Related papers: Ionic transport through a protein nanopore: a Coar…
It has been suggested that microtubules and other cytoskeletal filaments may act as electrical transmission lines. An electrical circuit model of the microtubule is constructed incorporating features of its cylindrical structure with…
Molecular dynamics (MD) simulations were performed to study the formation process of nanopores in a suspended graphene sheet irradiated by using energetic ions though a mask. By controlling the ion parameters including mass, energy and…
Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the…
Modulating ion transport through nanoporous membranes is critical to many important chemical and biological separation processes. The corresponding transport timescales, however, are often too long to capture accurately using conventional…
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…
Previously reported nanodosimetric measurements of therapeutic-energy carbon ions penetrating simulated tissue have produced results that are incompatible with the predicted mean energy of the carbon ions in the nanodosimeter and previous…
Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental…
Functoinal polymers can be used as electrolyte and binder materials in solid-state batteries. This often requires performance targets in terms of both transport and mechanical properties. In this work, a model ionic conductive polymer…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
The number of precise conductance measurements in nanopores is quickly growing. In order to clarify the dominant mechanisms at play and facilitate the characterization of such systems for which there is still no clear consensus, we propose…
Using continuous time Monte-Carlo method we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have…
We have developed a coarse-grained (CG) model of a polymer-clay system consisting of organically modified montmorillonite nanoclay as the nanoparticle in accordance with the MARTINI forcefield. We have used mechanical properties and…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
Under many conditions, macroscopic grains flow like a fluid; kinetic theory pred icts continuum equations of motion for this granular fluid. In order to test the theory, we perform event driven molecular simulations of a two-dimensional gas…
We use space-charge (SC) theory (also called the capillary pore model) to describe the ionic conductance, $G$, of charged carbon nanotubes (CNTs). Based on the reversible adsorption of hydroxyl ions to CNT pore walls, we use a Langmuir…
The requirement to boost the resolution of nanopore-based biosequencing devices necessitates the integration of novel biosensing techniques with reduced sensitivity to background noise. In this article, we probe the signatures of…
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic counterpart. Here, we investigate extensively this phenomenon using all-atom molecular dynamics of ionic transport…