Related papers: Frustration in Biomolecules
A misfit parameter is used to characterize the degree of frustration of ordered and disordered systems. It measures the increase of the ground-state energy due to frustration in comparison with that of a relevant reference state. The misfit…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
Geometric frustration is recognized to generate complex morphologies in self-assembling particulate and molecular systems. In bulk states, frustrated drives structured arrays of topological defects. In the dilute limit, these systems have…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Neurons in the brain are often finely tuned for specific task variables. Moreover, such disentangled representations are highly sought after in machine learning. Here we mathematically prove that simple biological constraints on neurons,…
Geometric frustration leads to complex phases of matter with exotic properties. Antiferromagnets on triangular lattices and square ice are two simple models of geometrical frustration. We map their highly degenerated ground-state phase…
Ginzburg-Landau theory of continuous phase transitions implicitly assumes that microscopic changes are negligible in determining the thermodynamic properties of the system. In this work we provide an example that clearly contrasts with this…
The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
From multicellular tissues to bacterial colonies, three dimensional cellular structures arise through the interaction of cellular activities and mechanical forces. Simple bacterial communities provide model systems for analyzing such…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
The design of desired behaviors in mechanical metamaterials has produced remarkable advances but has generally neglected two aspects - the inevitable presence of undesired behaviors and the role of dynamics in avoiding such behaviors.…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Quantum spin chains - the prototypical model for coupled two-level systems - offer a fertile playground both for fundamental and technological applications, ranging from the theory of thermalization to quantum computation. The effects of…
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior…