Modelling novel resonant X-ray spectroscopy for transition metal biological complexes and nano-particles
Lead Research Organisation:
King's College London
Department Name: Physics
Abstract
This is a theoretical proposal aiming at developing novel numerical approaches to describe quantum excitations and their out-of-equilbrium dynamics in materials and molecules. This project brings the complementary expertise from Dr Cedric Weber on quantum modeling approaches for molecular transition metal systems, and Dr Rafael T. M. de Rosales on functional nano-particles used in the context of medical imaging.
Here, we will model the dynamics of a core-hole state induced in hard core X-ray spectroscopy, used to probe chemical and magnetic properties of molecules and nano-scopic systems.
The student will develop a new modeling approach to describe typical X-ray spectroscopy methods, such as X-ray absorption spectroscopy (XAS) and extend the formalism to model resonant inelastic X- ray scattering (RIXS).
A canonical system, photo-system II (PSII), will be considered throughout the project. PSII has been investigated for decades, but the mechanism underpinning the water-splitting mechanism is still lacking. The modeling difficulties stem from the non-trivial quantum physics induced by the transition metal atoms (the four Mn atoms), which require state-of-the-art approaches.
The first set of theoretical techniques will be based on density functional theory (DFT) and time-dependent DFT (TD-DFT) [1], which accounts for the dynamic screening of the X-ray and the core-hole fields. In particular, a typical problem for TD-DFT is the presence of multiplets, and the student will explore extensions of DFT to obtain an accurate descriptions of multi determinantal effects in DFT [2].
The student will then extend the methodology to nano-scopic systems, and in particular focus on super pagramagnetic iron oxide nano-particles (SPIONs). SPIONs have a range of applications, in particular they are used as contrast agents in magnetic resonant imaging (MRI). In this project, the student will focus at understanding magnetic excitations in nano-particles, and how they could be resolved in the future via the RIXS technique.
The relaxation of the magnetic moment of nano-particles is a complex out-of-equilibrium process, and there is a subtle interplay between the dynamics and the conformation properties. In particular, the quantum confinement stemming from their spatial reduction is expected to provide new and complex out-of-equilibrium properties, as the external magnetic field is quenched. There are many major unanswered questions, such as the role of the magnetic frustration induced by the broken bonds in the outer-layers, and the role of the ligand bonding between the core of the nano-particle and the coating.
The purpose of the project is to guide the design of better contrast agents, via optimizing the magnetic relaxivities of the nano-particle. Indeed, a current limitation is that large nano-particles have optimal magnetic relaxivities, but tend to agglomerate due to surface effects, which hinders the relaxation of their magnetic moments and their application as contrast agents. We provide here a consistent theory based on quantum ab-initio simulations, including dynamical effects.
This project is also connected to the construction of a new X-ray beam line at the Diamond Light Source facility, that will be key to probe excitations in these new materials, as well as in a wide range of molecules and other materials of importance in chemistry and bio-chemistry.
Here, we will model the dynamics of a core-hole state induced in hard core X-ray spectroscopy, used to probe chemical and magnetic properties of molecules and nano-scopic systems.
The student will develop a new modeling approach to describe typical X-ray spectroscopy methods, such as X-ray absorption spectroscopy (XAS) and extend the formalism to model resonant inelastic X- ray scattering (RIXS).
A canonical system, photo-system II (PSII), will be considered throughout the project. PSII has been investigated for decades, but the mechanism underpinning the water-splitting mechanism is still lacking. The modeling difficulties stem from the non-trivial quantum physics induced by the transition metal atoms (the four Mn atoms), which require state-of-the-art approaches.
The first set of theoretical techniques will be based on density functional theory (DFT) and time-dependent DFT (TD-DFT) [1], which accounts for the dynamic screening of the X-ray and the core-hole fields. In particular, a typical problem for TD-DFT is the presence of multiplets, and the student will explore extensions of DFT to obtain an accurate descriptions of multi determinantal effects in DFT [2].
