxiang Li ◽  
Haoyu WU ◽  
Wenfeng Zhang ◽  
Xiuying Zhao ◽  
Yangyang Gao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Polymer Nanocomposites ◽  
Shear Viscosity ◽  
Rheological Behavior ◽  
Molecular Level ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Shear Rates ◽  
The Mean

<div><div>It is very urgent to understand the rheological behavior of polymer nanocomposites (PNCs) on the molecular level, which is very important for their processing and application. Thus, here the reverse nonequilibrium molecular dynamics simulation isemployed to explore it by tuning the nanoparticle (NP) concentration, the polymer-NPinteraction and the NP size. The shear viscosity (η~-m) exhibits a power law with theshear rate where m varies from 0.42 to 0.53 at high shear rates. By adopting the Carreau-Yasuda model, the obtained zero-shear viscosity gradually rises with increasing the NPconcentration, polymer-NP interaction or reducing the NP size. This is attributed to thestrong adsorption of chains by NPs and the formed network, which leads to the retarded dynamics. In addition, both the first and second normal stress differences also show power laws on the shear rates. The chains are gradually extended as the increase of shear rates, which is characterized by the mean-square end-to-end distance and the mean square radius of gyration. Especially, the evolution process of the NP network and the polymer- NP network is analyzed to deeply understand the shear thinning behavior. The number ofthe direct contact structure of NPs increases while the number of polymer-NP bridgedstructure is reduced. This is further proved by the increase of the formation probability of the NP network and the decrease of the polymer-NP interaction energy. Finally, the chain dynamics is found to be enhanced due to the shear flow. In summary, this work provides a further understanding on the mechanism of the shear thinning of PNCs on the molecular level. <br></div></div>

In-Vitro Adsorption Studies of Isoniazid

1991 ◽  
Vol 10 (2) ◽  
pp. 133-135 ◽  
Author(s):  
O.E. Orisakwe ◽  
A. Akintonwa
Keyword(s):  
Activated Carbon ◽  
Carbon Black ◽  
Adsorption Capacity ◽  
Adsorption Isotherms ◽  
Activated Charcoal ◽  
Binding Capacity ◽  
In Vitro Experiments ◽  
Adsorption Studies ◽  
The Mean

In-vitro experiments were performed to investigate the extent of adsorption of isoniazid to activated charcoal and locally produced activated carbon black (N220) and to explore the effect of varying pH on this adsorption. The results of the study indicated that activated charcoal and activated carbon black adsorbed isoniazid effectively. Adsorption was dependent upon the quantity of charcoal used. With charcoal quantity at 0.5 g, adsorption was virtually completed within 60 min. The mean or composite adsorption capacity of activated charcoal and activated carbon black (?g ml-1 of charcoal) were 325 and 278, respectively. The result of adsorption isotherms indicated no change in binding capacity of the drug from solutions of different pH.

Tight-Binding Quantum Chemical Molecular Dynamics of Oxygen Migration of Rh-supporting CeO2 Surfaces

2014 ◽  
Vol 1704 ◽  
Author(s):  
Ai Suzuki ◽  
Ryuji Miura ◽  
Nozomu Hatakeyama ◽  
Akira Miyamoto
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical ◽  
Oxygen Vacancies ◽  
Tight Binding ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Oxygen Mobility ◽  
Oxygen Migration ◽  
The Mean ◽  
Quantum Chemical Molecular Dynamics

ABSTRACTThe electronic properties of the interface between Rh clusters and CeO2 (111), (110) and (100) surfaces were studied using an isothermal-isobaric (NPT) ensemble at 773 K and 101.343 kPa using the tight binding-quantum chemical molecular dynamics (TB-QCMD) method. The amount of electronic exchange by interaction at the interface between the supported Rh55 clusters and each CeO2 surface was investigated quantitatively. A comparison of the mean square displacement (MSD) showed that the topmost oxygens on the Rh-supporting CeO2 surface exhibited higher mobility than those of the bare CeO2 surface. Although the mobility of the topmost oxygens on the bare CeO2 surface was in the order (100) > (110) > (111), this sequence was altered by the presence of Rh, so that the oxygen mobility for the more open (110) surface was the largest. The amount of electron exchange that occurred between Rh and the CeO2 (110) surface was also larger than for the (111) or (100) surface. The Ce 4f orbitals on the CeO2 (110) surface exhibited the strongest mixing with Rh 4d orbitals, which simultaneously caused restructuring and instability of the topmost Ce-O bonds. This enhancement of oxygen migration in the presence of Rh was occurred together with an increase in the number of oxygen vacancies on the ceria surface. This was because the topmost oxygens was shifted to have a stronger affinity with Rh and thus formed stronger bonds with Rh than with Ce.

