182 research outputs found
Diagnosing weakly first-order phase transitions by coupling to order parameters
The hunt for exotic quantum phase transitions described by emergent
fractionalized degrees of freedom coupled to gauge fields requires a precise
determination of the fixed point structure from the field theoretical side, and
an extreme sensitivity to weak first-order transitions from the numerical side.
Addressing the latter, we revive the classic definition of the order parameter
in the limit of a vanishing external field at the transition. We demonstrate
that this widely understood, yet so far unused approach provides a diagnostic
test for first-order versus continuous behavior that is distinctly more
sensitive than current methods. We first apply it to the family of -state
Potts models, where the nature of the transition is continuous for and
turns (weakly) first order for , using an infinite system matrix product
state implementation. We then employ this new approach to address the unsettled
question of deconfined quantum criticality in the N\'eel to valence
bond solid transition in two dimensions, focusing on the square lattice -
model. Our quantum Monte Carlo simulations reveal that both order parameters
remain finite at the transition, directly confirming a first-order scenario
with wide reaching implications in condensed matter and quantum field theory.Comment: Published versio
Extracting the Speed of Light from Matrix Product States
We provide evidence that the spectrum of the local effective Hamiltonian and
the transfer operator in infinite-system matrix product state simulations are
identical up to a global rescaling factor, i.e.~the speed of light of the
system, when the underlying system is described by a 1+1 dimensional CFT. We
provide arguments for this correspondence based on a path integral point of
view. This observation turns out to yield very precise estimates for the speed
of light in practice, confirming exact results to high precision where
available, but also allowing us to finally determine the speed of light of the
non-integrable, critical Heisenberg chains with half-integer spin
with unprecedented accuracy. We also show that the same technology
applied to doped Hubbard ladders provides highly accurate velocities for a
range of dopings. Combined with measurements of compressibilities we present
new results for the Luttinger liquid parameter in the Luther-Emery regime of
doped Hubbard ladders, outperforming earlier approaches based on the fitting of
real-space correlation functions.Comment: 6 pages, 4 figures, 1 table, published versio
Kinetic proofreading of gene activation by chromatin remodeling
Gene activation in eukaryotes involves the concerted action of histone tail
modifiers, chromatin remodellers and transcription factors, whose precise
coordination is currently unknown. We demonstrate that the experimentally
observed interactions of the molecules are in accord with a kinetic
proofreading scheme. Our finding could provide a basis for the development of
quantitative models for gene regulation in eukaryotes based on the
combinatorical interactions of chromatin modifiers.Comment: 8 pages, 2 Figures; application adde
Programmable quantum simulation of 2D antiferromagnets with hundreds of Rydberg atoms
Quantum simulation using synthetic systems is a promising route to solve
outstanding quantum many-body problems in regimes where other approaches,
including numerical ones, fail. Many platforms are being developed towards this
goal, in particular based on trapped ions, superconducting circuits, neutral
atoms or molecules. All of which face two key challenges: (i) scaling up the
ensemble size, whilst retaining high quality control over the parameters and
(ii) certifying the outputs for these large systems. Here, we use programmable
arrays of individual atoms trapped in optical tweezers, with interactions
controlled by laser-excitation to Rydberg states to implement an iconic
many-body problem, the antiferromagnetic 2D transverse field Ising model. We
push this platform to an unprecedented regime with up to 196 atoms manipulated
with high fidelity. We probe the antiferromagnetic order by dynamically tuning
the parameters of the Hamiltonian. We illustrate the versatility of our
platform by exploring various system sizes on two qualitatively different
geometries, square and triangular arrays. We obtain good agreement with
numerical calculations up to a computationally feasible size (around 100
particles). This work demonstrates that our platform can be readily used to
address open questions in many-body physics.Comment: Main text: 6 pages, 4 figures. Supplementary information: 10 pages,
16 figure
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Complete field-induced spectral response of the spin-1/2 triangular-lattice antiferromagnet CsYbSe2
Fifty years after Anderson’s resonating valence-bond proposal, the spin-1/2 triangular-lattice Heisenberg antiferromagnet (TLHAF) remains the ultimate platform to explore highly entangled quantum spin states in proximity to magnetic order. Yb-based delafossites are ideal candidate TLHAF materials, which allow experimental access to the full range of applied in-plane magnetic fields. We perform a systematic neutron scattering study of CsYbSe2, first proving the Heisenberg character of the interactions and quantifying the second-neighbor coupling. We then measure the complex evolution of the excitation spectrum, finding extensive continuum features near the 120°-ordered state, throughout the 1/3-magnetization plateau and beyond this up to saturation. We perform cylinder matrix-product-state (MPS) calculations to obtain an unbiased numerical benchmark for the TLHAF and spectacular agreement with the experimental spectra. The measured and calculated longitudinal spectral functions reflect the role of multi-magnon bound and scattering states. These results provide valuable insight into unconventional field-induced spin excitations in frustrated quantum materials
Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data
<p>Abstract</p> <p>Background</p> <p>Using gene co-expression analysis, researchers were able to predict clusters of genes with consistent functions that are relevant to cancer development and prognosis. We applied a weighted gene co-expression network (WGCN) analysis algorithm on glioblastoma multiforme (GBM) data obtained from the TCGA project and predicted a set of gene co-expression networks which are related to GBM prognosis.</p> <p>Methods</p> <p>We modified the Quasi-Clique Merger algorithm (QCM algorithm) into edge-covering Quasi-Clique Merger algorithm (eQCM) for mining weighted sub-network in WGCN. Each sub-network is considered a set of features to separate patients into two groups using K-means algorithm. Survival times of the two groups are compared using log-rank test and Kaplan-Meier curves. Simulations using random sets of genes are carried out to determine the thresholds for log-rank test p-values for network selection. Sub-networks with p-values less than their corresponding thresholds were further merged into clusters based on overlap ratios (>50%). The functions for each cluster are analyzed using gene ontology enrichment analysis.</p> <p>Results</p> <p>Using the eQCM algorithm, we identified 8,124 sub-networks in the WGCN, out of which 170 sub-networks show p-values less than their corresponding thresholds. They were then merged into 16 clusters.</p> <p>Conclusions</p> <p>We identified 16 gene clusters associated with GBM prognosis using the eQCM algorithm. Our results not only confirmed previous findings including the importance of cell cycle and immune response in GBM, but also suggested important epigenetic events in GBM development and prognosis.</p
MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure
Abstract Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw.http://deepblue.lib.umich.edu/bitstream/2027.42/78256/1/1471-2105-11-504.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/2/1471-2105-11-504-S1.PDFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/3/1471-2105-11-504-S2.ZIPhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/4/1471-2105-11-504.pdfPeer Reviewe
An in vitro assay to study the recruitment and substrate specificity of chromatin modifying enzymes
Post-translational modifications of core histones play an important role in regulating fundamental biological processes such as DNA repair, transcription and replication. In this paper, we describe a novel assay that allows sequential targeting of distinct histone modifying enzymes to immobilized nucleosomal templates using recombinant chimeric targeting molecules. The assay can be used to study the histone substrate specificity of chromatin modifying enzymes as well as whether and how certain enzymes affect each other's histone modifying activities. As such the assay can help to understand how a certain histone code is established and interpreted
Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI
Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo
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