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Publications (10 of 69) Show all publications
Sinelnikova, A., Niemi, A., Nilsson, J. & Ulybyshev, M. (2018). Multiple scales and phases in discrete chains with application to folded proteins. Physical review. E, 97(5), Article ID 052107.
Open this publication in new window or tab >>Multiple scales and phases in discrete chains with application to folded proteins
2018 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 5, article id 052107Article in journal (Refereed) Published
Abstract [en]

Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein. Here we address this impending problem. We develop a methodology with the potential to systematically identify different length scales, in the general case of a linear polymer chain. For this we introduce and analyze the properties of an order parameter that can both reveal the presence of different length scales and can also probe the phase structure. We first develop our concepts in the case of chiral homopolymers. We introduce a variant of Kadanoff's block-spin transformation to coarse grain piecewise linear chains, such as the C alpha backbone of a protein. We derive analytically, and then verify numerically, a number of properties that the order parameter can display, in the case of a chiral polymer chain. In particular, we propose that in the case of a chiral heteropolymer the order parameter can reveal traits of several different phases, contingent on the length scale at which it is scrutinized. We confirm that this is the case with crystallographic protein structures in the Protein Data Bank. Thus our results suggest relations between the scales, the phases, and the complexity of folding pathways.

Place, publisher, year, edition, pages
American Physical Society, 2018
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-357014 (URN)10.1103/PhysRevE.97.052107 (DOI)000432978200001 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2018-08-13 Created: 2018-08-13 Last updated: 2018-08-13Bibliographically approved
Molochkov, A., Begun, A. & Niemi, A. (2017). Gauge symmetries and structure of proteins. In: Foka, Y Brambilla, N Kovalenko, V (Ed.), XIITH QUARK CONFINEMENT AND THE HADRON SPECTRUM: . Paper presented at 12th Conference on Quark Confinement and the Hadron Spectrum, AUG 29-SEP 03, 2016, Thessaloniki, GREECE. E D P SCIENCES, Article ID UNSP 04004.
Open this publication in new window or tab >>Gauge symmetries and structure of proteins
2017 (English)In: XIITH QUARK CONFINEMENT AND THE HADRON SPECTRUM / [ed] Foka, Y Brambilla, N Kovalenko, V, E D P SCIENCES , 2017, article id UNSP 04004Conference paper, Published paper (Refereed)
Abstract [en]

We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is considered, what allows to derive Abelian Higgs model of protein backbone, correct folding of which is defined by gauge symmetry breaking due hydrophobic forces. Within this model structure of protein backbone is defined by superposition of one-dimensional topological solitons (kinks), what allows to reproduce the three-dimensional structure of the protein backbone with precision up to 1A and to predict its dynamics.

Place, publisher, year, edition, pages
E D P SCIENCES, 2017
Series
EPJ Web of Conferences, ISSN 2100-014X ; 137
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-341866 (URN)10.1051/epjconf/201713704004 (DOI)000404126100052 ()
Conference
12th Conference on Quark Confinement and the Hadron Spectrum, AUG 29-SEP 03, 2016, Thessaloniki, GREECE
Available from: 2018-02-16 Created: 2018-02-16 Last updated: 2018-02-16
Liu, J., Dai, J., He, J., Niemi, A. J. & Ilieva, N. (2017). Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example. Physical review. E, 95(3), Article ID 032406.
Open this publication in new window or tab >>Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example
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2017 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 95, no 3, article id 032406Article in journal (Refereed) Published
Abstract [en]

We propose to combine a mean-field approach with all-atom molecular dynamics ( MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques. We argue that a room-temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the C alpha backbone of Myc in a crystallographic heteromer as an initial ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy to describe the C alpha profile with ultrahigh precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground-state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyze the thermal stability of this Glauber attractor using room-temperature molecular dynamics. We identify and scrutinize a particularly stable subset in which the two helical segments of the original multisoliton align in parallel next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal alpha helix, some of which resemble a translating Davydov's Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2017
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-320251 (URN)10.1103/PhysRevE.95.032406 (DOI)000396040800010 ()
Available from: 2017-04-19 Created: 2017-04-19 Last updated: 2017-04-19Bibliographically approved
Rasmusson, M., Fagerlund, F., Rasmusson, K., Tsang, Y. & Niemi, A. (2017). Refractive-Light-Transmission Technique Applied to Density-Driven Convective Mixing in Porous Media With Implications for Geological CO2 Storage. Water resources research, 53(11), 8760-8780
Open this publication in new window or tab >>Refractive-Light-Transmission Technique Applied to Density-Driven Convective Mixing in Porous Media With Implications for Geological CO2 Storage
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2017 (English)In: Water resources research, ISSN 0043-1397, E-ISSN 1944-7973, Vol. 53, no 11, p. 8760-8780Article in journal (Refereed) Published
Abstract [en]

