Abstract

In this paper, Local Absorbing Boundary Conditions are presented for wave propagation through the viscoelastic media. This method is an extension of Local Absorbing Boundary Condition (ABC) proposed by Lysmer and Kuhlemeyer (1969). The proposed method does not converge for Kelvin type of viscoelastic materials but converges for Maxwell type of viscoelastic material model. This method is verified with 1D and 2D finite element models using explicit solver and the accuracy is compared with standard solutions. This study concluded that better responses can be obtained for the viscoelastic wave propagation using present approach when compared with traditional Local Absorbing Boundary Conditions. This study also concluded that the proposed method is suitable for low to medium viscous damping materials. For high viscous materials, the proposed method can be applied to transient wave propagation problems.

Abstract

Structural pounding may occur between two structures or at different parts of the same building during ground motions. Among all the structural damages, structural pounding has been commonly observed during several earthquakes in the past, which have lead to minor damage till complete collapse of the structure. The main focus of this paper is to study pounding responses and impact effects on structures subjected to ground motions. It is observed from the study that the response of stiff structure is more than flexible structure at dominant period of ground motion, irrespective of equal and unequal heights. If the structures vibrate at a non-dominant period of ground motion, then the response of flexible structure is observed more than the stiff structure.

Abstract

This paper is concerned with the study of effect of opening in infills on RC framed structures. Reinforced concrete buildings with masonry infill walls have been widely constructed for commercial, industrial, buildings. In this paper presents the results of analytical program showing behaviour of frames with different masonry infill i.e semi-interlocked masonry & Unreinforced masonry. The effect infill opening on seismic response of frame buildings were evaluated. A nonlinear static analysis has been carried out on different model frames by using finite element analysis software, seismostruct. The results obtained show that calculation of response reduction factor of RC infilled frames with & without opening on infill.

Abstract

Radiating boundary condition is an important consideration in the finite element modelling of unbounded media. Absorbing layer techniques such as Perfectly Matched Layers (PML) and Absorbing Layers by Increasing Damping (ALID) becoming popular as they are efficient in absorbing outward propagating waves energy. In this study, a comparative analysis has been carried out between PML and ALID+VABC (Absorbing Boundary conditions for Viscoelastic materials) methods. The methods are analyzed using LSDYNA explicit solver and the efficiency is compared with standard solutions. The study concluded that PML requires less number of elements to model the boundary conditions when compared with ALID+VABC. But PML requires a smaller element length which increases overall computational time. Both the methods are efficient in absorbing the wave energy. However, PML requires additional implementation cost to solve the complex equations.

Abstract

We developed a set of conformationally locked molecules each of which makes a single CH⋯O H-bond/short contact and has different electron density at the acceptor oxygen atom. The downfield shift of the 1H NMR signals due to the hydrogen involved in the CH⋯O H-bond varied from 0.93–1.6 ppm, and the magnitude of Δδ is in correlation with the hybridization state of the acceptor oxygen and with the CH⋯O H-bond strengths quantified using a computational method.

Abstract

Urea-assisted denaturation of protein and RNA has been shown to be a valuable tool to study their stabilities and folding phenomena. It has been shown that stacking interactions between nucleobases and urea are one of the driving forces of denaturation. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated by performing high-level quantum calculations (RI-MP2/aug-ccpVDZ level) on a few thousands of model systems. Four systems were considered based on the RNA nucleobases (GUA, ADE, CYT, and URA) for the investigation. For each system, a set of models were designed to study the role of hetero-atoms/groups of the nucleobases on stacking interactions with urea moiety with respect to every possible pair. Several plane-parallel complexes were generated with urea on top of aromatic systems to exhaustively study all possible factors for urea-nucleobases stacking interactions. Energy decomposition analysis (EDA), atoms in molecules (AIM) and natural bond orbital (NBO) analysis were performed to gain better insights on non-covalent stacking interactions. Dispersion component was found to be heavily stabilizing, while the EHF was found to be repulsive for all the four systems indicating lack of hydrogen bonding (HB) type interactions and presence of dispersion type interactions. Amide and carbonyl groups of urea molecule were found to play a major role in favourable stacking interactions. We demonstrate that along with functional groups present on the nucleobases, the orientation of urea molecules plays a vital role in stabilizing the urea-nucleobase non-covalent interactions. The proposed study quantifies and provides a comprehensive theoretical description of urea nucleobase unconventional stacking interactions which helps to unravel urea driven RNA unfolding mechanism.

