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Sample records for nonlinear poisson-boltzmann equation

  1. Solution of the nonlinear Poisson-Boltzmann equation: Application to ionic diffusion in cementitious materials

    SciTech Connect

    Arnold, J.; Kosson, D.S.; Garrabrants, A.; Meeussen, J.C.L.; Sloot, H.A. van der

    2013-02-15

    A robust numerical solution of the nonlinear Poisson-Boltzmann equation for asymmetric polyelectrolyte solutions in discrete pore geometries is presented. Comparisons to the linearized approximation of the Poisson-Boltzmann equation reveal that the assumptions leading to linearization may not be appropriate for the electrochemical regime in many cementitious materials. Implications of the electric double layer on both partitioning of species and on diffusive release are discussed. The influence of the electric double layer on anion diffusion relative to cation diffusion is examined.

  2. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves.

    PubMed Central

    Oberoi, H; Allewell, N M

    1993-01-01

    Although knowledge of the pKa values and charge states of individual residues is critical to understanding the role of electrostatic effects in protein structure and function, calculating these quantities is challenging because of the sensitivity of these parameters to the position and distribution of charges. Values for many different proteins which agree well with experimental results have been obtained with modified Tanford-Kirkwood theory in which the protein is modeled as a sphere (reviewed in Ref. 1); however, convergence is more difficult to achieve with finite difference methods, in which the protein is mapped onto a grid and derivatives of the potential function are calculated as differences between the values of the function at grid points (reviewed in Ref. 6). Multigrid methods, in which the size of the grid is varied from fine to coarse in several cycles, decrease computational time, increase rates of convergence, and improve agreement with experiment. Both the accuracy and computational advantage of the multigrid approach increase with grid size, because the time required to achieve a solution increases slowly with grid size. We have implemented a multigrid procedure for solving the nonlinear Poisson-Boltzmann equation, and, using lysozyme as a test case, compared calculations for several crystal forms, different refinement procedures, and different charge assignment schemes. The root mean square difference between calculated and experimental pKa values for the crystal structure which yields best agreement with experiment (1LZT) is 1.1 pH units, with the differences in calculated and experimental pK values being less than 0.6 pH units for 16 out of 21 residues. The calculated titration curves of several residues are biphasic. Images FIGURE 8 PMID:8369451

  3. A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation.

    PubMed

    Colmenares, José; Galizia, Antonella; Ortiz, Jesús; Clematis, Andrea; Rocchia, Walter

    2014-01-01

    The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs. PMID:25013789

  4. A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation

    PubMed Central

    Colmenares, José; Galizia, Antonella; Ortiz, Jesús; Clematis, Andrea; Rocchia, Walter

    2014-01-01

    The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs. PMID:25013789

  5. Solution of the nonlinear Poisson-Boltzmann equation using pseudo-transient continuation and the finite element method.

    PubMed

    Shestakov, A I; Milovich, J L; Noy, A

    2002-03-01

    The nonlinear Poisson-Boltzmann (PB) equation is solved using Newton-Krylov iterations coupled with pseudo-transient continuation. The PB potential is used to compute the electrostatic energy and evaluate the force on a user-specified contour. The PB solver is embedded in a existing, 3D, massively parallel, unstructured-grid, finite element code. Either Dirichlet or mixed boundary conditions are allowed. The latter specifies surface charges, approximates far-field conditions, or linearizes conditions "regulating" the surface charge. Stability and robustness are proved using results for backward Euler differencing of diffusion equations. Potentials and energies of charged spheres and plates are computed and results compared to analysis. An approximation to the potential of the nonlinear, spherical charge is derived by combining two analytic formulae. The potential and force due to a conical probe interacting with a flat plate are computed for two types of boundary conditions: constant potential and constant charge. The second case is compared with direct force measurements by chemical force microscopy. The problem is highly nonlinear-surface potentials of the linear and nonlinear PB equations differ by over an order of magnitude. Comparison of the simulated and experimentally measured forces shows that approximately half of the surface carboxylic acid groups, of density 1/(0.2 nm2), ionize in the electrolyte implying surface charges of 0.4 C/m2, surface potentials of 0.27 V, and a force of 0.6 nN when the probe and plate are 8.7 nm apart. PMID:16290441

  6. Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers.

    PubMed

    Cai, Qin; Hsieh, Meng-Juei; Wang, Jun; Luo, Ray

    2010-01-12

    We implemented and optimized seven finite-difference solvers for the full nonlinear Poisson-Boltzmann equation in biomolecular applications, including four relaxation methods, one conjugate gradient method, and two inexact Newton methods. The performance of the seven solvers was extensively evaluated with a large number of nucleic acids and proteins. Worth noting is the inexact Newton method in our analysis. We investigated the role of linear solvers in its performance by incorporating the incomplete Cholesky conjugate gradient and the geometric multigrid into its inner linear loop. We tailored and optimized both linear solvers for faster convergence rate. In addition, we explored strategies to optimize the successive over-relaxation method to reduce its convergence failures without too much sacrifice in its convergence rate. Specifically we attempted to adaptively change the relaxation parameter and to utilize the damping strategy from the inexact Newton method to improve the successive over-relaxation method. Our analysis shows that the nonlinear methods accompanied with a functional-assisted strategy, such as the conjugate gradient method and the inexact Newton method, can guarantee convergence in the tested molecules. Especially the inexact Newton method exhibits impressive performance when it is combined with highly efficient linear solvers that are tailored for its special requirement. PMID:24723843

  7. Multilevel Methods for the Poisson-Boltzmann Equation

    NASA Astrophysics Data System (ADS)

    Holst, Michael Jay

    We consider the numerical solution of the Poisson -Boltzmann equation (PBE), a three-dimensional second order nonlinear elliptic partial differential equation arising in biophysics. This problem has several interesting features impacting numerical algorithms, including discontinuous coefficients representing material interfaces, rapid nonlinearities, and three spatial dimensions. Similar equations occur in various applications, including nuclear physics, semiconductor physics, population genetics, astrophysics, and combustion. In this thesis, we study the PBE, discretizations, and develop multilevel-based methods for approximating the solutions of these types of equations. We first outline the physical model and derive the PBE, which describes the electrostatic potential of a large complex biomolecule lying in a solvent. We next study the theoretical properties of the linearized and nonlinear PBE using standard function space methods; since this equation has not been previously studied theoretically, we provide existence and uniqueness proofs in both the linearized and nonlinear cases. We also analyze box-method discretizations of the PBE, establishing several properties of the discrete equations which are produced. In particular, we show that the discrete nonlinear problem is well-posed. We study and develop linear multilevel methods for interface problems, based on algebraic enforcement of Galerkin or variational conditions, and on coefficient averaging procedures. Using a stencil calculus, we show that in certain simplified cases the two approaches are equivalent, with different averaging procedures corresponding to different prolongation operators. We also develop methods for nonlinear problems based on a nonlinear multilevel method, and on linear multilevel methods combined with a globally convergent damped-inexact-Newton method. We derive a necessary and sufficient descent condition for the inexact-Newton direction, enabling the development of extremely

  8. Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Harris, Robert C.; Boschitsch, Alexander H.; Fenley, Marcia O.

    2014-02-01

    Experimental results have demonstrated that the numbers of counterions surrounding nucleic acids differ from those predicted by the nonlinear Poisson-Boltzmann equation, NLPBE. Some studies have fit these data against the ion size in the size-modified Poisson-Boltzmann equation, SMPBE, but the present study demonstrates that other parameters, such as the Stern layer thickness and the molecular surface definition, can change the number of bound ions by amounts comparable to varying the ion size. These parameters will therefore have to be fit simultaneously against experimental data. In addition, the data presented here demonstrate that the derivative, SK, of the electrostatic binding free energy, ΔGel, with respect to the logarithm of the salt concentration is sensitive to these parameters, and experimental measurements of SK could be used to parameterize the model. However, although better values for the Stern layer thickness and ion size and better molecular surface definitions could improve the model's predictions of the numbers of ions around biomolecules and SK, ΔGel itself is more sensitive to parameters, such as the interior dielectric constant, which in turn do not significantly affect the distributions of ions around biomolecules. Therefore, improved estimates of the ion size and Stern layer thickness to use in the SMPBE will not necessarily improve the model's predictions of ΔGel.

  9. Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation.

    PubMed

    Harris, Robert C; Boschitsch, Alexander H; Fenley, Marcia O

    2014-02-21

    Experimental results have demonstrated that the numbers of counterions surrounding nucleic acids differ from those predicted by the nonlinear Poisson-Boltzmann equation, NLPBE. Some studies have fit these data against the ion size in the size-modified Poisson-Boltzmann equation, SMPBE, but the present study demonstrates that other parameters, such as the Stern layer thickness and the molecular surface definition, can change the number of bound ions by amounts comparable to varying the ion size. These parameters will therefore have to be fit simultaneously against experimental data. In addition, the data presented here demonstrate that the derivative, SK, of the electrostatic binding free energy, ΔGel, with respect to the logarithm of the salt concentration is sensitive to these parameters, and experimental measurements of SK could be used to parameterize the model. However, although better values for the Stern layer thickness and ion size and better molecular surface definitions could improve the model's predictions of the numbers of ions around biomolecules and SK, ΔGel itself is more sensitive to parameters, such as the interior dielectric constant, which in turn do not significantly affect the distributions of ions around biomolecules. Therefore, improved estimates of the ion size and Stern layer thickness to use in the SMPBE will not necessarily improve the model's predictions of ΔGel. PMID:24559370

  10. Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Watanabe, Hirofumi; Okiyama, Yoshio; Nakano, Tatsuya; Tanaka, Shigenori

    2010-11-01

    We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17 β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation.

  11. A new Green's function Monte Carlo algorithm for the solution of the two-dimensional nonlinear Poisson-Boltzmann equation: Application to the modeling of the communication breakdown problem in space vehicles during re-entry

    NASA Astrophysics Data System (ADS)

    Chatterjee, Kausik; Roadcap, John R.; Singh, Surendra

    2014-11-01

    The objective of this paper is the exposition of a recently-developed, novel Green's function Monte Carlo (GFMC) algorithm for the solution of nonlinear partial differential equations and its application to the modeling of the plasma sheath region around a cylindrical conducting object, carrying a potential and moving at low speeds through an otherwise neutral medium. The plasma sheath is modeled in equilibrium through the GFMC solution of the nonlinear Poisson-Boltzmann (NPB) equation. The traditional Monte Carlo based approaches for the solution of nonlinear equations are iterative in nature, involving branching stochastic processes which are used to calculate linear functionals of the solution of nonlinear integral equations. Over the last several years, one of the authors of this paper, K. Chatterjee has been developing a philosophically-different approach, where the linearization of the equation of interest is not required and hence there is no need for iteration and the simulation of branching processes. Instead, an approximate expression for the Green's function is obtained using perturbation theory, which is used to formulate the random walk equations within the problem sub-domains where the random walker makes its walks. However, as a trade-off, the dimensions of these sub-domains have to be restricted by the limitations imposed by perturbation theory. The greatest advantage of this approach is the ease and simplicity of parallelization stemming from the lack of the need for iteration, as a result of which the parallelization procedure is identical to the parallelization procedure for the GFMC solution of a linear problem. The application area of interest is in the modeling of the communication breakdown problem during a space vehicle's re-entry into the atmosphere. However, additional application areas are being explored in the modeling of electromagnetic propagation through the atmosphere/ionosphere in UHF/GPS applications.

