In this work we study the entropy of the Gibbs state corresponding to a graph. The Gibbs state is obtained from the Laplacian, normalized Laplacian or adjacency matrices associated with a graph. We calculated the entropy of the Gibbs state for a few classes of graphs and studied their behavior with changing graph order and temperature. We illustrate our analytical results with numerical simulations for Erdős-Rényi, Watts-Strogatz, Barabási-Albert and Chung-Lu graph models and a few real-world graphs. Our results show that the behavior of Gibbs entropy as a function of the temperature differs for a choice of real networks when compared to the random Erdős-Rényi graphs.
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http://dx.doi.org/10.1038/s41598-020-78626-2 | DOI Listing |
Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells.
View Article and Find Full Text PDFBinding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions.
View Article and Find Full Text PDFIn studies of individuals of primarily European genetic ancestry, common and low-frequency variants and rare coding variants have been found to be associated with the risk of bipolar disorder (BD) and schizophrenia (SZ). However, less is known for individuals of other genetic ancestries or the role of rare non-coding variants in BD and SZ risk. We performed whole genome sequencing of African American individuals: 1,598 with BD, 3,295 with SZ, and 2,651 unaffected controls (InPSYght study).
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Centre for Surface Science, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata 700032, India.
Interaction of a novel dihydroxy dibenzoazacrown (HDTC) with various surfactants of different charges, for example, anionic (sodium dodecylsulfate, SDS), cationic (dodecyl trimethylammonium bromide, DTAB), cationic gemini (butanediyl-1,4-bis(dimethylcetylammonium bromide), 16-4-16), ionic liquid (1-hexadecyl-3-methylimidazolium chloride, CMImCl), and nonionic (polyoxyethylene sorbitan monostearate, Tween-60), has been investigated at a widespread range of surfactant concentrations (including premicellar, micellar, and postmicellar regime) in 15% (v/v) EtOH medium at room temperature. Several experimental techniques, viz., tensiometry, UV-vis spectroscopy, and steady-state fluorimetry, are implemented to explicate these interactions.
View Article and Find Full Text PDFACS Omega
December 2024
Faculty of Health Science, University of Ss. Cyril and Methodius, 91701 Trnava, Slovakia.
A hybrid B3LYP version of the Density Functional Theory was applied in full geometry optimization followed by vibrational analysis of mustard-type molecules acting as antiblood cancer agents: melphalan and bendamustine. All calculations were performed with water as a solvent. In addition to the ground-state properties (dipole moment, quadrupole moment, dipole polarizability, solvated surface and volume, zero-point vibration energy, total entropic term), properties that characterize adiabatic redox processes (ionization energy, electron affinity, molecular electronegativity, chemical hardness, electrophilicity index) together with the absolute oxidation and reduction potentials were evaluated.
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