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Study on Antibody-Virus Interaction using Molecular Dynamics: Two Dimensional Simulation on Immunoglobulin Reaction against Human Papillomavirus

Human Papillomavirus (HPV) has been known as one of the cause of virus-induced cancer such as cervical cancer and carcinoma. Among other types of cancer, this type has higher chance in being prevented earlier. The main idea is to eradicate the virus as soon as it enters the body by marking it with antibodies; signaling the immune system to dispose of it. However, the antibodies must be trained to recognize the virus. They can be trained by inserting an object similar to the virus allowing them to learn to recognize and surround the inserted object. In response to this, molecular dynamics simulation was chosen to study the antibody-virus interaction. In this work, two-dimensional case that involves HPV and immunoglobulin (Ig) was studied and observed. Two types of objects will be defined; one stands for HPV while another stands for antibodies. The interaction between the two objects will be governed by two forces; Coulomb force and repulsive contact force. Through the definition of some rules and condition, the antibodies' motion was observed. The influence of antibody concentration, and the antibody's type and their appearance sequence were observed both quantitatively and visually. Keywords: antibody-virus interaction, molecular dynamics, HPV, immunoglobulin.