Kinetically limited valence of colloidal particles with surface mobile DNA linkers

Sánchez, Pedro A.; Caciagli, Alessio; Kantorovich, Sofia S.; Eiser, Erika

doi:10.1016/j.molliq.2023.121895

Cited by 5 publications

(7 citation statements)

References 62 publications

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“…The model presented in Section 2 is simulated using a reaction–diffusion algorithm 25,45–48 whose chart flow reads as follows…”

Section: Simulating the Reaction–diffusion Dynamicsmentioning

confidence: 99%

“…The model presented in Section 2 is simulated using a reaction-diffusion algorithm 25,[45][46][47][48] whose chart flow reads as follows 1: t ' 0 2: while t o t E do 3: Reaction(Dt) 4: Diffusion(Dt) 5: t ' t + Dt 6: end while where t is the time variable, Dt the simulation timestep, and t E the time at the end of the simulation. Reaction(Dt) implements ligands/receptors reactions, while Diffusion(Dt) updates the particle's and the receptors' position (when mobile) for a given set of HA-SA linkages.…”

Section: Simulation Chart Flowmentioning

confidence: 99%

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The sliding motility of the bacilliform virions of Influenza A viruses

2023

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“…The model presented in Section 2 is simulated using a reaction–diffusion algorithm 25,45–48 whose chart flow reads as follows…”

Section: Simulating the Reaction–diffusion Dynamicsmentioning

confidence: 99%

Section: Simulation Chart Flowmentioning

confidence: 99%

The sliding motility of the bacilliform virions of Influenza A viruses

2023

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“…The model presented in Sec. II is simulated using a reaction-diffusion algorithm 24,[45][46][47][48] whose chart flow reads as follows…”

Section: Simulating the Reaction-diffusion Dynamics A Simulation Char...mentioning

confidence: 99%

The sliding motility of the bacilliform virions of Influenza A Viruses

Stevens

Buyl

Mognetti

2023

Preprint

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Influenza A virus (IAV) infection relies on the action of the hemagglutinin (HA) and neuraminidase (NA) membrane proteins. The HA ligands anchor the IAV virion to the cell's surface by binding the sialic acid (SA) present on the host's receptors while NA is an enzyme capable of cleaving the SA from the extracellular environment. It is believed that the activity of NA ligands increases the motility of the virions favoring the propagation of the infection. In this work, we develop a numerical framework to study the dynamics of a virion moving across the cell surface for timescales much bigger than the typical ligand-receptor reaction times. We find that the rates controlling the ligand-receptor reactions and the maximal distance at which a pair of ligand-receptor molecules can interact greatly affect the motility of the virions. We also report on how different ways of organizing the two types of ligands on the virions' surface result in different types of motion that we rationalize using general principles. In particular, we show how the emerging motility of the virion is less sensitive to the rate controlling the enzymatic activity when NA ligands are clustered. These results help to assess how variations in the biochemical properties of the ligand-receptor interactions (as observed across different IAV subtypes) affect the dynamics of the virions at the cell surface.

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“…Prior work on these types of systems used implicit models of binding between neighboring droplets via the formation of adhesion patches, and some models included approximations to account for the dynamics of adhesion. 26,36,[50][51][52][53] The use of explicit mobile binders allows us to test the underlying assumptions in a more realistic model, albeit at the cost of additional complexity. For example, our model explicitly shows how steric repulsion between binders (designed to mimic electrostatic repulsion between DNA strands) affects the adhesion patch size and the concentration of binders therein.…”

Section: Introductionmentioning

confidence: 99%