Shape Influence of Active Material Micro-Structure on Diffusion and Contact Stress in Lithium-Ion Batteries

Electrochemical-mechanical modelling is a key issue to estimate the damage of active material, as direct measurements cannot be performed due to the particles nanoscale. The aim of this paper is to overcome the common assumptions of spherical and standalone particle, proposing a general approach that considers a parametrized particle shape and studying its influence on the mechanical stresses which arise in active material particles during battery operation. The shape considered is a set of ellipsoids with variable aspect ratio (elongation), which aims to approximate real active material particles. Active material particle is divided in two domains: non-contact domain and contact domain, whether contact with neighbouring particles affects stress distribution or not. Non-contact areas are affected by diffusion stress, caused by lithium concentration gradient inside particles. Contact areas are affected simultaneously by diffusion stress and contact stress, caused by contact with neighbouring particles as a result of particle expansion due to lithium insertion. A finite element model is developed in Ansys™APDL to perform the multi-physics computation in non-spherical domain. The finite element model is validated in the spherical case by analytical models of diffusion and contact available for simple geometry. Then, the shape factor is derived to describe how particle shape affects mechanical stress in non-contact and contact domains.

Analysis of Two Colliding Thin Spherical Shells

In the present paper, the collision of two elastic spherical shells is investigated using the wave theory of impact. The model developed here suggests that after the moment of impact quasi-longitudinal and quasi-transverse shock waves are generated, which then propagate along the spherical shells. The solution behind the wave fronts is constructed with the help of the theory of discontinuities. Since the local bearing of the materials of the colliding elastic shells is taken into account, then the solution in the contact domain is found via the Hertz contact theory.

Mutation patterns of human SARS-COV-2 and bat RaTG13 coronaviruses genomes are strongly biased towards C>U indicating rapid evolution in their hosts

Background: The world pandemy caused by SARS-CoV-2 spreading has raised considerable interest about its evolutionary origin and genome structure. Here we analysed mutation patterns in 13 human SARS-COV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis bat. We also evaluated the CpG dinucleotide contents in SARS-COV-2 and other human and animal coronavirus genomes. Results: Out of 1107 single nucleotide differences (c. 4% divergence) between human SARS-COV-2 and bat RaTG13, 672 (61%) can be attributed to C>U and U>T substitutions significantly (P<0.001) exceeding other types of SNPs. A similar trend was observed among the 13 sequenced SARS-COV-2 genomes. Accumulation of C>U mutations was also observed in a highly variable subregion encoding the ACE2 receptor contact domain. Contrast to most other coronaviruses both SARS-COV-2 and RaTG13 exhibited CpG depletion in their genomes. Conclusion: The data support that the C-to-U conversion played a significant role in the evolution of pathogenic RNA coronaviruses including SARS-COV-2. These mutations apparently also influenced amino acid composition of the SARS-Cov-2 spike protein domain receptor implicated in virus pathogenicity. We propose that SARS-COV-2 was evolving relatively long in humans following the transfer from animals before spreading world-wide.

Formulation of the pextension finite elements for the solution of normal contact problems

This work deals with normal contact problems. After a wide literature review, we look for the possibility of achieving a high-precision solution using the principle of minimum potential energy and the Hellinger-Reissner variational principle with penalty and augmented Lagrangian techniques. By positioning of the border of the contact elements, the whole surfaces of the eligible elements fall in contact or in gap regions. This reduces the error of the singularity in the border of the contact domain. Computations with $h$-, $p$- and $rp$-versions are performed. For the $rp$-version, the pre-fixed number of finite elements are moved so that small elements are placed in one or two element layers at the ends of the contact zone. A number of diagrams and tables showing the convergence of the solution (by increasing the number of polynomial degrees p) demonstrate the high efficiency of the proposed solution procedure.

Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture

The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, which utilize mult-restriction enzyme digestions for ultrafine mapping of targeted and genome-wide chromatin interaction, respectively, at up to one hundred basepair resolution. Tri-4C identified CRE loop interaction networks and quantifatively revealed their alterations underlying dynamic gene control. Tri-HiC uncovered global fine-gage regulatory interaction networks, identifying > 20-fold more enhancer:promoter (E:P) loops than in situ HiC. In addition to vasly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.

Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition

Higher-order chromatin organization such as A/B compartments, TADs and chromatin loops are temporarily disrupted during mitosis. These structures are thought to organize aspects of gene regulation, and thus it is important to understand how they are re-established after mitosis. We examined the dynamics of chromosome reorganization by Hi-C at defined time points following exit from mitosis in highly purified, synchronous cell populations. We observed that A/B compartments are rapidly established and progressively gain in strength following mitotic exit. Contact domain formation occurs from the “bottom-up” with smaller sub-TADs forming initially, followed by convergence into multi-domain TAD structures. CTCF is strongly retained at a significant fraction of sites on mitotic chromosomes and immediately resumes full binding at ana/telophase, the earliest tested time point. In contrast, cohesin is completely evicted from mitotic chromosomes and resumes focal binding with delayed kinetics. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contacts anchored by CTCF grow in length, consistent with a loop extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, preceding CTCF/cohesin anchored structural loops. Strikingly, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase, that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering loops. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin re-configuration to shape compartments, contact domains, cis-element contacts, and CTCF/cohesin dependent loops.

Mathematical Model to Study the Impact Response of a Viscoelastic Auxetic Plate

In the present paper, a mathematical model has been constructed in order to describe the impact response of a linear Kirchhoff-Love plate made of viscoelastic auxetic material possessing fractional viscosity. Auxetic’s Poisson’s ratio is a time-dependent value changing from negative to positive magnitudes with time. In the case of a linear plate, the solution out of the contact domain is found through the Green function, and within the contact zone via the modified Hertz contact theory. Integral equations for the contact force and local indentation have been obtained.

ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization

ChIA-PET enables the genome-wide discovery of chromatin interactions involving specific protein factors, with base-pair resolution. Interpreting ChIA-PET data depends on having a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, analysis, and visualization. ChIA-PIPE performs linker filtering, read mapping, peak calling, loop calling, chromatin-contact-domain calling, and can resolve allele-specific peaks and loops. ChIA-PIPE also automates quality-control assessment for each dataset. Furthermore, ChIA-PIPE generates input files for visualizing 2D contact maps with Juicebox and HiGlass, and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. With minimal adjusting, ChIA-PIPE can also be suited for the analysis of other related chromatin-mapping data.