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204 results on '"Vilhena, J."'

1. In-beam γ94-ray spectroscopy of γ94Ag

Author

Pereira-López, X., Bentley, M. A., Wadsworth, R., Ruotsalainen, P., Lenzi, S. M., Forsberg, U., Auranen, K., Blazhev, A., Cederwall, B., Grahn, T., Greenlees, P., Illana, A., Jenkins, D. G., Julin, R., Jutila, H., Juutinen, S., Liu, X., Llewelyn, R., Luoma, M., Moschner, K., Müller-Gatermann, C., Singh, B. S. Nara, Nowacki, F., Ojala, J., Pakarinen, J., Papadakis, P., Rahkila, P., Romero, J., Sandzelius, M., Sarén, J., Tann, H., Uthayakumaar, S., Uusitalo, J., Vega-Romero, J. G., Vilhena, J. M., Yajzey, R., Zhang, W., and Zimba, G.

Published
2023
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2. Conformation And Mechanical Response of Spray Deposited Single Strand DNA on Gold

Author

Pawlak, Remy, Vilhena, J. G., Hinaut, Antoine, Meier, Tobias, Glatzel, Thilo, Baratoff, Alexis, Moreno-Herrero, Fernando, Gnecco, Enrico, Perez, Ruben, and Meyer, Ernst

Subjects
Condensed Matter - Soft Condensed Matter, Physics - Biological Physics, Quantitative Biology - Biomolecules
Abstract

Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far, single base detection might be possible in more drastic cleanliness conditions such as ultra high vacuum. Here, we report on high resolution imaging and pulling attempts at low temperature (5K) of a single strand DNA (ssDNA) molecules composed of 20 cytosine bases adsorbed on Au(111) by scanning probe microscopy and numerical calculations. Using electrospray deposition technique, the ssDNA were successfully transferred from solution onto a surface kept in ultra high vacuum. Real space characterizations reveal that the ssDNA have an amorphous structure on gold in agreement with numerical calculations. Subsequent substrate annealing promotes the desorption of solvent molecules, DNA as individual molecules as well as the formation of DNA self assemblies. Furthermore, pulling experiments by force spectroscopy have been conducted to measure the mechanical response of the ssDNA while detaching. A periodic pattern of 0.2 to 0.3nm is observed in the force curve which arises from the stick slip of single nucleotide bases over the gold. Although an intra molecular response is obtained in the force curve, a clear distinction of each nucleotide detachment is not possible due the complex structure of ssDNA adsorbed on gold.

Published
2017

3. Quantum Mechanical Derived (VdW‐DFT) Transferable Lennard–Jones and Morse Potentials to Model Cysteine and Alkanethiol Adsorption on Au(111).

Author

Ventura‐Macias, Emiliano, Martinez, P. M., Pérez, Rubén, and Vilhena, J. G.

Subjects
POTENTIAL energy surfaces, DENSITY functional theory, MOLECULAR dynamics, SURFACE energy, INTERFACE dynamics
Abstract

The cysteine and alkanethiol adsorption on Au(111) surfaces is investigated using density functional theory (DFT) and classic molecular dynamics (MD). Understanding the S–Au interaction across different scales poses major challenges. DFT provides atomic‐level precision but it hardly provides insight on nanosecond scale dynamics of this interface. Alternatively, MD, although it enables modeling larger systems for longer periods, its accuracy heavily relies on the parameterization of the force fields (FF). To address this, an MD potential is fitted using DFT calculations, bridging the gap in accuracy and efficiency. At the DFT level, it is found that PBE with DFT‐D3 reproduces complex approaches at a fraction of the computational cost. Separating PBE and DFT‐D3 contributions reveals consistent PBE energy across molecules (chemisorption), while dispersion varies (physisorption). Thus, the interaction energy of cysteine and two short‐chain alkanethiols is calculated to parameterize both Morse and Lennard–Jones (LJ) potentials. The parameterization improves the potential energy in the preferred adsorption sites: the threefold hcp and fcc with respect to the previous proposals in the literature. Furthermore, the transferability is here demonstrated. At last, these results show that LJ potentials outperform more complex Morse potentials. The procedure is general, and the codes and supporting inputs are publicly available, allowing swift generation of potential energy surfaces (PES) at the DFT level, and fitted LJ or Morse potentials to any molecular interface. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Tailoring the thermal expansion of graphene via controlled defect creation

Author

López-Polín, Guillermo, Ortega, Maria, Vilhena, J. G., Alda, Irene, Gomez-Herrero, J., Serena, Pedro A., Gomez-Navarro, C., and Pérez, Rubén

Subjects
Condensed Matter - Materials Science
Abstract

Contrary to most materials, graphene exhibits a negative thermal expansion coefficient (TEC), i.e it contracts when heated. This contraction is due to the thermal excitation of low energy out-of-plane vibration modes. These flexural modes have been reported to govern the electronic transport and the mechanical response of suspended graphene. In this work, we systematically investigate the influence of defects in the TEC of suspended graphene membranes. Controlled introduction of low densities of mono-vacancies reduces the graphene TEC, up to one order of magnitude for a defect density of $5\times10^{12}$~cm$^{-2}$ . Our molecular dynamics simulations reproduce the observed trend and show that TEC reduction is due to the suppression of out-of-plane fluctuations caused by the strain fields created by mono-vacancies in their surrounding areas. These results highlight the key role of defects in the properties of "real-life" graphene, and pave the way for future proposals of electronic and mechanical defect engineering., Comment: 19

Published
2016
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5. Broken seniority symmetry in the semimagic proton mid-shell nucleus Rh95

Author

Das, B., primary, Cederwall, B., additional, Qi, C., additional, Górska, M., additional, Regan, P. H., additional, Aktas, Ö., additional, Albers, H. M., additional, Banerjee, A., additional, Chishti, M. M. R., additional, Gerl, J., additional, Hubbard, N., additional, Jazrawi, S., additional, Jolie, J., additional, Mistry, A. K., additional, Nowacki, F., additional, Polettini, M., additional, Yaneva, A., additional, Ahmed, U., additional, Alhomaidhi, S., additional, Algora, A., additional, Appleton, C., additional, Arici, T., additional, Bagchi, S., additional, Benzoni, G., additional, Benito, J., additional, Blazhev, A., additional, Boutachkov, P., additional, Bracco, A., additional, Bruce, A. M., additional, Brunet, M., additional, Canavan, R., additional, Davinson, T., additional, Dickel, T., additional, Esmaylzadeh, A., additional, Fraile, L. M., additional, Haettner, E., additional, Hall, O., additional, Häfner, G., additional, Heggen, H., additional, Hornung, Ch., additional, Hucka, J. P., additional, John, P. R., additional, Kahl, D., additional, Karayonchev, V., additional, Kern, R., additional, Knöbel, R., additional, Korgul, A., additional, Kosir, G., additional, Kojouharov, I., additional, Kostyleva, D., additional, Kuzminchuk, N., additional, Kurz, N., additional, Liotta, R., additional, Lozeva, R., additional, Mikolajczuk, M., additional, Mukha, I., additional, Napiralla, P., additional, Page, R., additional, Petrache, C. M., additional, Pietralla, N., additional, Pietri, S., additional, Plaß, W. R., additional, Podolyák, Zs., additional, Régis, J.-M., additional, Rudigier, M., additional, Rösch, H., additional, Ruotsalainen, P., additional, Sahin, E., additional, Sánchez-Tembleque, V., additional, Schaffner, H., additional, Scheidenberger, C., additional, Schirru, F., additional, Sexton, L., additional, Singh, B. S. Nara, additional, Sharma, A., additional, Shearman, R., additional, Si, M., additional, Tanaka, Y. K., additional, Vasiljević, J., additional, Vesić, J., additional, Vilhena, J., additional, Weick, H., additional, Wollersheim, H. J., additional, Werner, V., additional, Wiederhold, J., additional, Witt, W., additional, Woods, P. J., additional, Zimba, G., additional, and Zhao, J., additional

Published
2024
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6. A charge plunger device to measure the lifetimes of excited nuclear states where transitions are dominated by internal conversion

Author

Barber, L., Heery, J., Cullen, D.M., Singh, B.S. Nara, Herzberg, R.-D., Müller-Gatermann, C., Beeton, G., Bowry, M., Dewald, A., Grahn, T., Greenlees, P.T., Illana, A., Julin, R., Juutinen, S., Keatings, J.M., Luoma, M., O’Donnell, D., Ojala, J., Pakarinen, J., Rahkila, P., Ruotsalainen, P., Sandzelius, M., Sarén, J., Sinclair, J., Smith, J.F., Sorri, J., Spagnoletti, P., Tann, H., Uusitalo, J., Vilhena, J., and Zimba, G.

Published
2020
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8. Construction of the B88 exchange-energy functional in two dimensions

Author

Vilhena, J. G., Rasanen, E., Marques, M. A. L., and Pittalis, S.

Subjects
Condensed Matter - Strongly Correlated Electrons, Physics - Chemical Physics
Abstract

We construct a generalized-gradient approximation for the exchange-energy density of finite two-dimensional systems. Guided by non-empirical principles, we include the proper small-gradient limit and the proper tail for the exchange-hole potential. The observed performance is superior to that of the two-dimensional local-density approximation, which underlines the usefulness of the approach in practical applications.

