Theoretical calculations of atomic scale structure and dynamics at solid surfaces

Guest: Prof. Hannes Jónsson, University of Iceland, Reykjavik.

Hosted by:  Dr. Jörg Meyer and Dr. Thanja Lamberts (Leiden University) and Prof. dr. Peter Bolhuis (University of Amsterdam).

A visit of two months.

Processes that take place on the surfaces of solids play an important role in many different contexts, for example catalysis of chemical reactions and growth of crystals. An understanding of such processes at the atomic scale can help understand processes in nature and help in the development of improved technology for various purposes. A prerequisite is knowledge of the arrangement of the atoms at the surface, which can be quite different from what one would expect from the atomic structure of the crystal. The dynamics of the atoms are on a short timescale characterized as vibrations about well defined average positions, while on a longer timescale the atoms can migrate on the surface, visit different types of surface sites and eventually react or form various types of structures on the surface. This determines the functionality of the surface and its properties.

A particularly interesting and challenging solid surface is that of regular ice, i.e. ice Ih. The ice crystal is proton disordered, which means that while the oxygen atoms in the H2O molecules are arranged on a regular lattice, the position of the hydrogen atoms is random but subject to the rule that only one hydrogen atom can be placed in between two adjacent oxygen atoms (the so-called Bjerrum rules). Each hydrogen atom is covalently bonded to one of the oxygen atoms and hydrogen bonded to the other. As a results of the disorder, no two sites on the ice surface are the same. Earlier simulation studies by the Jónsson group have shown that the distribution of binding energy of an additional molecule at the surface is extremely broad and there are special sites where it form three strained hydrogen bonds with surface molecules, thereby having higher binding energy than the cohesive energy of the solid. Such admolecules will be particularly stable and likely to stay put  rather than migrate over the surface. Furthermore, such additional H2O molecule will not sit in a location corresponding to a site in the ice lattice, only after six additional molecules on the surface form an island will their location be consistent with the crystal structure. This complexity and richness of the ice surface opens up many interesting possibilities and challenges. The project will in particular be devoted to gain an understanding of the results of experimental measurements carried out by others relating to the dynamics at ice surfaces, such as dispersionless modes in the surface phonon spectrum and laser induced desorption at slow photon energy. The research project will combine complementary expertise of the research groups involved in order to improve our understanding of this complex surface and the dynamics of atoms there. Given the abundance and importance of ice on our planet and in outer space, the insight gained can have implications for a wide range of phenomena in nature.

From nano to macro: Intrinsically disordered proteins in the cellular environment

Guest: Dr. Divya Nayar, Department of Materials Science and Engineering, Indian Institute of Technology Delhi.

Hosted by: Dr. Ioana-Mariuca Ilie (Computational Chemistry, University of Amsterdam).

A visit of 2 months.

Neurodegenerative diseases, such as Parkinson’s and Alzheimer’s, affect millions of people world-wide, and are predicted to become the second leading cause of death (after cardiovascular disease) by 2040. In Parkinson’s disease, α-synuclein (α-syn) undergoes conformational changes to form condensates, which are found in the diseased brain. α-syn is a 140-residue intrinsically disordered protein (IDP), characterized by a rugged conformational space in its soluble monomeric state and by ordered configurations when involved in different types of (insoluble) condensates. The cellular environment is tightly packed with high concentrations of macromolecules and co-solutes, which affects the thermodynamics and kinetics of the system. The molecular origins of crowding effects remain unknown.

Here, we aim to unravel the folding and condensation mechanisms of -synuclein in presence of macromolecular crowders. To achieve this goal, we will employ a multiscale computational approach, spanning from full atomistic to mesoscale resolution linked via machine learning techniques. Importantly, the experimental validation will be done in collaboration with the group of Prof. Sander Woutersen.

This project stems as part of Dr. Ilie’s research lines on intrinsically disordered proteins and development of novel strategies to control IDP condensation. During her visit, Dr. Nayar will focus on the atomistic perspective of the problem. The work will involve evaluating the binding free energy surface (FES) of the α-synuclein protein oligomers, as shaped by the presence of crowders, using all-atom models and advanced molecular dynamics simulations. Dr. Nayar’s experience in elucidation of thermodynamic driving forces underlying crowding effects and Dr. Ilie’s expertise in coarse-grained modeling of IDPs will jointly bridge the gap in solving the mechanisms of IDP accumulation in the intracellular milieu at different spatiotemporal resolutions.

The multiscale approach in this collaboration will provide insights into the higher-order aggregate formation of IDPs in presence of macromolecular crowders replicating the cellular environment, highlighting the intermolecular driving forces underlying this process. Additionally, it will aid in the development of novel techniques to control the structural rearrangement of a protein by enriching the solvent with macromolecules, potentially leading to novel therapeutic strategies.

Emerging contaminants removal from wastewater: understanding from the molecular scale to the application

Guest: Dr. Vincenzo Russo, University of Naples Federico II, Italy.

Hosted by: Dr. Ştefania Grecea and Dr. David Dubbeldam (University of Amsterdam).

A visit of 4 months.

Removal of emerging contaminants from wastewater posseses signficant challenges to recycle water sources. Emerging contaminants include among others antibiotics, illicit drugs, cosmetics, personal care products, pesticides, microplastics, nanoparticles, and nanomaterials. Removing such contaminants is not easy task because classical wastewater treatment systems are not designed to handle emerging contaminants. Liquid–solid adsorption using commercial activated carbons is broadly applicable to produces high quality water. Although the high adsorption capacity of active carbons is widely recognized, these adsorbent materials have some drawbacks, including their rapid saturation and regeneration.
In this project, an in-depth study of emerging contaminants (i.e., ketoprofen, ibuprofen) will be conducted  using different sorbents (e.g., porous materials). The motivation is to develop sustainable technologies for wastewater treatment when facing with ECs. The expected outcome of the research is to develop a realistic and sustainable application for water purification field, using novel porous sorbents. The synthesis will be tailored by molecular simulations that will also help to understand how the contaminants interact with the solid surfaces.

The project is a collaboration between the groups of Dr. Grecea (UvA) with expertise in materials design, the group of Dr. Dubbeldam (UvA) with expertise in molecular simulations and the group of Dr. Russo (UniNa) with expertise in water treatment technologies, aiming in strengthening the collaboration between these research groups and within HRSMC and the University of Naples Federico II.