Sigbjørn Løland Bore

Doctoral Research Fellow - Theoretical chemistry
Image of Sigbjørn Løland Bore
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Room V 226
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Visiting address Sem Sælands vei 26 None 0371 OSLO
Postal address Postboks 1033 0315 OSLO

Description of my work:

The Hybrid particle-field (MD-SCF) method has proven to be a powerful tool in the study of soft matter systems.[1] In this method nonbonded interactions are treated in a mean field formalism. Computational efficiency is gained by avoiding pair interactions and is efficiently parallelizable. [2] I work on the extension of MD-SCF to study polypeptide chains. Our model is based on a two-bead coarse grained representation of amino acids, and explicit electrostatics following the multipolar reconstruction method previously established.[3] The new model presents an accurate calibration of bonded interactions for the backbone by a combined bending and torsional potential. The reference potential of mean force (PMF) is obtained from metadynamics simulations of an atomistic model of polyglycine in water. Stabilization of secondary structures by hydrogen bonds are reproduced by dipole-dipole interactions. The  implemented algorithm rigorously distributes forces acting on the peptide dipoles onto the beads, thus not enlarging the number of degrees of freedom of the system. Amino acid structural propensity is introduced by appropriate torsional potentials between beads. The model is implemented in OCCAM, a hybrid MD and field simulation package.[2] The new implemented models will promote efficient study of protein dynamics in very large systems.

 

References

 

[1] G. Milano and T. Kawakatsu, Phys. Biol., 2013, 10, 45007

[2] Zhao Y., De Nicola A., Kawakatsu T., Milano G., Journal of Computational Chemistry,2012

[3] M. Cascella, M. A. Neri, P. Carloni, and M. Dal Peraro Journal of Chemical Theory and Computation 2008 4 (8), 1378-1385

Additional academic interests:

  • Numerical simulation of  proteins and membranes
  • Statistical physics
  • Molecular dynamics
  • Monte carlo method 

Publications

  • Bore, Sigbjørn Løland; Schindler, Michael; Nguyen Thu Lam, Khanh-Dang; Bertin, Eric & Dauchot, Olivier (2016). Coupling spin to velocity: collective motion of Hamiltonian polar particles. Journal of Statistical Mechanics: Theory and Experiment.  ISSN 1742-5468. . doi: 10.1088/1742-5468/2016/03/033305 Show summary

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  • Bore, Sigbjørn Løland; Støvneng, Jon Andreas & Flåtten, Tore (2015). High-Resolution Large Time-Step Schemes for Hyperbolic Conservation Laws.

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Published Dec. 8, 2015 5:16 PM - Last modified May 18, 2016 2:47 PM

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