Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens

This repository contains original code and data created for the study titled "Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens" by Yang, Caradonna, Schmidt, and Chakraborty in Cell Reports (2023).

There are three folders for the code, each containing (1) Code for simulations of antigen capture by B cells at the FDC-B cell immune interface (2) Code for simulations of affinity maturation, upon immunization with cocktail or chimeric antigen (3) Code for the analysis of the data.

The data folder contains three datasets: (1) Result of B cell antigen capture simulations (2) Result of affinity maturation simulations (3) BnAb fractions extracted from the affinity maturation simulation.