The student will then extend the methodology to nano-scopic systems, and in particular focus on super pagramagnetic iron oxide nano-particles (SPIONs). SPIONs have a range of applications, in particular they are used as contrast agents in magnetic resonant imaging (MRI). In this project, the student will focus at understanding magnetic excitations in nano-particles, and how they could be resolved in the future via the RIXS technique.
The relaxation of the magnetic moment of nano-particles is a complex out-of-equilibrium process, and there is a subtle interplay between the dynamics and the conformation properties. In particular, the quantum confinement stemming from their spatial reduction is expected to provide new and complex out-of-equilibrium properties, as the external magnetic field is quenched. There are many major unanswered questions, such as the role of the magnetic frustration induced by the broken bonds in the outer-layers, and the role of the ligand bonding between the core of the nano-particle and the coating.
The purpose of the project is to guide the design of better contrast agents, via optimizing the magnetic relaxivities of the nano-particle. Indeed, a current limitation is that large nano-particles have optimal magnetic relaxivities, but tend to agglomerate due to surface effects, which hinders the relaxation of their magnetic moments and their application as contrast agents. We provide here a consistent theory based on quantum ab-initio simulations, including dynamical effects.
This project is also connected to the construction of a new X-ray beam line at the Diamond Light Source facility, that will be key to probe excitations in these new materials, as well as in a wide range of molecules and other materials of importance in chemistry and bio-chemistry.
Organisations
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M009513/1 | 01/10/2015 | 31/03/2024 | |||
| 1754398 | Studentship | BB/M009513/1 | 01/10/2016 | 14/04/2021 | Mohamed Al-Badri |
| Description | Using computational simulations, we have been able to accurately model the behaviour of the interface between nanomaterials and biological systems to atomic precision. In particular, we look at the interface between graphene-based nanomaterials and proteins, as well as nanomaterials in aqueous environments. Understanding the interactions of the bio-nano interface to a high degree of accuracy allows the advancement of biotechnology applications in a way that is inaccessible to conventional methods. We use this approach to study the formation of a protein corona around upon the introduction of a nanomaterial to a biological medium. The protein corona is an obstacle to exploiting the exotic properties of nanomaterials in clinical and biotechnology settings, with potential applications in DNA sequencing, point of care testing and drug delivery vehicles. One of our investigations unpicks the driving forces that induce the formation of a protein corona due to the small changes in the nanomaterial structure, particular changes in protein structure at the interface then induce the aggragation of many proteins on the nanomaterial surface, inhibiting its intended purpose. Another project that arose from this award was the use of methods employed in studying changes in protein structure, but were instead applied to investigating how the SARS-CoV-2 main protease can be inhibited by a drug molecule. This work conveys a methodology through which drug discovery efforts could be accelerated through taking advantage of a structure based information that we were able to derive. Finally, we studied the role of quantum biology in an oxygen-transporting protein using computational quantum simulations. There had been a discrepency between experiment and prior theoretical/computational work on the quantum state of the Hemocyanin protein core -- however, our work used novel methods to describe how a quantum entangled open shell ground state is stabilised by electronic correlation effects. |
| Exploitation Route | The biomimetic potential of the functional site of the hemocyanin protein is extraordinary, and can be utilised by both the medical (pharma) and engineering fields (catalysts). Accurate modelling of graphene-oxide in solution on a scale of hundreds of thousands of atoms has important implications not limited to biotechnology but also engineering. This may include desalination and gaseous separation. The knowledge of how proteins behave at the surface of nanomaterials -- to atomic precision and with calculations for each and every amino acid -- can help design better biotechnology applications of nanomaterials, without the unwanted effects such as the formation of aggregated proteins (protein corona). The SARS-CoV-2 work enables the acceleration of vast computational efforts to identify drug inhibitors for the main protease, which can aid in the efforts against not only COVID-19, but due to the lesser selective pressure of mutations on the protease, future evolutions of the corona virus. |
| Sectors | Chemicals,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |