We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model.
COBISS.SI-ID: 5421082
We propose the use of the Navier–Stokes equations subject to partial slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretizations of the Navier–Stokes equations are combined with slip lengths extracted from molecular dynamics (MD) simulations to predict the pressure losses at the CNT entrance as well as the enhancement of the flow rate in the CNT. The flow quantities calculated from the present hybrid approach are in excellent agreement with pure MD results while they are obtained at a fraction of the computational cost. The method enables simulations of system sizes and times well beyond the present capabilities of MD simulations. Our simulations provide an asymptotic flow rate enhancement and indicate that the pressure losses at the CNT ends can be reduced by reducing their curvature. More importantly, our results suggest that flows at nanoscale channels can be described by continuum solvers with proper boundary conditions that reflect the molecular interactions of the liquid with the walls of the nanochannel.
COBISS.SI-ID: 5529626
This paper reports the application of the adaptive resolution scheme (AdResS) for simulating aqueous salt solutions. The concurrent multiscale method AdResS allows for a dynamical change of molecular resolution by coupling atomistic and coarse-grained models of liquids. To this end, we have developed coarse-grained models of salt to be used with standard atomistic force fields and derive thermodynamic forces to ensure the thermodynamic equilibrium distribution of all molecular species across the simulation box.
COBISS.SI-ID: 5301530
We investigate condensation of a long confined chiral nematic polymer inside a spherical enclosure, mimicking condensation of DNA inside a viral capsid. The Landau-de Gennes nematic free-energy Ansatz appropriate for nematic polymers allows us to study the condensation process in detail with different boundary conditions at the enclosing wall that simulate repulsive and attractive polymer-surface interactions. By increasing the chirality, we observe a transformation of the toroidal condensate into a closed surface with an increasing genus, in some respects akin to the ordered domain formation observed in cryo-microscopy of bacteriophages.
COBISS.SI-ID: 2523492
We present adaptive resolution molecular dynamics simulations of aqueous and apolar solvents using coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes of solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent molecules change their resolution back and forth between the atomistic and coarse-grained representations according to their positions in the system. The difficulties that arise from coupling to a coarse-grained model with a multimolecule mapping, for example, 4 to 1 mapping in the case of the Simple Point Charge (SPC) and MARTINI water models, could be successfully circumvented by using bundled water models. We demonstrate that the presented multiscale approach faithfully reproduces the structural and dynamical properties computed by reference fully atomistic molecular dynamics simulations. Our approach is general and can be used with any atomistic force field to be linked with the MARTINI force field.
COBISS.SI-ID: 5465114