Abstract
This dissertation aims at advancing the capability of hybrid particle-field simulations of representing various physical phenomena relevant to biological systems. While hybrid particle-field simulations are computationally efficient and well adapted for studying mesoscale systems with molecular resolution, this approach has so far predominantly been applied to simple polymers. The computational investigation of systems of higher complexity, such as DNA and proteins, requires development of new models and an extension of the hybrid particle-field methodology. To this end, six research papers are presented. The main research output of these papers consists in both new methods for representing electrostatics and constant-pressure conditions, and new models for proteins and charged lipids within the hybrid particle-field formalism. The work contained in this thesis thus provides key steps towards large-scale realistic representations of biological systems
List of papers
| Paper I: Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains. Sigbjørn Løland Bore, Giuseppe Milano and Michele Cascella. Journal of Chemical Theory and Computation 14, 1120–1130 (2018) DOI: 10.1021/acs.jctc.7b01160. The article is not available in DUO due to publisher restrictions. The published version is available at: https://doi.org/10.1021/acs.jctc.7b01160 |
| Paper II: Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in Aqueous Environment. Hima Bindu Kolli, Antonio De Nicola, Sigbjørn Løland Bore, Ken Schäfer, Gregor Diezemann, Jürgen Gauss, Toshihiro Kawakatsu, Zhongyuan Lu, You-Liang Zhu, Giuseppe Milano and Michele Cascella. Journal of Chemical Theory and Computation 14, 4928–4937 (2018) DOI: 10.1021/acs.jctc.8b00466. The paper is included in the thesis. The published article is available at: https://doi.org/10.1021/acs.jctc.8b00466 |
| Paper III: Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics. Sigbjørn Løland Bore, Hima Bindu Kolli, Toshihiro Kawakatsu, Giuseppe Milano and Michele Cascella. Journal of Chemical Theory and Computation 14, 4928–4937 (2018). DOI: 10.1021/acs.jctc.8b01201. The paper is included in the thesis. The published article is available at: https://doi.org/10.1021/acs.jctc.8b01201 |
| Paper IV: Aggregation of Lipid A Variants: a Hybrid Particle-Field Model. Antonio De Nicola, Thereza A. Soares, Denys E. S. Santos, Sigbjørn Løland Bore, G. J. Agur Sevink, Michele Cascella and Giuseppe Milano. Accepted for publication in BBA – General Subjects (2020). (The paper is not available in DUO awaiting publishing.) |
| Paper V: Beyond the Molecular Packing Model: Understanding Morphological Transitions of Charged Surfactant Micelles. Ken Schäfer, Hima Bindu Kolli, Mikkel Killingmoe Christensen, Sigbjørn Løland Bore, Gregor Diezemann, Jürgen Gauss, Giuseppe Milano, Reidar Lund and Michele Cascella. (In preparation) (The paper is not available in DUO awaiting publishing.) |
| Paper VI: Hybrid Particle-Field Molecular Dynamics Under Constant Pressure. Sigbjørn Løland Bore, Hima Bindu Kolli, Antonio De Nicola, Maksym Byshkin, Toshihiro Kawakatsu, Giuseppe Milano and Michele Cascella. (In preparation) (The paper is not available in DUO awaiting publishing.) |