Charge fluctuations from molecular simulations in the constant-potential ensemble
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Recent findings identified electroencephalography (EEG) microstates as the electrophysiological correlates of fMRI resting-state networks. Microstates are defined as short periods (100 ms) during which the EEG scalp topography remains quasi-stable; that is ...
Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...
The present thesis is devoted to a detailed study of the Casimir force exerting between two parallel metallic plates whose conducting behaviour is described on the microscopic level. In the semi-classical regime, which corresponds to large separations and ...
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The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 and 400 K. Density-functional theory, p ...
The spectrum of exponentially weighted covariance matrices is studied here. We first give a formal way of obtaining the spectrum using annealed approximation frequently used in Statistical Mechanics. Using the method developed by Bai and Silverstein we obt ...
The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside ...
A method is described to extract a complete set of sequence-dependent material parameters for rigid base and basepair models of DNA in solution from atomistic molecular dynamics simulations. The method is properly consistent with equilibrium statistical me ...
We investigate the ground state properties of large atoms and quantum dots described by a d-dimensional N-body Hamiltonian of confinement ZV. In atoms, d = 3 and V is the Coulomb interaction; in dots, d = 2 and V is phenomenologically determined. We expres ...
In order to compute the thermodynamic weights of the different metastable conformations of a molecule, we want to approximate the molecule’s Boltzmann distribution π in a reasonable time. This is an essential issue in computational drug design. The energy l ...