Computational Approaches and Challenges in Spatial Transcriptomics

The development of spatial transcriptomics(ST)technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and function of various cell subsets in different environments and organs.The large-scale data generated by these ST technologies,which contain spatial gene expression information,have elicited the need for spatially resolved approaches to meet the requirements of computational and biological data interpretation.These requirements include dealing with the explosive growth of data to determine the cell-level and gene-level expression,correcting the inner batch effect and loss of expression to improve the data quality,conducting efficient interpretation and in-depth knowledge mining both at the single-cell and tissue-wide levels,and conducting multi-omics integration analysis to provide an extensible framework toward the in-depth understanding of biological processes.However,algorithms designed specifically for ST technologies to meet these requirements are still in their infancy.Here,we review computational approaches to these problems in light of corresponding issues and challenges,and present forward-looking insights into algorithm development.

Computational approaches for fast generation of digital 3D video holograms(Invited Paper)

Several approaches for fast generation of digital holograms of a three-dimensional （3D） object have been discussed. Among them, the novel look-up table （N-LUT） method is analyzed to dramatically reduce the number of pre-calculated fringe patterns required for computation of digital holograms of a 3D object by employing a new concept of principal fringe patterns, so that problems of computational complexity and huge memory size of the conventional ray-tracing and look-up table methods have been considerably alleviated. Meanwhile, as the 3D video images have a lot of temporally or spatially redundant data in their inter- and intra-frames, computation time of the 3D video holograms could be also reduced just by removing these redundant data. Thus, a couple of computational methods for generation of 3D video holograms by combined use of the N-LUT method and data compression algorithms are also presented and discussed. Some experimental results finally reveal that by using this approach a great reduction of computation time of 3D video holograms could be achieved.

Outline and computational approaches of protein misfolding

Protein misfolding is a general causation of classical conformational diseases and many pathogenic changes that are the result of structural conversion.Here I review recent progress in clinical and computational approaches for each stage of the misfolding process,aiming to present readers an outline for swift comprehension of this field.

COMPUTATIONALINTELLECTUAL ANALYTICAL THEORYOF COMPUTATIONAL ANALYTICAL APPROACH TOROTATING FLOW OF NON_NEWTONIAN FLUID

A combination of the computational symbolic calculation, mathematical approach and physico-mechanical model lends to a computational intellectual analytical approach developed by the author. There is a principal difference between the computer proof and the computer derivation completed by the computer, also difference between the numerical and symbolic calculations. In this investigation the computational analytical approach is extended, and an unsteady flow of non-Newtonian fluid in the gap between two rotating coaxial cylinders is studied. The Oldroyd fluid B model is used by which the Weissenberg effects are explained in a good comparison with the experiments. The governing equations are reduced to a partial differential equation of 3 rd order for the dimensionless velocity. Using the computer software Macsyma and an improved variational approach the problem with the initial and boundary conditions is then reduced to a problem of an ordinary differential equation for different approximations. The analytical solutions are given for the 1 st, 2 nd and 3 rd approximations. The present investigation shows the ability of the computational symbolic manipulation in solving the problems of non-Newtonian fluid flows. There is a possibility of that to solve the problems in mathematics and mechanics. An important conclusion can be drawn from the results that the transition from a steady state to another steady state is non-unique.

Computational Biology Approaches to Plant Metabolism and Photosynthesis:Applications for Corals in Times of Climate Change and Environmental Stress

Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress.

