Quantum, molecular and continuum modeling in nonlinear mechanics of viruses

Abstract

Introdution. Viruses are a large group of pathogens that have been identified to infect animals, plants, bacteria and even other viruses. The 2019 novel coronavirus SARS-CoV-2 remains a constant threat to the human population. Viruses are biological objects with nanometric dimensions (typically from a few tens to several hundreds of nanometers). They are considered as the biomolecular substances composed of genetic materials (RNA or DNA), protecting capsid proteins and sometimes also of envelopes. Objective. The goal of the present review is to help predict the response and even destructuration of viruses taking into account the influence of different environmental factors, such as, mechanical loads, thermal changes, electromagnetic field, chemical changes and receptor binding on the host membrane. These environmental factors have significant impact on the virus. Materials and methods. The study of viruses and virus-like structures has been analyzed using models and methods of nonlinear mechanics. In this regard, quantum, molecular and continuum descriptions in virus mechanics have been considered. Application of single molecule manipulation techniques, such as, atomic force microcopy, optical tweezers and magnetic tweezers has been discussed for a determination of the mechanical properties of viruses. Particular attention has been given to continuum damage–healing mechanics of viruses, proteins and virus-like structures. Also, constitutive modeling of viruses at large strains is presented. Nonlinear elasticity, plastic deformation, creep behavior, environmentally induced swelling (or shrinkage) and piezoelectric response of viruses were taken into account. Integrating a constitutive framework into ABAQUS, ANSYS and in-house developed software has been discussed. Conclusion. Link between virus structure, environment, infectivity and virus mechanics may be useful to predict the response and destructuration of viruses taking into account the influence of different environmental factors. Computational analysis using such link may be helpful to give a clear understanding of how neutralizing antibodies and T cells interact with the 2019 novel coronavirus SARS-CoV-2.

The Role of Cavities in Biological Structures

“…A virus capsid is an assembly of proteins that shields viral genomes, possessing remarkable mechanical properties that have captured scientific interest. This fascination has led to extensive studies of various capsids to unveil their elastic behavior [32][33][34]. Computer simulations of nanoindentation experiments [35][36][37][38] have revealed that virus capsids, especially those protecting single-stranded RNA, exhibit significant elasticity.…”