Topic: energy landscape

Hopfield networks are artificial neural networks which store memory patterns on the states of their neurons by choosing recurrent connection weights and update rules such that the energy landscape of the network forms attractors around the memories. How many stable, sufficiently-attracting memory patterns can we store in such a network using N neurons? The answer depends on the choice of weights and update rule. Inspired by setwise connectivity in biology, we extend Hopfield networks by adding setwise connections and embedding these connections in a simplicial complex. Simplicial complexes are

In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (the minimal chromatin model) explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data is presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. This model was generalized by u