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Cloud Application in Drug Development
Published in Rishabha Malviya, Pramod Kumar Sharma, Sonali Sundram, Rajesh Kumar Dhanaraj, Balamurugan Balusamy, Bioinformatics Tools and Big Data Analytics for Patient Care, 2023
Nitu Singh, Urvashi Sharma, Deepika Bairagee, Neelam Jain
Cloud Pharmaceuticals has developed JAK3 inhibitors that do not target other family members, resulting in more focused results with fewer side effects. By adopting a multi-scale, multi-resolution approach, the methods above help increase binding accuracies. This method uses an implicit solvation term with a high sample rate, as well as a flexible protein, flexible ligand, and explicit water model. For example, this technology was used for the Janus family of kinases to find new inhibitors of the JAK3 enzyme that are selective against other Janus family proteins. Each JAK protein is targeted for distinct disorders based on its activities: JAK3 for rheumatoid arthritis, immunosuppression, and inflammation, and JAK2 for cancer [45].
Variety of Shapes of Water Molecule Interactions
Published in Makoto Yasutomi, The Physics of Liquid Water, 2021
Several ideas similar to the binary mixture model described above have been proposed. Reference [Russo and Tanaka (2014)] proposed a water model with two states, S-state and ρ-state, to explain the thermodynamic properties of water. S-state is in a state of low energy, low density, and low degeneracy, but ρ-state is in a state of high degeneration, high energy, and high density. They reproduced the water density anomaly experimental results using molecular dynamics and showed that it was brought about by the change of the abundance ratio of S-state and ρ-state due to the temperature change. However, the relationship between the temperature change of the abundance ratios of the two states and the functional form of the intermolecular interaction has not been clarified. That is, below 4◦C, as the temperature decreases, negative thermal expansion is induced as a result of the S-state existence ratio exceeding the ρ-state existence ratio. But the reason for it remains a mystery. This mystery can be easily explained as follows based on the thermodynamic mechanism elucidated by the author in Section 2.2 and Section 3.7.
Transport Phenomena in Copper Bath Smelting and Converting Processes – A Review of Experimental and Modeling Studies
Published in Mineral Processing and Extractive Metallurgy Review, 2022
As a conclusion, the following factors and parameters seem to warrant further research: In the reported CFD modeling work on the SKS furnace, the effect of slag characteristics on mixing phenomena was ignored. Therefore, an investigation of high-temperature slag characteristics for SKS technology should be conducted first.Simulation work on the transport phenomena of Noranda and Mitsubishi technology is not of sufficient interest to the industry, and no relevant reports were found.Due to the different physical properties between water and a high-temperature melt, the water model results of surface waves are not accurate enough to describe the wave behavior in the matte-slag system. CFD modeling work to describe the surface waves in copper making bath reactors is required.
Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study
Published in Molecular Physics, 2020
Mahabir Prasad, Niall J. English, Somendra Nath Chakraborty
One-femtosecond time step was used for the integration. Nose-hoover thermostat [26–28] and Parrinello-Rahman barostat [29] was used to fix the temperature and pressure, respectively. The time step used for Barostats and Thermostats were 4 and 2 ps, respectively. The TIP4P/2005 water model [30] was used for all the simulations. In this four-site model, positive charges are located on the hydrogen atoms, with the negative charge of e not located on the oxygen atom but 0.1546 Å toward the hydrogens along the H–O–H angle bisector. The single LJ interaction site is centred on the oxygen atom. The O–H distance is 0.9572 Å, and the H–O–H angle is . The TIP4P/2005 water model is a reparameterisation of the TIP4P model [31]. TIP4P/2005 water model has been extensively used to study the properties of water [32–39]. At 1 bar, melting point of TIP4P/2005 water model is 252 K [30]. Here we perform molecular simulations in the temperature range 280–200 K. Our analysis covers liquid water over ambient, cooled and supercooled conditions.
Adsorption behaviour of NaCl solution on the surface of MgO: a molecular dynamics study
Published in Molecular Physics, 2019
Xiaoli Tang, Qingfei Bian, Qiuwang Wang, Min Zeng
The Clayff force field [26], developed by T. Cygan et al. is implemented to calculate the MgO and ions. In Clayff force field, the Lennard–Jones potential is chosen to describe Van der Waals interactions: The theory study indicates that the metal surface atoms’ vibrations do not have much influence on the adsorption properties of the liquid [19]. Therefore, all solid atoms are frozen to improve the calculation efficiency [27]. Even though the Clayff force field is derived from the SPC water model, using the SPC or the SPC/E model does not significantly affect the transferability of Clayff [18]. In this study, SPC/E [28] (only the partial charge assignments change is different from the SPC [28]) water model is chosen to simulate water. The force-field parameters used in this study are summarised in Table 1. The interaction parameters between unlike atoms are determined by Berthelot-Lorentz combining rules [29], i.e. the arithmetic mean rule is used for distance parameter, R0, and the geometric mean rule is used for the energy parameter, D0: The cut-off distance is set to 9 Å. To compute the long-range Coulomb interactions, particle mesh Ewald (PME) [30] method is adopted.