相关论文: Computational modeling of biological nanopores
Nanoscopic pores are used in various systems to attract nanoparticles. In general the behaviour is a result of two types of interactions: the material specific affinity and the solvent-mediated influence also called the depletion force. The…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
In tissues, cells in direct physical contact with each other can exchange ions or molecules via protein clusters called gap junctions that form channels across the membranes of adjacent cells. Here, we use a simplified biomimetic approach,…
Three-dimensional interconnected nanowire networks have recently attracted notable attention for the fabrication of new devices for energy harvesting/storage, sensing, catalysis, magnetic and spintronic applications and for the design of…
We use molecular dynamics simulations to investigate the displacement of a simple butterfly-like molecular motor inside nanopores of various radii filled with a viscous medium. The medium is modeled with a versatile potential that may be…
Modification of surface properties by polymer adsorption is a widely used technique to tune interactions in molecular experiments such as nanopore sensing. Here, we investigate how the ionic current noise through solid-state nanopores…
Cells offer numerous inspiring examples where proteins and membranes combine to form complex structures that are key to intracellular compartmentalization, cargo transport, and specialization of cell morphology. Despite this wealth of…
In fluid transport across nanopores, there is a fundamental dissipation that arises from the connection between the pore and the macroscopic reservoirs. This entrance effect can hinder the whole transport in certain situations, for short…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
Physical limit of molecular sensing has been extensively studied in biological systems. Biosensors are engineered equivalents of molecular sensors in living systems and play critical role in disease diagnosis and management. Investigation…
Understanding the dynamics of ions in nanopores is essential for applications ranging from single-molecule detection to DNA sequencing. We show both analytically and by means of molecular dynamics simulations that under specific conditions…
We propose two-terminal devices for DNA sequencing which consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
We use molecular simulations of an ionic liquid in contact with a range of nanoporous carbons to investigate correlations between ion size, pore size, pore topology and properties of the adsorbed ions. We show that diffusion coefficients…
Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
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…
Water desalination through nanopores has been shown to be a promising alternative to the currently water purification processes. In spite the results in this direction obtained by means of computational simulations were animating there are…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…