108 citations · 218 across the 10 of their papers we have counts for
10 papers
Solitons and Collapse in the lambda-repressor protein
Andrey Krokhotin, Martin Lundgren, Antti J. Niemi
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding -repressor (CI) and CRO prote…
Protein loops, solitons and side-chain visualization with applications to the left-handed helix region
Martin Lundgren, Antti J. Niemi, Fan Sha
Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we devel…
On correlation between protein secondary structure, backbone bond angles, and side-chain orientations
Martin Lundgren, Antti J. Niemi
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C carbon of a protein backbone, and…
Soliton driven relaxation dynamics and universality in protein collapse
Andrey Krokhotin, Martin Lundgren, Antti J. Niemi
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes…
Covalent bond symmetry breaking and protein secondary structure
Martin Lundgren, Antti J. Niemi
Both symmetry and organized breaking of symmetry have a pivotal rôle in our understanding of structure and pattern formation in physical systems, including the origin of mass in th…
On universal aspects of the left-handed helix region
Martin Lundgren, Antti J. Niemi, Fan Sha
We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the left-handed helix region of the Ramachandran map for non-glycyl residues cor…