Scale-free static and dynamical correlations in melts of monodisperse and Flory-distributed homopolymers: A review of recent bond-fluctuation model studies

It has been assumed until very recently that all long-range correlations are screened in three-dimensional melts of linear homopolymers on distances beyond the correlation length $\xi$ characterizing the decay of the density fluctuations. Summarizing simulation results obtained by means of a variant of the bond-fluctuation model with finite monomer excluded volume interactions and topology violating local and global Monte Carlo moves, we show that due to an interplay of the chain connectivity and the incompressibility constraint, both static and dynamical correlations arise on distances $r \gg \xi$. These correlations are scale-free and, surprisingly, do not depend explicitly on the compressibility of the solution. Both monodisperse and (essentially) Flory-distributed equilibrium polymers are considered.Comment: 60 pages, 49 figure

Classical Density Functional Study on Interfacial Structure and Differential Capacitance of Ionic Liquids near Charged Surfaces

We have implemented a generic coarse-grained model for the aromatic ionic liquid [CnMIM+][Tf2N-]. Various lengths for the alkyl chain on the cation define a homologous series, whose electric properties are expected to vary in a systematic way. Within the framework of a classical density functional theory, the interfacial structures of members of this series are compared over a range of surface charge densities, alkyl chain lengths, and surface geometries. The differential capacitance of the electric double layer, formed by ionic liquids against a charged electrode, is calculated as a function of the surface electric potential. A comparison of planar, cylindrical, and spherical surfaces confirms that the differential capacitance increases and varies less with surface potential as the surface curvature increases. Our results are in qualitative agreement with recent atomistic simulations

Molecular dynamics simulation studies of the interactions between ionic liquids and amino acids in aqueous solution

Although the understanding of the influence of ionic liquids (ILs) on the solubility behavior of biomolecules in aqueous solutions is relevant for the design and optimization of novel biotechnological processes, the underlying molecular-level mechanisms are not yet consensual or clearly elucidated. In order to contribute to the understanding of the molecular interactions established between amino acids and ILs in aqueous media, classical molecular dynamics (MD) simulations were performed for aqueous solutions of five amino acids with different structural characteristics (glycine, alanine, valine, isoleucine, and glutamic acid) in the presence of 1-butyl-3-methylimidazolium bis(trifluoromethyl)sulfonyl imide. The results from MD simulations enable to relate the properties of the amino acids, namely their hydrophobicity, to the type and strength of their interactions with ILs in aqueous solutions and provide an explanation for the direction and magnitude of the solubility phenomena observed in [IL + amino acid + water] systems by a mechanism governed by a balance between competitive interactions of the IL cation, IL anion, and water with the amino acids

The role of ATF-2 in oncogenesis

Activating Transcription Factor-2 is a sequence-specific DNA-binding protein that belongs to the bZIP family of proteins and plays diverse roles in the mammalian cells. In response to stress stimuli, it activates a variety of gene targets including cyclin A, cyclin D and c-jun, which are involved in oncogenesis in various tissue types. ATF-2 expression has been correlated with maintenance of a cancer cell phenotype. However, other studies demonstrate an antiproliferative or apoptotic role for ATF-2. In this review, we summarize the signaling pathways that activate ATF-2, as well as its downstream targets. We examine the role of ATF-2 in carcinogenesis with respect to other bZIP proteins, using data from studies in human cancer cell lines, human tumours and mouse models, and we propose a potential model for its function in carcinogenesis, as well as a theoretical basis for its utility in anticancer drug design. © 2008 Wiley Periodicals, Inc

In silico methods for the identification of diagnostic and favorable prognostic markers in acute myeloid leukemia

Acute myeloid leukemia (AML), the most common type of acute leukemia in adults, is mainly asymptomatic at early stages and progresses/recurs rapidly and frequently. These attributes necessitate the identification of biomarkers for timely diagnosis and accurate prognosis. In this study, differential gene expression analysis was performed on large-scale transcriptomics data of AML patients versus corresponding normal tissue. Weighted gene co-expression network analysis was conducted to construct networks of co-expressed genes, and detect gene modules. Finally, hub genes were identified from selected modules by applying network-based methods. This robust and integrative bioinformatics approach revealed a set of twenty-four genes, mainly related to cell cycle and immune response, the diagnostic significance of which was subsequently compared against two independent gene expression datasets. Furthermore, based on a recent notion suggesting that molecular characteristics of a few, unusual patients with exceptionally favorable survival can provide insights for improving the outcome of individuals with more typical disease trajectories, we defined groups of long-term survivors in AML patient cohorts and compared their transcriptomes versus the general population to infer favorable prognostic signatures. These findings could have potential applications in the clinical setting, in particular, in diagnosis and prognosis of AML. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Estrogen receptor α and β in uterine fibroids: a basis for altered estrogen responsiveness

Objective: To investigate the relative expression and the DNA-binding status of estrogen receptors α and β in fibroids and normal myometrial tissue to explore the molecular basis of altered estrogen responsiveness of leiomyomas. Design: Biopsy samples from uterine fibroids and adjacent normal myometrial tissue at the follicular phase of the menstrual cycle. Setting: Aretaieio University Hospital and the National Hellenic Research Foundation, Athens, Greece. Patient(s): Thirty-five patients who underwent hysterectomy or myomectomy because of myoma symptoms. Intervention(s): None. Main Outcome Measure(s): Deoxyribonucleic acid-binding status of estrogen receptors α and β. Result(s): The level of messenger RNA expression of estrogen receptor α and β and the level of estrogen receptor as a whole are increased on average to a similar extent in leiomyomas compared with normal myometrium. Occasionally, however, estrogen receptor α is disproportionately increased in leiomyomas, and this appears to increase the amount of estrogen receptor α that binds to the estrogen-responsive element of estrogen target genes as homodimer rather than as heterodimer with estrogen receptor β. Conclusion(s): The estrogen receptor α-to-estrogen receptor β expression ratio rather than the individual expression levels determines the fraction of DNA-binding homodimers of estrogen receptor α and possibly the growth potential of myomas. © 2008 American Society for Reproductive Medicine