Condensed Matter Theory

Abstract:

We consider the XY spin chain with arbitrary time-dependent magnetic field and anisotropy. We argue that a certain subclass of Gaussian states, called Coherent Ensemble (CE) following [1], provides a natural and unified framework for out-of-equilibrium physics in this model. We show that all correlation functions in the CE can be computed using form factor expansion and expressed in terms of Fredholm determinants. In particular, we present exact out-of-equilibrium expressions in the thermodynamic limit for the previously unknown order parameter 1-point function, dynamical 2-point function and equal-time 3-point function.

Abstract:

Biological cilia pump the surrounding fluid by asymmetric beating that is driven by dynein motors between sliding microtubule doublets. The complexity of biological cilia raises the question about minimal systems that can re-create similar patterns of motion. One such system consists of a pair of microtubules that are clamped at the proximal end. They interact through dynein motors that cover one of the filaments and pull against the other one. Here, we study theoretically the static shapes and the active dynamics of such a system. Using the theory of elastica, we analyse the shapes of two filaments of different lengths with clamped ends. Starting from equal lengths, we observe a transition similar to Euler buckling leading to a planar shape. When further increasing the length ratio, the system assumes a non-planar shape with spontaneously broken chiral symmetry after a secondary bifurcation and then transitions to planar again. The predicted curves agree with experimentally observed shapes of microtubule pairs. The dynamical system can have a stable fixed point, with either bent or straight filaments, or limit cycle oscillations. The latter match many properties of ciliary motility, demonstrating that a two-filament system can serve as a minimal actively beating model.

Abstract:

A classical wave-particle entity in the form of a millimetric walking droplet can emerge on the free surface of a vertically vibrating liquid bath. Such wave-particle entities have been shown to exhibit hydrodynamic analogs of quantum systems. Using an idealized theoretical model of this wave-particle entity in a tilted potential, we explore its transport behavior. The integro-differential equation of motion governing the dynamics of the wave-particle entity transforms to a Lorenz-like system of ordinary differential equations that drives the particle's velocity. Several anomalous transport regimes such as absolute negative mobility, differential negative mobility, and lock-in regions corresponding to force-independent mobility are observed. These observations motivate experiments in the hydrodynamic walking-droplet system for the experimental realizations of anomalous transport phenomena.

Abstract:

Background

Little is known about cytochrome P450 3A4 (CYP3A4) DNA methylation and transcription alterations in gastric cancer.

Objective

In this paper, we initially aimed to address the effect of diazinon pesticide on DNA methylation and transcription changes of the CYP3A4 gene in a human gastric cell line. In the next step, we studied the methylation differences of CpG sites within the upstream regulatory regions of the CYP3A4 gene among human gastric cancerous and healthy tissues.

Methods

For the in vitro assay, the methylation changes of the C/EBP response element and transcript level of the CYP3A4 gene were studied following treatment of the AGS cell line with various concentrations of diazinon pesticide. In the next phase, the methylation percentages of 24 CpG sites within or around the upstream regulatory elements, including near promoter, C/EBP binding site, XREM, and CLEM4, in 11 specimens of human gastric cancer tissue were compared to their adjacent healthy tissues.

Results

Treatment with 10 μM Diazinon significantly increased the CYP3A4 gene transcription by approximately 27-fold, which was correlated with the hypermethylation of 3 CpGs in C/EBP binding sites, including -5998, -5731 and -5725 (p<0.001 for all comparisons). Results of bisulfite sequencing revealed that the CpG sites which are located in -1521 (p=0.003), -1569 (p=0.027), -10813 (p=0.003), -10851 (p=0.001) and -10895 (p=0.0) bp from transcription start site, were significantly hypermethylated in cancerous tissues comparing to their healthy cohort.

Conclusion

Hypermethylation of CLEM4 and a region near the core promoter may have a significant association with gastric cancer incidence.