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Publications (10 of 73) Show all publications
Liu, J., Dai, J., He, J., Peng, X. & Niemi, A. (2019). Can the geometry of all-atom protein trajectories be reconstructed from the knowledge of Cα time evolution?: A study of peptide plane O and side chain Cβ atoms. Journal of Chemical Physics, 150(22), Article ID 225103.
Open this publication in new window or tab >>Can the geometry of all-atom protein trajectories be reconstructed from the knowledge of Cα time evolution?: A study of peptide plane O and side chain Cβ atoms
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2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 22, article id 225103Article in journal (Refereed) Published
Abstract [en]

We inquire to what extent can the geometry of protein peptide plane and side chain atoms be reconstructed from the knowledge of C time evolution. Due to the lack of experimental data, we analyze all atom molecular dynamics trajectories from the Anton supercomputer, and for clarity, we limit our attention to the peptide plane O atoms and side chain C atoms. We reconstruct their positions using four different approaches. Three of these are the publicly available reconstruction programs Pulchra, Remo, and Scwrl4. The fourth, Statistical Method, builds entirely on the statistical analysis of Protein Data Bank structures. All four methods place the O and C atoms accurately along the Anton trajectories; the Statistical Method gives results that are closest to the Anton data. The results suggest that when a protein moves under physiological conditions, its all atom structures can be reconstructed with high accuracy from the knowledge of the C atom positions. This can help to better understand and improve all atom force fields, and advance reconstruction and refinement methods for reduced protein structures. The results provide impetus for the development of effective coarse grained force fields in terms of reduced coordinates.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2019
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-390205 (URN)10.1063/1.5082627 (DOI)000471692400006 ()31202245 (PubMedID)
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2019-08-09 Created: 2019-08-09 Last updated: 2019-08-09Bibliographically approved
Hou, Y., Dai, J., He, J., Niemi, A., Peng, X. & Ilieva, N. (2019). Intrinsic protein geometry with application to non-proline cis peptide planes. Journal of Mathematical Chemistry, 57(1), 263-279
Open this publication in new window or tab >>Intrinsic protein geometry with application to non-proline cis peptide planes
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2019 (English)In: Journal of Mathematical Chemistry, ISSN 0259-9791, E-ISSN 1572-8897, Vol. 57, no 1, p. 263-279Article in journal (Refereed) Published
Abstract [en]

The shape of a protein can be modeled by the C atoms of its backbone, the mathematical description employing the notion of extrinsic geometry of a discrete piecewise linear chain. We advance differential geometry of a natively framed discrete chain to argue the existence of two additional, independent and intrinsic geometric structures, provided by the peptide planes and side chains, respectively. We develop our general methodology within a case study: analysis of the intrinsic geometry of atoms that are located around a non-proline cis peptide plane. We show that the native peptide plane framing allows for revealing of atomic positions anomalies. That way, we identify a number of entries that display such anomalies around their non-proline cis peptide planes within the ultrahigh-resolution structures in PDB. We propose that our approach can be extended into a visual analysis and refinement tool that is applicable even when resolution is limited or data is incomplete, for example when there are atoms missing in an experimental construct.

Keywords
Protein structure, Backbone geometry, Coordinate frames, Peptide planes
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-377371 (URN)10.1007/s10910-018-0949-7 (DOI)000456663400011 ()
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2019-02-25 Created: 2019-02-25 Last updated: 2019-02-25Bibliographically approved
Dai, J., Niemi, A. J., Peng, X. & Wilczek, F. (2019). Truncated dynamics, ring molecules, and mechanical time crystals. Physical Review A: covering atomic, molecular, and optical physics and quantum information, 99(2), Article ID 023425.
Open this publication in new window or tab >>Truncated dynamics, ring molecules, and mechanical time crystals
2019 (English)In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 99, no 2, article id 023425Article in journal (Refereed) Published
Abstract [en]

We identify circumstances where the effective descriptions of microscopic physical systems leads to a self-consistent reduced dynamics for a truncated subset of the original variables. The effective Hamiltonian involves unusual Poisson brackets that bring in noncommutative geometry. In idealized models of ring molecules, we find time crystal behavior is widespread.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2019
National Category
Other Physics Topics
Identifiers
urn:nbn:se:uu:diva-379590 (URN)10.1103/PhysRevA.99.023425 (DOI)000459900400014 ()
Funder
Swedish Research Council, 335-2014-7424EU, European Research Council, 742104
Available from: 2019-03-18 Created: 2019-03-18 Last updated: 2019-03-18Bibliographically approved
Begun, A., Gerasimenyuk, N., Korneev, A., Molochkov, A. & Niemi, A. (2018). Gauge theory: protein topology and dynamics. Paper presented at International Conference on Biomembranes (BIOMEMBRANES), OCT 01-05, 2018, RUSSIA. Journal of Bioenergetics and Biomembranes, 50(6), 500-501
Open this publication in new window or tab >>Gauge theory: protein topology and dynamics
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2018 (English)In: Journal of Bioenergetics and Biomembranes, ISSN 0145-479X, E-ISSN 1573-6881, Vol. 50, no 6, p. 500-501Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
SPRINGER/PLENUM PUBLISHERS, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-378240 (URN)000458294600028 ()
Conference
International Conference on Biomembranes (BIOMEMBRANES), OCT 01-05, 2018, RUSSIA
Funder
Swedish Research Council
Available from: 2019-03-15 Created: 2019-03-15 Last updated: 2019-03-15Bibliographically approved
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
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3408-5834

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