Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling
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Molecular dynamics simulations based on an empirical force field have been carried out to investigate the properties of a zwitter-ionic phospholipid (POPC) bilayer in contact with a water solution of [bmim][Cl], [bmim][PF6] and [bmim][Tf2N] at concentratio ...
We have developed a united atom (UA) nonpolarizable force field for 1-alkyl-3-methyl-imidazolium chloride ([Cnmim][Cl], n = 1, 2, 4, 6, 8), a potential solvent for the pretreatment of lignocellulosic biomass. The charges were assigned by fitting the electr ...
Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...
In this work, molecular simulations were performed to evaluate the separation performance of two typical zeolitic imidazolate frameworks (ZIFs), ZIF-68 and ZIF-69, for CO2/N2, CO2/CH 4, and CH4/N2 mixtures. To do this, we first identified a suitable force ...
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 ...
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 ...
Data reporting on structure and dynamics of cellular constituents are growing with increasing pace enabling, as never before, the understanding of fine mechanistic aspects of biological systems and providing the possibility to affect them in controlled way ...
We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, p ...
Sequence dependent mechanics of DNA is believed to play a central role in the functioning of the cell through the expression of genetic information. Nucleosome positioning, gene regulation, DNA looping and packaging within the cell are only some of the pro ...
Impurities are known to have a significant impact on materials properties. In particular, the presence of impurities can change mechanical properties and stabilize the microstructure by reducing grain growth and recrystallization processes. In the past ato ...