Related papers: Modeling Protein Diffusion Across ER-Nuclear Envel…
The biotransport of the intravascular nanoparticle (NP) is influenced by both the complex cellular flow environment and the NP characteristics. Being able to computationally simulate such intricate transport phenomenon with high efficiency…
Though membrane trafficking of cell junction proteins has been studied extensively for more than two decades, the accumulated knowledge remains fragmentary. The goal of this review is to synthesize published studies on the membrane…
Diffusion models are important in tissue engineering as they enable an understanding of molecular delivery to cells in tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically…
The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H$\&$E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large…
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…
Proteins are large and complex molecular machines. In order to perform their function, most of them need energy, e.g. either in the form of a photon, like in the case of the visual pigment rhodopsin, or through the breaking of a chemical…
Protein inverse folding, the design of an amino acid sequence based on a target protein structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external…
The transport of particles across lipid-bilayer membranes is important for biological cells to exchange information and material with their environment. Large particles often get wrapped by membranes, a process which has been intensively…
Eukaryotic cells adhere to extracellular matrix during the normal development of the organism, forming static adhesion as well as during cell motility. We study this process by considering a simplified coarse-grained model of a vesicle that…
Optical nanoantennas can efficiently confine light into nanoscopic hotspots, enabling single-molecule detection sensitivity at biological relevant conditions. This innovative approach to breach the diffraction limit offers a versatile…
A great possible achievement for the MMS mission would be crossing electron diffusion regions (EDR). EDR are regions in proximity of reconnection sites where electrons decouple from field lines, breaking the frozen in condition. Decades of…
All materials enter or exit the cell nucleus through nuclear pore complexes (NPCs), efficient transport devices that combine high selectivity and throughput. A central feature of this transport is the binding of cargo-carrying soluble…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
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,…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Several neurological disorders are associated with the aggregation of aberrant proteins, often localized in intracellular organelles such as the endoplasmic reticulum. Here we study protein aggregation kinetics by mean-field reactions and…
Non-Hermitian systems hosting exceptional points (EPs) exhibit signal enhancement and unconventional mode dynamics. Going beyond isolated EPs, here we report on the existence of exceptional rings (ERs) in planar optical resonators with…
Diffusion-based and neural communication are two interesting domains in molecular communication. Both of them have distinct advantages and are exploited separately in many works. However, in some cases, neural and diffusion-based ways have…
Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…
The transport of nanoparticles (NPs) in polymer networks, as a typical simplified model describing various structures in living systems, is profoundly important in biomedical engineering and nanotechnology. Predicting the effective…