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Papers by Dineli Ranathunga

Water condensation plays a major role in a wide range of industrial applications. Over the past f... more Water condensation plays a major role in a wide range of industrial applications. Over the past few years, many studies have shown interest in designing surfaces with enhanced water condensation and removal properties. To advance these designs a molecular scale understanding of the water behavior as a function of surface hydrophobicity is strongly needed. Using molecular dynamics computer simulations of well-characterized alkanethiol self- assembled monolayers with different head group chemistries, here we quantify the role of surface hydrophobicity on water condensation. We measured the water condensation rates on different surfaces and linked that behavior to well established surface characteristics to give a more complete picture of the role of surface hydrophobicity on the behavior of water. We observed a remarkable correlation between our results and the role of surface hydrophobicity on the water compressibility, interfacial thermal conductance and contact angle when we compare data across different studies. Examining the total interaction energy between water and the surface, density fluctuations near the surface, the formation, growth mechanism and stability of water clusters, and the wetting process on the surface we are able to provide insight into the water condensation process on different surfaces as a function of surface hydrophobicity.

Langmuir, Jun 5, 2020

Water condensation plays a major role in a wide range of industrial applications. Over the past f... more Water condensation plays a major role in a wide range of industrial applications. Over the past few years, many studies have shown interest in designing surfaces with enhanced water condensation and removal properties. It is well known that heterogeneous nucleation outperforms homogeneous nucleation in the condensation process. Because heterogeneous nucleation initiates on a surface at a small scale, it is highly desirable to characterize water-surface interactions at the molecular level. Molecular dynamics (MD) simulations can provide direct insight into heterogeneous nucleation and advance surface designs. Existing MD simulations of water condensation on surfaces were conducted by tuning the solid-water van der Waals interaction energy as a substitute for modeling surfaces with different wettabilities. However, this approach cannot reflect the real intermolecular interactions between the surface and water molecules. Here, we report MD simulations of water condensation on realistic surfaces of alkanethiol self-assembled monolayers with different head group chemistries. We show that decreasing surface hydrophobicity significantly increases the electrostatic forces between water molecules and the surface, thus increasing the water condensation rate. We observe a strong correlation between our rate of condensation results and the results from other surface characterization metrics, such as the interfacial thermal conductance, contact angle, and the molecular-scale wettability metric of Garde and co-workers. This work provides insight into the water condensation process at the molecular scale on surfaces with tunable wettability.

Physical Chemistry Chemical Physics, 2023

Histone tail electrostatics affect conformational transitions of BRCA1/BARD1-UbcH5c (E3-E2) enzym... more Histone tail electrostatics affect conformational transitions of BRCA1/BARD1-UbcH5c (E3-E2) enzymes on the nucleosome surface that regulate H2A C-tail dynamics and ubiquitination.

Water condensation plays a major role in a wide range of industrial applications. Over the past f... more Water condensation plays a major role in a wide range of industrial applications. Over the past few years, many studies have shown interest in designing surfaces with enhanced water condensation and removal properties. It is well known that heterogeneous nucleation outperforms homogeneous nucleation in the condensation process. Because heterogeneous nucleation initiates on a surface at a small scale, it is highly desirable to characterize water-surface interactions at the molecular level. Molecular dynamics (MD) simulations can provide direct insight into heterogeneous nucleation and advance surface designs. Existing MD simulations of water condensation on surfaces were conducted by tuning the solid-water van der Waals interaction energy as a substitute for modeling surfaces with different wettabilities. However, this approach cannot reflect the real intermolecular interactions between the surface and water molecules. Here, we report MD simulations of water condensation on realistic surfaces of alkanethiol self-assembled monolayers with different head group chemistries. We show that decreasing surface hydrophobicity significantly increases the electrostatic forces between water molecules and the surface, thus increasing the water condensation rate. We observe a strong correlation between our rate of condensation results and the results from other surface characterization metrics, such as the interfacial thermal conductance, contact angle, and the molecular-scale wettability metric of Garde and co-workers. This work provides insight into the water condensation process at the molecular scale on surfaces with tunable wettability.

