China
Africa
Explore chapters and articles related to this topic
Molecular Dynamics Simulations for the Extraction of Aromatics and Pesticide
Published in Papu Kumar Naik, Nikhil Kumar, Nabendu Paul, Tamal Banerjee, Deep Eutectic Solvents in Liquid–Liquid Extraction, 2023
Papu Kumar Naik, Nikhil Kumar, Nabendu Paul, Tamal Banerjee
For DES + nitenpyram + water system, the experimental compositions were used from an earlier work by Florindo et al. [23]. Here, the DES consists of DL-menthol and octanoic acid at a 1:1 molar ratio. The ternary system was prepared for the simulation study of pesticide extraction from the corresponding mole fraction in line with the respective molecules of the experiment. The exact mimicking of the experimental number of molecules was not possible due to the computational limit. As a result, the equal mass of DES and water for the simulated system with 5 molecules of nitenpyram in the aqueous phase has been considered initially. The chemical structures of these species are shown in Figure 3.2 and composition of the systems has been presented in Table 3.3. Nanoscale Molecular Dynamics (NAMD) was used for simulation. A sample NAMD configuration file is given in the Appendix. The Lennard–Jones (L-J) parameters used are reported in Table 3.4.
Numerical Methods for Modeling of Nanosystems
Published in Alexander V. Vakhrushev, Computational Multiscale Modeling of Multiphase Nanosystems, 2017
A widely used program Nanoscale Molecular Dynamics (NAMD) is developed by the group of biophysicists from Illinois University together with Backman University. NAMD is intended for parallel modeling of biomolecular systems with the method of molecular dynamics. This program is supplemented with the visualization program of calculation results— Visual Molecular Dynamics (VMD). VMD is specially developed for the visualization and analysis of such biological systems as proteins, nucleic acids, molecular systems based on lipids (e.g., components of cell membranes). The program understands the format Protein Data Bank (PDB) and allows using various variants and methods of visualization and coloring of molecules. VMD can be applied for the animation and analysis of phase theory obtained in the result of molecular-dynamic modeling. An interesting feature of the program is the fact that it can be used as the graphic component of computer modeling system and operates on a distant computer.
Measuring stiffness of soils in situ
Published in Fusao Oka, Akira Murakami, Ryosuke Uzuoka, Sayuri Kimoto, Computer Methods and Recent Advances in Geomechanics, 2014
Fusao Oka, Akira Murakami, Ryosuke Uzuoka, Sayuri Kimoto
processing computer systems at Center for Computationally Assisted Science and Technology, North Dakota State University. Molecular dynamics software NAMD was used for the simulations. Each solvation model was minimized using 100,000 iterations. Models were first minimized by allowing atoms to move freely in all directions; the same models were minimized again by restraining clay sheets and Na+ions in X-Y directions and keeping them free in Z-direction The clay models were placed in a solvation box containing water molecules and having density of bulk water at room temperature and pressure. Throughout the simulation, water molecules were kept free in all directions. Total minimum potential energy of the system was observed after 50,000 iterations; these simulations were carried at simulated conditions vacuum and 0K temperature. Next, the temperature was increased from 0K to 300K in three equal increments, each time the simulation was performed for 100,000 time steps. Nose-Hoover piston method (Feller et al, 1995; Martyna et al. 1994) to increase the pressure in constant pressure simulations; in this study pressure was increased form 0 bar to one bar in four equal increments. Periodic boundary conditions are required to perform NPT simulations.
