63 citations · 81 across the 4 of their papers we have counts for
4 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…
Efficient generation of random rotation matrices in four dimensions
Jakob Tómas Bullerjahn, Balázs Fábián, Gerhard Hummer
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 r…
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments
Jakob Tómas Bullerjahn, Gerhard Hummer
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting…
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure
Sören von Bülow, Jakob Tómas Bullerjahn, Gerhard Hummer
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using th…