Group for molecular dynamics simulations

Theme #1  Exploring the function and structure of aggregates formed by antimicrobial peptides
The rapid emergence of antibiotic-resistant bacteria is a serious and growing problem, which if it remains unsolved will result in increased mortality and expenditure by national health systems. It has been attributed, to a large extent, to the overuse and misuse of available antibiotics, but also to the lack of new treatments. Antimicrobial peptides (AMPs), which are the first line of defence against infection in all living organisms, may represent part of the solution.
Uncovering the details of the mechanism of action of some AMPs has revealed a staggering level of complexity and sophistication in their mode of actions, as well as in the responses of bacteria to this challenge. Here we investigate AMPs by using molecular dynamics simulations, spectroscopic (e.g. CD, fluorescence) and biophysical measurements (e.g. surface plasmon resonance), in the presence of model membranes, and relate the results to AMPs activity on real membranes in microbial or host cells (e.g. via biological assays to probe cellular integrity and vitality). By simulations and experiments of AMPs in various conditions and environments we i) explore the properties and mode of action of peptides that have been designed or identified in our laboratory as well as well-characterized ranid antimicrobial peptides including also those that are of bacterial origin; ii) investigate AMPs that due to their structure have a strong propensity to form aggregates, and may form liquid droplets as part of their mechanism of action.

Theme #2 Characterisation of the associations in multicomponent solutions
In molecular mixtures, associations are driven by the differences in mutual affinity between constitutive molecules. Well-known examples are aqueous solutions, where the high propensity of water molecules to form hydrogen bonding causes solute molecules with a lower propensity to form microheterogeneous (MH) structure. Some of the anomalous features presented in MH systems are explained by an atomistic description of the underlying structure, such as entropy of mixing and heat capacity. One of the recent examples of molecular heterogeneity are surfactant-free microemulsions (SFME) which show enhanced nanostructuring at an intermediate concentration range, near the two-phase boundary which precedes microemulsion formation. By using the molecular dynamics simulations, we describe the heterogeneous structure in binary and ternary solutions. In parallel by experimental techniques such as light scattering, we determine the concentrations at which the nanostructuring in different SFME emerge. Our final goal is to connect the physical-chemical properties of studied systems with underlying structuring and discuss the possible applications.