Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling
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Atomistic simulations are a powerful complement to experimental probes for understanding the nanoscale processes associated with the effects of hydrogen (H) on plasticity and fracture that are the underlying causes of hydrogen embrittlement (HE). Current e ...
Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as a statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the mo ...
This paper reviews atomistic force field parameterizations for molecular simulations of cementitious minerals, such as tricalcium silicate (C3S), portlandite (CH), tobermorites (model C-S-H). Computational techniques applied to these materials include clas ...
We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specifi ...
Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, b ...
Polarizable quantum mechanical (QM)/molecular mechanics (MM)-embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of ...
A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water. The method consists of two additive contributions: (i) ...
Huntington disease is a neurodegenerative disease characterized by a polymorphic tract of polyglutamine repeats in exon 1 of the huntingtin protein, which is thought to be responsible for protein aggregation and neuronal death. The polyglutamine tract is p ...
Hydrocarbon chains are important intermediates in various aqueous-phase surface processes, such as CO2 electroreduction, aqueous Fischer-Tropsch synthesis, and aqueous phase reforming of biomass-derived molecules. Further, the interaction between water and ...
Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a ...