Institute of Fundamental Technological Research

Nucleosomes are recognized as key regulators of transcription. However, the relationship between slow nucleosome unwrapping dynamics and bulk transcriptional properties has not been thoroughly explored. Here, an agent-based model that we call the dynamic defect Totally Asymmetric Simple Exclusion Process (ddTASEP) was constructed to investigate the effects of nucleosome-induced pausing on transcriptional dynamics. Pausing due to slow nucleosome dynamics induced RNAPII convoy formation, which would cooperatively prevent nucleosome rebinding leading to bursts of transcription. The mean first passage time (MFPT) and the variance of first passage time (VFPT) were analytically expressed in terms of the nucleosome rate constants, allowing for the direct quantification of the effects of nucleosome-induced pausing on pioneering polymerase dynamics. The mean first passage elongation rate γ(hc, ho) is inversely proportional to the MFPT and can be considered to be a new axis of the ddTASEP phase diagram, orthogonal to the classical αβ-plane (where α and β are the initiation and termination rates). Subsequently, we showed that, for β = 1, there is a novel jamming transition in the αγ-plane that separates the ddTASEP dynamics into initiation-limited and nucleosome pausing-limited regions. We propose analytical estimates for the RNAPII density ρ, average elongation rate v, and transcription flux J and verified them numerically. We demonstrate that the intra-burst RNAPII waiting times tin follow the time-headway distribution of a max flux TASEP and that the average inter-burst interval correlates with the index of dispersion De. In the limit γ→0, the average burst size reaches a maximum set by the closing rate hc. When α≪1, the burst sizes are geometrically distributed, allowing large bursts even while the average burst size is small. Last, preliminary results on the relative effects of static and dynamic defects are presented to show that dynamic defects can induce equal or greater pausing than static bottle necks.

Constitutive theory of plasticity coupled with orthotropic damage for geomaterials was established in the framework of irreversible thermodynamics. Prime results include: 1) evolution laws are presented for coupled evolution of plasticity and orthotropic damage; 2) the orthotropic damage tensor is introduced into the Mohr-Coulomb criterion through homogenization. Both the degradation of shear strength and degradation of friction angle caused by damage are included in this model. The dilatancy is calculated with the so-called damage strain.

damage plasticity, coupling, dilatancy, geomaterial

The propagation of interlayer cracks and the resulting failure of the interface is a typical mode occurring in rock engineering and masonry structure. On the basis of the theory of elastoplasticity and fracture mechanics, the shear beam model for the solution of interface failure was presented. The concent of ‘cohesive crack’ was adopted to describe the constitutive behavior of the cohesive interfacial layer. Related fundamental equations such as equilibrium equation, constitutive equations were presented. The behavior of a double shear beam bonded through cohesive layer was analytically calculated. The stable propagation of interface crack and process zone was investigated.

interface layer, cohesive layer, anti-plane shear, shear beam model, failure, instability, damage

Based on the (I) of the present work, the behavior of shear beam model at crack initiation stage andat instable propagation stage was studied. The prime results include:1) discriminant equation which clarifies the mode of instability, snap-back or snap-through, was established;2) analytical solution was given out for the double shear beam and the load-displacement diagram for monotonic loading was presented for a full process; and3) the problem of the energy release induced by instability was discussed.

interface layer, antiplane shear, failure, shear beam model, instability, snapthrough, snap-back, damage