108 citations · 187 across the 9 of their papers we have counts for
9 papers
Classification of Saccharomyces cerevisiae promoter regions into distinct chromatin classes reveals the existence of nucleosome-depleted hotspots of transcription factor occupancy
Junbai Wang, Lucas D. Ward, Harmen J. Bussemaker
Transcription factors (TF) play an essential role in the cell as locus- and condition-specific recruiters of transcriptional machinery or chromatin-modifying complexes. However, pr…
Thermodynamic stability of folded proteins against mutations
H. J. Bussemaker, D. Thirumalai, J. K. Bhattacharjee
By balancing the average energy gap with its typical change due to mutations for protein-like heteropolymers with M residues, we show that native states are unstable to mutations o…
Mean-field analysis of a dynamical phase transition in a cellular automaton model for collective motion
H. J. Bussemaker, A. Deutsch, E. Geigant
A cellular automaton model is presented for random walkers with biologically motivated interactions favoring local alignment and leading to collective motion or swarming behavior.…
Effective-field-theory approach to persistent currents
H. J. Bussemaker, T. R. Kirkpatrick
Using an effective-field-theory (nonlinear sigma model) description of interacting electrons in a disordered metal ring enclosing magnetic flux, we calculate the moments of the per…
Theory for Diffusion-Limited Oscillating Chemical Reactions
H. J. Bussemaker, R. Brito
A kinetic description of lattice-gas automaton models for reaction-diffusion systems is presented. It provides corrections to the mean-field rate equations in the diffusion-limited…
Microscopic Theory for Long Range Spatial Correlations in Lattice Gas Automata
H. J. Bussemaker, M. H. Ernst
Lattice gas automata with collision rules that violate the conditions of semi-detailed-balance exhibit algebraic decay of equal time spatial correlations between fluctuations of co…
Algebraic Spatial Correlations and Non-Gibbsian Equilibrium States
M. H. Ernst, H. J. Bussemaker
Non-Gibbsian stationary states occur in dissipative non-equilibrium systems. They are closely connected with the lack of detailed balance and the absence of a fluctuation-dissipati…
Generalized Boltzmann Equation for Lattice Gas Automata
H. J. Bussemaker, M. H. Ernst, J. W. Dufty
In this paper, for the first time a theory is formulated that predicts velocity and spatial correlations between occupation numbers that occur in lattice gas automata violating sem…
Instabilities and Patterns (minor technical modifications)
M. H. Ernst, H. J. Bussemaker
Violation of (semi)-detailed balance conditions in lattice gas automata gives rise to unstable spatial fluctuations that lead to phase separation and pattern formation in spinodal…