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Electrokinetic flows of an aqueous NaCl solution in nanochannels with negatively charged surfaces are studied using molecular dynamics (MD) simulations. The four transport coefficients that characterise the response to weak electric and…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
We use all-atom molecular dynamics simulations informed by density functional theory calculations to investigate aqueous ion transport across sub-nanoporous monolayer molybdenum disulfide (MoS$_2$) membranes subject to varying tensile…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
We model and simulate a nanopore sensor that selectively binds analyte ions. This binding leads to the modulation of the local concentrations of the ions of the background electrolyte (KCl), and, thus, to the modulation of the ionic current…
Even though atomistic and coarse-grained (CG) models have been used to simulate liquid nanodroplets in vapor, very few rigorous studies of the liquid-liquid interface structure are available, and most of them are limited to planar…
Continuum simulations become an important tool to uncover the mysteries in nanofluidic experiments. However, fluid flow in simulation models is usually unconsidered. Here, systematical simulations are conducted to provide a quantitative…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
We present a coarse-graining method applicable to dry scalar active matter with motility regulation. Our approach, based on a multiscale perturbative expansion of the backward Kolmogorov equation, does not rely on any specific microscopic…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Coarse-graining (CG) enables molecular dynamics (MD) simulations of larger systems and longer timescales that are otherwise infeasible with atomistic models. Machine learning potentials (MLPs), with their capacity to capture many-body…
Iontronics is a burgeoning paradigm that employs ions in solution as information carriers for sensing and computing, e.g., in neuromorphic devices. The fundamentally different working principle as compared to electronics requires novel…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
Predicting the molecular friction and energy landscapes under nonequilibrium conditions is key to coarse-graining the dynamics of selective solute transport through complex, fluctuating and responsive media, e.g., polymeric materials such…
Using molecular dynamics simulations, we show that, when subject to a periodic external electric field, a nanopore in ionic solution acts as a capacitor with memory (memcapacitor) at various frequencies and strengths of the electric field.…
Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule…