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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function

Neurodegeneration causes a significant disease burden and there are few therapeutic interventions available for reversing or slowing the disease progression. Induced pluripotent stem cells (iPSCs) hold significant potential since they are sourced from adult tissue and have the capacity to be differentiated into numerous cell lineages, including motor neurons. This differentiation process traditionally relies on cell lineage patterning factors to be supplied in the differentiation media. Genetic engineering of iPSC with the introduction of recombinant master regulators of motor neuron (MN) differentiation has the potential to shorten and streamline cell developmental programs. We have established stable iPSC cell lines with transient induction of exogenous LHX3 and ISL1 from the Tet-activator regulatory region and have demonstrated that induction of the transgenes is not sufficient for the development of mature MNs in the absence of neuron patterning factors. Comparative global transcriptome analysis of MN development from native and Lhx-ISL1 modified iPSC cultures demonstrated that the genetic manipulation helped to streamline the neuronal patterning process. However, leaky gene expression of the exogenous MN master regulators in iPSC resulted in the premature activation of genetic pathways characteristic of the mature MN function. Dysregulation of metabolic and regulatory pathways within the developmental process affected the MN electrophysiological responses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Legendre-Tau approximations for functional differential equations

The numerical approximation of solutions to linear functional differential equations are considered using the so called Legendre tau method. The functional differential equation is first reformulated as a partial differential equation with a nonlocal boundary condition involving time differentiation. The approximate solution is then represented as a truncated Legendre series with time varying coefficients which satisfy a certain system of ordinary differential equations. The method is very easy to code and yields very accurate approximations. Convergence is established, various numerical examples are presented, and comparison between the latter and cubic spline approximations is made.

Ito, K.↗
NASA NTRS1980

Nonlinear grid error effects on numerical solution of partial differential equations

Finite difference solutions of nonlinear partial differential equations require discretizations and consequently grid errors are generated. These errors strongly affect stability and convergence properties of difference models. Previously such errors were analyzed by linearizing the difference equations for solutions. Properties of mappings of decadence were used to analyze nonlinear instabilities. Such an analysis is directly affected by initial/boundary conditions. An algorithm was developed, applied to nonlinear Burgers equations, and verified computationally. A preliminary test shows that Navier-Stokes equations may be treated similarly.

Dey, S. K.↗
NASA NTRS1983

A new explicit method for the numerical solution of parabolic differential equations

A new method is derived for solving parabolic partial differential equations arising in transient heat conduction or in boundary-layer flows. The method is based on a combination of the modified differential quadrature (MDQ) method with the rational Runge-Kutta time-integration scheme. It is fully explicit, requires no matrix inversion, and is stable for any time-step for the heat equations. Burgers equation and the one- and two-dimensional heat equations are solved to demonstrate the accuracy and efficiency of the proposed algorithm. The present method is found to be very accurate and efficient when results are compared with analytic solutions.

Satofuka, N.↗
NASA NTRS1986

On substructuring algorithms and solution techniques for the numerical approximation of partial differential equations

Substructuring methods are in common use in mechanics problems where typically the associated linear systems of algebraic equations are positive definite. Here these methods are extended to problems which lead to nonpositive definite, nonsymmetric matrices. The extension is based on an algorithm which carries out the block Gauss elimination procedure without the need for interchanges even when a pivot matrix is singular. Examples are provided wherein the method is used in connection with finite element solutions of the stationary Stokes equations and the Helmholtz equation, and dual methods for second-order elliptic equations.

Gunzburger, M. D.↗
NASA NTRS2002

A Numerical Scheme for Ordinary Differential Equations Having Time Varying and Nonlinear Coefficients Based on the State Transition Matrix

A variable order method of integrating initial value ordinary differential equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. While it is more complex than most other methods, it produces exact solutions at arbitrary time step size when the time variation of the system can be modeled exactly by a polynomial. Solutions to several nonlinear problems exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with an exact solution and with solutions obtained by established methods.

Bartels, Robert E.↗
NASA NTRS1976

Numerical solution of nonlinear partial differential equations of mixed type

A review is presented of some recently developed numerical methods for the solution of nonlinear equations of mixed type. The methods considered use finite difference approximations to the differential equation. Central difference formulas are employed in the subsonic zone and upwind difference formulas are used in the supersonic zone. The relaxation method for the small disturbance equation is discussed and a description is given of difference schemes for the potential flow equation in quasi-linear form. Attention is also given to difference schemes for the potential flow equation in conservation form, the analysis of relaxation schemes by the time dependent analogy, the accelerated iterative method, and three-dimensional calculations.

