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Sieradzan, Adam K.
Publications (2 of 2) Show all publications
Sieradzan, A. K. (2015). Introduction of Periodic Boundary Conditions into UNRES Force Field. Journal of Computational Chemistry, 36(12), 940-946
Open this publication in new window or tab >>Introduction of Periodic Boundary Conditions into UNRES Force Field
2015 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 12, p. 940-946Article in journal (Refereed) Published
Abstract [en]

In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the hetero tetramer 1 protein system.

multi-chain systems, periodicity, coarse-grain force field, electrostatic interaction cutoff, proteins
National Category
Physical Sciences Chemical Sciences
urn:nbn:se:uu:diva-252670 (URN)10.1002/jcc.23864 (DOI)000352579100009 ()25753584 (PubMedID)
Available from: 2015-05-26 Created: 2015-05-11 Last updated: 2017-12-04Bibliographically approved
Sieradzan, A. K., Niemi, A. & Peng, X. (2014). Peierls-Nabarro barrier and protein loop propagation. Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 90(6), 062717
Open this publication in new window or tab >>Peierls-Nabarro barrier and protein loop propagation
2014 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 90, no 6, p. 062717-Article in journal (Refereed) Published
Abstract [en]

When a self-localized quasiparticle excitation propagates along a discrete one-dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy no longer enables the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the C-alpha backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink that solves a variant of the discrete nonlinear Schrodinger equation. We study the propagation of such a kink in the case of the protein G related albumin-binding domain, using the united residue coarse-grained molecular-dynamics force field. We estimate the height of the energy barriers that the kink needs to cross over in order to propagate along the backbone lattice. We analyze how these barriers give rise to both stresses and reliefs, which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone toward the native location. We observe that the dissipative forces that are exerted on the kink by the various energy barriers have a pivotal role in determining how a protein folds toward its native state.

National Category
Other Physics Topics
urn:nbn:se:uu:diva-242863 (URN)10.1103/PhysRevE.90.062717 (DOI)000347207000013 ()
Available from: 2015-02-04 Created: 2015-02-02 Last updated: 2017-12-05Bibliographically approved

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