Related papers: Entropic contributions to the splicing process
In this Letter, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale,…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…
A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules.…
We present a deterministic way of finding contraction maps for candidate holographic entanglement entropy inequalities modulo choices due to actual degeneracy. We characterize its complexity and give an argument for the completeness of the…
We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids…
Biomolecular condensates are cellular phase-separated droplets that usually exhibit a viscoelastic mechanical response. A behavior rationalized by modeling the complex molecules that make up a condensate as stickers and spacers, which…
Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently several high-resolution imaging techniques…
We investigate the effect of mobile polymer brushes on proteins embedded in biological membranes by employing both Asakura-Oosawa type of theoretical model and coarse-grained molecular dynamics simulations. The brush polymer-induced…
Membrane organization is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is to understand the lateral heterogeneous structures in membranes and membrane fluidity in the presence of…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
This paper is concerned with designing self-driven fitness functions for Embedded Evolutionary Robotics. The proposed approach considers the entropy of the sensori-motor stream generated by the robot controller. This entropy is computed…
I consider motivation and value-alignment in AI systems from the perspective of (constrained) entropy maximization. Though the structures encoding knowledge in any physical system can be understood as energetic constraints, only living…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
Self-organization is the autonomous assembly of a network of interacting components into a stable, organized pattern. This article shows that the process of self-assembly can be encoded in terms of evolutionary entropy, a statistical…
Transformers are strong baselines in both vision and language because self-attention captures long-range dependencies across tokens. However, the cost of self-attention grows quadratically with the number of tokens. Patch pruning mitigates…
We live within an increasingly technological, information-laden environment for the first time in human evolution.This subjects us, and will continue to subject us in an accelerating fashion, to an unremitting exposure to meaningful…