Inhibitory potentials of phytocompounds from Ocimum gratissimum against anti-apoptotic BCL-2 proteins associated with cancer: an integrated computational study
Published in Egyptian Journal of Basic and Applied Sciences, 2022
Gideon A. Gyebi, Oludare M. Ogunyemi, Ibrahim M. Ibrahim, Saheed O. Afolabi, Rotimi J. Ojo, Uju D.I. Ejike, Joseph O. Adebayo
Molecular Dynamic Simulation utilizing Nanoscale Molecular Dynamics (NAMD) V2.13 [30] was performed on 3ZLR (unbound), 3ZLR-luteolin complex, 4LVT (unbound) and 4LVT-ursolic acid complex. Prior to the MDS analysis, necessary files were prepared using CHARMM-GUI webserver [31,32]. The water model TIP3P was used in the solvation while the physiological concentration of 0.154 M was set by neutralized NaCl ions. The systems were minimized for 10,000 steps using CHARMM 36 force field as conjugate gradient algorithm in constant number of atoms, volume, and temperature ensemble (NVT). System equilibration was started afterward for 1 ns in NPT (constant number of atoms, constant pressure, and constant temperature ensemble). A 310 K temperature was set and maintained by langevin dynamics, while A 1 atm pressure was set and maintained by Nose-Hoover langevin piston. Eventually, All the systems were run for 100 ns in NVT ensemble. Periodic Boundary Conditions (PBC) were applied throughout the simulation. The trajectories were saved for each 0.1 ns with a 2 femto second time step. VMD scripts were used to analyze the trajectories by calculating the various thermodynamic parameters [33].
New development of atomic layer deposition: processes, methods and applications
Published in Science and Technology of Advanced Materials, 2019
Peter Ozaveshe Oviroh, Rokhsareh Akbarzadeh, Dongqing Pan, Rigardt Alfred Maarten Coetzee, Tien-Chien Jen
Other software, such as LAMMPS [38,106–109], NAMD [53], GROMACS, CHARMM [53] and AMBER [95,100] is also used for molecular dynamics simulation. For instance, by using LAMMPS for molecular dynamics simulation, Hieranian et al. [109] demonstrated that a single layer of molybdenum disulfide (MoS2) can effectively separate ions from water. They investigated the desalination of water through (MoS2) as a function of chemistry, pore size, hydrostatic pressure and geometry. To have efficient desalination, the sizes of pores should be such that both the water filtration and ion rejection are optimized. In one hand large pores do not effectively reject ions while very small pores permeation rate is low. Atomic layer deposition is effective in addressing such situations. Hu et al. [110] used MD to study and predict the influence of the initial surface composition and process temperature on the roughness of the surface, the growth rate and growth mode of the film deposition. Timo and Kari [111] in the study of the atomic layer deposition of alumina by TMA–H2O-process, they used MD simulation to study the water reaction mechanism with alumina to obtain more insight on the surface mechanisms and energetics which according to them is essential in the design and optimization of the ALD process.
Modelling nucleation from solution with the string method in the osmotic ensemble
Published in Molecular Physics, 2018
Chengxiang Liu, Geoffrey P. F. Wood, Erik E. Santiso
In each step of the SMCV simulation, the OPs of each image were maintained close to their ‘target value’ by adding a set of harmonic restraints. Short NPT simulations of 0.2 ns at 295 K and 1 atm were then run for each replica to calculate the mean force needed to keep it close to ‘target’ value. Finally, each image was propagated by following the mean force. To avoid images clustering at the end points of the pathway, which is what would happen if each of them was to evolve indefinitely along the gradient vector, we then reinterpolated (‘reparameterised’) the target OPs to keep the distance between images in OP space constant. This procedure was repeated until the Fréchet distance [40] between two neighbouring strings was stabilised. We determined the SMCV to reach convergence when the difference between the Fréchet distances in two successive steps was <4.0 (even for a converged string, the Fréchet distance between successive steps will remain finite due to thermal fluctuations). All the SMCV simulations were performed using a modified version of the NAMD [41] software that included the implementations of the OPs and SMCV in C++ libraries. Periodic boundary conditions were applied in all dimensions. The simulations to obtain the mean force at each image took approximately 5–6 hours running on Intel Xeon 12 core E5-2650 v4 processors, with all images running as separate simulations. Converging each SMCV calculation took in total approximately 2–3 weeks.