260 citations · 2.2k across the 37 of their papers we have counts for
37 papers
Unwrapping NPT simulations to calculate diffusion coefficients
Jakob Tómas Bullerjahn, Sören von Bülow, Maziar Heidari +2
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…
Structural ensembles of disordered proteins from hierarchical chain growth and simulation
Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer
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 dynamic…
Rebinding kinetics from single-molecule force spectroscopy experiments close to equilibrium
Jakob Tómas Bullerjahn, Gerhard Hummer
Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. Howev…
Small ionic radii limit time step in Martini 3 molecular dynamics simulations
Balázs Fábián, Sebastian Thallmair, Gerhard Hummer
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…
Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations
Karen Palacio-Rodriguez, Hadrien Vroylandt, Lukas S. Stelzl +3
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…
Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments
Hendrik Jung, Roberto Covino, A Arjun +2
Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Understanding the physical mech…