A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported

dae-cpp: A simple but powerful C++ solver for Differential Algebraic Equation (DAE) systems

A cross-platform, parallel C++ library for solving a user-defined system of DAEs (an initial value problem). </span

Heat generation and a conservation law for chemical energy in Li-ion batteries

Present theories of irreversible energy losses and heat generation within Li-ion cells are unsatisfactory because they are not compatible with energy conservation and typ- ically give rise to significant errors in the estimation of these quantities. This work aims to provide a consistent theoretical treatment of energy transport and losses in such devices. An energy conservation law is derived from the Doyle-Fuller-Newman (DFN) model of a Li-ion cell using a rigorous mathematical approach. The resulting law allows irreversible chemical energy losses to be located to seven different regions of the cell, namely: (i) the electrolyte, (ii) the anode particles, (iii) the cathode parti- cles, (iv) the solid parts of the anode (ohmic losses), (v) the solid parts of the cathode (ohmic losses), (vi) the surfaces of the anode particles (polarisation losses), and (vii) the surfaces of the cathode particles (polarisation losses). Numerical solutions to the DFN model are used to validate the conservation law in the cases of a drive cycle and constant current discharges, and to compare the energy losses occurring in different lo- cations. It is indicated how cell design can be improved, for a specified set of operating conditions, by comparing the magnitude of energy losses in the different regions of the cell

Lateral migration of peptides in transversely sheared flows in water: an atomistic-scale-resolving simulation

For atomistic scale-resolving simulations of peptide diffusion, which are representative of molecular sorting in micro-fluidic device, a hybrid Fluctuating Hydrodynamics - Molecular Dynamics (FH/MD) model is implemented based on the two-phase flow analogy framework. Thanks to the used framework, in comparison with existing simulations in the literature, the suggested model captures inter-atomic forces between the peptides and the surrounding shell of water atoms at atomistic resolution while concurrently taking into account the non-uniform flow effect. In comparison with previous applications of the hybrid two-phase flow analogy method, multiple moving atomic-resolution zones are implemented for the first time here. The moving zones comprise one and two peptides solvated in water with a Poiseuille flow applied, where each diffusing peptide and the surrounding water shell are dynamically resolved. The models are validated in comparison with the pure all-atom molecular dynamics simulations for the no flow case and then used to investigate how the flow rate and the starting location of peptides in the parabolic flow profile affect their lateral migration over a range of flow Reynolds numbers. It is estimated that for the Poiseuille flows considered, the FH/MD model is 2–20 times faster in comparison with the conventional all-atom non-equilibrium molecular dynamics simulations.</p