Quantifying disorder through conditional entropy: an application to fluid mixing.
Giovanni B. Brandani,Marieke Schor,Cait E. MacPhee,Helmut Grubmüller,Ulrich Zachariae,Ulrich Zachariae,Davide Marenduzzo +6 more
TLDR
In this article, the authors present a method to quantify the extent of disorder in a system by using conditional entropies, and apply it to mixing and demixing in multicomponent fluid membranes.Abstract:
In this paper, we present a method to quantify the extent of disorder in a system by using conditional entropies. Our approach is especially useful when other global, or mean field, measures of disorder fail. The method is equally suited for both continuum and lattice models, and it can be made rigorous for the latter. We apply it to mixing and demixing in multicomponent fluid membranes, and show that it has advantages over previous measures based on Shannon entropies, such as a much diminished dependence on binning and the ability to capture local correlations. Further potential applications are very diverse, and could include the study of local and global order in fluid mixtures, liquid crystals, magnetic materials, and particularly biomolecular systems.read more
Citations
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Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi,Aaron T. L. Lun,Michael D Morgan,John C. Marioni,John C. Marioni,John C. Marioni +5 more
TL;DR: This work presents a strategy for batch correction based on the detection of mutual nearest neighbors (MNNs) in the high-dimensional expression space and demonstrates the superiority of this approach compared with existing methods by using both simulated and real scRNA-seq data sets.
Journal ArticleDOI
Systems protobiology: origin of life in lipid catalytic networks.
TL;DR: The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.
Journal ArticleDOI
Stochastic Model of Supercoiling-Dependent Transcription
Chris A. Brackley,J. Johnson,A. Bentivoglio,Samuel Corless,Nick Gilbert,Giuseppe Gonnella,Davide Marenduzzo +6 more
TL;DR: There is a sharp crossover from a regime where torsional stresses relax quickly and gene transcription is random, to one where gene expression is highly correlated and tightly regulated by supercoiling.
Journal ArticleDOI
Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures
TL;DR: A critical study of system size impact on lipid domain phase separation into liquid-ordered and liquid-disordered macroscale domains in ternary lipid mixtures is presented and an analytical Flory-Huggins model is developed which is recursively validated using simulation and experimental data.
Journal ArticleDOI
The mixing-demixing phase diagram of ultracold heteronuclear mixtures in a ring trimer.
TL;DR: This study derives the complete mixing-demixing phase-diagram relevant to a bosonic binary mixture confined in a ring trimer and modeled within the Bose-Hubbard picture and proposes an experimental realization based on a realistic optical-tweezers system and on the bosonic mixture 23Na + 39K, thanks to the large tunability of their intra- and inter-species scattering lengths.
References
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