Published
2014

9. Minimal hypersurfaces in $\mathbb{S}^5$ with vanishing Gauss-Kronecker curvature

Author

Diniz, M. M., Vilhena, J. A. M., and Zapata, J. F. Z.

Subjects
Mathematics - Differential Geometry, 53C42
Abstract

In this paper we present a local description for complete minimal hypersurfaces in $\mathbb{S}^5$ with zero Gauss-Kronecker curvature, zero $3$-mean curvature and nowhere zero second fundamental form., Comment: 16 pages, 4 figures, submitted paper

Published
2014

10. On the violation of a local form of the Lieb-Oxford bound

Author

Vilhena, J. G., Rasanen, E., Lehtovaara, L., and Marques, M. A. L.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

In the framework of density-functional theory, several popular density functionals for exchange and correlation have been constructed to satisfy a local form of the Lieb-Oxford bound. In its original global expression, the bound represents a rigorous lower limit for the indirect Coulomb interaction energy. Here we employ exact-exchange calculations for the G2 test set to show that the local form of the bound is violated in an extensive range of both the dimensionless gradient and the average electron density. Hence, the results demonstrate the severity in the usage of the local form of the bound in functional development. On the other hand, our results suggest alternative ways to construct accurate density functionals for the exchange energy., Comment: (Submitted on 27 April 2012)

Published
2012
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11. On the Kirzhnits gradient expansion in two dimensions

Author

Putaja, A., Rasanen, E., van Leeuwen, R., Vilhena, J. G., and Marques, M. A. L.

Subjects
Condensed Matter - Strongly Correlated Electrons, Mathematical Physics
Abstract

We derive the semiclassical Kirzhnits expansion of the D-dimensional one-particle density matrix up to the second order in $\hbar$. We focus on the two-dimensional (2D) case and show that all the gradient corrections both to the 2D one-particle density and to the kinetic energy density vanish. However, the 2D Kirzhnits expansion satisfies the consistency criterion of Gross and Proetto [J. Chem. Theory Comput. 5, 844 (2009)] for the functional derivatives of the density and the noninteracting kinetic energy with respect to the Kohn-Sham potential. Finally we show that the gradient correction to the exchange energy diverges in agreement with the previous linear-response study.

Published
2011
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12. Excitonic effects in the optical properties of CdSe nanowires

Author

Vilhena, J. G., Botti, S., and Marques, M. A. L.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Materials Science
Abstract

Using a first-principle approach beyond density functional theory we calculate the electronic and optical properties of small diameter CdSe nanowires.Our results demonstrate how some approximations commonly used in bulk systems fail at this nano-scale level and how indispensable it is to include crystal local fields and excitonic effects to predict the unique optical properties of nanowires. From our results, we then construct a simple model that describes the optical gap as a function of the diameter of the wire, that turns out to be in excellent agreement with experiments for intermediate and large diameters., Comment: submitted

Published
2010
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13. Semi-local density functional for the exchange-correlation energy of electrons in two dimensions

Author

Rasanen, E., Pittalis, S., Vilhena, J. G., and Marques, M. A. L.

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

We present a practical and accurate density functional for the exchange-correlation energy of electrons in two dimensions. The exchange part is based on a recent two-dimensional generalized-gradient approximation derived by considering the limits of small and large density gradients. The fully local correlation part is constructed following the Colle-Salvetti scheme and a Gaussian approximation for the pair density. The combination of these expressions is shown to provide an efficient density functional to calculate the total energies of two-dimensional electron systems such as semiconductor quantum dots. Excellent performance of the functional with respect to numerically exact reference data for quantum dots is demonstrated., Comment: to appear in Int. J. Quantum Chem. (2010)

Published
2010
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14. Density gradients for the exchange energy of electrons in two dimensions

Author

Pittalis, S., Rasanen, E., Vilhena, J. G., and Marques, M. A. L.

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

We derive a generalized gradient approximation to the exchange energy to be used in density functional theory calculations of two-dimensional systems. This class of approximations has a long and successful history, but it has not yet been fully investigated for electrons in two dimensions. We follow the approach originally proposed by Becke for three-dimensional systems [Int. J. Quantum Chem. 23, 1915 (1983), J. Chem. Phys. 85, 7184 (1986)]. The resulting functional depends on two parameters that are adjusted to a test set of parabolically confined quantum dots. Our exchange functional is then tested on a variety of systems with promising results, reducing the error in the exchange energy by a factor of 4 with respect to the simple local density approximation.

Published
2008
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15. PSICANÁLISE IMPLICADA E ADOLESCÊNCIA: modos de intervenção e testemunhos clínicos

Author

GUERRA, A. M. C., primary, BEMFICA, A. G., additional, CASTRO, A. C. S., additional, MALTA, A. L., additional, FIGUEIREDO, A. C. C., additional, CUNHA, B. S. O., additional, GALAN, CAMILA CAMPOS BOTELHO, additional, ROSA, C. M., additional, FERNANDES, CHRISTIENE, additional, ZEFERINO, C. S. M., additional, MASSA, E. S. C., additional, SIQUEIRA, F. G., additional, SAUVAGNAT, FRANÇOIS, additional, DEL DEBBIO, G. M., additional, Lisita, Helena Greco, additional, GREISER, IRENE, additional, NOVAES, J. V., additional, GASPAR, J. P., additional, VILHENA, J., additional, PEREIRA, M.R., additional, VIEIRA, M. A., additional, ZAMORA, M. H., additional, ARANHA, M. C., additional, RAMIREZ, MÁRIO ELKIN, additional, PENNA, P. D. M., additional, AZEVEDO, POLIANE P. FERREIRA, additional, LAIA, S., additional, Goulart, T. S., additional, SILVA, TELMA NARA DA, additional, SOUZA, VANESSA DO CARMO FERREIRA DE, additional, DARRIBA, V. A., additional, and SALES JUNIOR, V. L., additional

Published
2020
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16. Lifetime measurements of yrast states in 178Pt using the charge plunger method with a recoil separator

Author

Heery, J., Barber, L., Vilhena, J., Singh, B. S. Nara, Herzberg, R.-D., Cullen, D. M., Müller-Gatermann, C., Beeton, G., Bowry, M., Dewald, A., Grahn, T., Greenlees, P. T., Illana, A., Julin, R., Juutinen, S., Keatings, J. M., Leino, M., Luoma, M., O’Donnell, D., Ojala, J., Pakarinen, J., Rahkila, P., Ruotsalainen, P., Sandzelius, M., Sarén, J., Sinclair, J., Smith, J. F., Sorri, J., Spagnoletti, P., Tann, H., Uusitalo, J., and Zimba, G.

Published
2021
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20. Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects

Author

Swiss National Science Foundation, University of Zurich, Suomalainen, Maarit [0000-0002-3276-3008], Volle, Romain [0000-0002-4442-4652], Bauer, Michael [0000-0002-8156-4603], Pachlopnik Schmid, Jana [0000-0002-6653-9047], Vilhena, J. G. [0000-0001-8338-9119], Pérez, Rubén [0000-0001-5896-541X], Mering, Christian von [0000-0001-7734-9102], Greber, Urs F. [0000-0003-2278-120X], Kannan, Abhilash, Suomalainen, Maarit, Volle, Romain, Bauer, Michael, Amsler, Marco, Trinh, Hung V., Vavassori, Stefano, Pachlopnik Schmid, Jana, Vilhena, J. G., Marin-González, Alberto, Pérez, Rubén, Franceschini, Andrea, Mering, Christian von, Hemmi, Silvia, Greber, Urs F., Swiss National Science Foundation, University of Zurich, Suomalainen, Maarit [0000-0002-3276-3008], Volle, Romain [0000-0002-4442-4652], Bauer, Michael [0000-0002-8156-4603], Pachlopnik Schmid, Jana [0000-0002-6653-9047], Vilhena, J. G. [0000-0001-8338-9119], Pérez, Rubén [0000-0001-5896-541X], Mering, Christian von [0000-0001-7734-9102], Greber, Urs F. [0000-0003-2278-120X], Kannan, Abhilash, Suomalainen, Maarit, Volle, Romain, Bauer, Michael, Amsler, Marco, Trinh, Hung V., Vavassori, Stefano, Pachlopnik Schmid, Jana, Vilhena, J. G., Marin-González, Alberto, Pérez, Rubén, Franceschini, Andrea, Mering, Christian von, Hemmi, Silvia, and Greber, Urs F.

