Second messengers, cyclic adenosine 3'-5'-monophosphate (cAMP) and cyclic guanosine 3'-5'-monophosphate (cGMP) are playing important roles in many animal cells by regulating intracellular signaling pathways and modulating cell physiology. Environmental cues like temperature, light and chemical compounds can stimulate cell surface receptors and trigger the generation of second messengers and the following regulations. Spread of cAMP and cGMP is further shaped by cyclic nucleotide phosphodiesterases (PDEs) for orchestration of intracellular microdomain signaling. However, localized intracellular cAMP and cGMP signaling requires further investigation. Optogenetic manipulation of cAMP and cGMP offers new opportunities of spatio-temporally precise study of their signaling mechanism. Light-gated nucleotide cyclases are well developed and applied for cAMP/cGMP manipulation. Recently discovered rhodopsin phosphodiesterase gene from protists established new and direct biological connection between light and PDEs. Light-regulated PDEs are under development and of demand to complete the toolkit of cAMP/cGMP manipulation. In this review, we summarize the state of the art, pros and cons of artificial and natural light-regulated PDEs and discuss potential new strategies of developing light-gated PDEs for optogenetic manipulation.

The aim of this survey is to review some recent developements in devising efficient preconditioners for sequences of linear systems A x = b. Such a problem arise in many scientific applications, such as discretization of transient PDEs, solution of eigenvalue problems, (Inexact) Newton method applied to nonlinear systems, rational Krylov methods for computing a function of a matrix. Full purpose preconditioners such as the Incomplete Cholesky (IC) factorization or approximate inverses are aimed at clustering eigenvalues of the preconditioned matrices around one. In this paper we will analyze a number of techniques of updating a given IC preconditioner (which we denote as P0 in the sequel) by a low-rank matrix with the aim of further improving this clustering. The most popular low-rank strategies are aimed at removing the smallest eigenvalues (deflation) or at shifting them towards the middle of the spectrum. The low-rank correction is based on a (small) number of linearly independent vectors whose choice is crucial for the effectiveness of the approach. In many cases these vectors are approximations of eigenvectors corresponding to the smallest eigenvalues of the preconditioned matrix P0 A. We will also review some techniques to efficiently approximate these vectors when incorporated within a sequence of linear systems all possibly having constant (or slightly changing) coefficient matrices. Numerical results concerning sequences arising from discretization of linear/nonlinear PDEs and iterative solution of eigenvalue problems show that the performance of a given iterative solver can be very much enhanced by the use of low-rank updates.

The deep energy method (DEM), a type of physics-informed neural network, is evolving as an alternative to finite element analysis. This method employs the principle of minimum potential energy to predict deformations under static loading conditions. However, the model’s accuracy is contingent upon choosing the appropriate architecture for the model, which can be challenging due to the high interactions between hyperparameters, large search space, difficulty in identifying objective functions, and non-convex relationships with the objective functions. To improve DEM’s accuracy, we first introduce random Fourier feature (RFF) mapping. RFF mapping helps with the training of the model by reducing bias towards high frequencies. The effects of six hyperparameters are then studied under compression, tension, and bending loads in planar linear elasticity. Based on this study, a systematic automated hyperparameter optimization approach is proposed. Due to the high interaction between hyperparameters and the non-convex nature of the optimization problem, Bayesian optimization algorithms are used. The models trained using optimized hyperparameters and having Fourier feature mapping can accurately predict deflections compared to finite element analysis. Additionally, the deflections obtained for tension and compression load cases are more sensitive to variations in hyperparameters than bending.

