Zobrazeno 1 - 10
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pro vyhledávání: '"Hummer, Gerhard"'
Autor:
Nüesch, Mark F., Pietrek, Lisa, Holmstrom, Erik D., Nettels, Daniel, von Roten, Valentin, Kronenberg-Tenga, Rafael, Medalia, Ohad, Hummer, Gerhard, Schuler, Benjamin
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecul
Externí odkaz:
http://arxiv.org/abs/2312.14734
In molecular dynamics simulations in the NPT ensemble at constant pressure, the size and shape of the periodic simulation box fluctuate with time. For particle images far from the origin, the rescaling of the box by the barostat results in unbounded
Externí odkaz:
http://arxiv.org/abs/2303.09418
Markov-chain Monte Carlo algorithms rely on trial moves that are either rejected or accepted based on certain criteria. Here, we provide an efficient algorithm to generate random rotation matrices in four dimensions (4D) covering an arbitrary pre-def
Externí odkaz:
http://arxiv.org/abs/2302.06230
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain growth (HCG
Externí odkaz:
http://arxiv.org/abs/2210.16167
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments it is now
Externí odkaz:
http://arxiv.org/abs/2205.05991
Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the representation
Externí odkaz:
http://arxiv.org/abs/2204.05121
Autor:
Wang, Jianhui, Heinz, Marcel, Han, Kang, Shah, Varun J., Hasselbeck, Sebastian, Schwalm, Martin P., Rathore, Rajeshwari, Hummer, Gerhard, Zhou, Jun, Dikic, Ivan, Cheng, Xinlai
Publikováno v:
In Cell Reports Physical Science 15 May 2024 5(5)
Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations
Autor:
Palacio-Rodriguez, Karen, Vroylandt, Hadrien, Stelzl, Lukas S., Pietrucci, Fabio, Hummer, Gerhard, Cossio, Pilar
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent metadynamics it is
Externí odkaz:
http://arxiv.org/abs/2109.11360
Autor:
Köfinger, Jürgen, Hummer, Gerhard
Publikováno v:
Journal of Chemical Physics; 3/21/2024, Vol. 160 Issue 11, p1-12, 12p
Publikováno v:
Nat Comput Sci 3, 334 345 (2023)
Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Understanding the physical mechanisms that govern the formation of molecular complexes and crystals i
Externí odkaz:
http://arxiv.org/abs/2105.06673