Abstract

Pathogen-associated molecular patterns, including cytoplasmic DNA and double-strand (ds)RNA trigger the induction of interferon (IFN) and antiviral states protecting cells and organisms from pathogens. Here we discovered that the transfection of human airway cell lines or non-transformed fibroblasts with 24mer dsRNA mimicking the cellular micro-RNA (miR)29b-1* gives strong anti-viral effects against human adenovirus type 5 (AdV-C5), influenza A virus X31 (H3N2), and SARS-CoV-2. These anti-viral effects required blunt-end complementary RNA strands and were not elicited by corresponding single-strand RNAs. dsRNA miR-29b-1* but not randomized miR-29b-1* mimics induced IFN-stimulated gene expression, and downregulated cell adhesion and cell cycle genes, as indicated by transcriptomics and IFN-I responsive Mx1-promoter activity assays. The inhibition of AdV-C5 infection with miR-29b-1* mimic depended on the IFN-alpha receptor 2 (IFNAR2) and the RNA-helicase retinoic acid-inducible gene I (RIG-I) but not cytoplasmic RNA sensors MDA5 and ZNFX1 or MyD88/TRIF adaptors. The antiviral effects of miR29b-1* were independent of a central AUAU-motif inducing dsRNA bending, as mimics with disrupted AUAU-motif were anti-viral in normal but not RIG-I knock-out (KO) or IFNAR2-KO cells. The screening of a library of scrambled short dsRNA sequences identified also anti-viral mimics functioning independently of RIG-I and IFNAR2, thus exemplifying the diverse anti-viral mechanisms of short blunt-end dsRNAs

Published
2022

21. In-beam $$\gamma $$-ray spectroscopy of $$^{94}$$Ag

Author

Pereira-López, X., primary, Bentley, M. A., additional, Wadsworth, R., additional, Ruotsalainen, P., additional, Lenzi, S. M., additional, Forsberg, U., additional, Auranen, K., additional, Blazhev, A., additional, Cederwall, B., additional, Grahn, T., additional, Greenlees, P., additional, Illana, A., additional, Jenkins, D. G., additional, Julin, R., additional, Jutila, H., additional, Juutinen, S., additional, Liu, X., additional, Llewelyn, R., additional, Luoma, M., additional, Moschner, K., additional, Müller-Gatermann, C., additional, Singh, B. S. Nara, additional, Nowacki, F., additional, Ojala, J., additional, Pakarinen, J., additional, Papadakis, P., additional, Rahkila, P., additional, Romero, J., additional, Sandzelius, M., additional, Sarén, J., additional, Tann, H., additional, Uthayakumaar, S., additional, Uusitalo, J., additional, Vega-Romero, J. G., additional, Vilhena, J. M., additional, Yajzey, R., additional, Zhang, W., additional, and Zimba, G., additional

Published
2023
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22. In-beam γ -ray spectroscopy of 94 Ag

Author

Pereira-Lopez, X., Bentley, M. A., Wadsworth, R., Ruotsalainen, P., Lenzi, S. M., Forsberg, U., Auranen, K., Blazhev, A., Cederwall, B., Grahn, T., Greenlees, P., Illana, A., Jenkins, D. G., Julin, R., Jutila, H., Juutinen, S., Liu, X., Llewelyn, R., Luoma, M., Moschner, K., Müller-Gatermann, C., Singh, B. S. Nara, Nowacki, F., Ojala, J., Pakarinen, J., Papadakis, P., Rahkila, P., Romero, J., Sandzelius, M., Saren, J., Tann, H., Uthayakumaar, S., Uusitalo, J., Vega-Romero, J. G., Vilhena, J. M., Yajzey, R., Zhang, W., Zimba, G., and Helsinki Institute of Physics

Subjects
Coulomb energy differences, Excited-states, Proton, Decay, Ag, 114 Physical sciences, Isomer
Published
2023

24. In-beam γ-ray spectroscopy of 94Ag

Author

Pereira-López, X., Bentley, M. A., Wadsworth, R., Ruotsalainen, P., Lenzi, S. M., Forsberg, U., Auranen, K., Blazhev, A., Cederwall, B., Grahn, T., Greenlees, P., Illana, A., Jenkins, D. G., Julin, R., Jutila, H., Juutinen, S., Liu, X., Llewelyn, R., Luoma, M., Moschner, K., Müller-Gatermann, C., Nara Singh, B. S., Nowacki, F., Ojala, J., Pakarinen, J., Papadakis, P., Rahkila, P., Romero, J., Sandzelius, M., Sarén, J., Tann, H., Uthayakumaar, S., Uusitalo, J., Vega-Romero, J. G., Vilhena, J. M., Yajzey, R., Zhang, W., and Zimba, G.

Subjects
spektroskopia, hopea, ydinfysiikka
Abstract

A recoil-beta-tagging experiment has been per formed to study the excited T = 0 and T = 1 states in the odd–odd N = Z nucleus 94Ag, populated via the 40Ca(58Ni,1p3n)94Ag reaction. The experiment was con ducted using the MARA recoil separator and JUROGAM3 array at the Accelerator Laboratory of the University of Jyväskylä. Through correlating fast, high-energy beta decays at the MARA focal plane with prompt γ rays emitted at the reaction target, a number of transitions between excited states in 94Ag have been identified. The timing characteris tics of these transitions confirm that they fall within decay sequences that feed the short-lived T = 1 ground state of 94Ag. The transitions are proposed to proceed within and between the sets of states with T = 0 and T = 1. Possi ble correspondence between some of these transitions from analog states in 94Pd has been discussed, and shell-model cal culations including multipole and monopole electromagnetic effects have been presented, in order to enable predictions of the decay patterns between the T = 0 and T = 1 states and to allow a theoretical set of Coulomb energy differences to be calculated for the A = 94 T = 1 analog states. peerReviewed

Published
2023

26. Decay studies in the A similar to 225 Po-Fr region from the DESPEC campaign at GSI in 2021

Author

Polettini, M, Pellumaj, J, Benzoni, G, Zhang, G, Mengoni, D, Vidal, RM Perez, Genna, D, Bracco, A, Aggez, G, Al Aqueel, M, Alayed, B, Albers, HM, Algora, A, Alhomaidhi, S, Appleton, C, Arici, T, Armstrong, M, Arnswald, K, Balogh, M, Banerjee, A, Blazhev, A, Bottoni, S, Boutachkov, P, Bruce, A, Bruno, C, Camera, F, Cederwall, B, Chishti, MMR, Cox, DM, Crespi, FCL, Das, B, Davinson, T, De Angelis, G, Dickel, T, Doncel, M, Donthi, R, Ertoprak, A, Escudeiro, R, Esmaylzadeh, A, Fraile, LM, Gaffney, L, Gamba, ER, Gerl, J, Gottardo, A, Ha, J, Haettner, E, Hall, O, Heggen, H, Hrabar, Y, Hubbard, N, Jazrawi, S, John, PR, Jolie, J, Jones, C, Joss, D, Judson, D, Kahl, D, Karayonchev, V, Kazantseva, E, Kern, R, Knafla, L, Kojouharov, I, Korgul, A, Korten, W, Koseoglou, P, Kosir, G, Kostyleva, D, Kurtukian-Nieto, T, Kurz, N, Kuzminchuk, N, Labiche, M, Lenzi, S, Leoni, S, Lozeva, R, Mertzimekis, TJ, Mikolajczuk, M, Million, B, Mistry, AK, Morales, A, Mukha, I, Murias, JR, Napoli, D, NaraSingh, BS, O'Donnell, D, Orrigo, SEA, Page, R, Pelonis, S, Petrovic, J, Pietralla, N, Pietri, S, Pigliapoco, S, Podolyak, Zs, Porzio, C, Quintana Arnes, B, Recchia, F, Regan, PH, Reiter, P, Rezynkina, K, Roy, P, Rudigier, M, Ruotsalainen, P, Sahin, E, Sarmiento, LG, Satrazani, M-M, Schaffner, H, Scheidenberger, C, Sexton, L, Sharma, A, Smallcombe, J, Sood, A, Vasileiou, P, Vesic, J, Vilhena, J, Waring, L, Weick, H, Werner, V, Wiederhold, J, Wieland, O, Wimmer, K, Wollersheim, HJ, Woods, P, Yaneva, A, Zanon, I, Zhao, J, Zidarova, R, Ziliani, S, Zimba, G, and Zyriliou, A

Subjects
Science & Technology, Physics, Physical Sciences, Physics, Multidisciplinary
Abstract

ispartof: NUOVO CIMENTO C-COLLOQUIA AND COMMUNICATIONS IN PHYSICS vol:45 issue:5 status: published

Published
2022

29. A molecular view of DNA flexibility

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Comunidad de Madrid, European Research Council, La Caixa, Marin-González, Alberto [0000-0002-9076-1270], Vilhena, J. G. [0000-0001-8338-9119], Moreno-Herrero, Fernando [0000-0003-4083-1709], Marin-González, Alberto, Vilhena, J. G., Pérez, Rubén, Moreno-Herrero, Fernando, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Comunidad de Madrid, European Research Council, La Caixa, Marin-González, Alberto [0000-0002-9076-1270], Vilhena, J. G. [0000-0001-8338-9119], Moreno-Herrero, Fernando [0000-0003-4083-1709], Marin-González, Alberto, Vilhena, J. G., Pérez, Rubén, and Moreno-Herrero, Fernando

Abstract

DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general ‘rules’ that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.