  12. AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.

    PubMed

    Koehl, Patrice; Delarue, Marc

    2010-02-14

    The Poisson-Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson-Boltzmann-Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE

  13. The charge conserving Poisson-Boltzmann equations: Existence, uniqueness, and maximum principle

    SciTech Connect

    Lee, Chiun-Chang

    2014-05-15

    The present article is concerned with the charge conserving Poisson-Boltzmann (CCPB) equation in high-dimensional bounded smooth domains. The CCPB equation is a Poisson-Boltzmann type of equation with nonlocal coefficients. First, under the Robin boundary condition, we get the existence of weak solutions to this equation. The main approach is variational, based on minimization of a logarithm-type energy functional. To deal with the regularity of weak solutions, we establish a maximum modulus estimate for the standard Poisson-Boltzmann (PB) equation to show that weak solutions of the CCPB equation are essentially bounded. Then the classical solutions follow from the elliptic regularity theorem. Second, a maximum principle for the CCPB equation is established. In particular, we show that in the case of global electroneutrality, the solution achieves both its maximum and minimum values at the boundary. However, in the case of global non-electroneutrality, the solution may attain its maximum value at an interior point. In addition, under certain conditions on the boundary, we show that the global non-electroneutrality implies pointwise non-electroneutrality.

  14. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION

    PubMed Central

    HOLST, MICHAEL; MCCAMMON, JAMES ANDREW; YU, ZEYUN; ZHOU, YOUNGCHENG; ZHU, YUNRONG

    2011-01-01

    We consider the design of an effective and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the two-term regularization technique for the continuous problem recently proposed by Chen, Holst, and Xu based on the removal of the singular electrostatic potential inside biomolecules; this technique made possible the development of the first complete solution and approximation theory for the Poisson-Boltzmann equation, the first provably convergent discretization, and also allowed for the development of a provably convergent AFEM. However, in practical implementation, this two-term regularization exhibits numerical instability. Therefore, we examine a variation of this regularization technique which can be shown to be less susceptible to such instability. We establish a priori estimates and other basic results for the continuous regularized problem, as well as for Galerkin finite element approximations. We show that the new approach produces regularized continuous and discrete problems with the same mathematical advantages of the original regularization. We then design an AFEM scheme for the new regularized problem, and show that the resulting AFEM scheme is accurate and reliable, by proving a contraction result for the error. This result, which is one of the first results of this type for nonlinear elliptic problems, is based on using continuous and discrete a priori L∞ estimates to establish quasi-orthogonality. To provide a high-quality geometric model as input to the AFEM algorithm, we also describe a class of feature-preserving adaptive mesh generation algorithms designed specifically for constructing meshes of biomolecular structures, based on the intrinsic local structure tensor of the molecular surface. All of the algorithms described in the article are implemented in the Finite Element Toolkit (FETK), developed and maintained at UCSD. The stability advantages of the new regularization scheme

  15. Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.

    PubMed

    Botello-Smith, Wesley M; Luo, Ray

    2015-10-26

    Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membranes into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multigrid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations. PMID:26389966

  16. Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation

    PubMed Central

    Botello-Smith, Wesley M.; Luo, Ray

    2016-01-01

    Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membrane into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multi-grid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations. PMID:26389966

  17. Membrane potential and ion partitioning in an erythrocyte using the Poisson-Boltzmann equation.

    PubMed

    Barbosa, Nathalia S V; Lima, Eduardo R A; Boström, Mathias; Tavares, Frederico W

    2015-05-28

    In virtually all mammal cells, we can observe a much higher concentration of potassium ions inside the cell and vice versa for sodium ions. Classical theories ignore the specific ion effects and the difference in the thermodynamic reference states between intracellular and extracellular environments. Usually, this differential ion partitioning across a cell membrane is attributed exclusively to the active ion transport. Our aim is to investigate how much the dispersion forces contribute to active ion pumps in an erythrocyte (red blood cell) as well as the correction of chemical potential reference states between intracellular and extracellular environments. The ionic partition and the membrane potential in an erythrocyte are analyzed by the modified Poisson-Boltzmann equation, considering nonelectrostatic interactions between ions and macromolecules. Results show that the nonelectrostatic potential calculated by Lifshitz theory has only a small influence with respect to the high concentration of K(+) in the intracellular environment in comparison with Na(+). PMID:25941952

  18. Exact solution of the unidimensional Poisson-Boltzmann equation for a 1:2 (2:1) electrolyte.

    PubMed Central

    Andrietti, F; Peres, A; Pezzotta, R

    1976-01-01

    The unidimensional Poisson-Boltzmann equation for a 1:2 (2:1) electrolyte has been solved analytically. The results have been compared with those obtained from the linearized equation. It is shown that in physiological conditions the difference may be greater than 10%. The value of the derivative of the potential in x=0, (dpsi/dx)x=0, has been used by many authors in the evaluation of the superficial charges of biological membranes. The value of (dpsi/dx)x-0 have also been compared with the ones derived from the linearized equation. The difference may be greater than 25%. Our results suggest that the linearization of the Poisson-Boltzmann equation for a 1:2(2:1) electrolyte may be greatly misleading. PMID:963209

  19. Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation.

    PubMed

    Harris, Robert C; Boschitsch, Alexander H; Fenley, Marcia O

    2013-08-13

    Grid-based solvers of the Poisson-Boltzmann, PB, equation are routinely used to estimate electrostatic binding, ΔΔGel, and solvation, ΔGel, free energies. The accuracies of such estimates are subject to grid discretization errors from the finite difference approximation to the PB equation. Here, we show that the grid discretization errors in ΔΔGel are more significant than those in ΔGel, and can be divided into two parts: (i) errors associated with the relative positioning of the grid and (ii) systematic errors associated with grid spacing. The systematic error in particular is significant for methods, such as the molecular mechanics PB surface area, MM-PBSA, approach that predict electrostatic binding free energies by averaging over an ensemble of molecular conformations. Although averaging over multiple conformations can control for the error associated with grid placement, it will not eliminate the systematic error, which can only be controlled by reducing grid spacing. The present study indicates that the widely-used grid spacing of 0.5 Å produces unacceptable errors in ΔΔGel, even though its predictions of ΔGel are adequate for the cases considered here. Although both grid discretization errors generally increase with grid spacing, the relative sizes of these errors differ according to the solute-solvent dielectric boundary definition. The grid discretization errors are generally smaller on the Gaussian surface used in the present study than on either the solvent-excluded or van der Waals surfaces, which both contain more surface discontinuities (e.g., sharp edges and cusps). Additionally, all three molecular surfaces converge to very different estimates of ΔΔGel. PMID:23997692

  20. Efficient quantum mechanical calculation of solvation free energies based on density functional theory, numerical atomic orbitals and Poisson Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Wang, Mingliang; Wong, Chung F.; Liu, Jianhong; Zhang, Peixin

    2007-07-01

    We have successfully coupled the Kohn-Sham with Poisson-Boltzmann equations to predict the solvation free energy, where the Kohn-Sham equations were solved by implementing the flexible pseudo atomic orbitals as in S IESTA package. It was found that the calculated solvation free energy is in good agreement with experimental results for small neutral molecules, and its standard error is 1.33 kcal/mol, the correlation coefficient is 0.97. Due to its high efficiency and accuracy, the proposed model can be a promising tool for computing solvation free energies in computer aided drug design in future.

  1. Electrostatic forces in the Poisson-Boltzmann systems

    PubMed Central

    Xiao, Li; Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

    2013-01-01

    Continuum modeling of electrostatic interactions based upon numerical solutions of the Poisson-Boltzmann equation has been widely used in structural and functional analyses of biomolecules. A limitation of the numerical strategies is that it is conceptually difficult to incorporate these types of models into molecular mechanics simulations, mainly because of the issue in assigning atomic forces. In this theoretical study, we first derived the Maxwell stress tensor for molecular systems obeying the full nonlinear Poisson-Boltzmann equation. We further derived formulations of analytical electrostatic forces given the Maxwell stress tensor and discussed the relations of the formulations with those published in the literature. We showed that the formulations derived from the Maxwell stress tensor require a weaker condition for its validity, applicable to nonlinear Poisson-Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models. PMID:24028101

  2. Langevin Poisson-Boltzmann equation: point-like ions and water dipoles near a charged surface.

    PubMed

    Gongadze, Ekaterina; van Rienen, Ursula; Kralj-Iglič, Veronika; Iglič, Aleš

    2011-06-01

    Water ordering near a charged membrane surface is important for many biological processes such as binding of ligands to a membrane or transport of ions across it. In this work, the mean-field Poisson-Boltzmann theory for point-like ions, describing an electrolyte solution in contact with a planar charged surface, is modified by including the orientational ordering of water. Water molecules are considered as Langevin dipoles, while the number density of water is assumed to be constant everywhere in the electrolyte solution. It is shown that the dielectric permittivity of an electrolyte close to a charged surface is decreased due to the increased orientational ordering of water dipoles. The dielectric permittivity close to the charged surface is additionally decreased due to the finite size of ions and dipoles. PMID:21613667

  3. The Poisson-Boltzmann model for tRNA

    PubMed Central

    Gruziel, Magdalena; Grochowski, Pawel; Trylska, Joanna

    2008-01-01

    Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA. PMID:18432617

  4. Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT.

    PubMed

    Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten

    2016-08-01

    The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol. PMID:27323006

  5. Polyelectrolyte Microcapsules: Ion Distributions from a Poisson-Boltzmann Model

    NASA Astrophysics Data System (ADS)

    Tang, Qiyun; Denton, Alan R.; Rozairo, Damith; Croll, Andrew B.

    2014-03-01

    Recent experiments have shown that polystyrene-polyacrylic-acid-polystyrene (PS-PAA-PS) triblock copolymers in a solvent mixture of water and toluene can self-assemble into spherical microcapsules. Suspended in water, the microcapsules have a toluene core surrounded by an elastomer triblock shell. The longer, hydrophilic PAA blocks remain near the outer surface of the shell, becoming charged through dissociation of OH functional groups in water, while the shorter, hydrophobic PS blocks form a networked (glass or gel) structure. Within a mean-field Poisson-Boltzmann theory, we model these polyelectrolyte microcapsules as spherical charged shells, assuming different dielectric constants inside and outside the capsule. By numerically solving the nonlinear Poisson-Boltzmann equation, we calculate the radial distribution of anions and cations and the osmotic pressure within the shell as a function of salt concentration. Our predictions, which can be tested by comparison with experiments, may guide the design of microcapsules for practical applications, such as drug delivery. This work was supported by the National Science Foundation under Grant No. DMR-1106331.

  6. Beyond Poisson-Boltzmann: fluctuations and fluid structure in a self-consistent theory.

    PubMed

    Buyukdagli, S; Blossey, R

    2016-09-01

    Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics and has been applied to numerous physical chemistry and biophysics problems. Its essential limitations are in its neglect of correlation effects and fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical review, we provide an update on the developments achieved in the self-consistent formulations of correlation-corrected Poisson-Boltzmann theory. We introduce a corresponding system of coupled non-linear equations for both continuum electrostatics with a uniform dielectric constant, and a structured solvent-a dipolar Coulomb fluid-including non-local effects. While the approach is only approximate and also limited to corrections in the so-called weak fluctuation regime, it allows us to include physically relevant effects, as we show for a range of applications of these equations. PMID:27357125

  7. A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments.

    PubMed

    Fisicaro, G; Genovese, L; Andreussi, O; Marzari, N; Goedecker, S

    2016-01-01

    The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes. PMID:26747797

  8. Numerical Considerations in the Computation of the Electrostatic Free Energy of Interaction within the Poisson-Boltzmann Theory

    NASA Astrophysics Data System (ADS)

    Micu, Alexandru M.; Bagheri, Babak; Ilin, Andrew V.; Scott, Ridgway; Pettitt, B. Montgomery

    1997-09-01

    We evaluate two different ways of calculating the contribution of the electrostatic stress to the free energy integral based on Sharp and Hönig's method within the finite difference nonlinear Poisson-Boltzmann equation method with the University of Houston Brownian Dynamics program. We show that only one of these approaches gives consistent results in the limit of zero ionic concentration for interactions of the order of magnitude of the hydrogen bond. The results are compared with results from both the linear Poisson-Boltzmann equation and the Debye-Hückel theory, for ion concentrations within the limits of validity of these approximate methods. We demonstrate this by application to DNA molecules.

