4,637 research outputs found
Unsupervised machine learning for detection of phase transitions in off-lattice systems I. Foundations
We demonstrate the utility of an unsupervised machine learning tool for the
detection of phase transitions in off-lattice systems. We focus on the
application of principal component analysis (PCA) to detect the freezing
transitions of two-dimensional hard-disk and three-dimensional hard-sphere
systems as well as liquid-gas phase separation in a patchy colloid model. As we
demonstrate, PCA autonomously discovers order-parameter-like quantities that
report on phase transitions, mitigating the need for a priori construction or
identification of a suitable order parameter--thus streamlining the routine
analysis of phase behavior. In a companion paper, we further develop the method
established here to explore the detection of phase transitions in various model
systems controlled by compositional demixing, liquid crystalline ordering, and
non-equilibrium active forces
Unsupervised machine learning for detection of phase transitions in off-lattice systems II. Applications
We outline how principal component analysis (PCA) can be applied to particle
configuration data to detect a variety of phase transitions in off-lattice
systems, both in and out of equilibrium. Specifically, we discuss its
application to study 1) the nonequilibrium random organization (RandOrg) model
that exhibits a phase transition from quiescent to steady-state behavior as a
function of density, 2) orientationally and positionally driven equilibrium
phase transitions for hard ellipses, and 3) compositionally driven demixing
transitions in the non-additive binary Widom-Rowlinson mixture
Treating random sequential addition via the replica method
While many physical processes are non-equilibrium in nature, the theory and
modeling of such phenomena lag behind theoretical treatments of equilibrium
systems. The diversity of powerful theoretical tools available to describe
equilibrium systems has inspired strategies that map non-equilibrium systems
onto equivalent equilibrium analogs so that interrogation with standard
statistical mechanical approaches is possible. In this work, we revisit the
mapping from the non-equilibrium random sequential addition process onto an
equilibrium multi-component mixture via the replica method, allowing for
theoretical predictions of non-equilibrium structural quantities. We validate
the above approach by comparing the theoretical predictions to numerical
simulations of random sequential addition.Comment: 32 pages, 3 figure
The Rhetoric of Restraint and the Ideology of Activism
Part of Symposium: The Rehnquist Court in Empirical and Statistical Retrospectiv
Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock
During heat shock and other proteotoxic stresses, cells regulate multiple steps in gene expression in order to globally repress protein synthesis and selectively upregulate stress response proteins. Splicing of several mRNAs is known to be inhibited during heat stress, often meditated by SRp38, but the extent and specificity of this effect have remained unclear. Here, we examined splicing regulation genome-wide during heat shock in mouse fibroblasts. We observed widespread retention of introns in transcripts from ~1,700 genes, which were enriched for tRNA synthetase, nuclear pore, and spliceosome functions. Transcripts with retained introns were largely nuclear and untranslated. However, a group of 580+ genes biased for oxidation reduction and protein folding functions continued to be efficiently spliced. Interestingly, these unaffected transcripts are mostly cotranscriptionally spliced under both normal and stress conditions, whereas splicing-inhibited transcripts are mostly spliced posttranscriptionally. Altogether, our data demonstrate widespread repression of splicing in the mammalian heat stress response, disproportionately affecting posttranscriptionally spliced genes.Weizmann Institute of Science (Postdoctoral Award for Advancing Women in Science)European Molecular Biology Organization (Long-term Fellowship)Machiah FoundationNational Science Foundation (U.S.) (Grant 0821391)National Institutes of Health (U.S.
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