Published
2021

31. Decay studies in the A∼225 Po-Fr region from the DESPEC campaign at GSI in 2021

Author

Polettini, M., Pellumaj, J., Benzoni, G., Zhang, G., Mengoni, D., Perez Vidal, R. M., Genna, D., Bracco, A., Aggez, G., Al Aqueel, M., Alayed, B., Albers, H. M., Algora, A., Alhomaidhi, S., Appleton, C., Arici, T., Armstrong, M., Arnswald, K., Balogh, M., Banerjee, A., Blazhev, A., Bottoni, S., Boutachkov, P., Bruce, A., Bruno, C., Camera, F., Cederwall, B., Chishti, M. M. R., Cox, D. M., Crespi, F. C. L., Das, B., Davinson, T., De Angelis, G., Dickel, T., Doncel, Maria, Donthi, R., Ertoprak, A., Escudeiro, R., Esmaylzadeh, A., Fraile, L. M., Gaffney, L., Gamba, E. R., Gerl, J., Gottardo, A., Ha, J., Haettner, E., Hall, O., Heggen, H., Hrabar, Y., Hubbard, N., Jazrawi, S., John, P. R., Jolie, J., Jones, C., Joss, D., Judson, D., Kahl, D., Karayonchev, V., Kazantseva, E., Kern, R., Knafla, L., Kojouharov, I., Korgul, A., Korten, W., Koseoglou, P., Kosir, G., Kostyleva, D., Kurtukian-Nieto, T., Kurz, N., Kuzminchuk, N., Labiche, M., Lenzi, S., Leoni, S., Lozeva, R., Mertzimekis, T. J., Mikolajczuk, M., Million, B., Mistry, A. K., Morales, A., Mukha, I., Murias, J. R., Napoli, D., NaraSingh, B. S., O'Donnell, D., Orrigo, S. E. A., Page, R., Pelonis, S., Petrovic, J., Pietralla, N., Pietri, S., Pigliapoco, S., Podolyak, Zs., Porzio, C., Quintana Arnes, B., Recchia, F., Regan, P. H., Reiter, P., Rezynkina, K., Roy, P., Rudigier, M., Ruotsalainen, P., Sahin, E., Sarmiento, L. G., Satrazani, M.-M., Schaffner, H., Scheidenberger, C., Sexton, L., Sharma, A., Smallcombe, J., Sood, A., Vasileiou, P., Vesic, J., Vilhena, J., Waring, L., Weick, H., Werner, V., Wiederhold, J., Wieland, O., Wimmer, K., Wollersheim, H. J., Woods, P., Yaneva, A., Zanon, I., Zhao, J., Zidarova, R., Ziliani, S., Zimba, G., Zyriliou, A., Polettini, M., Pellumaj, J., Benzoni, G., Zhang, G., Mengoni, D., Perez Vidal, R. M., Genna, D., Bracco, A., Aggez, G., Al Aqueel, M., Alayed, B., Albers, H. M., Algora, A., Alhomaidhi, S., Appleton, C., Arici, T., Armstrong, M., Arnswald, K., Balogh, M., Banerjee, A., Blazhev, A., Bottoni, S., Boutachkov, P., Bruce, A., Bruno, C., Camera, F., Cederwall, B., Chishti, M. M. R., Cox, D. M., Crespi, F. C. L., Das, B., Davinson, T., De Angelis, G., Dickel, T., Doncel, Maria, Donthi, R., Ertoprak, A., Escudeiro, R., Esmaylzadeh, A., Fraile, L. M., Gaffney, L., Gamba, E. R., Gerl, J., Gottardo, A., Ha, J., Haettner, E., Hall, O., Heggen, H., Hrabar, Y., Hubbard, N., Jazrawi, S., John, P. R., Jolie, J., Jones, C., Joss, D., Judson, D., Kahl, D., Karayonchev, V., Kazantseva, E., Kern, R., Knafla, L., Kojouharov, I., Korgul, A., Korten, W., Koseoglou, P., Kosir, G., Kostyleva, D., Kurtukian-Nieto, T., Kurz, N., Kuzminchuk, N., Labiche, M., Lenzi, S., Leoni, S., Lozeva, R., Mertzimekis, T. J., Mikolajczuk, M., Million, B., Mistry, A. K., Morales, A., Mukha, I., Murias, J. R., Napoli, D., NaraSingh, B. S., O'Donnell, D., Orrigo, S. E. A., Page, R., Pelonis, S., Petrovic, J., Pietralla, N., Pietri, S., Pigliapoco, S., Podolyak, Zs., Porzio, C., Quintana Arnes, B., Recchia, F., Regan, P. H., Reiter, P., Rezynkina, K., Roy, P., Rudigier, M., Ruotsalainen, P., Sahin, E., Sarmiento, L. G., Satrazani, M.-M., Schaffner, H., Scheidenberger, C., Sexton, L., Sharma, A., Smallcombe, J., Sood, A., Vasileiou, P., Vesic, J., Vilhena, J., Waring, L., Weick, H., Werner, V., Wiederhold, J., Wieland, O., Wimmer, K., Wollersheim, H. J., Woods, P., Yaneva, A., Zanon, I., Zhao, J., Zidarova, R., Ziliani, S., Zimba, G., and Zyriliou, A.

Abstract

The HISPEC-DESPEC collaboration aims at investigating the structure of exotic nuclei formed in fragmentation reactions with decay spectroscopy measurements, as part of the FAIR Phase-0 campaign at GSI. This paper reports on first results of an experiment performed in spring 2021, with a focus on beta-decaystudies in the Po-Fr nuclei in the 220 < A <230 island of octupole deformation exploiting the DESPEC setup. Ion-beta correlations and fast-timing techniques are being employed, giving an insight into this difficult-to-reach region.

Published
2022
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32. Decay studies in the A similar to 225 Po-Fr region from the DESPEC campaign at GSI in 2021

Author

Polettini, M., Pellumaj, J., Benzoni, G., Zhang, G., Mengoni, D., Vidal, R. M. Perez, Genna, D., Bracco, A., Aggez, G., Al Aqueel, M., Alayed, B., Albers, H. M., Algora, A., Alhomaidhi, S., Appleton, C., Arici, T., Armstrong, M., Arnswald, K., Balogh, M., Banerjee, A., Blazhev, A., Bottoni, S., Boutachkov, P., Bruce, A., Bruno, C., Camera, F., Cederwall, B., Chishti, M. M. R., Cox, D. M., Crespi, F. C. L., Das, B., Davinson, T., De Angelis, G., Dickel, T., Doncel, M., Donthi, R., Ertoprak, A., Escudeiro, R., Esmaylzadeh, A., Fraile, L. M., Gaffney, L., Gamba, E. R., Gerl, J., Gottardo, A., Ha, J., Haettner, E., Hall, O., Heggen, H., Hrabar, Y., Hubbard, N., Jazrawi, S., John, P. R., Jolie, J., Jones, C., Joss, D., Judson, D., Kahl, D., Karayonchev, V, Kazantseva, E., Kern, R., Knafla, L., Kojouharov, I, Korgul, A., Korten, W., Koseoglou, P., Kosir, G., Kostyleva, D., Kurtukian-Nieto, T., Kurz, N., Kuzminchuk, N., Labiche, M., Lenzi, S., Leoni, S., Lozeva, R., Mertzimekis, T. J., Mikolajczuk, M., Million, B., Mistry, A. K., Morales, A., Mukha, I, Murias, J. R., Napoli, D., NaraSingh, B. S., O'Donnell, D., Orrigo, S. E. A., Page, R., Pelonis, S., Petrovic, J., Pietralla, N., Pietri, S., Pigliapoco, S., Podolyak, Zs, Porzio, C., Quintana Arnes, B., Recchia, F., Regan, P. H., Reiter, P., Rezynkina, K., Roy, P., Rudigier, M., Ruotsalainen, P., Sahin, E., Sarmiento, L. G., Satrazani, M-M, Schaffner, H., Scheidenberger, C., Sexton, L., Sharma, A., Smallcombe, J., Sood, A., Vasileiou, P., Vesic, J., Vilhena, J., Waring, L., Weick, H., Werner, V, Wiederhold, J., Wieland, O., Wimmer, K., Wollersheim, H. J., Woods, P., Yaneva, A., Zanon, I, Zhao, J., Zidarova, R., Ziliani, S., Zimba, G., Zyriliou, A., Polettini, M., Pellumaj, J., Benzoni, G., Zhang, G., Mengoni, D., Vidal, R. M. Perez, Genna, D., Bracco, A., Aggez, G., Al Aqueel, M., Alayed, B., Albers, H. M., Algora, A., Alhomaidhi, S., Appleton, C., Arici, T., Armstrong, M., Arnswald, K., Balogh, M., Banerjee, A., Blazhev, A., Bottoni, S., Boutachkov, P., Bruce, A., Bruno, C., Camera, F., Cederwall, B., Chishti, M. M. R., Cox, D. M., Crespi, F. C. L., Das, B., Davinson, T., De Angelis, G., Dickel, T., Doncel, M., Donthi, R., Ertoprak, A., Escudeiro, R., Esmaylzadeh, A., Fraile, L. M., Gaffney, L., Gamba, E. R., Gerl, J., Gottardo, A., Ha, J., Haettner, E., Hall, O., Heggen, H., Hrabar, Y., Hubbard, N., Jazrawi, S., John, P. R., Jolie, J., Jones, C., Joss, D., Judson, D., Kahl, D., Karayonchev, V, Kazantseva, E., Kern, R., Knafla, L., Kojouharov, I, Korgul, A., Korten, W., Koseoglou, P., Kosir, G., Kostyleva, D., Kurtukian-Nieto, T., Kurz, N., Kuzminchuk, N., Labiche, M., Lenzi, S., Leoni, S., Lozeva, R., Mertzimekis, T. J., Mikolajczuk, M., Million, B., Mistry, A. K., Morales, A., Mukha, I, Murias, J. R., Napoli, D., NaraSingh, B. S., O'Donnell, D., Orrigo, S. E. A., Page, R., Pelonis, S., Petrovic, J., Pietralla, N., Pietri, S., Pigliapoco, S., Podolyak, Zs, Porzio, C., Quintana Arnes, B., Recchia, F., Regan, P. H., Reiter, P., Rezynkina, K., Roy, P., Rudigier, M., Ruotsalainen, P., Sahin, E., Sarmiento, L. G., Satrazani, M-M, Schaffner, H., Scheidenberger, C., Sexton, L., Sharma, A., Smallcombe, J., Sood, A., Vasileiou, P., Vesic, J., Vilhena, J., Waring, L., Weick, H., Werner, V, Wiederhold, J., Wieland, O., Wimmer, K., Wollersheim, H. J., Woods, P., Yaneva, A., Zanon, I, Zhao, J., Zidarova, R., Ziliani, S., Zimba, G., and Zyriliou, A.

