lncRNAs are involved in many biological processes, and their mutations and disorders are closely related to many diseases. Identification of LncRNA-Disease Associations (LDAs) helps us understand the pathogenesis of d...
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Finding index-1 saddle points is crucial for understanding phase transitions. In this work, we propose a simple yet efficient approach, the spring pair method (SPM), to accurately locate saddle points. Without requiri...
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Finding index-1 saddle points is crucial for understanding phase transitions. In this work, we propose a simple yet efficient approach, the spring pair method (SPM), to accurately locate saddle points. Without requiring the Hessian information, the SPM evolves a single pair of spring-coupled particles on an energy surface. By designing complementary drifting and climbing dynamics based on gradient decomposition, the spring pair converges onto the minimum energy path (MEP) and spontaneously aligns its orientation with the MEP tangent, providing a reliable ascent direction for efficient convergence to saddle points. The SPM fundamentally differs from traditional surface walking methods that rely on the eigenvectors of the Hessian, which may deviate from the MEP tangent and potentially lead to convergence failure or undesired saddle points. The efficiency of the SPM for finding saddle points is verified by ample examples, including Lennard-Jones clusters, Morse clusters, water clusters, and the Landau energy functional involving quasicrystal phase transitions.
In this paper spectral Galerkin approximation of optimal control problem governed by fractional elliptic equation is *** deal with the nonlocality of fractional Laplacian operator the Caffarelli-Silvestre extension is...
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In this paper spectral Galerkin approximation of optimal control problem governed by fractional elliptic equation is *** deal with the nonlocality of fractional Laplacian operator the Caffarelli-Silvestre extension is *** first order optimality condition of the extended optimal control problem is derived.A spectral Galerkin discrete scheme for the extended problem based on weighted Laguerre polynomials is developed.A priori error estimates for the spectral Galerkin discrete scheme is *** experiments are presented to show the effectiveness of our methods and to verify the theoretical findings.
By transforming the Caputo tempered fractional advection-diffusion equation into the Riemann–Liouville tempered fractional advection-diffusion equation,and then using the fractional-compact Grünwald–Letnikov te...
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By transforming the Caputo tempered fractional advection-diffusion equation into the Riemann–Liouville tempered fractional advection-diffusion equation,and then using the fractional-compact Grünwald–Letnikov tempered difference operator to approximate the Riemann–Liouville tempered fractional partial derivative,the fractional central difference operator to discritize the space Riesz fractional partial derivative,and the classical central difference formula to discretize the advection term,a numerical algorithm is constructed for solving the Caputo tempered fractional advection-diffusion *** stability and the convergence analysis of the numerical method are *** experiments show that the numerical method is effective.
This paper is devoted to examining the stability of Runge-Kutta methods for solving stiff nonlinear Volterra delay-integro-differential-algebraic equations (DIDAEs) with constant delay. Hybrid numerical schemes combin...
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Newton-type solvers have been extensively employed for solving a variety of nonlinear system of algebraic equations. However, for some complex nonlinear system of algebraic equations, efficiently solving these systems...
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The aim of this paper is to develop a refined error estimate of L1/finite element scheme for a reaction-subdiffusion equation with constant delay τ and uniform time mesh. Under the non-uniform multi-singularity assum...
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The numerical stability of nonlinear equations has been a long-standing concern and there is no standard framework for analyzing long-term qualitative behavior. In the recent breakthrough work [XX23], a rigorous numer...
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The numerical stability of nonlinear equations has been a long-standing concern and there is no standard framework for analyzing long-term qualitative behavior. In the recent breakthrough work [XX23], a rigorous numerical analysis was conducted on the numerical solution of a scalar ODE containing a cubic polynomial derived from the Allen-Cahn equation. It was found that only the implicit Euler method converge to the correct steady state for any given initial value u0 under the unique solvability and energy stability. But all the other commonly used second-order numerical schemes exhibit sensitivity to initial conditions and may converge to an incorrect equilibrium state as tn → ∞. This indicates that energy stability may not be decisive for the long-term qualitative correctness of numerical solutions. We found that using another fundamental property of the solution, namely monotonicity instead of energy stability, is sufficient to ensure that many common numerical schemes converge to the correct equilibrium state. This leads us to introduce the critical step size constant h∗ = h∗(u0, ϵ) that ensures the monotonicity and unique solvability of the numerical solutions, where the scaling parameter ϵ ∈ (0, 1). For a given numerical method, if the initial value u0 is given, no matter how large it is, we prove that h∗ > 0. As long as the actual simulation step 0 ∗, the numerical solution preserves monotonicity and converges to the correct equilibrium state. On the other hand, we prove that the implicit Euler scheme h∗ = h∗(ϵ), which is independent of u0 and only depends on ϵ. Hence regardless of the initial value taken, the simulation can be guaranteed to be correct when h ∗. But for various other numerical methods, no mater how small the step size h is in advance, there will always be initial values that cause simulation errors. In fact, for these numerical methods, we prove that infu0∈R h∗(u0, ϵ) = 0. Various numerical experiments are used to confirm the theoretical anal
In this paper,we present a two-grid discretization scheme for semilinear parabolic integro-differential equations by H1-Galerkin mixed finite element *** use the lowest order Raviart-Thomas mixed finite elements and c...
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In this paper,we present a two-grid discretization scheme for semilinear parabolic integro-differential equations by H1-Galerkin mixed finite element *** use the lowest order Raviart-Thomas mixed finite elements and continuous linear finite element for spatial discretization,and backward Euler scheme for temporal ***,a priori error estimates and some superclose properties are ***,a two-grid scheme is presented and its convergence is *** the proposed two-grid scheme,the solution of the nonlinear system on a fine grid is reduced to the solution of the nonlinear system on a much coarser grid and the solution of two symmetric and positive definite linear algebraic equations on the fine grid and the resulting solution still maintains optimal ***,a numerical experiment is implemented to verify theoretical results of the proposed *** theoretical and numerical results show that the two-grid method achieves the same convergence property as the one-grid method with the choice h=H^(2).
The iterative solution of the sequence of linear systems arising from threetemperature(3-T)energy equations is an essential component in the numerical simulation of radiative hydrodynamic(RHD)***,due to the complicate...
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The iterative solution of the sequence of linear systems arising from threetemperature(3-T)energy equations is an essential component in the numerical simulation of radiative hydrodynamic(RHD)***,due to the complicated application features of the RHD problems,solving 3-T linear systems with classical preconditioned iterative techniques is *** address this difficulty,a physicalvariable based coarsening two-level(PCTL)preconditioner has been proposed by dividing the fully coupled system into four individual easier-to-solve *** its nearly optimal complexity and robustness,the PCTL algorithm suffers from poor efficiency because of the overhead associatedwith the construction of setup phase and the solution of ***,the PCTL algorithm employs a fixed strategy for solving the sequence of 3-T linear systems,which completely ignores the dynamically and slowly changing features of these linear *** address these problems and to efficiently solve the sequence of 3-T linear systems,we propose an adaptive two-level preconditioner based on the PCTL algorithm,referred to as α*** adaptive strategies of the αSetup-PCTL algorithm are inspired by those of αSetup-AMG algorithm,which is an adaptive-setup-based AMG solver for sequence of sparse linear *** proposed αSetup-PCTL algorithm could adaptively employ the appropriate strategies for each linear system,and thus increase the overall *** results demonstrate that,for 36 linear systems,the αSetup-PCTL algorithm achieves an average speedup of 2.2,and a maximum speedup of 4.2 when compared to the PCTL algorithm.
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