MicroRNAs identification and bioinformatics analysis in large yellow croaker Larimichthys crocea using an integrated comparative and ab initio approach

MicroRNAs(miRNAs) are a group of small, endogenous, single-stranded non-coding RNAs that post-transcriptionally regulate gene expression levels. Previous studies have revealed that miRNAs play key roles in multiple biological processes, such as growth and development in both animals and plants. Computational identification is an efficient method for miRNA prediction in organisms with a reference genome before high-throughput miRNA sequencing experiments. In this study, we employed an integrated strategy combining the homology-based and ab initio approaches to predict miRNAs from the genome and transcriptome of large yellow croaker, one of the most commercially important marine fish in China and East Asia. A total of 418 miRNA molecules, including 287 miRNAs by the homology-based method and 131 miRNAs by the ab initio approach, were identified for large yellow croaker. Additionally, 16 053 target genes were predicted and annotated for Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) databases. Meanwhile, we analysed single nucleotide polymorphisms(SNPs) around large yellow croaker miRNA and found that the miRNA seed regions were significantly less prone to mutations, indicating that the miRNA sequences were under strict natural selection based on their essential regulation functions in living cells. Twenty-two SNPs were identified in large yellow croaker miRNA seed regions, which dramatically influenced the miRNA-gene regulation networks. This is the first reported miRNA detection from both the genome and transcriptome using the integrated strategy for large yellow croaker species, and the miRNA and SNP analyses in this work provide important resources and a reference for subsequent miRNA functional investigations in large yellow croaker.

Complex network perspective on modelling chaotic systems via machine learning

Recent advances have demonstrated that a machine learning technique known as "reservoir computing" is a significantly effective method for modelling chaotic systems. Going beyond short-term prediction, we show that long-term behaviors of an observed chaotic system are also preserved in the trained reservoir system by virtue of network measurements. Specifically, we find that a broad range of network statistics induced from the trained reservoir system is nearly identical with that of a learned chaotic system of interest. Moreover, we show that network measurements of the trained reservoir system are sensitive to distinct dynamics and can in turn detect the dynamical transitions in complex systems. Our findings further support that rather than dynamical equations, reservoir computing approach in fact provides an alternative way for modelling chaotic systems.

Hierarchical Visual Analysis and Steering Framework for Astrophysical Simulations

A framework for accelerating modern long-running astrophysical simulations is presented, which is based on a hierarchical architecture where computational steering in the high-resolution run is performed under the guide of knowledge obtained in the gradually refined ensemble analyses. Several visualization schemes for facilitating ensemble management, error analysis, parameter grouping and tuning are also integrated owing to the pluggable modular design. The proposed approach is prototyped based on the Flash code, and it can be extended by introducing userdefined visualization for specific requirements. Two real-world simulations, i.e., stellar wind and supernova remnant, are carried out to verify the proposed approach.

Multiple rational rogue waves for higher dimensional nonlinear evolution equations via symbolic computation approach

The paper investigates the multiple rogue wave solutions associated with the generalized Hirota-Satsuma-Ito(HSI)equation and the newly proposed extended(3+1)-dimensional Jimbo-Miwa(JM)equation with the help of a symbolic computation technique.By incorporating a direct variable trans-formation and utilizing Hirota’s bilinear form,multiple rogue wave structures of different orders are ob-tained for both generalized HSI and JM equation.The obtained bilinear forms of the proposed equations successfully investigate the 1st,2nd and 3rd-order rogue waves.The constructed solutions are verified by inserting them into original equations.The computations are assisted with 3D graphs to analyze the propagation dynamics of these rogue waves.Physical properties of these waves are governed by different parameters that are discussed in details.

Assessing the spatiotemporal malaria transmission intensity with heterogeneous risk factors:A modeling study in Cambodia

Malaria control can significantly benefit from a holistic and precise way of quantitatively measuring the transmission intensity,which needs to incorporate spatiotemporally varying risk factors.In this study,we conduct a systematic investigation to characterize malaria transmission intensity by taking a spatiotemporal network perspective,where nodes capture the local transmission intensities resulting from dominant vector species,the population density,and land cover,and edges describe the cross-region human mobility patterns.The inferred network enables us to accurately assess the transmission intensity over time and space from available empirical observations.Our study focuses on malaria-severe districts in Cambodia.The malaria transmission intensities determined using our transmission network reveal both qualitatively and quantitatively their seasonal and geographical characteristics:the risks increase in the rainy season and decrease in the dry season;remote and sparsely populated areas generally show higher transmission intensities than other areas.Our findings suggest that:the human mobility(e.g.,in planting/harvest seasons),environment(e.g.,temperature),and contact risk(coexistences of human and vector occurrence)contribute to malaria transmission in spatiotemporally varying degrees;quantitative relationships between these influential factors and the resulting malaria transmission risk can inform evidence-based tailor-made responses at the right locations and times.