  9. Assessment of linear finite-difference Poisson-Boltzmann solvers.

    PubMed

    Wang, Jun; Luo, Ray

    2010-06-01

    CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study, we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. PMID:20063271

  10. Assessment of Linear Finite-Difference Poisson-Boltzmann Solvers

    PubMed Central

    Wang, Jun; Luo, Ray

    2009-01-01

    CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. PMID:20063271

  11. A comparison between simulation and poisson-boltzmann fields

    NASA Astrophysics Data System (ADS)

    Pettitt, B. Montgomery; Valdeavella, C. V.

    1999-11-01

    The electrostatic potentials from molecular dynamics (MD) trajectories and Poisson-Boltzmann calculations on a tetra peptide are compared to understand the validity of the resulting free energy surface. The Tuftsin peptide with sequence, Thr-Lys-Pro-Arg, in water is used for the comparison. The results obtained from the analysis of the MD trajectories for the total electrostatic potential at points on a grid using the Ewald technique are compared with the solution to the Poisson-Boltzmann (PB) equation averaged over the same set of configurations. The latter was solved using an optimal set of dielectric constant parameters. Structural averaging of the field over the MD simulation was examined in the context of the PB results. The detailed spatial variation of the electrostatic potential on the molecular surface are not qualitatively reproducible from MD to PB. Implications of using such field calculations and the implied free energies are discussed.

  12. Poisson-Boltzmann thermodynamics of counterions confined by curved hard walls

    NASA Astrophysics Data System (ADS)

    Šamaj, Ladislav; Trizac, Emmanuel

    2016-01-01

    We consider a set of identical mobile pointlike charges (counterions) confined to a domain with curved hard walls carrying a uniform fixed surface charge density, the system as a whole being electroneutral. Three domain geometries are considered: a pair of parallel plates, the cylinder, and the sphere. The particle system in thermal equilibrium is assumed to be described by the nonlinear Poisson-Boltzmann theory. While the effectively one-dimensional plates and the two-dimensional cylinder have already been solved, the three-dimensional sphere problem is not integrable. It is shown that the contact density of particles at the charged surface is determined by a first-order Abel differential equation of the second kind which is a counterpart of Enig's equation in the critical theory of gravitation and combustion or explosion. This equation enables us to construct the exact series solutions of the contact density in the regions of small and large surface charge densities. The formalism provides, within the mean-field Poisson-Boltzmann framework, the complete thermodynamics of counterions inside a charged sphere (salt-free system).

  13. Poisson-Boltzmann thermodynamics of counterions confined by curved hard walls.

    PubMed

    Šamaj, Ladislav; Trizac, Emmanuel

    2016-01-01

    We consider a set of identical mobile pointlike charges (counterions) confined to a domain with curved hard walls carrying a uniform fixed surface charge density, the system as a whole being electroneutral. Three domain geometries are considered: a pair of parallel plates, the cylinder, and the sphere. The particle system in thermal equilibrium is assumed to be described by the nonlinear Poisson-Boltzmann theory. While the effectively one-dimensional plates and the two-dimensional cylinder have already been solved, the three-dimensional sphere problem is not integrable. It is shown that the contact density of particles at the charged surface is determined by a first-order Abel differential equation of the second kind which is a counterpart of Enig's equation in the critical theory of gravitation and combustion or explosion. This equation enables us to construct the exact series solutions of the contact density in the regions of small and large surface charge densities. The formalism provides, within the mean-field Poisson-Boltzmann framework, the complete thermodynamics of counterions inside a charged sphere (salt-free system). PMID:26871116

  14. Poisson-Boltzmann-Nernst-Planck model

    NASA Astrophysics Data System (ADS)

    Zheng, Qiong; Wei, Guo-Wei

    2011-05-01

    The Poisson-Nernst-Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst-Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst-Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst-Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson-Boltzmann and Nernst-Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external

  15. Poisson-Boltzmann-Nernst-Planck model.

    PubMed

    Zheng, Qiong; Wei, Guo-Wei

    2011-05-21

    The Poisson-Nernst-Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst-Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst-Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst-Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson-Boltzmann and Nernst-Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external

  16. Poisson-Boltzmann-Nernst-Planck model

    SciTech Connect

    Zheng Qiong; Wei Guowei

    2011-05-21

    The Poisson-Nernst-Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst-Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst-Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst-Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson-Boltzmann and Nernst-Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external

  17. Understanding of the Effects of Ionic Strength on the Bimolecular Rate Constant between Structurally Identified Redox Enzymes and Charged Substrates Using Numerical Simulations on the Basis of the Poisson-Boltzmann Equation.

    PubMed

    Sugimoto, Yu; Kitazumi, Yuki; Shirai, Osamu; Yamamoto, Masahiro; Kano, Kenji

    2016-03-31

    To understand electrostatic interactions in biomolecules, the bimolecular rate constants (k) between redox enzymes and charged substrates (in this study, redox mediators in the electrode reaction) were evaluated at various ionic strengths (I) for the mediated bioelectrocatalytic reaction. The k value between bilirubin oxidase (BOD) and positively charged mediators increased with I, while that between BOD and negatively charged mediators decreased with I. The opposite trend was observed for the reaction of glucose oxidase (GOD). In the case of noncharged mediators, the k value was independent of I for both BOD and GOD. These results reflect the electrostatic interactions between the enzymes and the mediators. Furthermore, we estimated k/k° (k° being the thermodynamic rate constant) by numerical simulation (finite element method) based on the Poisson-Boltzmann (PB) equation. By considering the charges of individual atoms involved in the amino acids around the substrate binding sites in the enzymes, the simulated k/k° values well reproduced the experimental data. In conclusion, k/k° can be predicted by PB-based simulation as long as the crystal structure of the enzyme and the substrate binding site are known. PMID:26956542

  18. Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies.

    PubMed

    Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

    2011-10-01

    Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first reviewed the theory for the computation of dielectric boundary forces based on the definition of the Maxwell stress tensor. This is followed by a new formulation of the dielectric boundary force suitable for the finite-difference Poisson-Boltzmann methods. We have validated the new formulation with idealized analytical systems and realistic molecular systems. PMID:22125339

  19. Dielectric boundary force in numerical Poisson-Boltzmann methods: Theory and numerical strategies

    NASA Astrophysics Data System (ADS)

    Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

    2011-10-01

    Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first reviewed the theory for the computation of dielectric boundary force based on the definition of the Maxwell stress tensor. This is followed by a new formulation of the dielectric boundary force suitable for the finite-difference Poisson-Boltzmann methods. We have validated the new formulation with idealized analytical systems and realistic molecular systems.

  20. Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations.

    PubMed

    Poitevin, Frédéric; Delarue, Marc; Orland, Henri

    2016-07-01

    We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the mean-field solution given by the Poisson-Boltzmann equation, an original approach is proposed to numerically sample fluctuations around it, through the propagation of a Langevin-like stochastic partial differential equation (SPDE). The diffusion tensor of the SPDE can be chosen so as to avoid the numerical complexity linked to long-range Coulomb interactions, effectively rendering the theory completely local. A finite-volume implementation of the SPDE is described, and the approach is illustrated with preliminary results on the study of a system made of two like-charge ions immersed in a bath of counterions. PMID:27075231

  1. Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum

    PubMed Central

    Schnieders, Michael J.; Baker, Nathan A.; Ren, Pengyu; Ponder, Jay W.

    2008-01-01

    Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager used vacuum properties of small molecules, including polarizability, dipole moment and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation (PBE). Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here we describe the theory underlying a newly developed Polarizable Multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pKa prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2–13 kcal/mole, depending on the formal charge of the protein, but had only a

  2. Unsteady electroosmosis in a microchannel with Poisson-Boltzmann charge distribution.

    PubMed

    Chang, Chien C; Kuo, Chih-Yu; Wang, Chang-Yi

    2011-11-01

    The present study is concerned with unsteady electroosmotic flow (EOF) in a microchannel with the electric charge distribution described by the Poisson-Boltzmann (PB) equation. The nonlinear PB equation is solved by a systematic perturbation with respect to the parameter λ which measures the strength of the wall zeta potential relative to the thermal potential. In the small λ limits (λ<1), we recover the linearized PB equation - the Debye-Hückel approximation. The solutions obtained by using only three terms in the perturbation series are shown to be accurate with errors <1% for λ up to 2. The accurate solution to the PB equation is then used to solve the electrokinetic fluid transport equation for two types of unsteady flow: transient flow driven by a suddenly applied voltage and oscillatory flow driven by a time-harmonic voltage. The solution for the transient flow has important implications on EOF as an effective means for transporting electrolytes in microchannels with various electrokinetic widths. On the other hand, the solution for the oscillatory flow is shown to have important physical implications on EOF in mixing electrolytes in terms of the amplitude and phase of the resulting time-harmonic EOF rate, which depends on the applied frequency and the electrokinetic width of the microchannel as well as on the parameter λ. PMID:22072500

  3. A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.

    PubMed

    Boschitsch, Alexander H; Fenley, Marcia O

    2011-05-10

    An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent - analytical solutions are available for this case, thus allowing rigorous

  4. Calculation of electron transfer reorganization energies using the finite difference Poisson-Boltzmann model.

    PubMed Central

    Sharp, K A

    1998-01-01

    A description is given of a method to calculate the electron transfer reorganization energy (lambda) in proteins using the linear or nonlinear Poisson-Boltzmann (PB) equation. Finite difference solutions to the linear PB equation are then used to calculate lambda for intramolecular electron transfer reactions in the photosynthetic reaction center from Rhodopseudomonas viridis and the ruthenated heme proteins cytochrome c, myoglobin, and cytochrome b and for intermolecular electron transfer between two cytochrome c molecules. The overall agreement with experiment is good considering both the experimental and computational difficulties in estimating lambda. The calculations show that acceptor/donor separation and position of the cofactors with respect to the protein/solvent boundary are equally important and, along with the overall polarizability of the protein, are the major determinants of lambda. In agreement with previous studies, the calculations show that the protein provides a low reorganization environment for electron transfer. Agreement with experiment is best if the protein polarizability is modeled with a low (<8) average effective dielectric constant. The effect of buried waters on the reorganization energy of the photosynthetic reaction center was examined and found to make a contribution ranging from 0.05 eV to 0.27 eV, depending on the donor/acceptor pair. PMID:9512022

  5. Ionic screening of charged impurities in electrolytically gated graphene: A partially linearized Poisson-Boltzmann model.

