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Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
Granular aluminium is a high kinetic inductance thin film superconductor which, when formed into nanowires can undergo an intrinsic electromigration process. We use a combination of experimental and computational approaches to investigate…
Ionic Coulomb blockade is one of the mesoscopic effects in ion transport revealing the quantized nature of ionic charges, which is of crucial importance to our understanding of the sub-continuum transport in nanofluidics and the mechanism…
Ionic transport in nanopores is a fundamentally and technologically important problem in view of its occurrence in biological processes and its impact on novel DNA sequencing applications. Using microscopic calculations, here we show that…
Transport properties of concentrated electrolytes have been analyzed using classical molecular dynamics simulations with the algorithms and parameters typical of simulations describing complex electrokinetic phenomena. The electrical…
Recently synthesized Porous 12-Atom-Wide Armchair Graphene Nanoribbons Nano Lett. 2024, 24, 10718-10723 exhibit tunable properties through periodic porosity, enabling precise control over their electronic, optical, thermal, and mechanical…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
Recent advances in nanofluidics have enabled the confinement of water down to a single molecular layer. Such monolayer electrolytes show promise in achieving bio-inspired functionalities through molecular control of ion transport. However,…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
In a recent paper, J. Chem. Phys. 162, 214101 (2025), a novel approach for the rigidification of a molecular cluster was proposed, in which starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
We describe a method to simulate the dynamics of charged colloidal particles suspended in a liquid containing dissociated ions and salt ions. Regimes of prime current interest are those of large volume fraction of colloids, highly charged…
Molecular dynamics simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous…
We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD)…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
The paper constructs a coarse-grained model to investigate dry sliding friction of the body-centered-cubic Fe micron-scale system by smoothed particle hydrodynamics simulations and examines influences of the spring force on the characters…
Mechanosensitive ion nanochannels regulate transport by undergoing conformational changes within nanopores. However, achieving precise control over these conformational states remains a major challenge for both artificial soft or solid…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
In this paper, we present a molecular theory analysis of ions and potential distribution, degree of ionization of polyelectrolyte (PE) brushes, velocity profile, volumetric flow rate, ionic selectivity, ionic conduction and advection by…