ORCID
0009-0003-3718-0930
Date of Award
2025
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Physics
First Advisor
Juan M. Vanegas
Second Advisor
Frederic Sansoz
Abstract
Modeling the elastic and mechanical properties soft materials such as lipidmembranes play an essential role in understanding numerous biological functions including membrane fission and fusion, organelle and cellular shaping, cardiovascular control and development, osmotic regulation, and touch and pain sensing. Obtaining these properties from molecular dynamics (MD) simulations allows for the estimation of the elastic coefficients from first principles. There have been many ways of approaching the problem of determining these properties using MD simulations, most common of which are the explicit deformation (ED) and the volume fluctuation (VF) methods. Although widely used in literature, these methods have numerous challenges when modeling soft materials such as finding an adequate deformation regime where the elastic properties are linear. One method that overcomes many of these challenges is the stress-stress fluctuation formula for the elasticity tensor. This formulation, which originates from the changes in free energy with respect to deformation, can provide the complete elasticity tensor of any simulated material from an equilibrium simulation at constant volume and temperature. In the literature the method has been shown to work well for solids, but there hasn't been much exploration into the realm of fluids due to the sensitivity and complexity of the computations. In this work we demonstrate the efficacy stress-stress fluctuation formula for fluids with careful analysis of the convergence of the elastic coefficients using various techniques. We then discuss the necessary measures required to avoid pitfalls which make modeling fluids difficult. Finally, we present our results demonstrating the precision, advantages and effectiveness of this procedure in modeling simple fluids and other soft materials such as Argon across its different states. We compare the elastic coefficients, the bulk modulus and the Poisson ratio computed with the stress-stress fluctuation formula against results obtained from volume fluctuation formulas and explicit deformation methods. We then focus on the properties of bulk materials and interfaces using coarse-grained MARTINI fluids that incorporate 2 and 3 body bonded potentials.
Language
en
Number of Pages
132 p.
Recommended Citation
Lewis, Andrew Lawrence, "Computation of Elastic Properties of Soft Materials from Molecular Dynamics Simulations" (2025). Graduate College Dissertations and Theses. 2062.
https://scholarworks.uvm.edu/graddis/2062