    PubMed

    Sharma, P; Mišković, Z L

    2015-10-01

    We present a model describing the electrostatic interactions across a structure that consists of a single layer of graphene with large area, lying above an oxide substrate of finite thickness, with its surface exposed to a thick layer of liquid electrolyte containing salt ions. Our goal is to analyze the co-operative screening of the potential fluctuation in a doped graphene due to randomness in the positions of fixed charged impurities in the oxide by the charge carriers in graphene and by the mobile ions in the diffuse layer of the electrolyte. In order to account for a possibly large potential drop in the diffuse later that may arise in an electrolytically gated graphene, we use a partially linearized Poisson-Boltzmann (PB) model of the electrolyte, in which we solve a fully nonlinear PB equation for the surface average of the potential in one dimension, whereas the lateral fluctuations of the potential in graphene are tackled by linearizing the PB equation about the average potential. In this way, we are able to describe the regime of equilibrium doping of graphene to large densities for arbitrary values of the ion concentration without restrictions to the potential drop in the electrolyte. We evaluate the electrostatic Green's function for the partially linearized PB model, which is used to express the screening contributions of the graphene layer and the nearby electrolyte by means of an effective dielectric function. We find that, while the screened potential of a single charged impurity at large in-graphene distances exhibits a strong dependence on the ion concentration in the electrolyte and on the doping density in graphene, in the case of a spatially correlated two-dimensional ensemble of impurities, this dependence is largely suppressed in the autocovariance of the fluctuating potential. PMID:26450303

  6. A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules

    NASA Astrophysics Data System (ADS)

    Geng, Weihua; Krasny, Robert

    2013-08-01

    We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a well-conditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid collocation. The linear system is solved by GMRES iteration and the matrix-vector product is carried out by a Cartesian treecode which reduces the cost from O(N2) to O(NlogN), where N is the number of faces in the triangulation. The TABI solver is applied to compute the electrostatic solvation energy in two cases, the Kirkwood sphere and a solvated protein. We present the error, CPU time, and memory usage, and compare results for the Poisson-Boltzmann and Poisson equations. We show that the treecode approximation error can be made smaller than the discretization error, and we compare two versions of the treecode, one with uniform clusters and one with non-uniform clusters adapted to the molecular surface. For the protein test case, we compare TABI results with those obtained using the grid-based APBS code, and we also present parallel TABI simulations using up to eight processors. We find that the TABI solver exhibits good serial and parallel performance combined with relatively simple implementation, efficient memory usage, and geometric adaptability.

  7. Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.

    PubMed

    Fenley, Marcia O; Harris, Robert C; Mackoy, Travis; Boschitsch, Alexander H

    2015-02-01

    The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software. PMID:25430617

  8. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.

    PubMed

    Botello-Smith, Wesley M; Liu, Xingping; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

    2013-01-01

    Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions. PMID:23439886

  9. Poisson-Boltzmann study of the effective electrostatic interaction between colloids at an electrolyte interface

    NASA Astrophysics Data System (ADS)

    Majee, Arghya; Bier, Markus; Dietrich, S.

    2016-08-01

    The effective electrostatic interaction between a pair of colloids, both of them located close to each other at an electrolyte interface, is studied by employing the full, nonlinear Poisson-Boltzmann (PB) theory within classical density functional theory. Using a simplified yet appropriate model, all contributions to the effective interaction are obtained exactly, albeit numerically. The comparison between our results and those obtained within linearized PB theory reveals that the latter overestimates these contributions significantly at short inter-particle separations. Whereas the surface contributions to the linear and the nonlinear PB results differ only quantitatively, the line contributions show qualitative differences at short separations. Moreover, a dependence of the line contribution on the solvation properties of the two adjacent fluids is found, which is absent within the linear theory. Our results are expected to enrich the understanding of effective interfacial interactions between colloids.

  10. Electrostatic interactions in protein solution--a comparison between Poisson-Boltzmann and Monte Carlo calculations.

    PubMed

    Fushiki, M; Svensson, B; Jönsson, B; Woodward, C E

    1991-09-01

    The accuracy of the Poisson-Boltzmann (PB) approximation and its linearized version is investigated by comparison to results obtained from Monte Carlo simulations. The dependence of the calcium binding constant of the protein calbindin as a function of salt concentration and mutation is used as a test case. The protein is modeled as a collection of charged and neutral spheres immersed in the electrolyte solution. The PB equation is solved using a finite difference technique on a grid in a spherical polar coordinate system, which is the preferred choice for a globular protein like calbindin. Both MC and PB give quantitative agreement with experimental results. The linearized PB equation is almost as accurate, but it becomes less reliable in systems with divalent ions. However, the linearized PB equation fails to describe the concentration profiles for cations and anions outside the protein even in a 1:1 salt solution. PMID:1790295

  11. AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems

    SciTech Connect

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, Jonathan

    2010-01-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.

  12. Analytic Thermodynamic Calculations for an Immobilized Molecule under Poisson-Boltzmann Interactions using a Spheroidal Geometry

    NASA Astrophysics Data System (ADS)

    Ambia-Garrido, Joaquin; Pettitt, Montgomery

    2008-03-01

    The change in some thermodynamic quantities such as Gibbs' free energy, entropy and enthalpy of the binding of a particle tethered to a surface or particle are analytically calculated. These particles are considered ellipsoids and submerged in a liquid. The ionic strength of the media allows the linearized version of the Poisson-Boltzmann equation (from the theory of the double layer interaction) to properly describe the interactions between an ion penetrable spheroid and a hard plate. We believe that this is an adequate model for a DNA chip and the predicted electrostatic effects suggest the feasibility of electronic control and detection of DNA hybridization and design of chips underline avoiding the DNA folding problem.

  13. Electro-osmosis of non-Newtonian fluids in porous media using lattice Poisson-Boltzmann method.

    PubMed

    Chen, Simeng; He, Xinting; Bertola, Volfango; Wang, Moran

    2014-12-15

    Electro-osmosis in porous media has many important applications in various areas such as oil and gas exploitation and biomedical detection. Very often, fluids relevant to these applications are non-Newtonian because of the shear-rate dependent viscosity. The purpose of this study was to investigate the behaviors and physical mechanism of electro-osmosis of non-Newtonian fluids in porous media. Model porous microstructures (granular, fibrous, and network) were created by a random generation-growth method. The nonlinear governing equations of electro-kinetic transport for a power-law fluid were solved by the lattice Poisson-Boltzmann method (LPBM). The model results indicate that: (i) the electro-osmosis of non-Newtonian fluids exhibits distinct nonlinear behaviors compared to that of Newtonian fluids; (ii) when the bulk ion concentration or zeta potential is high enough, shear-thinning fluids exhibit higher electro-osmotic permeability, while shear-thickening fluids lead to the higher electro-osmotic permeability for very low bulk ion concentration or zeta potential; (iii) the effect of the porous medium structure depends significantly on the constitutive parameters: for fluids with large constitutive coefficients strongly dependent on the power-law index, the network structure shows the highest electro-osmotic permeability while the granular structure exhibits the lowest permeability on the entire range of power law indices considered; when the dependence of the constitutive coefficient on the power law index is weaker, different behaviors can be observed especially in case of strong shear thinning. PMID:25278358

  14. Progress in developing Poisson-Boltzmann equation solvers.

    PubMed

    Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil

    2013-03-01

    This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects. PMID:24199185

  15. Progress in developing Poisson-Boltzmann equation solvers

    PubMed Central

    Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil

    2013-01-01

    This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects. PMID:24199185

  16. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics

    SciTech Connect

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, Jonathan

    2009-01-01

    The numerical solution of the Poisson Boltzmann (PB) equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. Recently, we have described a boundary integral equation-based PB solver accelerated by a new version of the fast multipole method (FMM). The overall algorithm shows an order N complexity in both the computational cost and memory usage. Here, we present an updated version of the solver by using an adaptive FMM for accelerating the convolution type matrix-vector multiplications. The adaptive algorithm, when compared to our previous nonadaptive one, not only significantly improves the performance of the overall memory usage but also remarkably speeds the calculation because of an improved load balancing between the local- and far-field calculations. We have also implemented a node-patch discretization scheme that leads to a reduction of unknowns by a factor of 2 relative to the constant element method without sacrificing accuracy. As a result of these improvements, the new solver makes the PB calculation truly feasible for large-scale biomolecular systems such as a 30S ribosome molecule even on a typical 2008 desktop computer.

  17. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

    NASA Astrophysics Data System (ADS)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2013-11-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/lubz/afmpb.html for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.

  18. A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver

    NASA Astrophysics Data System (ADS)

    Geng, Weihua; Jacob, Ferosh

    2013-06-01

    In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up our method, we take advantage of the parallel nature of the boundary integral formulation and parallelize the schemes within CUDA shared memory architecture on GPU. The schemes use only 11N+6Nc size-of-double device memory for a biomolecule with N triangular surface elements and Nc partial charges. Numerical tests of these schemes show well-maintained accuracy and fast convergence. The GPU implementation using one GPU card (Nvidia Tesla M2070) achieves 120-150X speed-up to the implementation using one CPU (Intel L5640 2.27 GHz). With our approach, solving PB equations on well-discretized molecular surfaces with up to 300,000 boundary elements will take less than about 10 min, hence our approach is particularly suitable for fast electrostatics computations on small to medium biomolecules.

  19. Features of CPB: A Poisson-Boltzmann Solver that Uses an Adaptive Cartesian Grid

    PubMed Central

    Harris, Robert C.; Mackoy, Travis

    2014-01-01

    The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other PBE solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software. PMID:25430617

  20. Binding of phosphorus-containing inhibitors to thermolysin studied by the Poisson-Boltzmann method.

    PubMed Central

    Shen, J.; Wendoloski, J.

    1995-01-01

    Zinc endopeptidase thermolysin can be inhibited by a series of phosphorus-containing peptide analogues, Cbz-Gly-psi (PO2)-X-Leu-Y-R (ZGp(X)L(y)R), where X = NH, O, or CH2; Y = NH or O; R = Leu, Ala, Gly, Phe, H, or CH3. The affinity correlation as well as an X-ray crystallography study suggest that these inhibitors bind to thermolysin in an identical mode. In this work, we calculate the electrostatic binding free energies for a series of 13 phosphorus-containing inhibitors with modifications at X, Y, and R moieties using finite difference solution to the Poisson-Boltzmann equation. A method has been developed to include the solvation entropy changes due to binding different ligands to a macromolecule. We demonstrate that the electrostatic energy and empirically derived solvation entropy can account for most of the binding energy differences in this series. By analyzing the binding contribution from individual residues, we show that the energy of a hydrogen bond is not confined to the donor and acceptor. In particular, the positive charges on Zn and Arg 203, which are not the acceptors, contribute significantly to the hydrogen bonds between two amides of ZGpLL and the thermolysin. PMID:7795520

  1. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver

    SciTech Connect

    Konecny, Robert; Baker, Nathan A.; McCammon, J. A.

    2012-07-26

    The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a Fortran or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages -- Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.

  2. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).

    PubMed

    Konecny, Robert; Baker, Nathan A; McCammon, J Andrew

    2012-07-26

    The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a FORTRAN or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages - Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS. PMID:22905037

  3. Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach

    PubMed Central

    Robbins, Timothy J.; Ziebarth, Jesse D.; Wang, Yongmei

    2014-01-01

    The ion atmosphere created by monovalent (Na+) or divalent (Mg2+) cations surrounding a B-form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson-Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and two-dimensional cation concentrations and by calculating the total number of cations and net solution charge surrounding the DNA. Na+ ion distributions near the DNA were more diffuse in PB calculations than in corresponding MD simulations, with PB calculations predicting lower concentrations near DNA groove sites and phosphate groups and a higher concentration in the region between these locations. Other than this difference, the Na+ distributions generated by the two methods largely agreed, as both predicted similar locations of high Na+ concentration and nearly identical values of the number of cations and the net solution charge at all distances from the DNA. In contrast, there was greater disagreement between the two methods for Mg2+ cation concentration profiles, as both the locations and magnitudes of peaks in Mg2+ concentration were different. Despite experimental and simulation observations that Mg2+ typically maintains its first solvation shell when interacting with nucleic acids, modeling Mg2+ as an unsolvated ion during PB calculations improved the agreement of the Mg2+ ion atmosphere predicted by the two methods and allowed for values of the number of bound ions and net solution charge surrounding the DNA from PB calculations that approached the values observed in MD simulations. PMID:24443090

  4. Incorporating Dipolar Solvents with Variable Density in Poisson-Boltzmann Electrostatics

    PubMed Central

    Azuara, Cyril; Orland, Henri; Bon, Michael; Koehl, Patrice; Delarue, Marc

    2008-01-01

    We describe a new way to calculate the electrostatic properties of macromolecules that goes beyond the classical Poisson-Boltzmann treatment with only a small extra CPU cost. The solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. The method effectively unifies both the Poisson-centric view and the Langevin Dipole model. The model results in a variable dielectric constant \\documentclass[10pt]{article} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{pmc} \\usepackage[Euler]{upgreek} \\pagestyle{empty} \\oddsidemargin -1.0in \\begin{document} \\begin{equation*}{\\epsilon}({\\vec{r}})\\end{equation*}\\end{document} in the solvent region and also in a variable solvent density \\documentclass[10pt]{article} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{pmc} \\usepackage[Euler]{upgreek} \\pagestyle{empty} \\oddsidemargin -1.0in \\begin{document} \\begin{equation*}{\\rho}({\\vec{r}})\\end{equation*}\\end{document} that depends on the nature of the closest exposed solute atoms. The model was calibrated using small molecules and ions solvation data with only two adjustable parameters, namely the size and dipolar moment of the solvent. Hydrophobicity scales derived from the solvent density profiles agree very well with independently derived hydrophobicity scales, both at the atomic or residue level. Dimerization interfaces in homodimeric proteins or lipid-binding regions in membrane proteins clearly appear as poorly solvated patches on the solute accessible surface. Comparison of the thermally averaged solvent density of this model with the one derived from molecular dynamics simulations shows qualitative agreement on a coarse-grained level. Because this calculation is much more

  5. PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

    PubMed

    Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

    2006-07-01

    We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations. PMID:16845031

  6. Nonlinear ordinary difference equations

    NASA Technical Reports Server (NTRS)

    Caughey, T. K.

