We examined real-time-propagation time-dependent density functional theory (rtp-TDDFT) coupled with molecular dynamics (MD), which uses single-particle representation of time-evolving wavefunctions allowing exchange of orbital characteristics between occupied and empty states making the effective Kohn-Sham Hamiltonian dependent on the potential energy surfaces (PESs). This scheme is expected to...

Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We ...

Molecular dynamics (MD) simulation is used increasingly often for materials design to reduce the costs associated with the pure experimental approach. Complex MD simulations are, however, notoriously hard to set up. It requires expertise in several distinct areas, including the peculiarities of a particular simulator tool, the chemical properties of the family of materials being studied, as wel...

We consider tracer diffusion in colloidal suspensions under solid loading conditions, where hydrodynamic interactions play an important role. To this end, we carry out computer simulations based on the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) technique. Many details of the simulation method are discussed in detail. In particular, our choices for the SRD-MD parameters and ...

serum albumin is the most aboundant protein in blood plasma. its two major roles aremaintaining osmotic pressure and depositing and transporting compounds. in this paper,albumin-methanol solution simulation is carried out by three techniques including montecarlo (mc), molecular dynamic (md) and langevin dynamic (ld) simulations. byinvestigating energy changes by time and temperature (between 27...

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to characterize the structure of aqueous guanidinium carbonate (Gdm2CO3) solutions. The MD simulations found very strong hetero-ion pairing in Gdm2CO3 solution and were used to determine the best structural experiment to demonstrate this ion pairing. The NDIS experiments conf...