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Lemkul et al. have used steered molecular dynamics simulations to calculate the potential of mean force to assess the stability of Alzheimer's amyloid protofibrils. [6] Gosai et al. have also used umbrella sampling simulations to show that potential of mean force decreases between thrombin and its aptamer (a protein-ligand complex) under the ...
An alternative to free-energy perturbation for computing potentials of mean force in chemical space is thermodynamic integration. Another alternative, which is probably more efficient, is the Bennett acceptance ratio method. Adaptations to FEP exist which attempt to apportion free-energy changes to subsections of the chemical structure. [5]
The electric potential and the magnetic vector potential together form a four-vector, so that the two kinds of potential are mixed under Lorentz transformations. Practically, the electric potential is a continuous function in all space, because a spatial derivative of a discontinuous electric potential yields an electric field of impossibly ...
calculation of () Radial distribution function for the Lennard-Jones model fluid at =, =.. In statistical mechanics, the radial distribution function, (or pair correlation function) () in a system of particles (atoms, molecules, colloids, etc.), describes how density varies as a function of distance from a reference particle.
There are various types of potential energy, each associated with a particular type of force. For example, the work of an elastic force is called elastic potential energy; work of the gravitational force is called gravitational potential energy; work of the Coulomb force is called electric potential energy; work of the nuclear force acting on the baryon charge is called nuclear potential ...
In electrochemistry, the Nernst equation is a chemical thermodynamical relationship that permits the calculation of the reduction potential of a reaction (half-cell or full cell reaction) from the standard electrode potential, absolute temperature, the number of electrons involved in the redox reaction, and activities (often approximated by concentrations) of the chemical species undergoing ...
In electrochemistry, the electrochemical potential of electrons (or any other species) is the total potential, including both the (internal, nonelectrical) chemical potential and the electric potential, and is by definition constant across a device in equilibrium, whereas the chemical potential of electrons is equal to the electrochemical ...
In thermodynamics, the Gibbs free energy (or Gibbs energy as the recommended name; symbol ) is a thermodynamic potential that can be used to calculate the maximum amount of work, other than pressure–volume work, that may be performed by a thermodynamically closed system at constant temperature and pressure.