Jameson, A.↗
NASA NTRS1978

The stability of numerical methods for second order ordinary differential equations

An important characterization of a numerical method for first order ODE's is the region of absolute stability. If all eigenvalues of the linear problem dy/dt = Ay are inside this region, the numerical method is stable. If the second order system d/dt(dy/dt) = 2Ady/dt - By is solved as a first order system, the same result applies to the eigenvalues of the generalized eigenvalue problem (lambda-squared)I 2(lambda)A + B. No such region exists for general methods for second order equations, but in some cases a region of absolute stability can be defined for methods for the single second order equation d/dt(dy/dt) = 2ady/dt - by. The absence of a region of absolute stability can occur when different members of a system of first order equations are solved by different methods.

Gear, C. W.↗
NASA NTRS1986

Legendre-tau approximations for functional differential equations

The numerical approximation of solutions to linear retarded functional differential equations are considered using the so-called Legendre-tau method. The functional differential equation is first reformulated as a partial differential equation with a nonlocal boundary condition involving time-differentiation. The approximate solution is then represented as a truncated Legendre series with time-varying coefficients which satisfy a certain system of ordinary differential equations. The method is very easy to code and yields very accurate approximations. Convergence is established, various numerical examples are presented, and comparison between the latter and cubic spline approximation is made.

Ito, K.↗
NASA NTRS1999

Numerical Study of Buoyancy and Differential Diffusion Effects on the Structure and Dynamics of Triple Flames

Triple flames arise in a number of practical configurations where fuel and oxidizer are partially premixed, such as in the base of a lifted jet flame. Past experimental studies, theoretical analyses, and numerical modeling of triple flames suggested the potential role of triple flames in stabilizing turbulent flames and in promoting flame propagation. From recent numerical simulations of laminar triple flames, a strong influence of differential diffusion among species and heat on the triple flame structure has been gradually appreciated. This paper reports preliminary numerical results on the influence of gravity and differential diffusion effects on the structure and dynamics of triple flames with a one-step global irreversible chemistry model.

Chen, J. -Y.↗
NASA NTRS1986

A combined integrating and differentiating matrix formulation for boundary value problems on rectangular domains

Integrating and differentiating matrices allow the numerical integration and differential of functions whose values are known at points of a discrete grid. Previous derivations of these matrices were restricted to one dimensional grids or to rectangular grids with uniform spacing in at least one direction. Integrating and differentiating matrices were developed for grids with nonuniform spacing in both directions. The use of these matrices as operators to reformulate boundary value problems on rectangular domains as matrix problems for a finite dimensional solution vector is considered. The method requires nonuniform grids which include near boundary points. An eigenvalue problem for the transverse vibrations of a simply supported rectangular plate is solved to illustrate the method.

Lakin, W. D.↗
NASA NTRS1986

A combined integrating- and differentiating-matrix formulation for boundary-value problems on rectangular domains

Integrating and differentiating matrices allow the numerical integration and differential of functions whose values are known at points of a discrete grid. Previous derivations of these matrices were restricted to one dimensional grids or to rectangular grids with uniform spacing in at least one direction. Integrating and differentiating matrices were developed for grids with nonuniform spacing in both directions. The use of these matrices as operators to reformulate boundary value problems on rectangular domains as matrix problems for a finite dimensional solution vector is considered. The method requires nonuniform grids which include near boundary points. An eigenvalue problem for the transverse vibrations of a simply supported rectangular plate is solved to illustrate the method.

Lakin, W. D.↗
DOE OSTI2023

Learning effective stochastic differential equations from microscopic simulations: Linking stochastic numerics to deep learning

We identify effective stochastic differential equations (SDEs) for coarse observables of fine-grained particle- or agent-based simulations; these SDEs then provide useful coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDEs through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler–Maruyama and Milstein); our approximations can thus benefit from backward error analysis of these underlying numerical schemes. They also lend themselves naturally to “physics-informed” gray-box identification when approximate coarse models, such as mean field equations, are available. Existing numerical integration schemes for Langevin-type equations and for stochastic partial differential equations can also be used for training; we demonstrate this on a stochastically forced oscillator and the stochastic wave equation. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

97 MATHEMATICS AND COMPUTING↗