Density-driven convection has been identified to accelerate the rate of CO2 solubility trapping during geological CO2 storage in deep saline aquifers. In this paper, we present an experimental method using the refractive properties of fluids (their impact on light transmission), and an analogous system design, which enables the study of transport mechanisms in saturated porous media. The method is used to investigate solutally induced density-driven convective mixing under conditions relevant to geological CO2 storage. The analogous system design allows us by choice of initial solute concentration and bead size to duplicate a wide range of conditions (Ra-values), making it possible to study the convective process in general, and as a laboratory analogue for systems found in the field. We show that the method accurately determines the solute concentration in the system with high spatial and temporal resolution. The onset time of convection (t(c)), mass flux (F), and flow dynamics are quantified and compared with experimental and numerical findings in the literature. Our data yield a scaling law for tc which gives new insight into its dependence on Ra, indicating t(c) to be more sensitive to large Ra than previously thought. Furthermore, our data show and explain why F is described equally well by a Ra-dependent or a Ra-independent scaling law. These findings improve the understanding of the physical process of convective mixing in saturated porous media in general and help to assess the CO2 solubility trapping rate under certain field conditions.

Place, publisher, year, edition, pages
American Geophysical Union (AGU), 2017
Keywords
carbon dioxide, CCS, density-driven convection, experiment, refraction, solubility trapping
National Category
Environmental Sciences Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:uu:diva-339703 (URN)10.1002/2017WR020730 (DOI)000418736700007 ()
Available from: 2018-01-26 Created: 2018-01-26 Last updated: 2018-03-03Bibliographically approved
Ioannidou, T. & Niemi, A. (2017). Relation between discrete Frenet frames and the bi- Hamiltonian structure of the discrete nonlinear Schrödinger equation. Physical Review D: covering particles, fields, gravitation, and cosmology, 95(8), Article ID 085003.
Open this publication in new window or tab >>Relation between discrete Frenet frames and the bi- Hamiltonian structure of the discrete nonlinear Schrödinger equation
2017 (English)In: Physical Review D: covering particles, fields, gravitation, and cosmology, ISSN 2470-0010, E-ISSN 2470-0029, Vol. 95, no 8, article id 085003Article in journal (Refereed) Published
Abstract [en]

The discrete Frenet equation entails a local framing of a discrete, piecewise linear polygonal chain in terms of its bond and torsion angles. In particular, the tangent vector of a segment is akin to the classical O(3) spin variable. Thus there is a relation to the lattice Heisenberg model that can be used to model physical properties of the chain. On the other hand, the Heisenberg model is closely related to the discrete nonlinear Schrodinger equation. Here we apply these interrelations to develop a perspective on discrete chains dynamics: We employ the properties of a discrete chain in terms of a spinorial representation of the discrete Frenet equation, to introduce a bi-Hamiltonian structure for the discrete nonlinear Schrodinger equation, which we then use to produce integrable chain dynamics.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2017
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-333415 (URN)10.1103/PhysRevD.95.085003 (DOI)000406742300009 ()
Funder
EU, FP7, Seventh Framework Programme, IRSES-606096
Available from: 2017-11-14 Created: 2017-11-14 Last updated: 2017-11-29Bibliographically approved
Nasedkin, A., Davidsson, J., Niemi, A. J. & Peng, X. (2017). Solution x-ray scattering and structure formation in protein dynamics. Physical review. E, 96(6), Article ID 062405.
Open this publication in new window or tab >>Solution x-ray scattering and structure formation in protein dynamics
2017 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 6, article id 062405Article in journal (Refereed) Published
Abstract [en]

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

National Category
Subatomic Physics
Identifiers
urn:nbn:se:uu:diva-339801 (URN)10.1103/PhysRevE.96.062405 (DOI)000417759900002 ()29347365 (PubMedID)
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2018-02-23 Created: 2018-02-23 Last updated: 2018-02-23Bibliographically approved
Ilieva, N., Liu, J., Marinova, R., Petkov, P., Litov, L., He, J. & Niemi, A. J. (2016). Are There Folding Pathways in the Functional Stages of Intrinsically Disordered Proteins?. In: Application Of Mathematics In Technical And Natural Sciences (AMITANS'16): . Paper presented at 8th International Conference on Promoting the Application of Mathematics in Technical and Natural Sciences (AMiTaNS), JUN 22-27, 2016, Albena, BULGARIA. , Article ID 110008.
Open this publication in new window or tab >>Are There Folding Pathways in the Functional Stages of Intrinsically Disordered Proteins?
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2016 (English)In: Application Of Mathematics In Technical And Natural Sciences (AMITANS'16), 2016, article id 110008Conference paper, Published paper (Refereed)
Abstract [en]

We proceed from the description of protein folding by means of molecular dynamics (MD) simulations with all-atom force fields, with folding pathways interpreted in terms of soliton structures, to identify possible systematic dynamical patterns of self-organisation that govern protein folding process. We perform in silico investigations of the conformational transformations of three different proteins MYC protein (an alpha-helical protein), amylin and indolicidin (IDPs with different length and binding dynamics). We discuss the emergence of soliton-mediated secondary motifs, in the case of IDPs in the context of their functional activity. We hypothesize that soliton-like quasi-ordered conformations appear as an important intermediate stage in this process.

