Browsing by Author "Antila, Hanne"

Filter results by typing the first few letters
Now showing 1 - 5 of 5
  • Electrostatics of a polarizable force based on the Thole point dipole model
    (2011) Antila, Hanne
     Perustieteiden korkeakoulu | Master's thesis
    Molecular dynamics (MD) simulations are widely used in the modeling of biomolecules because these models are able to provide information on those properties of biological systems which are hard to study by experimental means. The increase in computational power has provided the means to simulate more complex systems, but has also introduced both the possibility and the requirement to improve the force fields the simulations are based on. At present, electrostatic interactions in the common MD force fields are represented as interactions between fixed partial charges. The downside is that these charges cannot accurately reflect the dependence of a charge distribution on the state of the system nor can they respond to fluctuations in the electric field due to molecular motion. For this, one should explicitly include the effect polarizability into the force field. In this thesis, ways of parametrizing the electrostatics of a polarizable force field have been studied. It was examined how three different point charge fitting methods, MK, CHELPG, and RESP, and two multipole algorithms, DMA and GMM, perform when intra molecular polarizability contributions are self-consistently removed from the fitting done in the parametrization process. To this end, the different methods are combined with the induced point dipole model by Thole. MK and RESP were determined to be the most promising candidates for polarizable force field parametrization at the moment. They provide a good compromise between accuracy and computational efficiency not to mention the ease of force field implementation. To our surprise, DMA multipoles up to octupoles were required to reach the same level of accuracy. The applicability of GMM is hindered by the convergence issues that arose when GMM was combined with the Thole model. Also, the functional forms of the electric interactions resulting from the GMM multipoles makes it less appealing for force field purposes.
  • The influence of ionic strength and mixing ratio on the colloidal stability of PDAC/PSS polyelectrolyte complexes
    (2015) Zhang, Yanpu; Yildirim, E.; Antila, Hanne; Valenzuela, Luis D.; Sammalkorpi, Maria; Lutkenhaus, Jodie L.
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Polyelectrolyte complexes (PECs) form by mixing polycation and polyanion solutions together, and have been explored for a variety of applications. One challenge for PEC processing and application is that under certain conditions the as-formed PECs aggregate and precipitate out of suspension over the course of minutes to days. This aggregation is governed by several factors such as electrostatic repulsion, van der Waals attractions, and hydrophobic interactions. In this work, we explore the boundary between colloidally stable and unstable complexes as it is influenced by polycation/polyanion mixing ratio and ionic strength. The polymers examined are poly(diallyldimethylammonium chloride) (PDAC) and poly(sodium 4-styrenesulfonate) (PSS). Physical properties such as turbidity, hydrodynamic size, and zeta potential are investigated upon complex formation. We also perform detailed molecular dynamics simulations to examine the structure and effective charge distribution of the PECs at varying mixing ratios and salt concentrations to support the experimental findings. The results suggest that the colloidally stable/unstable boundary possibly marks the screening effects from added salt, resulting in weakly charged complexes that aggregate. At higher salt concentrations, the complexes initially form and then gradually dissolve into solution.
  • Polymeerin ja nanopartikkeleiden seokseen perustuva orgaaninen painesensori
    (2008) Antila, Hanne
     Informaatio- ja luonnontieteiden tiedekunta | Bachelor's thesis
  • Repulsion between oppositely charged rod-shaped macromolecules: role of overcharging and ionic confinement
    (2017-09) Antila, Hanne; van Tassel, Paul R.; Sammalkorpi, Maria
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
  • Simulations of Polyelectrolyte Interactions in Salt
    (2016) Antila, Hanne
     School of Chemical Technology | Doctoral dissertation (article-based)
    Charged polymers, polyelectrolytes (PEs), are versatile synthetic materials with applications ranging from water treatment to fuel cells. PEs are abundant also in nature as many biological macromolecules, most notably DNA, are charged polymers. A characteristic property of PEs is that oppositely charged PEs attract and readily form complexes with each other, or other charged molecules and surfaces. This ability to complex is the basis of many applications of PEs. It can be utilized to build up thin, multilayered films consisting of up to hundreds of layers of oppositely charged PEs. Another application of PE complexation is in gene therapy, where DNA-polycation complexes can be used as means of delivering the genetic material into a cell. PE complexation is sensitive to the presence of additional salt. Salt can e.g. speed up the equilibration of PE complexes and dissolve polyelectrolyte multilayers. This thesis aims to elucidate the mechanisms through which salt affects PE interactions in complexation. This is done by using both all-atom molecular dynamics (MD) simulations of PE complexes and Monte Carlo simulations of a simplified model where the opposite charge PEs are modelled as rigid, charged rods. The MD simulations of this thesis demonstrate how salt dissolves a DNA-polycation complex by breaking the PE-PE contacts, and explain why multivalent ions are more effective in dissolving the complex compared to monovalent ions. The connection between the polyanion-polycation charge ratio in the complex and the complex behavior in salt is also investigated. Decreasing the polycation charge density seems to destabilize complexes in salt solutions.The MC simulations are used to extensively map out the interactions of oppositely charged PEs as function of salt concentration, salt valency, and PE charge ratio. Two mechanism leading to repulsion between oppositely charged rods are discovered: asymmetric overcharging and repulsion due to osmotic contributions. The latter is accompanied by a formation of a double minimum in the free energy landscape of the two approaching, oppositely charged rods. The location and depth of the secondary minimum are affected by salt concentration, salt type and the ratio of rod charges. The results thus suggest ways of tuning the interactions in PE systems by controlling the PE charges and the salt content of the solution. The findings of this thesis can be used to better understand and design materials based on PE complexation, such as the polycationic DNA carriers. In addition, this thesis presents a methodological advance related to the modelling of electrostatics in simulations. This novel modification of the Ewald summation enables more efficient simulations of charged, cylindrical macromolecules and facilitates the comparison of the simulation results to approximate theories utilizing similar geometries.