The Influence of Graphene Sheet on the Dynamics of Cholesterol Molecules in the Lodgment Located near a Transmembrane Protein – MD Study

2008 ◽  
Vol 140 ◽  
pp. 141-146
Author(s):  
P. Raczynski ◽  
A. Dawid ◽  
Z. Gburski
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Graphene Sheet ◽  
Transmembrane Protein ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Mean Square ◽  
Velocity Autocorrelation ◽  
The Mean ◽  
Velocity Autocorrelation Functions

Molecular dynamics (MD) simulations have been made for a cluster of cholesterols localized near the transmembrane protein at the physiological temperature of 310 K. It was observed that the cholesterol molecules form a lodgment on the surface of protein. Additional studies were made of the influence of graphene sheet on several physical observables of cholesterol molecules including: the radial distribution function, the mean square displacement, diffusion coefficient and the linear and angular velocity autocorrelation functions.

scholarly journals Rheological Behavior of Polymer Nanocomposites Filled with Spherical Nanoparticles: Insights from Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Haoxiang Li ◽  
Haoyu WU ◽  
Wenfeng Zhang ◽  
Xiuying Zhao ◽  
Yangyang Gao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Polymer Nanocomposites ◽  
Shear Viscosity ◽  
Rheological Behavior ◽  
Molecular Level ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Shear Rates ◽  
The Mean

<div><div>It is very urgent to understand the rheological behavior of polymer nanocomposites (PNCs) on the molecular level, which is very important for their processing and application. Thus, here the reverse nonequilibrium molecular dynamics simulation isemployed to explore it by tuning the nanoparticle (NP) concentration, the polymer-NPinteraction and the NP size. The shear viscosity (η~-m) exhibits a power law with theshear rate where m varies from 0.42 to 0.53 at high shear rates. By adopting the Carreau-Yasuda model, the obtained zero-shear viscosity gradually rises with increasing the NPconcentration, polymer-NP interaction or reducing the NP size. This is attributed to thestrong adsorption of chains by NPs and the formed network, which leads to the retarded dynamics. In addition, both the first and second normal stress differences also show power laws on the shear rates. The chains are gradually extended as the increase of shear rates, which is characterized by the mean-square end-to-end distance and the mean square radius of gyration. Especially, the evolution process of the NP network and the polymer- NP network is analyzed to deeply understand the shear thinning behavior. The number ofthe direct contact structure of NPs increases while the number of polymer-NP bridgedstructure is reduced. This is further proved by the increase of the formation probability of the NP network and the decrease of the polymer-NP interaction energy. Finally, the chain dynamics is found to be enhanced due to the shear flow. In summary, this work provides a further understanding on the mechanism of the shear thinning of PNCs on the molecular level. <br></div></div>

scholarly journals Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11261
Author(s):  
Asim Kumar Bepari ◽  
Hasan Mahmud Reza
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Mean Square ◽  
Autodock Vina ◽  
Protein Ligand Interactions ◽  
Main Protease ◽  
Ligand Interactions ◽  
Dynamics Simulations

