Styliani Constas

My research group studies the stability of chemical and biochemical systems by investigating their dynamics using computer modelling. Sizes of systems that are examined range from small clusters to systems containing hundreds of thousand atoms. We focus on the development and application of Molecular Dynamics and Monte Carlo techniques to study rare event dynamics. These critical events, that are usually identified with the transition state of the process, are a bottle-neck in the simulations of a variety of systems of chemical and biological interest. Using these methods we examine conformational changes of macromolecules such as proteins and nucleic acids in solution, stability of non-covalently bound complexes of proteins, nucleic acids and other macromolecules, chemical reactions in solution, disintegration mechanisms of charged nanodrops. The systems are modelled at the atomic scale using different levels of description that range from quantum chemical to empirical in order to capture features defining the properties of the systems. Molecular interactions of macromolecules and their complexes in charged nanodrops Charged droplets are ubiquitous in atmospheric aerosols and experimental techniques such as electrospray ionization mass spectrometry. We study the solvent-macromolecule, ion-macromolecule interactions in the droplet environment and the dynamics of disintegration of the charged nanodrops. Examples of macromolecules that we examine are peptides, nucleic acids, poly(ethylene glycol) (PEG). PEG is also used in our studies as a model macromolecule to understand the behaviour of intrinsically disordered proteins. Our computational studies provide the molecular understanding in experiments that use electrospray ionization (ESI). Examples of such experiments are found in the usage of ESI in transfer of analytes from bulk solution into the gas phase for mass spectrometry (MS) analysis, deposition of materials and creation of nanoparticles with controlled morphologies. The outcome of these applications is vast. They lead to the understanding of the interactions among biological molecules, discovery of pharmaceuticals, increased security in transportation by detection of explosives in the airports, efficient chemical analysis, industry production. “Recoil-growth” Monte Carlo methods for high density polymer systems Polymers are ubiquitous in industrial and technological applications. Due to the extremely long relaxation times present in high density polymer systems such systems are impossible to simulate by conventional Molecular Dynamics and Monte Carlo methods. The first problem encountered in the computation of equilibrium and dynamic properties is the generation of equilibrated configurations. We develop biased Monte Carlo schemes that allow for rapid equilibration of these complex systems and we apply these schemes in the study of problems of biological interest.