Abstract

We compute the top quark threshold contributions to the γγ production at the LHC. They appear when the invariant mass of the photon pair, Mγ γ just exceeds two times the mass of the top quark and induce some feature in the Mγ γ distribution. We determine the magnitude of this threshold effect and characterize this feature with a simple empirical fitting function to show that it is possible to observe this effect at the LHC in future. We also explore some possible improvements that may enhance its significance.

Abstract

Alzheimer’s disease (AD) is a neurodegenerative disorder contributing to rapid decline in cognitive function and ultimately dementia. Most cases of AD occur in elderly and later years. There is a growing need for understanding the relationship between ageing and AD to identify shared and unique hallmarks associated with the disease in a region and cell-type specific manner. Although genomic studies on AD have been performed extensively, the molecular mechanism of disease progression is still not clear. The major objective of our study is to obtain a higher-order network-level understanding of ageing and AD, and their relationship using the hippocampal gene expression profiles of young (20-50yrs), ageing (70-99yrs) and AD (70-99yrs). The hippocampus is vulnerable to damage at early stages of AD and altered neurogenesis in the hippocampus is linked to the onset of AD. We combined the weighted gene co-expression network and weighted protein-protein interaction network-level approaches to study the transition from young to ageing to AD. The network analysis revealed the organization of co-expression network into functional modules that are cell-type specific in ageing and AD. We found that modules associated with astrocytes, endothelial cells and microglial cells are upregulated and significantly correlate with both ageing and AD. The modules associated with neurons, mitochondria and endoplasmic reticulum are downregulated and significantly correlate with AD than ageing. The oligodendrocytes module does not show significant correlation with neither aging nor disease. Further, we identified ageing- and AD-specific …

Abstract

In response to developmental and environmental conditions, cells exit the mitotic cell cycle and enter the meiosis program to generate haploid gametes from diploid germ cells. Once cells decide to enter the meiosis program they become irreversibly committed to the completion of meiosis irrespective of the presence of cue signals. How meiotic entry and commitment occur due to the dynamics of the regulatory network is not well understood. Therefore, we constructed a mathematical model of the regulatory network that controls the transition from mitosis to meiosis in Schizosaccharomyces pombe. Upon nitrogen starvation, yeast cells exit mitosis and undergo conjugation and meiotic entry. The model includes the regulation of Mei2, an RNA binding protein required for conjugation and meiotic entry, by multiple feedback loops involving Pat1, a kinase that keeps cells in mitosis, and Ste11, a transcription activator …

Abstract

Cells switch between quiescence and proliferation states for maintaining tissue homeostasis and regeneration. At the restriction point (R-point), cells become irreversibly committed to the completion of the cell cycle independent of mitogen. The mechanism involving hyper-phosphorylation of retinoblastoma (Rb) and activation of transcription factor E2F is linked to the R-point passage. However, stress stimuli trigger exit from the cell cycle back to the mitogen-sensitive quiescent state after Rb hyper-phosphorylation but only until APC/CCdh1 inactivation. In this study, we developed a mathematical model to investigate the reversible transition between quiescence and proliferation in mammalian cells with respect to mitogen and stress signals. The model integrates the current mechanistic knowledge and accounts for the recent experimental observations with cells exiting quiescence and proliferating cells. We show that Cyclin E:Cdk2 couples Rb-E2F and APC/CCdh1 bistable switches and temporally segregates the R-point and the G1/S transition. A redox-dependent mutual antagonism between APC/CCdh1 and its inhibitor Emi1 makes the inactivation of APC/CCdh1 bistable. We show that the levels of Cdk inhibitor (CKI) and mitogen control the reversible transition between quiescence and proliferation. Further, we propose that shifting of the mitogen-induced transcriptional program to G2-phase in proliferating cells might result in an intermediate Cdk2 activity at the mitotic exit and in the immediate inactivation of APC/CCdh1. Our study builds a coherent framework and generates hypotheses that can be further explored by experiments.