3.13 Computational methods related to molecular structure and reaction chemistry of biomaterials

S. Farokhirad, R. P. Bradley, A. Sarkar, A. Shih, S. Telesco, Y. Liu, R. Venkatramani, D. M. Eckmann, P. S. Ayyaswamy, R. Radhakrishnan

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations


In this article, we discuss the implementation of several computational techniques that are commonly employed to simulate interactions between biomaterials and cellular systems. These methods include molecular dynamics, biopolymer, and homology modeling, which focus on the atomic structure of biomaterials, electronic structure methods, and free-energy simulations. Challenges involved in applying these techniques and connections to cellular experiments are also addressed. These computational methods are important tools in delineating the molecular mechanisms involved in the interactions between biomaterials and tissue, which govern biocompatibility. They have also been applied in the rational design of biomaterials, as molecular-based models predict likely recognition sequences and the corresponding conformations at the interface between material surface and extracellular matrix and cell membrane. Focusing on these molecular mechanisms will lead to new insights into the bioactivity of existing biomaterials and to the development of improved biomaterials for use in bone tissue repair therapies and targeted drug delivery. The chapter concludes with a discussion of recent applications of computational methods to the rational design of biomaterials, including the creation of surfaces with tailored functionality, computational modeling of the attachment function of fibronectin, and model-based design of tunable nanocarriers for drug delivery.

Original languageEnglish (US)
Title of host publicationComprehensive Biomaterials II
Number of pages23
ISBN (Electronic)9780081006924
ISBN (Print)9780081006917
StatePublished - Jan 1 2017
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Engineering
  • General Materials Science


  • Arginine-glycine-aspartic acid (RGD)
  • Density functional theory (DFT)
  • Dextran hydrogel
  • Extracellular matrix (ECM)
  • Fibronectin (FN)
  • Functionalized nanocarriers
  • GROMOS (computer program)
  • Hyaluronic acid
  • Intracellular adhesion molecule 1 (ICAM-1) receptor
  • Physicochemical properties
  • Polysaccharide-based nanocarriers
  • Self-assembled monolayer (SAMs)
  • Targeted drug delivery
  • Thermodynamic properties
  • Titanium alloys


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