Abstract

The HISPEC-DESPEC collaboration aims at investigating the struc-ture of exotic nuclei formed in fragmentation reactions with decay spectroscopymeasurements, as part of the FAIR Phase-0 campaign at GSI. This paper reportson first results of an experiment performed in spring 2021, with a focus on beta-decaystudies in the Po-Fr nuclei in the 220 < A <230 island of octupole deformationexploiting the DESPEC setup. Ion-beta correlations and fast-timing techniques arebeing employed, giving an insight into this difficult-to-reach region.

Published
2022

33. Nature of seniority symmetry breaking in the semimagic nucleus Ru-94

Author

Das, B., Cederwall, B., Qi, C., Gorska, M., Regan, P. H., Aktas, O., Albers, H. M., Banerjee, A., Chishti, M. M. R., Gerl, J., Hubbard, N., Jazrawi, S., Jolie, J., Mistry, A. K., Polettini, M., Yaneva, A., Alhomaidhi, S., Zhao, J., Arici, T., Bagchi, S., Benzoni, G., Boutachkov, P., Davinson, T., Dickel, T., Haettner, E., Hall, O., Hornung, Ch, Hucka, J. P., John, P. R., Kojouharov, I, Knoebel, R., Kostyleva, D., Kuzminchuk, N., Mukha, I, Plass, W. R., Singh, B. S. Nara, Vasiljevic, J., Pietri, S., Podolyak, Zs, Rudigier, M., Roesch, H., Sahin, E., Schaffner, H., Scheidenberger, C., Schirru, F., Sharma, A., Shearman, R., Tanaka, Y., Vesic, J., Weick, H., Wollersheim, H. J., Ahmed, U., Algora, A., Appleton, C., Benito, J., Blazhev, A., Bracco, A., Bruce, A. M., Brunet, M., Canavan, R., Esmaylzadeh, A., Fraile, L. M., Haefner, G., Heggen, H., Kahl, D., Karayonchev, V, Kern, R., Korgu, A., Kosir, G., Kurz, N., Lozeva, R., Mikolajczuk, M., Napiralla, P., Page, R., Petrache, C. M., Pietralla, N., Regis, J-M, Ruotsalainen, P., Sexton, L., Sanchez-Temble, V, Si, M., Vilhena, J., Werner, V, Wiederhold, J., Witt, W., Woods, P. J., Zimba, G., Das, B., Cederwall, B., Qi, C., Gorska, M., Regan, P. H., Aktas, O., Albers, H. M., Banerjee, A., Chishti, M. M. R., Gerl, J., Hubbard, N., Jazrawi, S., Jolie, J., Mistry, A. K., Polettini, M., Yaneva, A., Alhomaidhi, S., Zhao, J., Arici, T., Bagchi, S., Benzoni, G., Boutachkov, P., Davinson, T., Dickel, T., Haettner, E., Hall, O., Hornung, Ch, Hucka, J. P., John, P. R., Kojouharov, I, Knoebel, R., Kostyleva, D., Kuzminchuk, N., Mukha, I, Plass, W. R., Singh, B. S. Nara, Vasiljevic, J., Pietri, S., Podolyak, Zs, Rudigier, M., Roesch, H., Sahin, E., Schaffner, H., Scheidenberger, C., Schirru, F., Sharma, A., Shearman, R., Tanaka, Y., Vesic, J., Weick, H., Wollersheim, H. J., Ahmed, U., Algora, A., Appleton, C., Benito, J., Blazhev, A., Bracco, A., Bruce, A. M., Brunet, M., Canavan, R., Esmaylzadeh, A., Fraile, L. M., Haefner, G., Heggen, H., Kahl, D., Karayonchev, V, Kern, R., Korgu, A., Kosir, G., Kurz, N., Lozeva, R., Mikolajczuk, M., Napiralla, P., Page, R., Petrache, C. M., Pietralla, N., Regis, J-M, Ruotsalainen, P., Sexton, L., Sanchez-Temble, V, Si, M., Vilhena, J., Werner, V, Wiederhold, J., Witt, W., Woods, P. J., and Zimba, G.

Abstract

Direct lifetime measurements via gamma -gamma coincidences using a fast timing detector array consisting of LaBr3(Ce) scintillators has been applied to determine the lifetime of low-lying states in the semimagic (N = 50) nucleus Ru-94. The experiment was carried out as the first in a series of FAIR-0 experiments with the DESPEC experimental setup at the Facility for Antiproton and Ion Research (FAIR). Excited states in Ru-94 were populated primarily via the beta-delayed proton emission of Pd-95 nuclei, produced in the projectile fragmentation of an 850 MeV/nucleon Xe-124 beam impinging on a 4 g/cm(2) Be-9 target. While the deduced E2 strength for the 2(+) -> 0(+) transition in the yrast cascade follows the expected behavior for conserved seniority symmetry, the intermediate 4(+) -> 2(+) transition exhibits a drastic enhancement of transition strength in comparison with pure-seniority model predictions as well as standard shell model predictions in the f pg proton hole space with respect to doubly magic Sn-100. The anomalous behavior is ascribed to a subtle interference between the wave function of the lowest seniority v = 2, I-pi = 4(+) state and that of a close-lying v = 4 state that exhibits partial dynamic symmetry. In addition, the observed strongly prohibitive 6(+) -> 4(+) transition can be attributed to the same mechanism but with a destructive interference. It is noted that such effects may provide stringent tests of the nucleon-nucleon interactions employed in state-of-the-art theoretical model calculations.

Published
2022

35. Flexible Superlubricity Unveiled in Sidewinding Motion of Individual Polymeric Chains

Author

Vilhena, J. G., primary, Pawlak, Rémy, additional, D’Astolfo, Philipp, additional, Liu, Xunshan, additional, Gnecco, Enrico, additional, Kisiel, Marcin, additional, Glatzel, Thilo, additional, Pérez, Rúben, additional, Häner, Robert, additional, Decurtins, Silvio, additional, Baratoff, Alexis, additional, Prampolini, Giacomo, additional, Liu, Shi-Xia, additional, and Meyer, Ernst, additional

Published
2022
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36. Nature of seniority symmetry breaking in the semimagic nucleus Ru94

Author

Das, B., primary, Cederwall, B., additional, Qi, C., additional, Górska, M., additional, Regan, P. H., additional, Aktas, Ö., additional, Albers, H. M., additional, Banerjee, A., additional, Chishti, M. M. R., additional, Gerl, J., additional, Hubbard, N., additional, Jazrawi, S., additional, Jolie, J., additional, Mistry, A. K., additional, Polettini, M., additional, Yaneva, A., additional, Alhomaidhi, S., additional, Zhao, J., additional, Arici, T., additional, Bagchi, S., additional, Benzoni, G., additional, Boutachkov, P., additional, Davinson, T., additional, Dickel, T., additional, Haettner, E., additional, Hall, O., additional, Hornung, Ch., additional, Hucka, J. P., additional, John, P. R., additional, Kojouharov, I., additional, Knöbel, R., additional, Kostyleva, D., additional, Kuzminchuk, N., additional, Mukha, I., additional, Plass, W. R., additional, Nara Singh, B. S., additional, Vasiljević, J., additional, Pietri, S., additional, Podolyák, Zs., additional, Rudigier, M., additional, Rösch, H., additional, Sahin, E., additional, Schaffner, H., additional, Scheidenberger, C., additional, Schirru, F., additional, Sharma, A., additional, Shearman, R., additional, Tanaka, Y., additional, Vesić, J., additional, Weick, H., additional, Wollersheim, H. J., additional, Ahmed, U., additional, Algora, A., additional, Appleton, C., additional, Benito, J., additional, Blazhev, A., additional, Bracco, A., additional, Bruce, A. M., additional, Brunet, M., additional, Canavan, R., additional, Esmaylzadeh, A., additional, Fraile, L. M., additional, Häfner, G., additional, Heggen, H., additional, Kahl, D., additional, Karayonchev, V., additional, Kern, R., additional, Korgul, A., additional, Kosir, G., additional, Kurz, N., additional, Lozeva, R., additional, Mikolajczuk, M., additional, Napiralla, P., additional, Page, R., additional, Petrache, C. M., additional, Pietralla, N., additional, Régis, J.-M., additional, Ruotsalainen, P., additional, Sexton, L., additional, Sanchez-Temble, V., additional, Si, M., additional, Vilhena, J., additional, Werner, V., additional, Wiederhold, J., additional, Witt, W., additional, Woods, P. J., additional, and Zimba, G., additional

