488 research outputs found
Combination of natural betanidin dye with synthetic organic sensitiser towards dye-sensitised solar cell application
A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Materials Science and Engineering of the Nelson Mandela African Institution of Science and TechnologyBetanidins belong to natural red-purple pigments betacyanins, which experimentally
demonstrated good light adsorption in a visible range and might be suitable for the dye sensitised solar cell (DSSCs). Instability is a well-known drawback of natural dyes, which
impedes their use for DSSCs. A thermodynamic approach helps to understand the betanidin
(Bd) instability which occurs due to spontaneous decarboxylation reaction with
decarboxylated betanidin (dBd) formation. The study considers the improvement of the
sensitiser’s functionality via combination of natural Bd/dBd dyes and synthetic 4-
(Diphenylamino)phenylcyanoacrylic acid (L0) dye. Novel complex D–π–A organic dyes,
L0–Bd and L0–dBd with structural isomers, have been designed via esterification reactions.
The DFT/B3LYP5/6‒31G(d,p) approach has been used to compute geometry, vibrational
spectra and thermodynamic characteristics of the individual isomers and their complexes with
L0. Implementation of TD–DFT method aids in obtaining optoelectronic properties. The
broader coverage of the solar spectrum with greater light-harvesting efficiency was achieved
for the complexes compared to individual dyes. The dyes attachment to the semiconductor
TiO2 was simulated in terms of different adsorption modes to hydrogenated (TiO2)6 cluster.
Binding energies and electronic spectra of the dye@TiO2 systems were computed, and
electron density distributions over frontier molecular orbitals analysed. Binding energy
magnitudes varied within 15‒21 eV for the dye@TiO2 systems
Electronic Structure Methods for Large Molecular Systems and Materials in Strong Magnetic Fields
The high-rank polynomial scaling of modern electronic structure methods can present significant limitations on the size of molecular systems that can be accurately studied. This issue is further exasperated when using non-perturbative approaches for studying systems within arbitrary strength magnetic fields due to the requirements for complex algebra and reduced permutational symmetry. One such attempt at overcoming this issue is the concept of fragmentation, which has shown promise in recent years for accurately determining the electronic structure of systems that can be sensibly fragmented into smaller subunits. The main aim in this work is to combine the concepts of one such method, the embedding fragment method (EFM), with recent advances in non-perturbative treatment of external fields, enabling the study of increasingly large or complex systems. The implementation of this approach is presented for systems in strong magnetic fields. The method is applied to determine energetic, structural and magnetic response properties of systems beyond the scope of more conventional methods. The EFM is shown to provide an accurate electronic structure approximation when studying systems within extremely strong magnetic fields, with errors generally 70000 Tesla. Its application to large water clusters is presented showing how external magnetic fields strengthen intermolecular interactions, as has previously been demonstrated through experiment, but that the origin of this strengthening is not as straightforward as the altering of the hydrogen bonding present at zero field, a rational often considered alongside experimental results. Also demonstrated is how this approach can be used to accurately model solvation effects when calculating magnetic properties of solute molecules. In this work the calculation of nuclear magnetic resonance chemical shifts is considered, using the EFM and comparing to both gas phase calculations and calculations including solvent effects using the polarisable continuum method. To aid in the interpretation of results, two additional tool sets have been development. The first is a suite of tools to analyse the complex current vector field induced by exposing a molecule to an external field. The second is a new molecular viewer software package, improving the ability to analyse the effects of external magnetic fields on molecular systems
MODELLING CELL POPULATION GROWTH
The growth of biological matter, e.g., tumor invasion, depends on various factors, mainly the tissue’s mechanical properties, implying elasticity, stiffness, or apparent viscosity. These properties are impacted by the characteristics of the tissue’s extracellular matrix and constituent cells, including, but not limited to, cell membrane stiffness, cell cytoskeleton mechanical properties, and the intensity and distribution of focal adhesions over the cell membrane. To compute and study the mechanical properties of tissues during growth and confluency, a theoretical and computational framework, called CellSim3D, was developed in our group based on a three-dimensional kinetic division model.