Series
AIP Conference Proceedings, ISSN 0094-243X ; 1773
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-316642 (URN)10.1063/14965012 (DOI)000392692400058 ()9780735414310 (ISBN)
Conference
8th International Conference on Promoting the Application of Mathematics in Technical and Natural Sciences (AMiTaNS), JUN 22-27, 2016, Albena, BULGARIA
Available from: 2017-03-06 Created: 2017-03-06 Last updated: 2017-03-06Bibliographically approved
Dai, J., Niemi, A., He, J., Sieradzan, A. & Ilieva, N. (2016). Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example. Physical review E, 93(3), Article ID 032409.
Open this publication in new window or tab >>Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example
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2016 (English)In: Physical review E, ISSN 2470-0045, Vol. 93, no 3, article id 032409Article in journal (Refereed) Published
Abstract [en]

We inquire how structure emerges during the process of protein folding. For this we scrutinize collective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop, and employ various topological techniques, in combination with analytic tools that we deduce from the concept of integrable models and structure of discrete nonlinear Schrödinger equation. The example we consider is an α-helical subunit of the HIV envelope glycoprotein gp41. The helical structure is stable when the subunit is part of the biological oligomer. But in isolation, the helix becomes unstable, and the monomer starts deforming. We follow the process computationally. We interpret the evolving structure both in terms of a backbone based Heisenberg spin chain and in terms of a side chain based XY spin chain. We find that in both cases the formation of protein supersecondary structure is akin the formation of a topological Bloch domain wall along a spin chain. During the process we identify three individual Bloch walls and we show that each of them can be modelled with a precision of tenths to several angstroms in terms of a soliton solution to a discrete nonlinear Schrödinger equation.

Place, publisher, year, edition, pages
American Physical Society, 2016
National Category
Subatomic Physics
Research subject
Theoretical Physics
Identifiers
urn:nbn:se:uu:diva-287901 (URN)10.1103/PhysRevE.93.032409 (DOI)000372425200004 ()
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2016-04-26 Created: 2016-04-26 Last updated: 2016-04-27Bibliographically approved
Gordeli, I., Melnikov, D., Niemi, A. & Sedrakyan, A. (2016). Chern-Simons Improved Hamiltonians for Strings in Three Space Dimensions. PHYSICAL REVIEW D, 94(2), Article ID 021701.
Open this publication in new window or tab >>Chern-Simons Improved Hamiltonians for Strings in Three Space Dimensions
2016 (English)In: PHYSICAL REVIEW D, ISSN 2470-0010, Vol. 94, no 2, article id 021701Article in journal (Other academic) Published
Abstract [en]

The Frenet equation governs the extrinsic geometry of a string in three-dimensional ambient space in terms of the curvature and torsion, which are both scalar functions under string reparameterisations. The description engages a local SO(2) gauge symmetry, which emerges from the invariance of the extrinsic string geometry under local frame rotations around the tangent vector. Here we inquire how to construct the most general SO(2) gauge invariant Hamiltonian of strings, in terms of the curvature and torsion. The construction instructs us to introduce a long-range (self-) interaction between strings, which is mediated by a three dimensional bulk gauge field with a Chern-Simons self-interaction. The results support the proposal that fractional statistics should be prevalent in the case of three dimensional string-like configurations.

National Category
Subatomic Physics
Research subject
Theoretical Physics
Identifiers
urn:nbn:se:uu:diva-287914 (URN)10.1103/PhysRevD.94.021701 (DOI)000379723900001 ()
Available from: 2016-04-26 Created: 2016-04-26 Last updated: 2016-08-09Bibliographically approved
Chen, S. & Niemi, A. J. (2016). On Ramachandran angles, closed strings and knots in protein structure. Journal of Physics D: Applied Physics, 49(31), Article ID 315401.
Open this publication in new window or tab >>On Ramachandran angles, closed strings and knots in protein structure
2016 (English)In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 49, no 31, article id 315401Article in journal (Refereed) Published
Abstract [en]

The Ramachandran angles (phi, psi) of a protein backbone form the vertices of a piecewise geodesic curve on the surface of a torus. When the ends of the curve are connected to each other similarly, by a geodesic, the result is a closed string that in general wraps around the torus a number of times both in the meridional and the longitudinal directions. The two wrapping numbers are global characteristics of the protein structure. A statistical analysis of the wrapping numbers in terms of crystallographic x-ray structures in the protein data bank (PDB) reveals that proteins have no net chirality in the phi direction but in the psi direction, proteins prefer to display chirality. A comparison between the wrapping numbers and the concept of folding index discloses a non-linearity in their relationship. Thus these three integer valued invariants can be used in tandem, to scrutinize and classify the global loop structure of individual PDB proteins, in terms of the overall fold topology.

Keywords
Ramachandran angles, knots in protein, topological classification
National Category
Physical Sciences Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-305939 (URN)10.1088/0022-3727/49/31/315401 (DOI)000384003000016 ()
Funder
Carl Tryggers foundation Swedish Research Council
Available from: 2016-11-07 Created: 2016-10-24 Last updated: 2017-11-29Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3408-5834

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