    1979-01-01

    Future space vehicles will be relatively large and flexible, and active control will be necessary to maintain geometrical configuration. While the stresses and strains in these space vehicles are not expected to be excessively large, their cumulative effects will cause significant geometrical nonlinearities to appear in the equations of motion, in addition to the nonlinearities caused by material properties. Since the only effective tool for the analysis of such large complex structures is the digital computer, it will be necessary to gain a better understanding of the nonlinear ordinary difference equations which result from the time discretization of the semidiscrete equations of motion for such structures.

  7. Nonlinear gyrokinetic equations

    SciTech Connect

    Dubin, D.H.E.; Krommes, J.A.; Oberman, C.; Lee, W.W.

    1983-03-01

    Nonlinear gyrokinetic equations are derived from a systematic Hamiltonian theory. The derivation employs Lie transforms and a noncanonical perturbation theory first used by Littlejohn for the simpler problem of asymptotically small gyroradius. For definiteness, we emphasize the limit of electrostatic fluctuations in slab geometry; however, there is a straight-forward generalization to arbitrary field geometry and electromagnetic perturbations. An energy invariant for the nonlinear system is derived, and various of its limits are considered. The weak turbulence theory of the equations is examined. In particular, the wave kinetic equation of Galeev and Sagdeev is derived from an asystematic truncation of the equations, implying that this equation fails to consider all gyrokinetic effects. The equations are simplified for the case of small but finite gyroradius and put in a form suitable for efficient computer simulation. Although it is possible to derive the Terry-Horton and Hasegawa-Mima equations as limiting cases of our theory, several new nonlinear terms absent from conventional theories appear and are discussed.

  8. Adapting Poisson-Boltzmann to the self-consistent mean field theory: Application to protein side-chain modeling

    NASA Astrophysics Data System (ADS)

    Koehl, Patrice; Orland, Henri; Delarue, Marc

    2011-08-01

    We present an extension of the self-consistent mean field theory for protein side-chain modeling in which solvation effects are included based on the Poisson-Boltzmann (PB) theory. In this approach, the protein is represented with multiple copies of its side chains. Each copy is assigned a weight that is refined iteratively based on the mean field energy generated by the rest of the protein, until self-consistency is reached. At each cycle, the variational free energy of the multi-copy system is computed; this free energy includes the internal energy of the protein that accounts for vdW and electrostatics interactions and a solvation free energy term that is computed using the PB equation. The method converges in only a few cycles and takes only minutes of central processing unit time on a commodity personal computer. The predicted conformation of each residue is then set to be its copy with the highest weight after convergence. We have tested this method on a database of hundred highly refined NMR structures to circumvent the problems of crystal packing inherent to x-ray structures. The use of the PB-derived solvation free energy significantly improves prediction accuracy for surface side chains. For example, the prediction accuracies for χ1 for surface cysteine, serine, and threonine residues improve from 68%, 35%, and 43% to 80%, 53%, and 57%, respectively. A comparison with other side-chain prediction algorithms demonstrates that our approach is consistently better in predicting the conformations of exposed side chains.

  9. Nonlinear differential equations

    SciTech Connect

    Dresner, L.

    1988-01-01

    This report is the text of a graduate course on nonlinear differential equations given by the author at the University of Wisconsin-Madison during the summer of 1987. The topics covered are: direction fields of first-order differential equations; the Lie (group) theory of ordinary differential equations; similarity solutions of second-order partial differential equations; maximum principles and differential inequalities; monotone operators and iteration; complementary variational principles; and stability of numerical methods. The report should be of interest to graduate students, faculty, and practicing scientists and engineers. No prior knowledge is required beyond a good working knowledge of the calculus. The emphasis is on practical results. Most of the illustrative examples are taken from the fields of nonlinear diffusion, heat and mass transfer, applied superconductivity, and helium cryogenics.

  10. Optimizing electrostatic field calculations with the adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces. I. Sampling and focusing.

    PubMed

    Ritchie, Andrew W; Webb, Lauren J

    2013-10-01

    Continuum electrostatics methods are commonly used to calculate electrostatic potentials in proteins and at protein-protein interfaces to aid many types of biophysical studies. Despite their ubiquity throughout the biophysical literature, these calculations are difficult to test against experimental data to determine their accuracy and validity. To address this, we have calculated the Boltzmann-weighted electrostatic field at the midpoint of a nitrile bond placed at a variety of locations on the surface of the protein RalGDS, both in its monomeric form as well as when docked to four different constructs of the protein Rap, and compared the computation results to vibrational absorption energy measurements of the nitrile oscillator. This was done by generating a statistical ensemble of protein structures using enhanced molecular dynamics sampling with the Amber03 force field, followed by solving the linear Poisson-Boltzmann equation for each structure using the Applied Poisson-Boltzmann Solver (APBS) software package. Using a two-stage focusing strategy, we examined numerous second stage box dimensions, grid point densities, box locations, and compared the numerical result to the result obtained from the sum of the numeric reaction field and the analytic Coulomb field. It was found that the reaction field method yielded higher correlation with experiment for the absolute calculation of fields, while the numeric solutions yielded higher correlation with experiment for the relative field calculations. Finer grid spacing typically improved the calculation, although this effect was less pronounced in the reaction field method. These sorts of calculations were also very sensitive to the box location, particularly for the numeric calculations of absolute fields using a 10(3) Å(3) box. PMID:24041016

  11. Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions.

    PubMed

    Xiao, Li; Wang, Changhao; Ye, Xiang; Luo, Ray

    2016-08-25

    Continuum solvation modeling based upon the Poisson-Boltzmann equation (PBE) is widely used in structural and functional analysis of biomolecules. In this work, we propose a charge-central interpretation of the full nonlinear PBE electrostatic interactions. The validity of the charge-central view or simply charge view, as formulated as a vacuum Poisson equation with effective charges, was first demonstrated by reproducing both electrostatic potentials and energies from the original solvated full nonlinear PBE. There are at least two benefits when the charge-central framework is applied. First the convergence analyses show that the use of polarization charges allows a much faster converging numerical procedure for electrostatic energy and forces calculation for the full nonlinear PBE. Second, the formulation of the solvated electrostatic interactions as effective charges in vacuum allows scalable algorithms to be deployed for large biomolecular systems. Here, we exploited the charge-view interpretation and developed a particle-particle particle-mesh (P3M) strategy for the full nonlinear PBE systems. We also studied the accuracy and convergence of solvation forces with the charge-view and the P3M methods. It is interesting to note that the convergence of both the charge-view and the P3M methods is more rapid than the original full nonlinear PBE method. Given the developments and validations documented here, we are working to adapt the P3M treatment of the full nonlinear PBE model to molecular dynamics simulations. PMID:27146097

  12. Solving Nonlinear Coupled Differential Equations

    NASA Technical Reports Server (NTRS)

    Mitchell, L.; David, J.

    1986-01-01

    Harmonic balance method developed to obtain approximate steady-state solutions for nonlinear coupled ordinary differential equations. Method usable with transfer matrices commonly used to analyze shaft systems. Solution to nonlinear equation, with periodic forcing function represented as sum of series similar to Fourier series but with form of terms suggested by equation itself.

  13. Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

    NASA Astrophysics Data System (ADS)

    Cooper, Christopher D.; Barba, Lorena A.

    2016-05-01

    Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. Protein adsorption, being a free-energy-driven process, is difficult to study experimentally. This paper develops and evaluates a computational model to study electrostatic interactions of proteins and charged nanosurfaces, via the Poisson-Boltzmann equation. We extended the implicit-solvent model used in the open-source code PyGBe to include surfaces of imposed charge or potential. This code solves the boundary integral formulation of the Poisson-Boltzmann equation, discretized with surface elements. PyGBe has at its core a treecode-accelerated Krylov iterative solver, resulting in O(N log N) scaling, with further acceleration on hardware via multi-threaded execution on GPUs. It computes solvation and surface free energies, providing a framework for studying the effect of electrostatics on adsorption. We derived an analytical solution for a spherical charged surface interacting with a spherical dielectric cavity, and used it in a grid-convergence study to build evidence on the correctness of our approach. The study showed the error decaying with the average area of the boundary elements, i.e., the method is O(1 / N) , which is consistent with our previous verification studies using PyGBe. We also studied grid-convergence using a real molecular geometry (protein G B1 D4‧), in this case using Richardson extrapolation (in the absence of an analytical solution) and confirmed the O(1 / N) scaling. With this work, we can now access a completely new family of problems, which no other major bioelectrostatics solver, e.g. APBS, is capable of dealing with. PyGBe is open

  14. Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

    NASA Astrophysics Data System (ADS)

    Cooper, Christopher D.; Barba, Lorena A.

    2016-05-01

    Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. Protein adsorption, being a free-energy-driven process, is difficult to study experimentally. This paper develops and evaluates a computational model to study electrostatic interactions of proteins and charged nanosurfaces, via the Poisson-Boltzmann equation. We extended the implicit-solvent model used in the open-source code PyGBe to include surfaces of imposed charge or potential. This code solves the boundary integral formulation of the Poisson-Boltzmann equation, discretized with surface elements. PyGBe has at its core a treecode-accelerated Krylov iterative solver, resulting in O(N log N) scaling, with further acceleration on hardware via multi-threaded execution on GPUs. It computes solvation and surface free energies, providing a framework for studying the effect of electrostatics on adsorption. We derived an analytical solution for a spherical charged surface interacting with a spherical dielectric cavity, and used it in a grid-convergence study to build evidence on the correctness of our approach. The study showed the error decaying with the average area of the boundary elements, i.e., the method is O(1 / N) , which is consistent with our previous verification studies using PyGBe. We also studied grid-convergence using a real molecular geometry (protein G B1 D4‧), in this case using Richardson extrapolation (in the absence of an analytical solution) and confirmed the O(1 / N) scaling. With this work, we can now access a completely new family of problems, which no other major bioelectrostatics solver, e.g. APBS, is capable of dealing with. PyGBe is open

  15. Solitons and nonlinear wave equations

    SciTech Connect

    Dodd, Roger K.; Eilbeck, J. Chris; Gibbon, John D.; Morris, Hedley C.