Background The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has ravaged lives across the globe since December 2019, and new cases are still on the rise. Peoples’ ongoing sufferings trigger scientists to develop safe and effective remedies to treat this deadly viral disease. While repurposing the existing FDA-approved drugs remains in the front line, exploring drug candidates from synthetic and natural compounds is also a viable alternative. This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime molecular target to treat coronavirus diseases. Methods We performed 100 ns GROMACS molecular dynamics simulations of three high-resolution X-ray crystallographic structures of 3CL-PRO. We extracted frames at 10 ns intervals to mimic conformational diversities of the target protein in biological environments. We then used AutoDock Vina molecular docking to virtual screen the Sigma–Aldrich MyriaScreen Diversity Library II, a rich collection of 10,000 druglike small molecules with diverse chemotypes. Subsequently, we adopted in silico computation of physicochemical properties, pharmacokinetic parameters, and toxicity profiles. Finally, we analyzed hydrogen bonding and other protein-ligand interactions for the short-listed compounds. Results Over the 100 ns molecular dynamics simulations of 3CL-PRO’s crystal structures, 6LZE, 6M0K, and 6YB7, showed overall integrity with mean Cα root-mean-square deviation (RMSD) of 1.96 (±0.35) Å, 1.98 (±0.21) Å, and 1.94 (±0.25) Å, respectively. Average root-mean-square fluctuation (RMSF) values were 1.21 ± 0.79 (6LZE), 1.12 ± 0.72 (6M0K), and 1.11 ± 0.60 (6YB7). After two phases of AutoDock Vina virtual screening of the MyriaScreen Diversity Library II, we prepared a list of the top 20 ligands. We selected four promising leads considering predicted oral bioavailability, druglikeness, and toxicity profiles. These compounds also demonstrated favorable protein-ligand interactions. We then employed 50-ns molecular dynamics simulations for the four selected molecules and the reference ligand 11a in the crystallographic structure 6LZE. Analysis of RMSF, RMSD, and hydrogen bonding along the simulation trajectories indicated that S51765 would form a more stable protein-ligand complexe with 3CL-PRO compared to other molecules. Insights into short-range Coulombic and Lennard-Jones potentials also revealed favorable binding of S51765 with 3CL-PRO. Conclusion We identified a potential lead for antiviral drug discovery against the SARS-CoV-2 main protease. Our results will aid global efforts to find safe and effective remedies for COVID-19.

scholarly journals CONFIRMATION OF ADS-B DATA IN THE AERODROME TRAFFIC ZONE BY GATING METHOD

T-Comm ◽  
2021 ◽  
Vol 15 (7) ◽  
pp. 39-49
Author(s):  
Andrey S. Kalintsev ◽  
◽  
Evgeny A. Rubtsov ◽  
Alexandr P. Plyasovskih ◽  
◽  
...  
Keyword(s):  
Mathematical Expectation ◽  
Low Cost ◽  
Time Interval ◽  
Surveillance Systems ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Validity Condition ◽  
Data Validity ◽  
The Mean ◽  
Aircraft Trajectory

The low cost of ADS-B stations in comparison with radars and multi-position surveillance systems allows to consider them as promising means, including for the airfield zone. However, at present, the ICAO does not recommend the use of the ADS-B as the main means of observation, since confirmation of the accuracy of the received coordinate information is required. The article presents a method of algorithmic confirmation of the ADS-B data, while providing flights in the aerodrome traffic zone. It is suggested to use method of the gating to estimate the fidelity of the ADS-B data by selecting the area of space around he extrapolated coordinate of the aircraft. According to the required flight procedure, request of the enhanced surveillance a Mode S is transmitted to the aircraft. On the coordinates of assigned track, according to the maneuvering scheme, aircraft trajectory is built, relative to which the calculation of location errors is performed. Estimation of the mathematical expectation and the mean square deviation of the location error is performed for different levels of reliability. Based on the size of the gate area, a check is performed for compliance of the obtained interval estimates with the data validity condition. The check is performed sequentially for reliability levels 0.9, 0.95, and 0.999. On exit the values of estimate of the error beyond the limit of tolerance for a target level of reliability, information about the unreliability of the received data is displayed, which allows to detect large deviations of the measured coordinates for a smaller number of observations. When performing imitation modelling for the obtained data were set various inaccuracy values: the mathematical expectation from 10 to 48 m and the mean square deviation from 20 to 100 m. The error estimation for the reliability level of 0.999 required from 5 to 22 observations, which corresponds to a time interval of 3 to 11 s real time. At values systematic error of 10 m and mean square deviation of 70 m, the accepted coordinates will be identified as untrusted and will display the information on prohibiting the use of ADS-B and necessary to use other surveillance equipment.

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