Higher-order rogue waves with controllable fission and asymmetry localized in a(3+1)-dimensional generalized Boussinesq equation

The purpose of this paper is to report the feasibility of constructing high-order rogue waves with controllable fission and asymmetry for high-dimensional nonlinear evolution equations.Such a nonlinear model considered in this paper as the concrete example is the(3+1)-dimensional generalized Boussinesq(gB)equation,and the corresponding method is Zhaqilao’s symbolic computation approach containing two embedded parameters.It is indicated by the(3+1)-dimensional gB equation that the embedded parameters can not only control the center of the first-order rogue wave,but also control the number of the wave peaks split from higher-order rogue waves and the asymmetry of higher-order rogue waves about the coordinate axes.The main novelty of this paper is that the obtained results and findings can provide useful supplements to the method used and the controllability of higher-order rogue waves.

Prediction of the Residual Welding Stress in 2.25Cr-1Mo Steel by Taking into Account the Effect of the Solid-State Phase Transformations

A computational approach based on the thermal elastic plastic finite element method was developed for predicting welding residual stress in low carbon alloyed steel welds by taking into account the effect of the solid-state phase transformations. The kinetics of phase transformations was described by Johnson Mehl Avrami Kolmogrov （JMAK） equation for bainitic transition and by Koistinen-Marburger （K-M） relationship for martensitic transition. Moreover, an additive rule depending on volumetric phase fraction was adopted to represent the material property changes during heating and cooling. Consequently, the residual welding stresses in a 2.25Cr1Mo steel TIG welded plate were computed. Early calculation results suggest that the bainitic and martensitic transformations took place in the weld the heat-affected zone drastically reduce the residual longitudinal tensile stress in the region.

Underworld-GT Applied to Guangdong,a Tool to Explore the Geothermal Potential of the Crust

Geothermal energy potential is usually discussed in the context of conventional or engineered systems and at the scale of an individual reservoir. Whereas exploration for conventional reservoirs has been relatively easy, with expressions of resource found close to or even at the surface, exploration for non-conventional systems relies on temperature inherently increasing with depth and searching for favourable geological environments that maximise this increase. To utilitise the information we do have, we often assimilate available exploration data with models that capture the physics of the domi- nant underlying processes. Here, we discuss computational modelling approaches to exploration at a regional or crust scale, with application to geothermal reservoirs within basins or systems of basins. Target reservoirs have （at least） appropriate temperature, permeability and are at accessible depths. We discuss the software development approach that leads to effective use of the tool Underworld. We explore its role in the process of modelling, understanding computational error, importing and exporting geological knowledge as applied to the geological system underpinning the Guangdong Province, China.

CFD simulation of solid-liquid stirred tanks for low to dense solid loading systems

The hydrodynamics of suspension of solids in liquids are critical to the design and performance of stirred tanks as mixing systems. Modelling a multiphase stirred tank at a high solids concentration is complex owing to particle-particle and particle-wall interactions which are generally neglected at low concentra- tions. Most models do not consider such interactions and deviate significantly from experimental data. Furthermore, drag force, turbulence and turbulent dispersion play a crucial role and need to be precisely known in predicting local hydrodynamics. Therefore, critical factors such as the modelling approach, drag, dispersion, coefficient of restitution and turbulence are examined and discussed exhaustively in this paper. The Euler-Euler approach with kinetic theory of granular flow, Syamlal-O＇Brien drag model and Reynolds stress turbulence model provide realistic predictions for such systems. The contribution of the turbulent dispersion force in improving the prediction is marginal but cannot be neglected at low solids volume fractions. Inferences drawn from the study and the finalised models will be instrumen- tal in accurately simulating the solids suspension in stirred tanks for a wide range of conditions. These models can be used in simulations to obtain precise results needed for an in-depth understanding of hydrodynamics in stirred tanks.

