Lead-Acid Battery Model Under Discharge with a Fast Splitting Method

A mathematical model of a valve-regulated lead-acid battery under discharge is presented as simplified from a standard electrodynamics model. This nonlinear reaction–diffusion model of a battery cell is solved using an operator splitting method to quickly and accurately simulate sulfuric acid concentration. This splitting method incorporates one-sided approximation schemes to preserve continuity over material interfaces encompassing discontinuous parameters. Numerical results are compared with measured data by calculating battery voltage from modeled acid concentration as derived from the Nernst equation

Modeling the Spread of COVID-19 in Enclosed Spaces

SEIR models are typically conjured for populations in open environments; however, there seems to be a lack of these types of models that deal with infection rates amongst enclosed spaces. We have also seen certain age groups struggle to deal with COVID-19 more than others, and to this end, we have constructed an age-structured SEIR model that incorporates the Gammaitoni–Nucci model, which is used for infective material in an enclosed space with ventilation. We apply some sensitivity analysis to better understand which parameters have the biggest impact on overall infection rates, as well as create a realistic scenario in which we apply our model to see the comparison in sickness rates amongst four different age groups with different ventilation filtration systems (UVGI, HEPA) and differing quanta production rates

Allostery through protein-induced DNA bubbles

Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription

Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome (PRRS) has devastated pig industries worldwide for many years. It is caused by a small RNA virus (PRRSV), which targets almost exclusively pig monocytes or macrophages. In the present study, five SAGE (serial analysis of gene expression) libraries derived from 0 hour mock-infected and 6, 12, 16 and 24 hours PRRSV-infected porcine alveolar macrophages (PAMs) produced a total 643,255 sequenced tags with 91,807 unique tags. Differentially expressed (DE) tags were then detected using the Bayesian framework followed by gene/mRNA assignment, arbitrary selection and manual annotation, which determined 699 DE genes for reactome analysis. The DAVID, KEGG and REACTOME databases assigned 573 of the DE genes into six biological systems, 60 functional categories and 504 pathways. The six systems are: cellular processes, genetic information processing, environmental information processing, metabolism, organismal systems and human diseases as defined by KEGG with modification. Self-organizing map (SOM) analysis further grouped these 699 DE genes into ten clusters, reflecting their expression trends along these five time points. Based on the number one functional category in each system, cell growth and death, transcription processes, signal transductions, energy metabolism, immune system and infectious diseases formed the major reactomes of PAMs responding to PRRSV infection. Our investigation also focused on dominant pathways that had at least 20 DE genes identified, multi-pathway genes that were involved in 10 or more pathways and exclusively-expressed genes that were included in one system. Overall, our present study reported a large set of DE genes, compiled a comprehensive coverage of pathways, and revealed system-based reactomes of PAMs infected with PRRSV. We believe that our reactome data provides new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV and lays a strong foundation for vaccine development to control PRRS incidence in pigs

Summary of differentially expressed genes in PAMs infected with PRRSV.

<p>All genes (A), up-regulated genes (B) and down-regulated genes at four time-points post-infection (C).</p

Pathway summary of DE genes that are related to six biological systems of PAMs infected with PRRSV.

<p>Pathway summary of DE genes that are related to six biological systems of PAMs infected with PRRSV.</p

Fold change in TPM for genes with multiple tags due to nucleotide polymorphisms.

<p>TPM and fold changes for two tags in <i>PLIN2</i> (A), <i>RPS13</i> (B) and <i>SLA-DRA</i> (C) genes representing different alleles at 0, 6, 12, 16 and 24 hours post-infection.</p

Ten expression trend clusters of 699 DE genes derived from PAMs during PRRSV infection.

<p>Ten expression trend clusters of 699 DE genes derived from PAMs during PRRSV infection.</p

DE gene distributions and interactions among functional categories associated with Human Diseases in PAMs infected with PRRSV.

<p>DE gene distributions and interactions among functional categories associated with Human Diseases in PAMs infected with PRRSV.</p

DE gene distributions and interactions among functional categories associated with Environmental Information Processing in PAMs infected with PRRSV.

<p>DE gene distributions and interactions among functional categories associated with Environmental Information Processing in PAMs infected with PRRSV.</p