In this work, CellSim3D is updated with a new set of cell mechanical parameters and force fields such as the asymmetric division rule, shape diversity, apoptosis process, and boundary conditions, e.g., periodic and Lees-Edwards boundary conditions. The package is upgraded to operate on multiple GPUs to further accelerate computations. This enables the inclusion of more complexity in the system. For instance, the simulation of macroscopic scale bicellular tissue growth with precise control over the mechanical properties of cells is now more feasible than before.
The effects of cell-cell adhesion strength and intermembrane friction on growth kinetics and interface roughness dynamics of epithelial tissue were studied. It is reported that with fine alterations of the mechanical parameters such as the cell-cell adhesion strength, one could reliably reproduce different interface roughness scaling behaviors such as Kardar–Parisi–Zhang (KPZ)-like and Molecular Beam Epitaxy (MBE)-like scaling. In addition, it was observed that substrate heterogeneity and geometry have significant impacts on the morphology and interface roughness scaling of epithelial tissue. The results suggest that the interface roughness scaling of epithelial tissues cannot be classified by any well-known scaling universality class. Instead, it strongly depends on several other factors, such as the cell-cell adhesion strength. This explains the controversies observed in earlier experimental works over the interface roughness scaling of expanding epithelial tissue
2011 GREAT Day Program
SUNY Geneseo’s Fifth Annual GREAT Day.https://knightscholar.geneseo.edu/program-2007/1005/thumbnail.jp
Recommended from our members
ATOMISTIC SIMULATIONS OF INTRINSICALLY DISORDERED PROTEIN FOLDING AND DYNAMICS
Intrinsically disordered proteins (IDPs) are crucial in biology and human diseases, necessitating a comprehensive understanding of their structure, dynamics, and interactions. Atomistic simulations have emerged as a key tool for unraveling the molecular intricacies and establishing mechanistic insights into how these proteins facilitate diverse biological functions. However, achieving accurate simulations requires both an appropriate protein force field capable of describing the energy landscape of functionally relevant IDP conformations and sufficient conformational sampling to capture the free energy landscape of IDP dynamics. These factors are fundamental in comprehending potential IDP structures, dynamics, and interactions.
I first conducted explicit solvent simulations to assess the performance of two state-of-the-art protein force fields, namely CHARMM36m and a99SB-disp, in capturing the stability of small protein-protein interactions. To evaluate their accuracy, I selected a set of 46 amino acid backbone and side chain pairs with representative configurations and computed the free energy profiles of their interactions. The results demonstrated that CHARMM36m consistently predicted stronger protein-protein interactions compared to a99SB-disp. Notably, the most significant overestimation in CHARMM36m occurred in charged pairs involving Arg and Glu side chains, with an overestimation of up to 2.9 kcal/mol. Through free energy decomposition analysis, I determined that these overestimations were primarily driven by protein-water electrostatic interactions rather than van der Waals (vdW) interactions. Consequently, these findings suggest that careful rebalancing of electrostatic interactions should be considered in the further optimization of protein force fields.
In order to enhance the conformational sampling of IDPs, I developed an integrated approach that combines an improved implicit solvent model called Generalized Born with molecular volume and solvent accessible surface area (GBMV2/SA) with a multiscale enhanced sampling (MSES) technique. To make this approach more efficient, I implemented it as a standalone OpenMM plugin on Graphics Processing Units (GPUs). The results demonstrated that the GPU-GBMV2/SA model achieved numerical equivalence to the original CPU-GBMV2/SA models, while providing a remarkable ~60x speedup on a single NVIDIA TITAN X (Pascal) graphics card for molecular dynamic simulations of both folded and unstructured proteins. This significant acceleration greatly facilitated the application of the approach in biomolecular simulations.
In addition, I conducted an evaluation of the reliability of GBMV2/SA models in simulating both folded and unfolded proteins. The results revealed that the GBMV2/SA model accurately describes small proteins, but its applicability is limited when it comes to larger proteins such as KID and p53-TAD proteins. This limitation can be attributed to the absence of long-range solute-solvent dispersion interactions in the model. To address this issue, I introduced a comprehensive treatment of nonpolar solvation free energy called GBMV2/NP model. Unfortunately, the GBMV2/NP model exhibited a destabilizing effect on well-folded proteins, particularly larger ones, due to an inaccurate representation of the repulsive solvent accessible surface area (SASA) model caused by the utilization of unphysical van der Waals volume. This observation highlights the need for further improvements in accurately describing the nonpolar term in the model
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