Quantum Discord in any Mixture of Two Bi-Qubit Arbitrary Product States

Quantum discord in any mixture of two bi-qubit arbitrary product states is studied with two different approaches. In the first approach the maximM classicM correlations are obtained via numerical computations, while in the second approach they are analytically derived. Quantum correlations captured with both approaches completely coincide, as is in accord with the conclusion of Cen et al. [Phys. Rev. A 83 （2011） 054101]. The symmetry reduction of the concerned states concerning quantum correlations is accomplished. The captured discords are amply analyzed so that some inherent distinct properties are revealed.

Effect of coefficient of restitution in Euler-Euler CFD simulation of fluidized-bed hydrodynamics

Collision between particles plays an important role in determining the hydrodynamic characteristics of gas-solid flow in a fluidized bed. In the present work, earlier work （Loha, Chattopadhyay, ＆ Chatterjee, 2013） was extended to study the effect of the elasticity of particle collision on the hydrodynamic behavior of a bubbling fluidized bed filled with 530-~m particles. The Eulerian-Eulerian two-fluid model was used to simulate the hydrodynamics of the bubbling fluidized bed, where the solid-phase properties were calculated by applying the kinetic theory of granular flow. To investigate the effect of the elasticity of particle collision, different values of the coefficient of restitution were applied in the simulation and their effects were studied in detail. Simulations were performed for two different solid-phase wall boundary conditions. No bubble formation was observed for perfectly elastic collision. The bubble formation started as soon as the coefficient of restitution was set below 1.0, and the space occupied by bubbles in the bed increased with a decrease in the coefficient of restitution. Simulation results were also compared with experimental data available in the literature, and good agreement was found for coefficients of restitution of 0.95 and 0.99.

Comparison of three different CFD methods for dense fluidized beds and validation by a cold flow experiment

This work focuses on a comparison between three different numerical CFD methods, namely Euler-Euler, Euler-Lagrange-stochastic, and Euler-Lagrange-deterministic, to treat a dense spouted bed, A simple cold flow experiment was used to investigate the hydrodynamics of a gas-solid flow in a three dimensional lab-scale spouted bed, In this context, two different air mass flow rates, 0,005 and 0.006 kg/s, were applied during fluidization. The experimental bed behaviour was recorded with a high-speed camera to validate the numerical predictions in terms of bubble size, bed expansion rate, and particle velocities at different reactor heights. The numerical setup was kept similar between all three modelling approaches, At both gas mass flow rates all three approaches are able to capture the overall bed expansion. However, at higher gas mass flow rates, discrepancies between experiment and simulation increase for the Euler-Euler and Euler-Lagrange-stochastic models. The Euler-Lagrange deterministic model most accurately predicts the flow pattern at both mass flow rates. The main reasons for discrepancies between simulation and experiment result from modelling of the collision and friction forces.

Multiple-order rogue wave solutions to a(2+1)-dimensional Boussinesq type equation

In this paper,based on the Hirota bilinear method and symbolic computation approach,multipleorder rogue waves of(2+1)-dimensional Boussinesq type equation are constructed.The reduced bilinear form of the equation is deduced by the transformation of variables.Three kinds of rogue wave solutions are derived by means of bilinear equation.The maximum and minimum values of the first-order rogue wave solution are given at a specific moment.Furthermore,the second-order and third-order rogue waves are explicitly derived.The dynamic characteristics of three kinds of rogue wave solutions are shown by three-dimensional plot.