Exploring the Mechanical Properties of Soft Materials: Beyond lipid membrane composition

In recent years, flat or curved lipid membranes, vesicles and lipid micelles have received attention due to the importance of these systems as nanostructured lipid carriers (NLC) and solid lipid nanoparticles (SLN) widely used in the area of drug delivery (drug delivery) for diagnosis and treatment of diseases. The knowledge of their biological functions and medical applications has led to a growing number of computational studies that aim to describe the conformational dynamics of vesicles and their elastic properties. Furthermore, the spatial structure of lipid membranes is a highly relevant factor in biological processes, being responsible for the interaction between membranes and proteins present in the cell environment. Not by chance, several mathematical models have emerged over the years, in line with the growing computational technical development, with the purpose of describing the structural dynamics of lipid membranes, and their energetic variations linked to the elastic deformations of their structure, resulting from their lipid composition and spatial arrangement. Several works have approached the general format of the models used in the last decades to study these characteristics. All these models have a common origin, the pioneering work of Helfrich (1973) on the elastic properties of lipid membranes. However, despite the great scientific effort employed in the development of these mathematical models, and the vertiginous improvement of computational simulations of biomolecules, until the present moment, there are still no computational tools capable of extracting more complete structural information from computational simulations of membranes, vesicles and micelles. This work proposes the implementation and validation of an algorithm for the calculation of elastic properties from molecular dynamics simulations of soft materials, with emphasis on bacterial membranes. The proposed algorithm was implemented as part of the SuAVE software (Surface Assessment Via grid Evaluation) which is developed in our research group (www.biomatsite.net/suave-software). SuAVE allows calculating geometric properties at chemical interfaces considering the morphology of the lipid aggregate and crystalline materials. The code was developed to handle any chemical interface (organic, inorganic or biological) exhibiting flat or curved surfaces, and allows the calculation, in an efficient and simple way, of a series of properties relevant to soft matter systems: area and volume per molecule, thickness of membranes and vesicles, radius of gyration and shape of vesicles and micelles, density profiles, curvature order parameters, and Gaussian curvatures.