BRCA1 (BReast Cancer-Associated protein 1), a human tumor suppressor, plays a key role in genome ... more BRCA1 (BReast Cancer-Associated protein 1), a human tumor suppressor, plays a key role in genome stability and DNA repair. Heterodimerization of BRCA1 with BARD1 is important for its stability, maximal Ub ligase (E3) activity and cooperative activation of UbcH5c (E2). Recent studies demonstrate the importance of ubiquitination of the nucleosomal H2A C-terminal tail by BRCA1/BARD1-UbcH5c (E3-E2) in which its mutations inhibit ubiquitination, predispose cells to chromosomal instability and greatly increase the likelihood of breast and ovarian cancer development. Due to the lack of molecular-level insight on the flexible and disordered H2A C-tail, its ubiquitination mechanism by BRCA1/BARD1-UbcH5c and its function and relationship to cancer susceptibility remain elusive. Here, we use molecular dynamics simulations to provide molecular-level insights into the dynamics of the less-studied H2A C-tail and BRCA1/BARD1-UbcH5c on the nucleosome surface. Our results precisely identify the key ...

Due to its excellent chemical and mechanical properties, titanium has become the material of choi... more Due to its excellent chemical and mechanical properties, titanium has become the material of choice for orthopedic and dental implants to promote rehabilitation via bone anchorage and osseointegration. Titanium osseointegration is partially related to its capability to form a TiO2 surface layer and its ability to interact with key endogenous proteins immediately upon implantation, establishing the first bone-biomaterial interface. Surgical trauma caused by implantation results in the release of High Mobility Group Box 1 (HMGB1) protein, which is a prototypic DAMP (Damage Associated Molecular Pattern) with multiple roles in inflammation and tissue healing. To develop different surface strategies that improve the clinical outcome of titanium-based implants by controlling their biological activity, a molecular-scale understanding of HMGB1-surface interactions is desired. Here, we use molecular dynamics (MD) computer simulations to provide direct insight into the HMGB1 interactions and ...

Supramolecular Chemistry, 2019

Aqueous anion recognition has been a long-standing challenge in molecular recognition. The use of... more Aqueous anion recognition has been a long-standing challenge in molecular recognition. The use of synthetic polymers is an emerging area of interest due to their conformational flexibility, creating microdomains that favor the desolvation and binding of anions in water. Here, we report that the fluorescence of off-the-shelf polyvinylpyrrolidone (PVP) can be used to detect the presence of not only nitrate, as previously reported, but also nitrite, iodide, and thiocyanate in aqueous media. The extent of quenching and anion affinity is dependent on the solution pH and the molecular weight of PVP, while showing close correlation with the Hofmeister series. Moreover, molecular dynamics simulations support our experimental findings, suggesting that anions associating closest to the surface of PVP quench its fluorescence to the greatest extent. Combined with the versatility of PVP, this fundamental study provides a starting point to confer anion binding properties with a fluorescence output in new materials.

Advanced Optical Materials, 2018

Plasmonic vesicle consists of multiple gold nanocrystals within a polymer coating or around a pho... more Plasmonic vesicle consists of multiple gold nanocrystals within a polymer coating or around a phospholipid core. As a multifunctional nanostructure, it has unique advantages of assembling small nanoparticles (<5 nm) for rapid renal clearance, strong plasmonic coupling for ultrasensitive biosensing and imaging, and near‐infrared light absorption for drug release. Thus, understanding the interaction of plasmonic vesicles with light is critically important for a wide range of applications. In this paper, a combined experimental and computational study is presented on the nanocrystal transformation in colloidal plasmonic vesicles induced by the ultrafast picosecond pulsed laser. Experimentally observed merging and transformation of small nanocrystals into larger nanoparticles when treated by laser pulses is first reported. The underlying mechanisms responsible for the experimental observations are investigated with a multiphysics computational approach featuring coupled electromagnet...

