Effect of delay on pattern formation of a Rosenzweig–MacArthur type reaction–diffusion model with spatiotemporal delay

In this paper, a predator–prey reaction–diffusion model with Rosenzweig–MacArthur type functional response and spatiotemporal delay is investigated through using the tool of Turing bifurcation theories. First, by taking the average time delay as a bifurcation parameter, conditions of occurrence of Turing bifurcation are obtained through employing the Routh–Hurwitz criteria. Second, as the average time delay varies the amplitude equations of Turing bifurcation patterns including spots pattern and stripes pattern are also obtained through the multiple scale perturbation method. Finally, the two kinds of spatiotemporal evolution distributions of species such as spots pattern and stripes pattern are shown to illustrate theoretical results.

Semi-numerical analysis of a two-stage series composite planetary transmission considering incremental harmonic balance and multi-scale perturbation methods

This study conducts an analytical investigation of the dynamic response characteristics of a two-stage series composite system (TsSCS) with a planetary transmission consisting of dual-power branches. An improved incremental harmonic balance (IHB) method, which solves the closed solution of incremental parameters passing through the singularity point of the analytical path, based on the arc length extension technique, is proposed. The results are compared with those of the numerical integration method to verify the feasibility and effectiveness of the improved method. Following that, the multi-scale perturbation (MsP) method is applied to the TsSCS proposed in this subject to analyze the parameter excitation and gap nonlinear equations and then to obtain the analytical frequency response functions including the fundamental, subharmonic, and superharmonic resonance responses. The frequency response equations of the primary resonance, subharmonic resonance, and superharmonic resonance are solved to generate the frequency response characteristic curves of the planetary gear system (PGS) in this method. A comparison between the results obtained by the MsP method and the numerical integration method proves that the former is ideal and credible in most regions. Considering the parameters of TsSCS excitation frequency and damping, the nonlinear response characteristics of steady-state motion are mutually converted. The effects of the time-varying parameters and the nonlinear deenthing caused by the gear teeth clearance on the amplitude–frequency characteristics of TsSCS components are studied in this special topic.

GeneTargeter: Automated in silico design for genome editing in the malaria parasite, Plasmodium falciparum

Functional characterization of the multitude of poorly-described proteins in the human malarial pathogen, Plasmodium falciparum, requires tools to enable genome-scale perturbation studies. Here we present GeneTargeter (genetargeter.mit.edu), a software tool for automating the design of homology-directed repair donor vectors to achieve gene knockouts, conditional knockdowns, and epitope tagging of P. falciparum genes. We demonstrate GeneTargeter facilitated genome-scale design of six different types of knockout and conditional knockdown constructs for the P. falciparum genome, and validate the computational design process experimentally with successful donor vector assembly. The software's modular, customizable nature makes it extendable to additional plasmids and genomes.

Study of Thermal Activity in The Mixing Layer During First Generated Single Cloud by Using Combined Observation From Boundary Layer Radar, Doppler Lidar and Time Lapse Camera

<p>Detailed observation of small scale perturbation in the atmospheric boundary layer during the first generated cumulus cloud are conducted. Our target is to study this small scale perturbation, especially related to the thermal activity at the first generated cumulus cloud. The observation is performed during the daytime on August 17, 2018, and September 03, 2018. Location is focused in the urban area of Kobe, Japan. High-resolution instruments such as Boundary Layer Radar, Doppler Lidar, and Time Lapse camera are used in this observation. Boundary Layer Radar, and Doppler Lidar are used for clear air observation. Meanwhile Time Lapse Camera are used for cloud existence observation. The atmospheric boundary layer structure is analyzed based on vertical velocity profile, variance, skewness, and estimated atmospheric boundary layer height. Wavelet are used to observe more of the period of the thermal activity. Furthermore, time correlation between vertical velocity time series from height 0.3 to 2 km and image pixel of generated cloud time series are also discussed in this study.</p>

Multi-Scale Localized Perturbation Method in OpenFOAM

A modified set of governing differential equations for geophysical fluid flows is derived. All of the simulation fields are decomposed into a nominal large-scale background state and a small-scale perturbation from this background, and the new system is closed by the assumption that the perturbation is one-way coupled to the background. The decomposition method, termed the multi-scale localized perturbation method (MSLPM), is then applied to the governing equations of stratified fluid flows, implemented in OpenFOAM, and exercised in order to simulate the interaction of a vertically-varying background shear flow with an axisymmetric perturbation in a turbulent ocean environment. The results demonstrate that the MSLPM can be useful in visualizing the evolution of a perturbation within a complex background while retaining the complex physics that are associated with the original governing equations. The simulation setup may also be simplified under the MSLPM framework. Further applications of the MSLPM, especially to multi-scale simulations that encompass a large range of spatial and temporal scales, may be beneficial for researchers.

Stochastic Modelling of Small-Scale Perturbation

In this paper we propose a stochastic model reduction procedure for deterministic equations from geophysical fluid dynamics. Once large-scale and small-scale components of the dynamics have been identified, our method consists in modelling stochastically the small scales and, as a result, we obtain that a transport-type Stratonovich noise is sufficient to model the influence of the small scale structures on the large scales ones. This work aims to contribute to motivate the use of stochastic models in fluid mechanics and identifies examples of noise of interest for the reduction of complexity of the interaction between scales. The ideas are presented in full generality and applied to specific examples in the last section.

A Review of Drug Repositioning Based Chemical-induced Cell Line Expression Data

Drug repositioning is an important area of biomedical research. The drug repositioning studies have shifted to computational approaches. Large-scale perturbation databases, such as the Connectivity Map and the Library of Integrated Network-Based Cellular Signatures, contain a number of chemical-induced gene expression profiles and provide great opportunities for computational biology and drug repositioning. One reason is that the profiles provided by the Connectivity Map and the Library of Integrated Network-Based Cellular Signatures databases show an overall view of biological mechanism in drugs, diseases and genes. In this article, we provide a review of the two databases and their recent applications in drug repositioning.

Genuine Dilatons in Gauge Theories

A genuine dilaton σ allows scales to exist even in the limit of exact conformal invariance. In gauge theories, these may occur at an infrared fixed point (IRFP) α IR through dimensional transmutation. These large scales at α IR can be separated from small scales produced by θ μ μ , the trace of the energy-momentum tensor. For quantum chromodynamics (QCD), the conformal limit can be combined with chiral S U ( 3 ) × S U ( 3 ) symmetry to produce chiral-scale perturbation theory χ PT σ , with f 0 ( 500 ) as the dilaton. The technicolor (TC) analogue of this is crawling TC: at low energies, the gauge coupling α goes directly to (but does not walk past) α IR , and the massless dilaton at α IR corresponds to a light Higgs boson at α ≲ α IR . It is suggested that the W ± and Z 0 bosons set the scale of the Higgs boson mass. Unlike crawling TC, in walking TC, θ μ μ produces all scales, large and small, so it is hard to argue that its “dilatonic” candidate for the Higgs boson is not heavy.