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The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. The ionic conductivity of CG ions in solution was computed and compared with experimental results.…
We present the state-of-the-art theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…
Solid-state nanopores have received substantial attention in the past years owing to their simplicity and potential applications expected in genomics, sensing, archival information storage, and computing. The underlying sensing technique of…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Janus --or two-sided, charged membranes offer promise as ionic current rectifiers. In such systems, pores consisting of two regions of opposite charge can be used to generate a current from a gradient in salinity. The efficiency of…
Single nanopores have attracted much scientific interest due to their versatile applications. The majority of experiments have been performed with nanopores being in contact with the same electrolyte on both sides of the membrane, while…
Nanopores in solid state membranes are a tool able to probe nanofluidic phenomena or can act as a single molecular sensor. They also have diverse applications in filtration, desalination or osmotic power generation. Many of these…
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Partitioning and transport of water and small solutes into and through nanopores is important to a variety of chemical and biological processes and applications. Here we study the partitioning of positive ions of increasing size into the…
Fundamental understanding of ionic transport at the nanoscale is essential for developing biosensors based on nanopore technology and new generation high-performance nanofiltration membranes for separation and purification applications. We…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Hydroxide ion transport in anion-exchange membranes fundamentally limits the efficiency of alkaline water electrolysis for green hydrogen production, yet the atomic-scale transport mechanisms remain poorly understood due to the…
Continuum simulation is employed to study ion transport and fluid flow through a nanopore in a solid-state membrane under an applied potential drop. Results show the existence of concentration polarization layers on the surfaces of the…
Molecular dynamics simulation is utilized to investigate the ionic transport of NaCl in solution through a graphene nanopore under an applied electric field. Results show the formation of concentration polarization layers in the vicinity of…