    1982-01-01

    A discussion of the theory and applications of classical solitons is presented with a brief treatment of quantum mechanical effects which occur in particle physics and quantum field theory. The subjects addressed include: solitary waves and solitons, scattering transforms, the Schroedinger equation and the Korteweg-de Vries equation, and the inverse method for the isospectral Schroedinger equation and the general solution of the solvable nonlinear equations. Also considered are: isolation of the Korteweg-de Vries equation in some physical examples, the Zakharov-Shabat/AKNS inverse method, kinks and the sine-Gordon equation, the nonlinear Schroedinger equation and wave resonance interactions, amplitude equations in unstable systems, and numerical studies of solitons. 45 references.

  16. Optimizing electrostatic field calculations with the Adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces II: explicit near-probe and hydrogen-bonding water molecules.

    PubMed

    Ritchie, Andrew W; Webb, Lauren J

    2014-07-17

    We have examined the effects of including explicit, near-probe solvent molecules in a continuum electrostatics strategy using the linear Poisson-Boltzmann equation with the Adaptive Poisson-Boltzmann Solver (APBS) to calculate electric fields at the midpoint of a nitrile bond both at the surface of a monomeric protein and when docked at a protein-protein interface. Results were compared to experimental vibrational absorption energy measurements of the nitrile oscillator. We examined three methods for selecting explicit water molecules: (1) all water molecules within 5 Å of the nitrile nitrogen; (2) the water molecule closest to the nitrile nitrogen; and (3) any single water molecule hydrogen-bonding to the nitrile. The correlation between absolute field strengths with experimental absorption energies were calculated and it was observed that method 1 was only an improvement for the monomer calculations, while methods 2 and 3 were not significantly different from the purely implicit solvent calculations for all protein systems examined. Upon taking the difference in calculated electrostatic fields and comparing to the difference in absorption frequencies, we typically observed an increase in experimental correlation for all methods, with method 1 showing the largest gain, likely due to the improved absolute monomer correlations using that method. These results suggest that, unlike with quantum mechanical methods, when calculating absolute fields using entirely classical models, implicit solvent is typically sufficient and additional work to identify hydrogen-bonding or nearest waters does not significantly impact the results. Although we observed that a sphere of solvent near the field of interest improved results for relative field calculations, it should not be consider a panacea for all situations. PMID:24446740

  17. Duffing's Equation and Nonlinear Resonance

    ERIC Educational Resources Information Center

    Fay, Temple H.

    2003-01-01

    The phenomenon of nonlinear resonance (sometimes called the "jump phenomenon") is examined and second-order van der Pol plane analysis is employed to indicate that this phenomenon is not a feature of the equation, but rather the result of accumulated round-off error, truncation error and algorithm error that distorts the true bounded solution onto…

  18. Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.

    PubMed

    Decherchi, Sergio; Colmenares, José; Catalano, Chiara Eva; Spagnuolo, Michela; Alexov, Emil; Rocchia, Walter

    2013-01-01

    The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. Results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view. PMID:23519863

  19. Linear superposition in nonlinear equations.

    PubMed

    Khare, Avinash; Sukhatme, Uday

    2002-06-17

    Several nonlinear systems such as the Korteweg-de Vries (KdV) and modified KdV equations and lambda phi(4) theory possess periodic traveling wave solutions involving Jacobi elliptic functions. We show that suitable linear combinations of these known periodic solutions yield many additional solutions with different periods and velocities. This linear superposition procedure works by virtue of some remarkable new identities involving elliptic functions. PMID:12059300

  20. Nonlinear SCHRÖDINGER-PAULI Equations

    NASA Astrophysics Data System (ADS)

    Ng, Wei Khim; Parwani, Rajesh R.

    2011-11-01

    We obtain novel nonlinear Schrüdinger-Pauli equations through a formal non-relativistic limit of appropriately constructed nonlinear Dirac equations. This procedure automatically provides a physical regularisation of potential singularities brought forward by the nonlinear terms and suggests how to regularise previous equations studied in the literature. The enhancement of contributions coming from the regularised singularities suggests that the obtained equations might be useful for future precision tests of quantum nonlinearity.

  1. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics

    NASA Astrophysics Data System (ADS)

    Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

    2015-12-01

    Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

  2. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

    PubMed

    Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

    2015-12-28

    Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

  3. Engineering integrable nonautonomous nonlinear Schroedinger equations

    SciTech Connect

    He Xugang; Zhao Dun; Li Lin; Luo Honggang

    2009-05-15

    We investigate Painleve integrability of a generalized nonautonomous one-dimensional nonlinear Schroedinger (NLS) equation with time- and space-dependent dispersion, nonlinearity, and external potentials. Through the Painleve analysis some explicit requirements on the dispersion, nonlinearity, dissipation/gain, and the external potential as well as the constraint conditions are identified. It provides an explicit way to engineer integrable nonautonomous NLS equations at least in the sense of Painleve integrability. Furthermore analytical solutions of this class of integrable nonautonomous NLS equations can be obtained explicitly from the solutions of the standard NLS equation by a general transformation. The result provides a significant way to control coherently the soliton dynamics in the corresponding nonlinear systems, as that in Bose-Einstein condensate experiments. We analyze explicitly the soliton dynamics under the nonlinearity management and the external potentials and discuss its application in the matter-wave dynamics. Some comparisons with the previous works have also been discussed.

  4. A differential equation for the Generalized Born radii.

    PubMed

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2013-06-28

    The Generalized Born (GB) model offers a convenient way of representing electrostatics in complex macromolecules like proteins or nucleic acids. The computation of atomic GB radii is currently performed by different non-local approaches involving volume or surface integrals. Here we obtain a non-linear second-order partial differential equation for the Generalized Born radius, which may be solved using local iterative algorithms. The equation is derived under the assumption that the usual GB approximation to the reaction field obeys Laplace's equation. The equation admits as particular solutions the correct GB radii for the sphere and the plane. The tests performed on a set of 55 different proteins show an overall agreement with other reference GB models and "perfect" Poisson-Boltzmann based values. PMID:23676843

  5. Spurious Solutions Of Nonlinear Differential Equations

    NASA Technical Reports Server (NTRS)

    Yee, H. C.; Sweby, P. K.; Griffiths, D. F.

    1992-01-01

    Report utilizes nonlinear-dynamics approach to investigate possible sources of errors and slow convergence and non-convergence of steady-state numerical solutions when using time-dependent approach for problems containing nonlinear source terms. Emphasizes implications for development of algorithms in CFD and computational sciences in general. Main fundamental conclusion of study is that qualitative features of nonlinear differential equations cannot be adequately represented by finite-difference method and vice versa.

  6. Nonlinear quantum equations: Classical field theory

    SciTech Connect

    Rego-Monteiro, M. A.; Nobre, F. D.

    2013-10-15

    An exact classical field theory for nonlinear quantum equations is presented herein. It has been applied recently to a nonlinear Schrödinger equation, and it is shown herein to hold also for a nonlinear generalization of the Klein-Gordon equation. These generalizations were carried by introducing nonlinear terms, characterized by exponents depending on an index q, in such a way that the standard, linear equations, are recovered in the limit q→ 1. The main characteristic of this field theory consists on the fact that besides the usual Ψ(x(vector sign),t), a new field Φ(x(vector sign),t) needs to be introduced in the Lagrangian, as well. The field Φ(x(vector sign),t), which is defined by means of an additional equation, becomes Ψ{sup *}(x(vector sign),t) only when q→ 1. The solutions for the fields Ψ(x(vector sign),t) and Φ(x(vector sign),t) are found herein, being expressed in terms of a q-plane wave; moreover, both field equations lead to the relation E{sup 2}=p{sup 2}c{sup 2}+m{sup 2}c{sup 4}, for all values of q. The fact that such a classical field theory works well for two very distinct nonlinear quantum equations, namely, the Schrödinger and Klein-Gordon ones, suggests that this procedure should be appropriate for a wider class nonlinear equations. It is shown that the standard global gauge invariance is broken as a consequence of the nonlinearity.

  7. Extended Trial Equation Method for Nonlinear Partial Differential Equations

    NASA Astrophysics Data System (ADS)

    Gepreel, Khaled A.; Nofal, Taher A.

    2015-04-01

    The main objective of this paper is to use the extended trial equation method to construct a series of some new solutions for some nonlinear partial differential equations (PDEs) in mathematical physics. We will construct the solutions in many different functions such as hyperbolic function solutions, trigonometric function solutions, Jacobi elliptic function solutions, and rational functional solutions for the nonlinear PDEs when the balance number is a real number via the Zhiber-Shabat nonlinear differential equation. The balance number of this method is not constant as we shown in other methods, but it is changed by changing the trial equation derivative definition. This method allowed us to construct many new types of solutions. It is shown by using the Maple software package that all obtained solutions satisfy the original PDEs.

  8. Markovian master equation for nonlinear systems

    NASA Astrophysics Data System (ADS)

    de los Santos-Sánchez, O.; Récamier, J.; Jáuregui, R.

    2015-06-01

    Within the f-deformed oscillator formalism, we derive a Markovian master equation for the description of the damped dynamics of nonlinear systems that interact with their environment. The applicability of this treatment to the particular case of a Morse-like oscillator interacting with a thermal field is illustrated, and the decay of quantum coherence in such a system is analyzed in terms of the evolution on phase space of its nonlinear coherent states via the Wigner function.

  9. Algorithms For Integrating Nonlinear Differential Equations

    NASA Technical Reports Server (NTRS)

    Freed, A. D.; Walker, K. P.

    1994-01-01

    Improved algorithms developed for use in numerical integration of systems of nonhomogenous, nonlinear, first-order, ordinary differential equations. In comparison with integration algorithms, these algorithms offer greater stability and accuracy. Several asymptotically correct, thereby enabling retention of stability and accuracy when large increments of independent variable used. Accuracies attainable demonstrated by applying them to systems of nonlinear, first-order, differential equations that arise in study of viscoplastic behavior, spread of acquired immune-deficiency syndrome (AIDS) virus and predator/prey populations.

  10. The non-linear MSW equation

    NASA Astrophysics Data System (ADS)

    Thomson, Mark J.; McKellar, Bruce H. J.

    1991-04-01

    A simple, non-linear generalization of the MSW equation is presented and its analytic solution is outlined. The orbits of the polarization vector are shown to be periodic, and to lie on a sphere. Their non-trivial flow patterns fall into two topological categories, the more complex of which can become chaotic if perturbed.

  11. Quantum nonlinear Schrodinger equation on a lattice

    SciTech Connect

    Bogolyubov, N.M.; Korepin, V.E.

    1986-09-01

    A local Hamiltonian is constructed for the nonlinear Schrodinger equation on a lattice in both the classical and the quantum variants. This Hamiltonian is an explicit elementary function of the local Bose fields. The lattice model possesses the same structure of the action-angle variables as the continuous model.

