Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Diversity against adversity: How adaptive immunity evolves potent
  antibodies   How does immune system evolve functional proteins - potent antibodies - in
such a short time? We address this question using a microscopic, protein-level,
sequence-based model of humoral immune response with explicitly defined
interactions between Immunoglobulins, host and pathogen proteins. Potent
Immunoglobulins are discovered in this model via clonal selection and affinity
maturation. Possible outcomes of an infection (extinction of cells, survival
with complete elimination of viruses, or persistent infection) crucially depend
on mutation rates of viral and Immunoglobulin proteins. The model predicts that
there is an optimal Somatic Hypermutation (SHM) rate close to experimentally
observed 10-3 per nucleotide per replication. Further, we developed an
analytical theory which explains the physical reason for an optimal SHM program
as a compromise between deleterious effects of random mutations on nascent
maturing Immunoglobulins (adversity) and the need to generate diverse pool of
mutated antibodies from which highly potent ones can be drawn (diversity). The
theory explains such effects as dependence of B cell fate on affinity for an
incoming antigen, ceiling in affinity of mature antibodies, Germinal Center
sizes and maturation times. The theory reveals the molecular factors which
determine the efficiency of affinity maturation, providing insight into
variability of immune response to cytopathic (direct response by germline
antibodies) and poorly cytopathic viruses (crucial role of SHM in response).
These results demonstrate the feasibility and promise of microscopic
sequence-based models of immune system, where population dynamics of evolving
Immunoglobulins is explicitly tied to their molecular properties.

37
The categories of this paper are: supr-con
11
The categories of this paper are: hep-lat
24
The categories of this paper are: dg-ga
3
The categories of this paper are: physics
2
The categories of this paper are: math
18
The categories of this paper are: econ
9
The categories of this paper are: nlin
8
The categories of this paper are: hep-ex
26
The categories of this paper are: bayes-an
22
The categories of this paper are: chao-dyn
25
The categories of this paper are: patt-sol
33
The categories of this paper are: plasm-ph
34
The categories of this paper are: chem-ph
31
The categories of this paper are: ao-sci
32
The categories of this paper are: atom-ph
13
The categories of this paper are: quant-ph