The Physics-Informed Neural Networks (PINNs) improve the efficiency of data utilization by combining physical principles with neural network algorithms and ensure that the predictions are consistent and stable with the physical laws. PINNs opens up a new approach to address inverse problems in fluid mechanics. Based on the single-relaxation-time lattice Boltzmann method (SRT-LBM) with the Bhatnagar-Gross-Krook (BGK) collision operator, the PINN-SRT-LBM model is proposed in this paper for solving the inverse problem in fluid mechanics. The PINN-SRT-LBM model consists of three components. The first component involves a deep neural network that predicts the equilibrium control equations in different discrete velocity directions within SRT-LBM. The second component employs another deep neural network to predict non-equilibrium control equations, enabling inference of the fluid's non-equilibrium characteristics. The third component, a physics informed function translates the outputs of the first two networks into physical infor-mation. By minimizing the residuals of the physical partial differential equations (PDEs), the physics informed function infers relevant macroscopic quantities of the flow. The model evolves two sub-models applicable to different dimensions, named PINN-SRT-LBM-I and PINN-SRT-LBM-II models according to the construction of the physical informed function. The innovation of this work is the introduction of SRT-LBM and discrete velocity models as physical drivers into the neural network through the interpretation function. Therefore, PINN-SRT-LBM allows the neural network to handle inverse problems of various dimensions and focus on problem-specific solving. Experimental results confirm the accurate prediction of flow infor-mation at different Reynolds numbers within the computational domain. Relying on the PINN-SRT-LBM models, inverse problems in fluid mechanics can be solved efficiently.

The subject of this paper is to analyse the Math Principia of Economic 3D Black Holes in Roegenian economics. This idea is totally new in the related literature, excepting our papers. In details, we study two special problems: (i) math origin of economic 3D black holes, (ii) entropy and internal political stability depending on national income and the total investment, for economic RN 3D black hole. To solve these problems, it was necessary to jump from macroeconomic side to microeconomic side (a substantial approach so different), to complete the thermodynamics-economics dictionary with new entities, to introduce the flow between two macroeconomic systems, to study the Schwarzschild type metric properties on an economic 4D system, together with Rindler coordinates, Einstein 4D PDEs, and economic RN 3D black hole. In addition, we introduce some economic Ricci type flows or waves, for further research.

Despite being small and simple structured in comparison to their victims, virus particles have the potential to harm severly and even kill highly developed species such as humans. To face upcoming virus pandemics, detailed quantitative biophysical understanding of intracellular virus replication mechanisms is inevitable. Unveiling the relationship of form and function might allow to determine putative attack points relevant for the systematic development of direct antiviral agents (DAA) and potent vaccines. Biophysical investigations of spatio-temporal dynamics of intracellular virus replication so far are rare. We are developing a framework to allow for fully spatio-temporal resolved virus replication dynamics simulations based on partial differential equations models (PDE) and evaluated with advanced numerical mathematical methods on leading supercomputers. This study presents an advanced highly nonlinear model of the genome replication cycle of a specific RNA virus, the Hepatitis C virus (HCV). The diffusion-reaction model mimics the interplay of the major components of the viral RNA (vRNA) cycle, namely non structural viral proteins (NSP), vRNA and a generic host factor. Technically, we couple surface PDEs (sufPDEs) on the 3D embedded 2D Endoplasmatic Reticulum (ER) manifold with PDEs in the 3D membranous web (MW) and cytosol volume. (The MWs are the replication factories growing on the ER induced by NSPs.) The sufPDE/PDE model is evaluated at realistic reconstructed cell geometries which are based on experimental data. The simulations couple the effects of NSPs which are restricted to the ER surface with effects appearing in the volume. The volume effects include the host factor supply from the cytosol and the MW dynamics. Special emphasis is put to the exchange of components between ER surface, MWs and cytosol volume. As the vRNA spatial properties are not fully understood so far in experiment, the model allows for vRNA both restricted to the ER and moving in the cytosol. The visualization of the simulation resembles a look into some sort of fully 3D resolved “in silico microscopes” to mirror and complement in vitro / in vivo experiments for the intracellular vRNA cycle dynamics. The output data are quantitatively consistent with experimental data and provoke advanced experimental studies to validate the model.