Published
2022
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37. Decay studies in the A ∼ 225 Po-Fr region from the DESPEC campaign at GSI in 2021

Author

Polettini, M., Pellumaj, J., Benzoni, G., Valiente-Dobon, J. J., Zhang, G., Mengoni, D., Vidal, R. M. P., Genna, D., Bracco, A., Aggez, G., Ahmed, U., Aktas, O., Al Aqueel, M., Alayed, B., Albers, H. M., Algora, A., Alhomaidhi, S., Appleton, C., Arici, T., Armstrong, M., Arnswald, K., Balogh, M., Banerjee, A., Garcia, J. B., Blazhev, A., Bottoni, S., Boutachkov, P., Bruce, A., Bruno, C., Camera, F., Cederwall, B., Chishti, M. M. R., Cortes, M. L., Cox, D. M., Crespi, F. C. L., Das, B., Davinson, T., De Angelis, G., Dickel, T., Doncel, M., Donthi, R., Ertoprak, A., Escudeiro, R., Esmaylzadeh, A., Fraile, L. M., Gaffney, L., Gamba, E. R., Gerl, J., Gorska, M., Gottardo, A., Ha, J., Haettner, E., Hall, O., Heggen, H., Hrabar, Y., Hubbard, N., Jazrawi, S., John, P. R., Jolie, J., Jones, C., Joss, D., Judson, D., Kahl, D., Karayonchev, V., Kazantseva, E., Kern, R., Knafla, L., Kojouharov, I., Korgul, A., Korten, W., Koseoglou, P., Kosir, G., Kostyleva, D., Kurtukian-Nieto, T., Kurz, N., Kuzminchuk, N., Labiche, M., Lenzi, S., Leoni, S., Exposito, M. L., Lozeva, R., Mertzimekis, T. J., Mikolajczuk, M., Million, B., Mistry, A. K., Morales, A., Mukha, I., Murias, J. R., Napoli, D., Singh, B. S. N., O'Donnell, D., Orrigo, S. E. A., Page, R., Pelonis, S., Petrovic, J., Pietralla, N., Pietri, S., Pigliapoco, S., Podolyak, Zs., Porzio, C., Arnes, B. Q., Recchia, F., Regan, P. H., Regis, J. -M., Reiter, P., Rezynkina, K., Roy, P., Rudigier, M., Ruotsalainen, P., Sahin, E., Sarmiento, L. G., Satrazani, M. -M., Schaffner, H., Scheidenberger, C., Sexton, L., Sharma, A., Smallcombe, J., Soderstrom, P. -A., Sood, A., Vasileiou, P., Vesic, J., Vilhena, J., Waring, L., Weick, H., Werner, V., Wiederhold, J., Wieland, O., Wimmer, K., Wollersheim, H. J., Woods, P., Yaneva, A., Zanon, I., Zhao, J., Zidarova, R., Ziliani, S., Zimba, G., and Zyriliou, A.

Published
2022

38. Nature of seniority symmetry breaking in the semimagic nucleus $^{94}Ru$

Author

Das, B., Cederwall, B., Qi, C., Górska, M., Regan, P. H., Aktas, Ö., Albers, H. M., Banerjee, A., Chishti, M. M. R., Gerl, J., Hubbard, N., Jazrawi, S., Jolie, J., Mistry, A. K., Polettini, M., Yaneva, A., Alhomaidhi, S., Zhao, Jianwei, Arici, T., Bagchi, S., Benzoni, G., Boutachkov, P., Davinson, T., Dickel, Timo, Haettner, E., Hall, O., Hornung, Ch., Hucka, J. P., John, P. R., Kojouharov, I., Knöbel, R., Kostyleva, D., Kuzminchuk, N., Mukha, I., Plass, W. R., Nara Singh, B. S., Vasiljević, J., Pietri, S., Podolyák, Zs., Rudigier, M., Rösch, H., Sahin, E., Schaffner, H., Scheidenberger, C., Schirru, Fabio, Sharma, A., Shearman, R., Tanaka, Y., Vesić, J., Weick, H., Wollersheim, H. J., Ahmed, U., Algora, A., Appleton, C., Benito, J., Blazhev, A., Bracco, A., Bruce, A. M., Brunet, M., Canavan, R., Esmaylzadeh, A., Fraile, L. M., Häfner, G., Heggen, H., Kahl, D., Karayonchev, V., Kern, R., Korgul, A., Kosir, G., Kurz, N., Lozeva, R., Mikolajczuk, M., Napiralla, P., Page, R., Petrache, C. M., Pietralla, N., Régis, J.-M., Ruotsalainen, P., Sexton, L., Sanchez-Temble, V., Si, M., Vilhena, J., Werner, V., Wiederhold, J., Witt, W., Woods, P. J., and Zimba, G.

Subjects
Nuclear Theory, ddc:530, Nuclear Experiment, ydinfysiikka
Abstract

Physical review / C 105(3), L031304 (2022). doi:10.1103/PhysRevC.105.L031304, Published by APS, Woodbury, NY

Published
2022

40. Decay studies in the A∼225 Po-Fr region from the DESPEC campaign at GSI in 2021

Author

Polettini, M., Pellumaj, J., Benzoni, G., Valiente-Dobón, J.J., Zhang, G., Mengoni, D., Vidal, R.M.Perez, Genna, D., Bracco, A., Aggez, G., Ahmed, U., Aktas, Ö., Aqueel, M.Al, Alayed, B., Albers, H.M., Algora, A., Alhomaidhi, S., Appleton, C., Arici, T., Armstrong, M., Arnswald, K., Balogh, M., Banerjee, A., Garcıa, J.Benito, Blazhev, A., Bottoni, S., Boutachkov, P., Bruce, A., Bruno, C., Camera, F., Cederwall, B., Chishti, M.M.R., Cortés, M.L., Cox, D.M., Crespi, F.C.L., Das, B., Davinson, T., Angelis, G.De, Dickel, T., Doncel, M., Donthi, R., Ertoprak, A., Escudeiro, R., Esmaylzadeh, A., Fraile, L.M., Gaffney, L., Gamba, E.R., Gerl, J., Górska, M., Gottardo, A., Ha, J., Haettner, E., Hall, O., Heggen, H., Hrabar, Y., Hubbard, N., Jazrawi, S., John, P.R., Jolie, J., Jones, C., Joss, D., Judson, D., Kahl, D., Karayonchev, V., Kazantseva, E., Kern, R., Knafla, L., Kojouharov, I., Korgul, A., Korten, W., Koseoglou, P., Kosir, G., Kostyleva, D., Kurtukian-Nieto, T., Kurz, N., Kuzminchuk, N., Labiche, M., Lenzi, S., Leoni, S., Expósito, M.Llanos, Lozeva, R., Mertzimekis, T.J., Mikolajczuk, M., Million, B., Mistry, A.K., Morales, A., Mukha, I., Murias, J.R., Napoli, D., Singh, B.S.Nara, O'Donnell, D., Orrigo, S.E.A., Page, R., Pelonis, S., Petrovic, J., Pietralla, N., Pietri, S., Pigliapoco, S., Podolyak, Zs., Porzio, C., Arnes, B.Quintana, Recchia, F., Regan, P.H., Régis, J.M., Reiter, P., Rezynkina, K., Roy, P., Rudigier, M., Ruotsalainen, P., Sahin, E., Sarmiento, L.G., Satrazani, M.M., Schaffner, H., Scheidenberger, C., Sexton, L., Sharma, A., Smallcombe, J., Söderström, P.A., Sood, A., Vasileiou, P., Vesic, J., Vilhena, J., Waring, L., Weick, H., Werner, V., Wiederhold, J., Wieland, O., Wimmer, K., Wollersheim, H.J., Woods, P., Yaneva, A., Zanon, I., Zhao, J., Zidarova, R., Ziliani, S., Zimba, G., Zyriliou, A., Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique des 2 Infinis Irène Joliot-Curie (IJCLab), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon

Subjects
[PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex]
Abstract

International audience; The HISPEC-DESPEC collaboration aims at investigating the structure of exotic nuclei formed in fragmentation reactions with decay spectroscopymeasurements, as part of the FAIR Phase-0 campaign at GSI. This paper reportson first results of an experiment performed in spring 2021, with a focus on β-decaystudies in the Po-Fr nuclei in the 220

Published
2021

42. Lifetime measurements of yrast states in ¹⁷⁸ Pt using the charge plunger method with a recoil separator

Author

Heery, J., Barber, L., Vilhena, J., Nara Singh, B. S., Herzberg, R.-D., Cullen, D. M., Müller-Gatermann, C., Beeton, G., Bowry, M., Dewald, A., Grahn, T., Greenlees, P. T., Illana, A., Julin, R., Juutinen, S., Keatings, J. M., Leino, M., Luoma, M., O’Donnell, D., Ojala, J., Pakarinen, J., Rahkila, P., Ruotsalainen, P., Sandzelius, M., Sarén, J., Sinclair, J., Smith, J. F., Sorri, J., Spagnoletti, P., Tann, H., Uusitalo, J., and Zimba, G.