Journal of Molecular Liquids, 2020

Dicationic ionic liquids have been attracting attention due to their high thermal storage density... more Dicationic ionic liquids have been attracting attention due to their high thermal storage density, which is attributed to an increase in the number of cations. However, there is no information about the effect that the dianionic structure has on the thermophysical properties of dicationic ionic liquids. Thus in this study, imidazolium-based dicationic dicarboxylate ionic liquids (C n (MIM) 2 [C m (CO 2) 2 ], n = 4, 6, 8, 10 and m = 0, 1, 2, 3, 4, 5) were synthesized and their thermal properties were determined. The results showed that the dicarboxylate's spacer length has no effect on the melting point; however, a trend in which the heat of fusion of ionic liquids increases with the increase in the spacer chain length of the dication and dianions was observed. Moreover, dicationic dicarboxylate ionic liquids have a greater heat capacity than monocationic ionic liquids, but a smaller heat capacity than analogous dicationic ionic liquids with bromine. Our results also showed that the anion has a strong effect on the heat capacity of dicationic ionic liquids. In terms of thermal storage, [C 6 (MIM) 2 ][C 2 ] and [C 6 (MIM) 2 ] [C 5 ] were the most promising ionic liquids, because they have thermal storage higher than monocationic ILs and mineral oil and compared with analogues ILs with bromine, they are potentially less toxic. All of the ionic liquids were soluble in protic polar solvents and DMSO, and were insoluble in aprotic and nonpolar-polar solvents. The study and determination of these properties is extremely important for future applications.

Langmuir, Jun 5, 2020

Water condensation plays a major role in a wide range of industrial applications. Over the past f... more Water condensation plays a major role in a wide range of industrial applications. Over the past few years, many studies have shown interest in designing surfaces with enhanced water condensation and removal properties. It is well known that heterogeneous nucleation outperforms homogeneous nucleation in the condensation process. Because heterogeneous nucleation initiates on a surface at a small scale, it is highly desirable to characterize water-surface interactions at the molecular level. Molecular dynamics (MD) simulations can provide direct insight into heterogeneous nucleation and advance surface designs. Existing MD simulations of water condensation on surfaces were conducted by tuning the solid-water van der Waals interaction energy as a substitute for modeling surfaces with different wettabilities. However, this approach cannot reflect the real intermolecular interactions between the surface and water molecules. Here, we report MD simulations of water condensation on realistic surfaces of alkanethiol self-assembled monolayers with different head group chemistries. We show that decreasing surface hydrophobicity significantly increases the electrostatic forces between water molecules and the surface, thus increasing the water condensation rate. We observe a strong correlation between our rate of condensation results and the results from other surface characterization metrics, such as the interfacial thermal conductance, contact angle, and the molecular-scale wettability metric of Garde and co-workers. This work provides insight into the water condensation process at the molecular scale on surfaces with tunable wettability.

Physical Chemistry Chemical Physics, 2023

Water condensation plays a major role in a wide range of industrial applications. Over the past f... more Water condensation plays a major role in a wide range of industrial applications. Over the past few years, many studies have shown interest in designing surfaces with enhanced water condensation and removal properties. It is well known that heterogeneous nucleation outperforms homogeneous nucleation in the condensation process. Because heterogeneous nucleation initiates on a surface at a small scale, it is highly desirable to characterize water-surface interactions at the molecular level. Molecular dynamics (MD) simulations can provide direct insight into heterogeneous nucleation and advance surface designs. Existing MD simulations of water condensation on surfaces were conducted by tuning the solid-water van der Waals interaction energy as a substitute for modeling surfaces with different wettabilities. However, this approach cannot reflect the real intermolecular interactions between the surface and water molecules. Here, we report MD simulations of water condensation on realistic surfaces of alkanethiol self-assembled monolayers with different head group chemistries. We show that decreasing surface hydrophobicity significantly increases the electrostatic forces between water molecules and the surface, thus increasing the water condensation rate. We observe a strong correlation between our rate of condensation results and the results from other surface characterization metrics, such as the interfacial thermal conductance, contact angle, and the molecular-scale wettability metric of Garde and co-workers. This work provides insight into the water condensation process at the molecular scale on surfaces with tunable wettability.

Supramolecular Chemistry, 2019

Advanced Optical Materials, 2018

Journal of Molecular Liquids, 2020