Computational methodologies for exploring nano-engineered materials

Abstract

​Biomimetic nano-engineered materials have emerged as new potential additives for biomedical therapies. However, one of the most critical challenges that remain is the ability to produce responsive nanostructures that respond to external stimuli, enhance existing properties, and introduce new functionalities. In this regard, the use of computational methodologies to design, simulate, and visualize the interaction between biological substrates and nanostructures provides a powerful tool for better understanding structure/function. This chapter focuses on the use of molecular modeling and molecular dynamics (MD) methods to assist the design of bio-nanomaterials and characterize the structural aspects of the interaction between nanostructures and biological molecules. Computational simulations allow the analysis of the behavior of atoms and molecules for a period of time employing integrated mathematical and physical equations. Here, we describe how these theoretical methods are used to design and model nanomaterials in a rational way, as well as to evaluate its functionalization and association with drug-like compounds. Methodologies used in the field of computational nanotechnology include de novo modeling, parametrization, molecular dynamics simulations under functional conditions, binding free energy calculations, as well as future perspectives oriented to use reactive force field techniques.