Subjects
platina, ydinfysiikka
Abstract

Lifetime measurements in \(^{178}\)Pt with excited states de-exciting through \(\gamma\)-ray transitions and internal electron conversions have been performed. Ionic charges were selected by the in-flight mass separator MARA and measured at the focal plane in coincidence with the \(4^{+}_{1}→2^{+}_{1}\) 257 keV γ-ray transition detected using the JUROGAM 3 spectrometer. The resulting charge-state distributions were analysed using the differential decay curve method (DDCM) framework to obtain a lifetime value of 430(20) ps for the \(2^{+}_{1}\) state. This work builds on a method that combines the charge plunger technique with the DDCM analysis. As an alternative analysis, ions were selected in coincidence with the \(^{178}\)Pt alpha decay (\(E_{\mathrm {alpha}} = 5.458(5)\) MeV) at the focal plane. Lifetime information was obtained by fitting a two-state Bateman equation to the decay curve with the lifetime of individual states defined by a single quadrupole moment. This yielded a lifetime value of 430(50) ps for the \(2^{+}_{1}\) state, and 54(6) ps for the \(4^{+}_{1}\) state. An analysis method based around the Bateman equation will become especially important when using the charge plunger method for the cases where utilising coincidences between prompt \(\gamma\) rays and recoils is not feasible.

Published
2021

43. Lifetime measurements of yrast states in ¹⁷⁸ Pt using the charge plunger method with a recoil separator

Author

Heery, J. (J.), Barber, L. (L.), Vilhena, J. (J.), Singh, B. S. (B. S. Nara), Herzberg, R. -. (R. -D.), Cullen, D. M. (D. M.), Mueller-Gatermann, C. (C.), Beeton, G. (G.), Bowry, M. (M.), Dewald, A. (A.), Grahn, T. (T.), Greenlees, P. T. (P. T.), Illana, A. (A.), Julin, R. (R.), Juutinen, S. (S.), Keatings, J. M. (J. M.), Leino, M. (M.), Luoma, M. (M.), O'Donnell, D. (D.), Ojala, J. (J.), Pakarinen, J. (J.), Rahkila, P. (P.), Ruotsalainen, P. (P.), Sandzelius, M. (M.), Saren, J. (J.), Sinclair, J. (J.), Smith, J. F. (J. F.), Sorri, J. (J.), Spagnoletti, P. (P.), Tann, H. (H.), Uusitalo, J. (J.), Zimba, G. (G.), Heery, J. (J.), Barber, L. (L.), Vilhena, J. (J.), Singh, B. S. (B. S. Nara), Herzberg, R. -. (R. -D.), Cullen, D. M. (D. M.), Mueller-Gatermann, C. (C.), Beeton, G. (G.), Bowry, M. (M.), Dewald, A. (A.), Grahn, T. (T.), Greenlees, P. T. (P. T.), Illana, A. (A.), Julin, R. (R.), Juutinen, S. (S.), Keatings, J. M. (J. M.), Leino, M. (M.), Luoma, M. (M.), O'Donnell, D. (D.), Ojala, J. (J.), Pakarinen, J. (J.), Rahkila, P. (P.), Ruotsalainen, P. (P.), Sandzelius, M. (M.), Saren, J. (J.), Sinclair, J. (J.), Smith, J. F. (J. F.), Sorri, J. (J.), Spagnoletti, P. (P.), Tann, H. (H.), Uusitalo, J. (J.), and Zimba, G. (G.)

Abstract

Lifetime measurements in \(^{178}\)Pt with excited states de-exciting through \(\gamma\)-ray transitions and internal electron conversions have been performed. Ionic charges were selected by the in-flight mass separator MARA and measured at the focal plane in coincidence with the \(4^{+}_{1}→2^{+}_{1}\) 257 keV γ-ray transition detected using the JUROGAM 3 spectrometer. The resulting charge-state distributions were analysed using the differential decay curve method (DDCM) framework to obtain a lifetime value of 430(20) ps for the \(2^{+}_{1}\) state. This work builds on a method that combines the charge plunger technique with the DDCM analysis. As an alternative analysis, ions were selected in coincidence with the \(^{178}\)Pt alpha decay (\(E_{\mathrm {alpha}} = 5.458(5)\) MeV) at the focal plane. Lifetime information was obtained by fitting a two-state Bateman equation to the decay curve with the lifetime of individual states defined by a single quadrupole moment. This yielded a lifetime value of 430(50) ps for the \(2^{+}_{1}\) state, and 54(6) ps for the \(4^{+}_{1}\) state. An analysis method based around the Bateman equation will become especially important when using the charge plunger method for the cases where utilising coincidences between prompt \(\gamma\) rays and recoils is not feasible.

Published
2021

44. DESPEC Phase-0 campaign at GSI

Author

Polettini, M., Jazrawi, S., Chishti, M. M. R., Yaneva, A., Das, B., Banerjee, A., Hubbard, N., Mistry, A. K., Albers, H. M., Shearman, R., Gorska, M., Gerl, J., Regan, P. H., Cederwall, B., Jolie, J., Alhomaidhi, S., Arici, T., Benzoni, G., Boutachkov, P., Davinson, T., Dickel, T., Haettner, E., Hall, O., Heggen, H., John, P. R., Kojouharov, I, Kurz, N., Singh, B. S. Nara, Pietri, S., Podolyak, Zs, Rudigier, M., Sahin, E., Schaffner, H., Scheidenberger, C., Sharma, A., Vesic, J., Weick, H., Wollersheim, H. J., Ahmed, U., Aktas, O., Algora, A., Appleton, C., Benito, J., Blazhev, A., Bracco, A., Bruce, A., Brunet, M., Canavan, R., Esmaylzadeh, A., Fraile, L. M., Grawe, H., Haefner, G., Kahl, D., Karayonchev, V, Kern, R., Kosir, G., Lozeva, R., Napiralla, P., Page, R., Petrache, C. M., Petrovic, J., Pietralla, N., Regis, J-M, Ruotsalainen, P., Sexton, L., Sanchez-Temble, V, Si, M., Vilhena, J., Werner, V, Wiederhold, J., Witt, W., Woods, P., Zimba, G., Polettini, M., Jazrawi, S., Chishti, M. M. R., Yaneva, A., Das, B., Banerjee, A., Hubbard, N., Mistry, A. K., Albers, H. M., Shearman, R., Gorska, M., Gerl, J., Regan, P. H., Cederwall, B., Jolie, J., Alhomaidhi, S., Arici, T., Benzoni, G., Boutachkov, P., Davinson, T., Dickel, T., Haettner, E., Hall, O., Heggen, H., John, P. R., Kojouharov, I, Kurz, N., Singh, B. S. Nara, Pietri, S., Podolyak, Zs, Rudigier, M., Sahin, E., Schaffner, H., Scheidenberger, C., Sharma, A., Vesic, J., Weick, H., Wollersheim, H. J., Ahmed, U., Aktas, O., Algora, A., Appleton, C., Benito, J., Blazhev, A., Bracco, A., Bruce, A., Brunet, M., Canavan, R., Esmaylzadeh, A., Fraile, L. M., Grawe, H., Haefner, G., Kahl, D., Karayonchev, V, Kern, R., Kosir, G., Lozeva, R., Napiralla, P., Page, R., Petrache, C. M., Petrovic, J., Pietralla, N., Regis, J-M, Ruotsalainen, P., Sexton, L., Sanchez-Temble, V, Si, M., Vilhena, J., Werner, V, Wiederhold, J., Witt, W., Woods, P., and Zimba, G.

Abstract

This paper reports preliminary results of the DESPEC campaign at GSI, focused on the study of neutron-deficient nuclei approaching Sn-100. The results presented show the isomeric decays of excited states with I-pi = 14(+) and 8(+) in Pd-96 and Pd-94, respectively. The detailed characterisation of the DESPEC set-up and analysis methodologies, proven in this experimental run, are crucial for the future campaigns.