  12. Solitary waves in the nonlinear Dirac equation with arbitrary nonlinearity.

    PubMed

    Cooper, Fred; Khare, Avinash; Mihaila, Bogdan; Saxena, Avadh

    2010-09-01

    We consider the nonlinear Dirac equations (NLDE's) in 1+1 dimension with scalar-scalar self interaction g{2}/k+1(ΨΨ){k+1} , as well as a vector-vector self interaction g{2}/k+1(Ψγ{μ}ΨΨγ{μ}Ψ){1/2(k+1)} . We find the exact analytic form for solitary waves for arbitrary k and find that they are a generalization of the exact solutions for the nonlinear Schrödinger equation (NLSE) and reduce to these solutions in a well defined nonrelativistic limit. We perform the nonrelativistic reduction and find the 1/2m correction to the NLSE, valid when |ω-m|<2m , where ω is the frequency of the solitary wave in the rest frame. We discuss the stability and blowup of solitary waves assuming the modified NLSE is valid and find that they should be stable for k<2 . PMID:21230200

  13. Taming the nonlinearity of the Einstein equation.

    PubMed

    Harte, Abraham I

    2014-12-31

    Many of the technical complications associated with the general theory of relativity ultimately stem from the nonlinearity of Einstein's equation. It is shown here that an appropriate choice of dynamical variables may be used to eliminate all such nonlinearities beyond a particular order: Both Landau-Lifshitz and tetrad formulations of Einstein's equation are obtained that involve only finite products of the unknowns and their derivatives. Considerable additional simplifications arise in physically interesting cases where metrics become approximately Kerr or, e.g., plane waves, suggesting that the variables described here can be used to efficiently reformulate perturbation theory in a variety of contexts. In all cases, these variables are shown to have simple geometrical interpretations that directly relate the local causal structure associated with the metric of interest to the causal structure associated with a prescribed background. A new method to search for exact solutions is outlined as well. PMID:25615299

  14. Explicit integration of Friedmann's equation with nonlinear equations of state

    NASA Astrophysics Data System (ADS)

    Chen, Shouxin; Gibbons, Gary W.; Yang, Yisong

    2015-05-01

    In this paper we study the integrability of the Friedmann equations, when the equation of state for the perfect-fluid universe is nonlinear, in the light of the Chebyshev theorem. A series of important, yet not previously touched, problems will be worked out which include the generalized Chaplygin gas, two-term energy density, trinomial Friedmann, Born-Infeld, two-fluid models, and Chern-Simons modified gravity theory models. With the explicit integration, we are able to understand exactly the roles of the physical parameters in various models play in the cosmological evolution which may also offer clues to a profound understanding of the problems in general settings. For example, in the Chaplygin gas universe, a few integrable cases lead us to derive a universal formula for the asymptotic exponential growth rate of the scale factor, of an explicit form, whether the Friedmann equation is integrable or not, which reveals the coupled roles played by various physical sectors and it is seen that, as far as there is a tiny presence of nonlinear matter, conventional linear matter makes contribution to the dark matter, which becomes significant near the phantom divide line. The Friedmann equations also arise in areas of physics not directly related to cosmology. We provide some examples ranging from geometric optics and central orbits to soap films and the shape of glaciated valleys to which our results may be applied.

  15. Solving Nonlinear Euler Equations with Arbitrary Accuracy

    NASA Technical Reports Server (NTRS)

    Dyson, Rodger W.

    2005-01-01

    A computer program that efficiently solves the time-dependent, nonlinear Euler equations in two dimensions to an arbitrarily high order of accuracy has been developed. The program implements a modified form of a prior arbitrary- accuracy simulation algorithm that is a member of the class of algorithms known in the art as modified expansion solution approximation (MESA) schemes. Whereas millions of lines of code were needed to implement the prior MESA algorithm, it is possible to implement the present MESA algorithm by use of one or a few pages of Fortran code, the exact amount depending on the specific application. The ability to solve the Euler equations to arbitrarily high accuracy is especially beneficial in simulations of aeroacoustic effects in settings in which fully nonlinear behavior is expected - for example, at stagnation points of fan blades, where linearizing assumptions break down. At these locations, it is necessary to solve the full nonlinear Euler equations, and inasmuch as the acoustical energy is of the order of 4 to 5 orders of magnitude below that of the mean flow, it is necessary to achieve an overall fractional error of less than 10-6 in order to faithfully simulate entropy, vortical, and acoustical waves.

  16. Forces Associated with Nonlinear Nonholonomic Constraint Equations

    NASA Technical Reports Server (NTRS)

    Roithmayr, Carlos M.; Hodges, Dewey H.

    2010-01-01

    A concise method has been formulated for identifying a set of forces needed to constrain the behavior of a mechanical system, modeled as a set of particles and rigid bodies, when it is subject to motion constraints described by nonholonomic equations that are inherently nonlinear in velocity. An expression in vector form is obtained for each force; a direction is determined, together with the point of application. This result is a consequence of expressing constraint equations in terms of dot products of vectors rather than in the usual way, which is entirely in terms of scalars and matrices. The constraint forces in vector form are used together with two new analytical approaches for deriving equations governing motion of a system subject to such constraints. If constraint forces are of interest they can be brought into evidence in explicit dynamical equations by employing the well-known nonholonomic partial velocities associated with Kane's method; if they are not of interest, equations can be formed instead with the aid of vectors introduced here as nonholonomic partial accelerations. When the analyst requires only the latter, smaller set of equations, they can be formed directly; it is not necessary to expend the labor to form the former, larger set first and subsequently perform matrix multiplications.

  17. Dark soliton solutions of (N+1)-dimensional nonlinear evolution equations

    NASA Astrophysics Data System (ADS)

    Demiray, Seyma Tuluce; Bulut, Hasan

    2016-06-01

    In this study, we investigate exact solutions of (N+1)-dimensional double sinh-Gordon equation and (N+1)-dimensional generalized Boussinesq equation by using generalized Kudryashov method. (N+1)-dimensional double sinh-Gordon equation and (N+1)-dimensional generalized Boussinesq equation can be returned to nonlinear ordinary differential equation by suitable transformation. Then, generalized Kudryashov method has been used to seek exact solutions of the (N+1)-dimensional double sinh-Gordon equation and (N+1)-dimensional generalized Boussinesq equation. Also, we obtain dark soliton solutions for these (N+1)-dimensional nonlinear evolution equations. Finally, we denote that this method can be applied to solve other nonlinear evolution equations.

  18. Using the scalable nonlinear equations solvers package

    SciTech Connect

    Gropp, W.D.; McInnes, L.C.; Smith, B.F.

    1995-02-01

    SNES (Scalable Nonlinear Equations Solvers) is a software package for the numerical solution of large-scale systems of nonlinear equations on both uniprocessors and parallel architectures. SNES also contains a component for the solution of unconstrained minimization problems, called SUMS (Scalable Unconstrained Minimization Solvers). Newton-like methods, which are known for their efficiency and robustness, constitute the core of the package. As part of the multilevel PETSc library, SNES incorporates many features and options from other parts of PETSc. In keeping with the spirit of the PETSc library, the nonlinear solution routines are data-structure-neutral, making them flexible and easily extensible. This users guide contains a detailed description of uniprocessor usage of SNES, with some added comments regarding multiprocessor usage. At this time the parallel version is undergoing refinement and extension, as we work toward a common interface for the uniprocessor and parallel cases. Thus, forthcoming versions of the software will contain additional features, and changes to parallel interface may result at any time. The new parallel version will employ the MPI (Message Passing Interface) standard for interprocessor communication. Since most of these details will be hidden, users will need to perform only minimal message-passing programming.

  19. The beam equation with nonlinear memory

    NASA Astrophysics Data System (ADS)

    D'Abbicco, Marcello; Lucente, Sandra

    2016-06-01

    In this paper, we study the critical exponent for the beam equation with nonlinear memory, i.e., {u_{tt}+Δ^2u = F(t, u)}, where F = intlimits0tf(t - s)N(u)(s, x) {d}s, quad N(u)≈ |u|^p. For suitable f and p, we prove the existence of local-in-time solutions and small data global solutions to the Cauchy problem, in homogeneous and nonhomogeneous Sobolev spaces. In some cases, we prove that the local solution cannot be extended to a global one. We also consider the limit case of power nonlinearity, i.e., {F = N(u)}.

  20. Exact and explicit solitary wave solutions to some nonlinear equations

    SciTech Connect

    Jiefang Zhang

    1996-08-01

    Exact and explicit solitary wave solutions are obtained for some physically interesting nonlinear evolutions and wave equations in physics and other fields by using a special transformation. These equations include the KdV-Burgers equation, the MKdV-Burgers equation, the combined KdV-MKdV equation, the Newell-Whitehead equation, the dissipative {Phi}{sup 4}-model equation, the generalized Fisher equation, and the elastic-medium wave equation.

  1. FAST TRACK COMMUNICATION Quasi self-adjoint nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Ibragimov, N. H.; Torrisi, M.; Tracinà, R.

    2010-11-01

    In this paper we generalize the classification of self-adjoint second-order linear partial differential equation to a family of nonlinear wave equations with two independent variables. We find a class of quasi self-adjoint nonlinear equations which includes the self-adjoint linear equations as a particular case. The property of a differential equation to be quasi self-adjoint is important, e.g. for constructing conservation laws associated with symmetries of the differential equation.

  2. Solution spectrum of nonlinear diffusion equations

    SciTech Connect

    Ulmer, W.

    1992-08-01

    The stationary version of the nonlinear diffusion equation -{partial_derivative}c/{partial_derivative}t+D{Delta}c=A{sub 1}c-A{sub 2}c{sup 2} can be solved with the ansatz c={summation}{sub p=1}{sup {infinity}} A{sub p}(cosh kx){sup -p}, inducing a band structure with regard to the ratio {lambda}{sub 1}/{lambda}{sub 2}. The resulting solution manifold can be related to an equilibrium of fluxes of nonequilibrium thermodynamics. The modification of this ansatz yielding the expansion c={summation}{sub p,q=1}{sup infinity}A{sub pa}(cosh kx){sup -p}[(cosh {alpha}t){sup -q-1} sinh {alpha}t+b(cosh {alpha}t){sup -q}] represents a solution spectrum of the time-dependent nonlinear equations, and the stationary version can be found from the asymptotic behaviour of the expansion. The solutions can be associated with reactive processes such as active transport phenomena and control circuit problems is discussed. There are also applications to cellular kinetics of clonogenic cell assays and spheriods. 33 refs., 1 tab.

  3. Nonlinear scattering term in the gyrokinetic Vlasov equation

    SciTech Connect

    Wang, Shaojie

    2013-08-15

    Nonlinear scattering term is found from the nonlinear gyrokinetic equation by decoupling the perturbed gyrocenter motion from the unperturbed motion. The gyro-center distribution function is determined by the well-understood unperturbed motion, with the effects of fields perturbation included in the nonlinear scattering term, which explicitly reveals the nonlinear stochastic dissipation on the time scale longer than the wave correlation time.

  4. Asymptotic behaviour of the Boltzmann equation as a cosmological model

    NASA Astrophysics Data System (ADS)

    Lee, Ho

    2016-08-01

    As a Newtonian cosmological model the Vlasov-Poisson-Boltzmann system is considered, and a slightly modified Boltzmann equation, which describes the stability of an expanding universe, is derived. Asymptotic behaviour of solutions turns out to depend on the expansion of the universe, and in this paper we consider the soft potential case and will obtain asymptotic behaviour.

  5. Role of non-ideality for the ion transport in porous media: Derivation of the macroscopic equations using upscaling

    NASA Astrophysics Data System (ADS)

    Allaire, Grégoire; Brizzi, Robert; Dufrêche, Jean-François; Mikelić, Andro; Piatnitski, Andrey

    2014-07-01

    This paper is devoted to the homogenization (or upscaling) of a system of partial differential equations describing the non-ideal transport of a N-component electrolyte in a dilute Newtonian solvent through a rigid porous medium. Realistic non-ideal effects are taken into account by an approach based on the mean spherical approximation (MSA) model which takes into account finite size ions and screening effects. We first consider equilibrium solutions in the absence of external forces. In such a case, the velocity and diffusive fluxes vanish and the equilibrium electrostatic potential is the solution of a variant of the Poisson-Boltzmann equation coupled with algebraic equations. Contrary to the ideal case, this nonlinear equation has no monotone structure. However, based on invariant region estimates for the Poisson-Boltzmann equation and for small characteristic value of the solute packing fraction, we prove existence of at least one solution. To our knowledge this existence result is new at this level of generality. When the motion is governed by a small static electric field and a small hydrodynamic force, we generalize O'Brien's argument to deduce a linearized model. Our second main result is the rigorous homogenization of these linearized equations and the proof that the effective tensor satisfies Onsager properties, namely is symmetric positive definite. We eventually make numerical comparisons with the ideal case. Our numerical results show that the MSA model confirms qualitatively the conclusions obtained using the ideal model but there are quantitative differences arising that can be important at high charge or high concentrations.

