Related papers: Frustration, dynamics and catalysis
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Biological cells are able to adapt their behaviour in response to environmental cues. Durotaxis is a phenomenon in which cells adjust their migration depending on the mechanical properties of a surrounding substrate. Although durotaxis has…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
The study of entanglement and magic properties in topologically frustrated systems suggests that, in the thermodynamic limit, these quantities decompose into two distinct contributions. One is determined by the specific nature of the model…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
We investigate the full phase diagram of a column of grains near jamming, as a function of varying levels of frustration. Frustration is modelled by the effect of two opposing fields on a grain, due respectively to grains above and below…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…
The importance of molecular-scale forces in sculpting biological form and function has been acknowledged for more than a century. Accounting for forces in biology is a problem that lies at the intersection of soft condensed matter physics,…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do…
Cognitive function depends on an adaptive balance between flexible dynamics and integrative processes in distributed cortical networks. Patterns of zero-lag synchrony likely underpin numerous perceptual and cognitive functions.…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…
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…
Active fluctuations are detected in a growing number of systems due to self-propulsion mechanisms or collisions with active environment. They drive the system far from equilibrium and can induce phenomena which at equilibrium states are…
By characterizing the dynamics of idealized lattice models with a tunable kinetic constraint, we explore the different ways in which dynamical facilitation manifests itself within the local dynamics of glassy materials. Dynamical…
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 apply to funnel design for a single conformation. The maximum…