Published
2021

45. Lifetime measurements of yrast states in Pt-178 using the charge plunger method with a recoil separator

Author

Heery, J., Barber, L., Vilhena, J., Singh, B. S. Nara, Herzberg, R. -D., Cullen, D. M., Mueller-Gatermann, C., Beeton, G., Bowry, M., Dewald, A., Grahn, T., Greenlees, P. T., Illana, A., Julin, R., Juutinen, S., Keatings, J. M., Leino, M., Luoma, M., O'Donnell, D., Ojala, J., Pakarinen, J., Rahkila, P., Ruotsalainen, P., Sandzelius, M., Saren, J., Sinclair, J., Smith, J. F., Sorri, J., Spagnoletti, P., Tann, H., Uusitalo, J., Zimba, G., Heery, J., Barber, L., Vilhena, J., Singh, B. S. Nara, Herzberg, R. -D., Cullen, D. M., Mueller-Gatermann, C., Beeton, G., Bowry, M., Dewald, A., Grahn, T., Greenlees, P. T., Illana, A., Julin, R., Juutinen, S., Keatings, J. M., Leino, M., Luoma, M., O'Donnell, D., Ojala, J., Pakarinen, J., Rahkila, P., Ruotsalainen, P., Sandzelius, M., Saren, J., Sinclair, J., Smith, J. F., Sorri, J., Spagnoletti, P., Tann, H., Uusitalo, J., and Zimba, G.

Abstract

Lifetime measurements in Pt-178 with excited states de-exciting through gamma-ray transitions and internal electron conversions have been performed. Ionic charges were selected by the in-flight mass separatorMARAand measured at the focal plane in coincidence with the 4(1)(+) -> 2(1)(+) 257 keV gamma-ray transition detected using the JUROGAM 3 spectrometer. The resulting charge-state distributions were analysed using the differential decay curve method (DDCM) framework to obtain a lifetime value of 430(20) ps for the 2(1)(+) state. This work builds on a method that combines the charge plunger technique with the DDCM analysis. As an alternative analysis, ions were selected in coincidence with the Pt-178 alpha decay (E-alpha = 5.458(5) MeV) at the focal plane. Lifetime informationwas obtained by fitting a two-state Bateman equation to the decay curve with the lifetime of individual states defined by a single quadrupolemoment. This yielded a lifetime value of 430(50) ps for the 2(1)(+) state, and 54(6) ps for the 4(1)(+) state. An analysis method based around the Bateman equation will become especially important when using the charge plunger method for the cases where utilising coincidences between prompt gamma rays and recoils is not feasible.

Published
2021

46. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G

Author

European Commission, Swiss National Science Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Comunidad de Madrid, Vilhena, J. G., Ortega, María, Uhlig, Manuel R., García García, Ricardo, Pérez, Rubén, European Commission, Swiss National Science Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Comunidad de Madrid, Vilhena, J. G., Ortega, María, Uhlig, Manuel R., García García, Ricardo, and Pérez, Rubén

Abstract

[EN] Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive - a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime - where the mechanical response is linked to the presence of the water environment - followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spec

Published
2021

47. Lifetime measurements of yrast states in $$^{\mathbf {178}}$$Pt using the charge plunger method with a recoil separator

Author

Heery, J., primary, Barber, L., additional, Vilhena, J., additional, Singh, B. S. Nara, additional, Herzberg, R.-D., additional, Cullen, D. M., additional, Müller-Gatermann, C., additional, Beeton, G., additional, Bowry, M., additional, Dewald, A., additional, Grahn, T., additional, Greenlees, P. T., additional, Illana, A., additional, Julin, R., additional, Juutinen, S., additional, Keatings, J. M., additional, Leino, M., additional, Luoma, M., additional, O’Donnell, D., additional, Ojala, J., additional, Pakarinen, J., additional, Rahkila, P., additional, Ruotsalainen, P., additional, Sandzelius, M., additional, Sarén, J., additional, Sinclair, J., additional, Smith, J. F., additional, Sorri, J., additional, Spagnoletti, P., additional, Tann, H., additional, Uusitalo, J., additional, and Zimba, G., additional

Published
2021
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48. DESPEC Phase-0 campaign at GSI

Author

Polettini, M, Jazrawi, S, Chishti, M, Yaneva, A, Das, B, Banerjee, A, Hubbard, N, Mistry, A, Albers, H, Shearman, R, Gorska, M, Gerl, J, Regan, P H, Cederwall, B., Jolie, J, Alhomaidhi, S, Arici, T, Benzoni, G., Boutachkov, P., Davinson, T., Dickel, T., Haettner, E., Hall, O, Heggen, H., John, P R, Kojouharov, I., Kurz, N, Nara Singh, B.S., Pietri, S, Podolyakn, Zs., Rudigier, M., Sahin, E, Schaffner, H, Scheidenberger, Ch., Sharma, A, Vesic, J., Weick, H, Wollersheimc, H.J., Ahmed, U, Algora, A., Benito, J, Blazhev, A., Bruce, A, BRUNET, M, Canavan, R., Esmaylzadeh, A., Frailel, L.M., Grawe, H., Häfner, G., Kahl, D, Karayonchev, V., Kern, R, Kosir, G, Lozeva, R., Napiralla, P., Page, R, Petrache, C.M., Petrovic, J, Pietralla, N., Régis, J.M., Ruotsalainen, P., Sexton, L, Sánchez-Tembleque, V., Si, M., Vilhena, J. G., Werner, V, Wiederhold, J., Witt, W, Woods, P.J., Zimba, G., Istituto Nazionale di Fisica Nucleare [Ferrara] (INFN), Istituto Nazionale di Fisica Nucleare (INFN), Laboratoire de Physique des 2 Infinis Irène Joliot-Curie (IJCLab), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS]Physics [physics], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

49. A charge plunger device to measure the lifetimes of excited nuclear states where transitions are dominated by internal conversion

Author

Barber, L. (L.), Heery, J. (J.), Cullen, D. M. (D. M.), Singh, B. S. (B. S. Nara), Herzberg, R.-D. (R.-D.), Müller-Gatermann, C. (C.), Beeton, G. (G.), Bowry, M. (M.), Dewald, A. (A.), Grahn, T. (T.), Greenlees, P. T. (P. T.), Illana, A. (A.), Julin, R. (R.), Juutinen, S. (S.), Keatings, J. M. (J. M.), Luoma, M. (M.), O’Donnell, D. (D.), Ojala, J. (J.), Pakarinen, J. (J.), Rahkila, P. (P.), Ruotsalainen, P. (P.), Sandzelius, M. (M.), Sarén, J. (J.), Sinclair, J. (J.), Smith, J. F. (J. F.), Sorri, J. (J.), Spagnoletti, P. (P.), Tann, H. (H.), Uusitalo, J. (J.), Vilhena, J. (J.), and Zimba, G. (G.)

Subjects
DDCM, Plunger, RDDS, Charge plunger, Nuclear-state lifetimes
Abstract

A charge plunger device has been commissioned based on the DPUNS plunger (Taylor et al., 2013) using the in-flight mass separator MARA at the University of Jyväskylä. The ¹⁵²Sm(³²S,4n)¹⁸⁰ reaction was used to populate excited states in ¹⁸⁰. A lifetime measurement of the state \(2_1^+\) was performed by applying the charge plunger technique, which relies on the detection of the charge state-distribution of recoils rather than the detection of the emitted γ rays. This state was a good candidate to test the charge plunger technique as it has a known lifetime and depopulates through a converted transition that competes strongly with γ-ray emission. The lifetime of the \(2_1^+\) state was measured to be 480(10)ps, which is consistent with previously reported lifetimes that relied on the standard γ-ray techniques. The charge plunger technique is a complementary approach to lifetime measurements of excited states that depopulate through both γ-ray emission and internal conversion. In cases where it is not possible to detect Doppler-shifted γ rays, for example, in heavy nuclei where internal conversion dominates, it may well be the only feasible lifetime analysis approach.

Published
2020

50. Double-stranded RNA bending by AU-tract sequences

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, European Commission, Swiss National Science Foundation, Marin-González, Alberto, Aicart-Ramos, Clara, Marin-Baquero, Mikel, Martín-González, Alejandro, Suomalainen, Maarit, Kannan, Abhilash, Vilhena, J. G., Greber, Urs F., Moreno-Herrero, Fernando, Pérez, Rubén, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, European Commission, Swiss National Science Foundation, Marin-González, Alberto, Aicart-Ramos, Clara, Marin-Baquero, Mikel, Martín-González, Alejandro, Suomalainen, Maarit, Kannan, Abhilash, Vilhena, J. G., Greber, Urs F., Moreno-Herrero, Fernando, and Pérez, Rubén

Abstract

Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. However, in contrast to dsDNA, sequence-dependent structural features of dsRNA have received little attention. In this work, we demonstrate that the nucleotide sequence can induce a bend in a canonical Watson-Crick base-paired dsRNA helix. Using all-atom molecular dynamics simulations, we identified a sequence motif consisting of alternating adenines and uracils, or AU-tracts, that strongly bend the RNA double-helix. This finding was experimentally validated using atomic force microscopy imaging of dsRNA molecules designed to display macroscopic curvature via repetitions of phased AU-tract motifs. At the atomic level, this novel phenomenon originates from a localized compression of the dsRNA major groove and a large propeller twist at the position of the AU-tract. Moreover, the magnitude of the bending can be modulated by changing the length of the AU-tract. Altogether, our results demonstrate the possibility of modifying the dsRNA curvature by means of its nucleotide sequence, which may be exploited in the emerging field of RNA nanotechnology and might also constitute a natural mechanism for proteins to achieve recognition of specific dsRNA sequences.

Published
2020

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