Related papers: TransPath: A Computational Method to Study the Ion…
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to…
Biological ion channels balance electrostatic and dehydration effects to yield large ion selectivities alongside high transport rates. These macromolecular systems are often interrogated through point mutations of their pore domain,…
Molecular motion through pores plays a crucial role in various natural and industrial processes. One of the most fascinating features of biological channel-facilitated transport is a stochastic gating process, when the channels dynamically…
Computational prediction of protein structures is a difficult task, which involves fast and accurate evaluation of candidate model structures. We propose to enhance single model quality assessment with a functionality evaluation phase for…
Ion transport through charged nanopores is commonly interpreted in terms of electrical double layer structure, leading to the expectation of cation-selective conduction in negatively charged pores. This picture can break down for…
Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. Design of diverse applications of bacterial cellulose films also relies on understanding…
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective…
Recent advances in machine learning have become increasingly popular in the applications of phase transitions and critical phenomena. By machine learning approaches, we try to identify the physical characteristics in the two-dimensional…
Accurate prediction of cancer progression remains a challenge due to the high heterogeneity of molecular omics data across patients. While biologically informed models have improved the interpretability of these predictions, a persistent…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as…
We present theory for ion and water transport through reverse osmosis membranes based on a Maxwell-Stefan framework combined with hydrodynamic theory for the reduced motion of particles in thin pores. We include all driving forces and…
Recent experiments have demonstrated that highly charged ions can be guided through insulating nanocapillaries along the direction of the capillary axis for a surprisingly wide range of injection angles. Even more surprisingly, the…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
Selective ion transport is a hallmark of biological ion channel behavior but is a major challenge to engineer into artificial membranes. Here, we demonstrate, with all-atom molecular dynamics simulations, that bare graphene nanopores yield…
We describe a method for modeling the geometry of porous materials. The approach enables the independent selection of crucial parameters, including porosity, pore size distribution, pore shape, and connectivity. Consequently, it can…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
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…
Currently, identification of crystallization pathways in polymers is being carried out using molecular simulation-based data on a preset cut-off point on a single order parameter (OP) to define nucleated or crystallized regions. Aside from…
An uncoupled multi-scale homogenization approach is used to estimate the effective thermal conductivities of plain weave C/C composites with a high degree of porosity. The geometrical complexity of the material system on individual scales…