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Theoretical Models for Investigating The Processes of Nanofilm Deposition onto Porous Templates of Aluminum Oxide
Published in Rishat G. Valeev, Alexander V. Vakhrushev, Aleksey Yu. Fedotov, Dmitrii I. Petukhov, A. N. Beltiukov, A. L. Trigub, A. V. Severyukhin, Nanostructured Semiconductors in Porous Alumina Matrices, 2019
Rishat G. Valeev, Alexander V. Vakhrushev, Aleksey Yu. Fedotov, Dmitrii I. Petukhov
The force field Assisted Model Building with Energy Refinement15–16 (AMBER) is used for modeling the behavior of proteins, nucleic acids, and a number of other classes of molecules. It is not recommended to use this field to calculate properties of materials. Force fields built based on the calculations of molecular systems with the help of quantum-mechanical methods are available. MMFF can serve as example of such field and which is detailed in Ref. [17]. The force field Consistent Valence Force Field (CVFF) includes the refining contributions of anharmonicity and interaction of the force field components. The field GROningen MOlecular Simulation8,19 (GROMOS) was developed within software package GROMACS and it comprises the parameters for wider family of chemical elements and their compounds.
Role of Computational Tools in Designing Enzymatic Biosensors for the Detection of Pesticides in Environment
Published in Chaudhery Mustansar Hussain, Ajay Kumar Mishra, Nanocomposites for Pollution Control, 2018
Mohd. Shahbaaz, Suvardhan Kanchi, Myalowenkosi Sabela, Krishna Bisetty
The generated docked complexes were subjected to MD simulations using GROMACS [45] (version 5.1.2, installed on the Center for High Performance Computing (CHPC), Cape Town, which provides 10 nodes with 24 cores per node of space for computation). The topologies of pesticide structures were generated by the means of GROMOS96 53a6 force field [46]. Due to the unavailability of suitable force field parameters for drug-like molecules in the GROMACS package, the PRODRG server [47] was used for the generation of the piperine in topologies and coordinate files. The partial charges were corrected by using DFT method of Gaussian which utilized the B3LYP 6-31G (d,p) basis set and CHELPG program [48]. After the successful topology generation, all docked complexes were immersed in SPC/E water model [49] and the systems were neutralized by adding the counter ions. The neutralized systems were energetically minimized by steepest descent and conjugate gradient algorithms with a convergence criterion of 0.005 kcal mol−1. In order to increase the reliability of the MD simulations the restraints were applied to the structure of the pesticides before the equilibration phase.
Atomic Force Microscope Force Spectroscopy
Published in Yuri L. Lyubchenko, An Introduction to Single Molecule Biophysics, 2017
Eric A. Josephs, Piotr E. Marszalek, Zackary N. Scholl
Furthermore, computational tools in various programs, such as NAMD (Phillips et al. 2005) or GROMACS (Pronk et al. 2013), can simulate the mechanical denaturing of proteins through a process called steered molecular dynamics (Isralewitz et al. 2000). These simulations allow researchers to model the unfolding of individual domains, their respective mechanical strengths, and the unfolding pathway of the entire protein (or the order in which the domains mechanically denature). A limitation of these simulations at present is that, for detailed simulations that model the behavior of all of the atoms of the protein subjected to applied forces and of the surrounding solution, pulling rates must be very fast (relative to experimental pulling rates) in order for the computations to complete after a practical period of time (in the order of days); otherwise coarse-grain simulations that make significant simplifying assumptions regarding the intramolecular behaviors of the protein must be performed. While the performance of high-speed SMFS experiments can help bridge this gap between computational and experimental studies (e.g., see Box 3.4), direct comparison of these “all-atom” simulations or these “coarse-grain” simulations with AFM SMFS experiments, therefore, can only provide qualitative guidance for the interpretation of F–X curves. Recent advances, such as the development of computational all-atom Monte Carlo pulling (MCP) (Zhang and Lyubchenko 2014), are addressing this challenge.
Ion effects on the extraction of cesium (I) by 1,3-Diisopropoxycalix [4] arenecrown-6(BPC6) and the highly efficient extraction under neutral conditions
Published in Solvent Extraction and Ion Exchange, 2022
Huifang Xing, Liangrong Yang, Lu Wang, Mengfang Li, Jiemiao Yu, Diannan Lu, Gang Ye, Huizhou Liu
The molecular dynamics simulations were carried out by means of the Gromacs 5.1.4 package.[27–31] The OPLS-AA (Optimized Parameters for Liquid Simulations-All Atoms) force field[32] was used for Cs+, I−, Cl− and octanol. The SPC/E model[33] was employed to describe water molecules. The force-field parameters and geometry parameters of ClO4−, NO3− and SO42− were taken from the works reported in other literature.[34,35]