Dynamical Models of Biology and Medicine

Mathematical and computational modeling approaches in biological and medical research are experiencing rapid growth globally. This Special Issue Book intends to scratch the surface of this exciting phenomenon. The subject areas covered involve general mathematical methods and their applications in biology and medicine, with an emphasis on work related to mathematical and computational modeling of the complex dynamics observed in biological and medical research. Fourteen rigorously reviewed papers were included in this Special Issue. These papers cover several timely topics relating to classical population biology, fundamental biology, and modern medicine. While the authors of these papers dealt with very different modeling questions, they were all motivated by specific applications in biology and medicine and employed innovative mathematical and computational methods to study the complex dynamics of their models. We hope that these papers detail case studies that will inspire many additional mathematical modeling efforts in biology and medicin

Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles

Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA

Evaluations of heterogeneous epidemic models with exponential and non-exponential distributions for latent period: the Case of COVID-19

Most of heterogeneous epidemic models assume exponentially distributed sojourn times in infectious states, which may not be practical in reality and could affect the dynamics of the epidemic. This paper investigates the potential discrepancies between exponential and non-exponential distribution models in analyzing the transmission patterns of infectious diseases and evaluating control measures. Two SEIHR models with multiple subgroups based on different assumptions for latency are established: Model Ⅰ assumes an exponential distribution of latency, while Model Ⅱ assumes a gamma distribution. To overcome the challenges associated with the high dimensionality of GDM, we derive the basic reproduction number ($R_{0}$) of the model theoretically, and apply numerical simulations to evaluate the effect of different interventions on EDM and GDM. Our results show that considering a more realistic gamma distribution of latency can change the peak numbers of infected and the timescales of an epidemic, and GDM may underestimate the infection eradication time and overestimate the peak value compared to EDM. Additionally, the two models can produce inconsistent predictions in estimating the time to reach the peak. Our study contributes to a more accurate understanding of disease transmission patterns, which is crucial for effective disease control and prevention

Dynamics of Bose-Einstein Condensates: Exact Representation and Topological Classification of Coherent Matter Waves

By using the bifurcation theory of dynamical systems, we present the exact representation and topological classification of coherent matter waves in Bose-Einstein condensates (BECs), such as solitary waves and modulate amplitude waves (MAWs). The existence and multiplicity of such waves are determined by the parameter regions selected. The results show that the characteristic of coherent matter waves can be determined by the “angular momentum” in attractive BECs while for repulsive BECs; the waves of the coherent form are all MAWs. All exact explicit parametric representations of the above waves are exhibited and numerical simulations support the result

Towards diluted magnetism in TaAs

Magnetism in Weyl semimetals is desired to investigate the interaction between the magnetic moments and Weyl fermions, e.g. to explore anomalous quantum Hall phenomena. Here we demonstrate that proton irradiation is an effective tool to induce ferromagnetism in the Weyl semimetal TaAs. The intrinsic magnetism is observed with a transition temperature above room temperature. The magnetic moments from d states are found to be localized around Ta atoms. Further, the first-principles calculations indicate that the d states localized on the nearest-neighbor Ta atoms of As vacancy sites are responsible for the observed magnetic moments and the long-ranged magnetic order. The results show the feasibility of inducing ferromagnetism in Weyl semimetals so that they may facilitate the applications of this material in spintronics.Comment: 20 pages, 6 figure

Optical waveguides in LiTaO3 crystals fabricated by swift C5+ ion irradiation

We report on the optical waveguides, in both planar and ridge configurations, fabricated in LiTaO3 crystal by using carbon (C5+) ions irradiation at energy of 15 MeV. The planar waveguide was produced by direct irradiation of swift C5+ ions, whilst the ridge waveguides were manufactured by using femtosecond laser ablation of the planar layer. The reconstructed refractive index profile of the planar waveguide has showed a barrier-shaped distribution, and the near-field waveguide mode intensity distribution was in good agreement with the calculated modal profile. After thermal annealing at 260 °C in air, the propagation losses of both the planar and ridge waveguides were reduced to 10 dB/cm.This work is supported by the National Natural Science Foundation of China (No. U1332121) and the 973 Project (No. 2010CB832906) of China. S.Z. acknowledges the funding by the Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF-VHNG-713). J.R.V. thanks supports from Junta de Castilla y León under project SA086A12-2 and the Centro de Láseres Pulsados (CLPU)

Tailoring Magnetic Features in Zigzag-Edged Nanographenes by Controlled Diels–Alder Reactions

Nanographenes (NGs) with tunable electronic and magnetic properties have attracted enormous attention in the realm of carbon-based nanoelectronics. In particular, NGs with biradical character at the ground state are promising building units for molecular spintronics. However, most of the biradicaloids are susceptible to oxidation under ambient conditions and photolytic degradation, which hamper their further applications. Herein, we demonstrated the feasibility of tuning the magnetic properties of zigzag-edged NGs in order to enhance their stability via the controlled Diels–Alder reactions of peri-tetracene (4-PA). The unstable 4-PA (y0=0.72; half-life, t1/2=3 h) was transformed into the unprecedented benzo-peri-tetracenes (BPTs) by a one-side Diels–Alder reaction, which featured a biradical character at the ground state (y0=0.60) and exhibited remarkable stability under ambient conditions for several months. In addition, the fully zigzag-edged circumanthracenes (CAs) were achieved by two-fold or stepwise Diels–Alder reactions of 4-PA, in which the magnetic properties could be controlled by employing the corresponding dienophiles. Our work reported herein opens avenues for the synthesis of novel zigzag-edged NGs with tailor-made magnetic properties. © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinhei

Receptor–ligand pair typing and prognostic risk model of response or resistance to immune checkpoint inhibitors in lung adenocarcinoma

IntroductionCurrently, programmed cell death-1 (PD-1)-targeted treatment is ineffective for a sizable minority of patients, and drug resistance still cannot be overcome.MethodsTo explore the mechanisms of immunotherapy and identify new therapeutic opportunities in lung adenocarcinoma (LUAD), data from patients who did and did not respond to the anti-PD-1 treatment were evaluated using single-cell RNA sequencing, and bulk RNA sequencing were collected.ResultsWe investigated the gene expression that respond or not respond to immunotherapy in diverse cell types and revealed transcriptional characteristics at the single-cell level. To ultimately explore the molecular response or resistance to anti-PD-1 therapy, cell-cell interactions were carried out to identify the different LRIs (ligand-receptor interactions) between untreated patients vs. no-responders, untreated patients vs. responders, and responders vs. non-responders. Next, two molecular subgroups were proposed based on 73 LRI genes, and subtype 1 had a poor survival status and was likely to be the immunosuppressive tumor subtype. Furthermore, based on the LASSO Cox regression analysis results, we found that TNFSF13, AXL, KLRK1, FAS, PROS1, and CDH1 can be distinct prognostic biomarkers, immune infiltration levels, and responses to immunotherapy in LUAD.DiscussionAltogether, the effects of immunotherapy were connected to LRIs scores, indicating that potential medications targeting these LRIs could contribute to the clinical benefit of immunotherapy. Our integrative omics analysis revealed the mechanisms underlying the anti-PD-1 therapy response and offered abundant clues for potential strategies to improve precise diagnosis and immunotherapy