Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins
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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 ...
Small-angle neutron scattering experiments and molecular dynamics simulations combined with an application of concepts from soft matter physics to complex protein mixtures provide new insight into the stability of eye lens protein mixtures. Exploring this ...
The need to perform large-scale molecular dynamics simulations of radiation defects in ferritic steels has stimulated the recent development of a 'magnetic' interatomic potential for body-centred cubic alpha-iron [1,2]. Here we describe the first applicati ...
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 review the state-of-the-art in computational molecular simulations for biological systems. We limit our discussion to three fields: all-atom simulations, coarse-grained models, and novel multiscale approaches. While molecular dynamics simulations are br ...
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 ...
Molecular dynamics simulations of collision cascades in pure tungsten are performed to assess the primary damage due to irradiation. For short-range interaction the universal potential is used [J.F. Ziegler, J.P. Biersack, U. Littmark, The Stopping and Ran ...
Chemoselective autoxidation of 4-imino-1,5-dimethyl-3-(4-nitrophenyl) imidazolidin-2-one (1b) to its 5-hydroxy derivative 2 occurred in solutions of DMSO-d(6), acetonitrile-d(3) or refluxing ethanol. Also bis(imidazolidin-5-yl) peroxide 5 was isolated as a ...
We discuss the static and dynamical properties of a model of short range attractive colloidal systems. Our model is a binary mixture of particles interacting with a modified Lennard-Jones potential that we simulated by molecular dynamics. As previously fou ...
Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the in ...