105 citations · 629 across the 35 of their papers we have counts for
12 papers · 1 filter
Surfactancy in a tadpole model of proteins
Oliver T. Dyer, Robin C. Ball
We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexib…
Influence of thermal fluctuations on active diffusion at large Péclet numbers
Oliver T. Dyer, Robin C. Ball
Wavelet Monte Carlo dynamics simulations are used to study the dynamics of passive particles in the presence of microswimmers, taking account of the often-omitted thermal motion al…
Why clothes don't fall apart: tension transmission in staple yarns
Patrick B. Warren, Robin C. Ball, Raymond E. Goldstein
The problem of how staple yarns transmit tension is addressed within abstract models in which the Amontons-Coulomb friction laws yield a linear programming (LP) problem for the ten…
Wavelet Monte Carlo dynamics: a new algorithm for simulating the hydrodynamics of interacting Brownian particles
Oliver T Dyer, Robin C Ball
We develop a new algorithm for the Brownian dynamics of soft matter systems that evolves time by spatially correlated Monte Carlo moves. The algorithm uses vector wavelets as its b…
Polymer Translocation out of Planar Confinements
Debabrata Panja, Gerard T. Barkema, Robin C. Ball
Polymer translocation in three dimensions out of planar confinements is studied in this paper. Three membranes are located at , and . These membranes are impenet…
Pore-blockade Times for Field-Driven Polymer Translocation
Henk Vocks, Debabrata Panja, Gerard T. Barkema +1
We study pore blockade times for a translocating polymer of length , driven by a field across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we con…
Effect of Anomalous Dynamics on Unbiased Polymer Translocation
Debabrata Panja, Gerard T. Barkema, Robin C. Ball
In this paper, we investigate the microscopic dynamics of a polymer of length translocating through a narrow pore. Characterization of its purportedly anomalous dynamics has so…
Folding and form: Insights from lattice simulations
P. F. N. Faisca, M. M. Telo da Gama, R. C. Ball
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding me…
Topological complexity, contact order and protein folding rates
P. F. N. Faisca, R. C. Ball
Monte Carlo simulations of protein folding show the emergence of a strong correlation between the relative contact order parameter, CO, and the folding time, t, of two-state foldin…
Thermodynamic control and dynamical regimes in protein folding
P. F. N. Faisca, R. C. Ball
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small p…
Kinetic Capacity of a Protein
Robin C Ball, Thomas M A Fink
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we app…
Thermodynamic Capacity of a Protein
Thomas M A Fink, Robin C Ball
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and in…