| 1. |
- Antonov, A. N., et al.
(author)
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The electron-ion scattering experiment ELISe at the International Facility for Antiproton and Ion Research (FAIR)-A conceptual design study
- 2011
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In: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. - : Elsevier BV. - 0168-9002 .- 0167-5087. ; 637:1, s. 60-76
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Journal article (peer-reviewed)abstract
- The electron-ion scattering experiment ELISe is part of the installations envisaged at the new experimental storage ring at the International Facility for Antiproton and Ion Research (FAIR) in Darmstadt, Germany. It offers an unique opportunity to use electrons as probe in investigations of the structure of exotic nuclei. The conceptual design and the scientific challenges of ELISe are presented. (C) 2011 Elsevier B.V. All rights reserved.
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| 2. |
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| 3. |
- Ramilowski, JA, et al.
(author)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Journal article (peer-reviewed)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 4. |
- Dyakov, Sergey, et al.
(author)
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Optical properties of silicon nanocrystals covered by periodic array of gold nanowires
- 2016
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In: Physical Review B. - : American Physical Society. - 2469-9950. ; 93:20
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Journal article (peer-reviewed)abstract
- Extinction and photoluminescence spectra are experimentally and theoretically studied for a periodic array of gold nanowires deposited on top of a dielectric substrate containing silicon nanocrystals. Quasiguided modes are observed in the substrate resulting in modification of optical properties of silicon nanocrystals. Our calculations of extinction and photoluminescence spectra are in good agreement with experimental results. The periodicity provides a powerful tool for achieving a high photoluminescence outcoupling efficiency of silicon nanocrystals.
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| 5. |
- Silanteva, I. A., et al.
(author)
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Equilibrium properties of 3-arm star-shaped polyions : an entropic sampling Monte Carlo study
- 2017
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In: Nanosystems: Physics, Chemistry, Mathematics. - : ITMO University. - 2220-8054. ; 8:1, s. 108-120
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Journal article (peer-reviewed)abstract
- The entropic sampling Monte Carlo method within Wang-Landau algorithm is applied to investigate properties of a lattice model of strongly charged flexible 3-arm star-shaped polyelectrolyte. The density of states is calculated, from which the canonical properties of the system in a wide temperature range are obtained by simple integration. The effects of the arm length and the short-range monomer-monomer potential on the thermal and structural properties of star polyions are studied. We calculate such characteristics as mean square radius of gyration and its components, the radius vector of the center of mass, components of the tensor of inertia and parameters characterizing the shape of the polyion. In this work, we focus on how these characteristics are influenced by the change of the reduced temperature which, within the considered model, is a parameter combining the effect of real temperature, linear charge density and solvent dielectric permittivity. The coil-globule transition is observed in most of the considered cases, and for the polyions with the longest length of arms ( 24), the transition from a liquid globule to a solid-like state is observed. Comparison of polyelectrolyte models with neutral ones is given.
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| 6. |
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| 7. |
- Vorontsov-Velyaminov, P. N., et al.
(author)
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Calculation of Canonical Properties and Excited States by Path Integral Numerical Methods
- 2011
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In: Contributions to Plasma Physics. - : Wiley. - 0863-1042 .- 1521-3986. ; 51:4, s. 382-385
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Journal article (peer-reviewed)abstract
- Path integral Monte Carlo method in the expanded ensemble is used for calculation of the ratio of partition functions for different classes of permutations treating the problem of several interacting identical particles (fermions) in an external field. Wang-Landau algorithm is used for adjustment of balancing factors. For systems consisting of greater than two number of particles we propose an advanced variant of our approach which implies calculation of the ratio of positive and negative contributions to the partition function. Densities and energies of the sequence of excited states starting from the ground state for a system of non interacting quantum particles are calculated in turn, one by one, by means of considering systems with artificially excluded lowest energy levels and further obtaining of the ground state of each next system constructed in this way. The idea of evaluation of densities of excited states for a quantum system with interparticle interaction by evaluating density difference between systems of different number of noninteracting Fermi-copies of the system of interest is realized in terms of cyclic expansion formalism for a simple 2D system of two spinless fermions interacting via Coulomb repulsion.
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| 8. |
- Nerstedt, Annika, 1960, et al.
(author)
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Lipid droplet-associated kinase STK25 regulates peroxisomal activity and metabolic stress response in steatotic liver
- 2020
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In: Journal of Lipid Research. - 0022-2275. ; 61:2, s. 178-191
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Journal article (peer-reviewed)abstract
- Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are emerging as leading causes of liver disease worldwide and have been recognized as one of the major unmet medical needs of the 21st century. Our recent translational studies in mouse models, human cell lines, and well-characterized patient cohorts have identified serine/threonine kinase (STK)25 as a protein that coats intrahepatocellular lipid droplets (LDs) and critically regulates liver lipid homeostasis and progression of NAFLD/NASH. Here, we studied the mechanism-of-action of STK25 in steatotic liver by relative quantification of the hepatic LD-associated phosphoproteome from high-fat diet-fed Stk25 knockout mice compared with their wild-type littermates. We observed a total of 131 proteins and 60 phosphoproteins that were differentially represented in STK25-deficient livers. Most notably, a number of proteins involved in peroxisomal function, ubiquitination-mediated proteolysis, and antioxidant defense were coordinately regulated in Stk25(-/-) versus wild-type livers. We confirmed attenuated peroxisomal biogenesis and protection against oxidative and ER stress in STK25-deficient human liver cells, demonstrating the hepatocyte-autonomous manner of STK25's action. In summary, our results suggest that regulation of peroxisomal function and metabolic stress response may be important molecular mechanisms by which STK25 controls the development and progression of NAFLD/NASH.
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| 9. |
- Polyakov, Eugeny A., et al.
(author)
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Centroid molecular dynamics : Comparison with exact results for model systems
- 2010
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:19, s. 194103-
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Journal article (peer-reviewed)abstract
- The relation between the accuracy of centroid molecular dynamics correlation functions, and the geometry of the centroid potential is investigated. It is shown that, depending on the temperature, there exist several regimes, and in each of them certain features of the exact Kubo correlation functions are reproduced. The change of regimes is related to the emergence of barriers in the centroid potential. In order to clarify how the above described picture of regimes is modified in real systems when dissipation is important, a methodology is developed to test the accuracy of centroid correlation functions for the model of a particle coupled to a harmonic heat bath. A modification of the centroid molecular dynamics method to include the influence of the heat bath is introduced. Preliminary results of comparison of centroid molecular dynamics with the numerically exact results of filtered propagator functional method are presented.
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| 10. |
- Voznesenskiy, M. A., et al.
(author)
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Path-integral-expanded-ensemble Monte Carlo method in treatment of the sign problem for fermions
- 2009
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In: PHYS REV E. - 1539-3755. ; 80:6
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Journal article (peer-reviewed)abstract
- Expanded-ensemble Monte Carlo method with Wang-Landau algorithm was used for calculations of the ratio of partition functions for classes of permutations in the problem of several interacting quantum particles (fermions) in an external field. Simulations for systems consisting of 2 up to 7 interacting particles in harmonic or Coulombic field were performed. The presented approach allows one to carry out calculations for low enough temperatures that makes it possible to extract data for the ground-state energy and low-temperature thermodynamics.
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