Results 11 to 20 of about 1,038,801 (318)

Molecular dynamics simulations [PDF]

Journal of Physics: Condensed Matter, 2004
38 pages, 11 figures, to appear in J.
Binder, K., Horbach, J., Kob, W., Paul, W., Varnik, F.   +4 more
openaire   +3 more sources

Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2

Nature Communications, 2023
NIPBL is considered the cohesin loader. Here, the authors report that a drastic reduction of NIPBL levels reduces chromatin-bound cohesin-STAG2 genome wide while cohesin-STAG1 increases and can still be found at CTCF-bound sites but cannot form loops.
Dácil Alonso-Gil, Ana Cuadrado, Daniel Giménez-Llorente, Miriam Rodríguez-Corsino, Ana Losada   +4 more
doaj   +1 more source

Molecular dynamics simulations in photosynthesis [PDF]

, 2020
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale.
Marrink, Siewert Jan, Liguori, Nicoletta; id_orcid, Marrink, Siewert J, Thallmair, Sebastian, Croce, Roberta, Marrink, Siewert J; id_orcid, Liguori, Nicoletta, Croce, Roberta; id_orcid   +7 more
core   +1 more source

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling [PDF]

, 2023
Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA.
Marrink, Siewert J, Lu, Senbao, Marrink, Siewert J; id_orcid, Wassenaar, Tsjerk A., Korkin, Dmitry, Pezeshkian, Weria; id_orcid, Marrink, Siewert J., Arkhipova, Valeria, Pezeshkian, Weria, Wassenaar, Tsjerk A, Narykov, Oleksandr, Solodovnikov, Alexey, Grünewald, Fabian   +12 more
core   +1 more source

Symmetric Molecular Dynamics

Journal of Chemical Theory and Computation, 2022
We derive a formulation of molecular dynamics that generates only symmetric configurations. We implement it for all 2D planar and 3D space groups. An atlas of 2D Lennard-Jones crystals under all planar groups is created with symmetric molecular dynamics.
Sam Cox, Andrew D. White
openaire   +3 more sources

Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages

eLife, 2022
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex,
Nadia M Huisjes, Thomas M Retzer, Matthias J Scherr, Rohit Agarwal, Lional Rajappa, Barbara Safaric, Anita Minnen, Karl E Duderstadt   +7 more
doaj   +1 more source

Unbiased PCR-free spatio-temporal mapping of the mtDNA mutation spectrum reveals brain region-specific responses to replication instability

BMC Biology, 2020
Background The accumulation of mtDNA mutations in different tissues from various mouse models has been widely studied especially in the context of mtDNA mutation-driven ageing but has been confounded by the inherent limitations of the most widely used ...
Emilie Kristine Bagge, Noriko Fujimori-Tonou, Mie Kubota-Sakashita, Takaoki Kasahara, Tadafumi Kato   +4 more
doaj   +1 more source

Molecular dynamics

The Journal of Logic and Algebraic Programming, 2002
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Bergstra, J.A., Bethke, I.
openaire   +5 more sources

Absolute entropies from molecular dynamics simulation trajectories [PDF]

, 2000
Absolute entropies was calculated using the molecular dynamics (MD) simulation trajectories. The heuristic formula for the calculation of entropies from the covariance matrix of atom-positional fluctuations was tested.
van Gunsteren, Wilfred F., Mark, A. E., Schafer, Heiko, van Gunsteren, W. F., Wilfred F. van Gunsteren, Mark, Alan E., Alan E. Mark, Heiko Schäfer, Schafer, H.   +8 more
core   +1 more source

Study on the temperature dependence of the bulk modulus of polyisoprene by molecular dynamics simulations [PDF]

, 2008
The temperature dependence of the bulk modulus of polyisoprene has been studied using molecular dynamics simulations. Virtual polyisoprenes have been submitted to volume contractions above and below the glass transition. Bulk modulus has been observed to
GILORMINI, Pierre, DIANI, Julie, FAYOLLE, Bruno   +2 more
core   +1 more source