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Solvent Extraction through the Lens of Advanced Modeling and Simulation
Published in Bruce A. Moyer, Ion Exchange and Solvent Extraction: Volume 23, 2019
Aurora E. Clark, Michael J. Servis, Zhu Liu, Ernesto Martinez-Baez, Jing Su, Enrique R. Batista, Ping Yang, Andrew Wildman, Torin Stetina, Xiaosong Li, Ken Newcomb, Edward J. Maginn, Jochen Autschbach, David A. Dixon
Rare-event sampling methods are implemented in molecular simulation to investigate states which are inaccessible through statistical sampling of feasible simulation time and length scales. One such method which is often applied to study of solvent extraction relevant systems is the potential of mean force. The potential of mean force (PMF) technique can be used to determine the free-energy surface along a coordinate. For studies on solvent extraction systems, a common coordinate is the transfer of a metal ion, extractant or extractant–metal complex across the aqueous–organic interface. While that transfer event may be sufficiently energetically unfavorable or inhibited by kinetic barriers so as to elude the nanometer and nanosecond length and time scales of simulation methods, the free-energy profile of that event can be studied with a PMF. For a discussion on constructing a potential of mean force and the techniques used to do so, such as umbrella sampling279, see ref 280.
Interactions Between 2D Graphene-Based Materials and the Nervous tissue
Published in Craig E. Banks, Dale A. C. Brownson, 2D MATERIALS, 2018
Mattia Bramini, Giulio Alberini, Fabio Benfenati, Luca Maragliano, Fabrizia Cesca
Firstly, in the work of Sun et al.,158 an atomistic description of the inhibitory action of GO on the activity of a-chymotrypsin (ChT),160 has been provided based on the deformation of its binding sites and supporting the hypothesis that GO can be considered as an ideal artificial receptor for enzyme inhibition. The distinct binding modalities of ChT to GR and GO substrates is shown in Fig. 5. Secondly, Zeng et al.159 show the details of the binding of GO to Vpr13-33, a fragment of the viral protein R (Vpr), that plays a key role in regulating nuclear import of HIV. In this process, the Vpr13-33 fragment can modify its conformation after the adsorbing process. The binding energy of the protein domain on GO was obtained using the potential of mean force (PMF) calculations with umbrella sampling calculations.161 The self aggregation of multiple copies of the Vpr13-33 peptide was strongly affected by the adsorption on GO substrate, with a weaker interaction between two of these peptides, while it is shown that a stable dimer can be obtained in water or on GR substrate.
Application of enhanced sampling approaches to the early stages of mineralization
Published in Elaine DiMasi, Laurie B. Gower, Biomineralization Sourcebook, 2014
that have each provided insight into the early stages of calcium carbonate formation and that will provide the reader with a rm introduction to enhanced sampling techniques. 18.3.1 UMBRELLA SAMPLING Umbrella sampling determines the potential of mean force (PMF) or equivalently the free energy (Helmholtz) along a speci ed reaction coordinate, . The full energy landscape along is sampled by segmenting the reaction coordinate into discrete windows that are simulated independently (Torrie and Valleau, 1974). In each window, a restraining potential, i() is applied so that the simulation does not drift away from the small segment of the reaction coordinate it is intended to sample. The restraining potential may take several forms; however, the harmonic variety is usually employed: i () = 1 K ( - i )2 2 (18.18)
Determining the occurrence time of different stages of asphaltene aggregation using molecular dynamics simulations
Published in Petroleum Science and Technology, 2019
Reza Aminzadeh, Manouchehr Nikazar, Bahram Dabir
The potential of mean force (PMF) is an effective tool to calculate the effective interactions between two complex molecules inside a liquid medium. A common method to calculate PMF along a given reaction coordinate is umbrella sampling, in which separate simulations are run in a series of windows along the reaction coordinate ξ, biased by umbrella potentials wi (ξ). The bias potentials can have any functional form. Often, harmonic potentials shown in Eq. (1) are applied for the sake of their simplicity, where is the position at which the system is restrained with a force constant .