  6. Complex PT-symmetric nonlinear Schrödinger equation and Burgers equation.

    PubMed

    Yan, Zhenya

    2013-04-28

    The complex -symmetric nonlinear wave models have drawn much attention in recent years since the complex -symmetric extensions of the Korteweg-de Vries (KdV) equation were presented in 2007. In this review, we focus on the study of the complex -symmetric nonlinear Schrödinger equation and Burgers equation. First of all, we briefly introduce the basic property of complex symmetry. We then report on exact solutions of one- and two-dimensional nonlinear Schrödinger equations (known as the Gross-Pitaevskii equation in Bose-Einstein condensates) with several complex -symmetric potentials. Finally, some complex -symmetric extension principles are used to generate some complex -symmetric nonlinear wave equations starting from both -symmetric (e.g. the KdV equation) and non- -symmetric (e.g. the Burgers equation) nonlinear wave equations. In particular, we discuss exact solutions of some representative ones of the complex -symmetric Burgers equation in detail. PMID:23509385

  7. Forced nonlinear Schrödinger equation with arbitrary nonlinearity

    NASA Astrophysics Data System (ADS)

    Cooper, Fred; Khare, Avinash; Quintero, Niurka R.; Mertens, Franz G.; Saxena, Avadh

    2012-04-01

    We consider the nonlinear Schrödinger equation (NLSE) in 1+1 dimension with scalar-scalar self-interaction (g2)/(κ+1)(ψψ)κ+1 in the presence of the external forcing terms of the form re-i(kx+θ)-δψ. We find new exact solutions for this problem and show that the solitary wave momentum is conserved in a moving frame where vk=2k. These new exact solutions reduce to the constant phase solutions of the unforced problem when r→0. In particular we study the behavior of solitary wave solutions in the presence of these external forces in a variational approximation which allows the position, momentum, width, and phase of these waves to vary in time. We show that the stationary solutions of the variational equations include a solution close to the exact one and we study small oscillations around all the stationary solutions. We postulate that the dynamical condition for instability is that dp(t)/dq˙(t)<0, where p(t) is the normalized canonical momentum p(t)=(1)/(M(t))(∂L)/(∂q˙), and q˙(t) is the solitary wave velocity. Here M(t)=∫dxψ(x,t)ψ(x,t). Stability is also studied using a “phase portrait” of the soliton, where its dynamics is represented by two-dimensional projections of its trajectory in the four-dimensional space of collective coordinates. The criterion for stability of a soliton is that its trajectory is a closed single curve with a positive sense of rotation around a fixed point. We investigate the accuracy of our variational approximation and these criteria using numerical simulations of the NLSE. We find that our criteria work quite well when the magnitude of the forcing term is small compared to the amplitude of the unforced solitary wave. In this regime the variational approximation captures quite well the behavior of the solitary wave.

  8. Capillary waves in the subcritical nonlinear Schroedinger equation

    SciTech Connect

    Kozyreff, G.

    2010-01-15

    We expand recent results on the nonlinear Schroedinger equation with cubic-quintic nonlinearity to show that some solutions are described by the Bernoulli equation in the presence of surface tension. As a consequence, capillary waves are predicted and found numerically at the interface between regions of large and low amplitude.

  9. Forced nonlinear Schrödinger equation with arbitrary nonlinearity.

    PubMed

    Cooper, Fred; Khare, Avinash; Quintero, Niurka R; Mertens, Franz G; Saxena, Avadh

    2012-04-01

    We consider the nonlinear Schrödinger equation (NLSE) in 1+1 dimension with scalar-scalar self-interaction g(2)/κ+1(ψ*ψ)(κ+1) in the presence of the external forcing terms of the form re(-i(kx+θ))-δψ. We find new exact solutions for this problem and show that the solitary wave momentum is conserved in a moving frame where v(k)=2k. These new exact solutions reduce to the constant phase solutions of the unforced problem when r→0. In particular we study the behavior of solitary wave solutions in the presence of these external forces in a variational approximation which allows the position, momentum, width, and phase of these waves to vary in time. We show that the stationary solutions of the variational equations include a solution close to the exact one and we study small oscillations around all the stationary solutions. We postulate that the dynamical condition for instability is that dp(t)/dq ̇(t)<0, where p(t) is the normalized canonical momentum p(t)=1/M(t)∂L/∂q ̇, and q ̇(t) is the solitary wave velocity. Here M(t)=∫dxψ*(x,t)ψ(x,t). Stability is also studied using a "phase portrait" of the soliton, where its dynamics is represented by two-dimensional projections of its trajectory in the four-dimensional space of collective coordinates. The criterion for stability of a soliton is that its trajectory is a closed single curve with a positive sense of rotation around a fixed point. We investigate the accuracy of our variational approximation and these criteria using numerical simulations of the NLSE. We find that our criteria work quite well when the magnitude of the forcing term is small compared to the amplitude of the unforced solitary wave. In this regime the variational approximation captures quite well the behavior of the solitary wave. PMID:22680598

  10. Exact Travelling Wave Solutions of the Nonlinear Evolution Equations by Auxiliary Equation Method

    NASA Astrophysics Data System (ADS)

    Kaplan, Melike; Akbulut, Arzu; Bekir, Ahmet

    2015-10-01

    The auxiliary equation method presents wide applicability to handling nonlinear wave equations. In this article, we establish new exact travelling wave solutions of the nonlinear Zoomeron equation, coupled Higgs equation, and equal width wave equation. The travelling wave solutions are expressed by the hyperbolic functions, trigonometric functions, and rational functions. It is shown that the proposed method provides a powerful mathematical tool for solving nonlinear wave equations in mathematical physics and engineering. Throughout the article, all calculations are made with the aid of the Maple packet program.

  11. Exact traveling wave solutions for system of nonlinear evolution equations.

    PubMed

    Khan, Kamruzzaman; Akbar, M Ali; Arnous, Ahmed H

    2016-01-01

    In this work, recently deduced generalized Kudryashov method is applied to the variant Boussinesq equations, and the (2 + 1)-dimensional breaking soliton equations. As a result a range of qualitative explicit exact traveling wave solutions are deduced for these equations, which motivates us to develop, in the near future, a new approach to obtain unsteady solutions of autonomous nonlinear evolution equations those arise in mathematical physics and engineering fields. It is uncomplicated to extend this method to higher-order nonlinear evolution equations in mathematical physics. And it should be possible to apply the same method to nonlinear evolution equations having more general forms of nonlinearities by utilizing the traveling wave hypothesis. PMID:27347461

  12. Stochastic differential equations for non-linear hydrodynamics

    NASA Astrophysics Data System (ADS)

    Español, Pep

    1998-02-01

    We formulate the stochastic differential equations for non-linear hydrodynamic fluctuations. The equations incorporate the random forces through a random stres tensor and random heat flux as in the Landau and Lifshitz theory. However, the equations are non-linear and the random forces are non-Gaussian. We provide explicit expressions for these random quantities in terms of the well-defined increments of the Wienner process.

  13. Collocation Method for Numerical Solution of Coupled Nonlinear Schroedinger Equation

    SciTech Connect

    Ismail, M. S.

    2010-09-30

    The coupled nonlinear Schroedinger equation models several interesting physical phenomena presents a model equation for optical fiber with linear birefringence. In this paper we use collocation method to solve this equation, we test this method for stability and accuracy. Numerical tests using single soliton and interaction of three solitons are used to test the resulting scheme.

  14. Analytic solutions of a general nonlinear functional equations near resonance

    NASA Astrophysics Data System (ADS)

    Xu, Bing; Zhang, Weinian

    2006-05-01

    Existence of analytic solutions of a general class of nonlinear functional equations is discussed. This general class includes some specific functional equations studied recently. Moreover, we can generalize this problem to finding analytic solutions of a general class of iterative equations.

  15. The zero dispersion limits of nonlinear wave equations

    SciTech Connect

    Tso, T.

    1992-01-01

    In chapter 2 the author uses functional analytic methods and conservation laws to solve the initial-value problem for the Korteweg-de Vries equation, the Benjamin-Bona-Mahony equation, and the nonlinear Schroedinger equation for initial data that satisfy some suitable conditions. In chapter 3 the energy estimates are used to show that the strong convergence of the family of the solutions of the KdV equation obtained in chapter 2 in H[sup 3](R) as [epsilon] [yields] 0; also, it is shown that the strong L[sup 2](R)-limit of the solutions of the BBM equation as [epsilon] [yields] 0 before a critical time. In chapter 4 the author uses the Whitham modulation theory and averaging method to find the 2[pi]-periodic solutions and the modulation equations of the KdV equation, the BBM equation, the Klein-Gordon equation, the NLS equation, the mKdV equation, and the P-system. It is shown that the modulation equations of the KdV equation, the K-G equation, the NLS equation, and the mKdV equation are hyperbolic but those of the BBM equation and the P-system are not hyperbolic. Also, the relations are studied of the KdV equation and the mKdV equation. Finally, the author studies the complex mKdV equation to compare with the NLS equation, and then study the complex gKdV equation.

  16. NA Nonlinear Equation-of-state Inversion

    NASA Astrophysics Data System (ADS)

    Jackson, I.; Kennett, B. L.

    2008-12-01

    A fully non-linear inversion scheme is introduced for the determination of the parameters controlling the equation-of-state and elasticity of mineral phases using the thermodynamically consistent finite-strain formulation introduced by Stixrude & Lithgow-Bertelloni (2005). This inversion exploits a directed search in an eight-dimensional parameter space using the Neighbourhood Algorithm (NA) of Sambridge (1999) to search for the minimum of an objective function representing the misfit to multiple data sets that constrain different aspects of the mineral behaviour. No derivatives are employed and the progress towards the minimum builds on the accumulated information on the character of the parameter space acquired as the inversion progresses. When only a limited range of experimental information is available there is a strong possibility of multiple minima in the objective function, which can pose problems for conventional iterative least-squares or other gradient methods. The addition of many different styles of data tends to produce a better defined minimum. The influence of different data types can be readily assessed by allowing differential weighting. The new procedure is illustrated by application to MgO, for which extensive experimental data are available. These include the variation of relative volume V with temperature T and pressure P from both static and shock-compression experiments, acoustic measurements of compressional and shear (and hence bulk) moduli, and calorimetric determinations of entropy as a function of temperature at atmospheric pressure. Preliminary NA modeling highlighted tensions between marginally incompatible subsets of data. We therefore excluded one-atmosphere V(T) data for T ≥ 1800 K for which the quasi-harmonic approximation is inadequate (Wu et al., 2008) along with elastic moduli derived from Brillouin spectroscopy under conditions (P ≥ 14 GPa) where significant departures from hydrostatic conditions are expected. With these

  17. Nonlinear modes of the tensor Dirac equation and CPT violation

    NASA Technical Reports Server (NTRS)

    Reifler, Frank J.; Morris, Randall D.

    1993-01-01

    Recently, it has been shown that Dirac's bispinor equation can be expressed, in an equivalent tensor form, as a constrained Yang-Mills equation in the limit of an infinitely large coupling constant. It was also shown that the free tensor Dirac equation is a completely integrable Hamiltonian system with Lie algebra type Poisson brackets, from which Fermi quantization can be derived directly without using bispinors. The Yang-Mills equation for a finite coupling constant is investigated. It is shown that the nonlinear Yang-Mills equation has exact plane wave solutions in one-to-one correspondence with the plane wave solutions of Dirac's bispinor equation. The theory of nonlinear dispersive waves is applied to establish the existence of wave packets. The CPT violation of these nonlinear wave packets, which could lead to new observable effects consistent with current experimental bounds, is investigated.

  18. Painlevé equations--nonlinear special functions

    NASA Astrophysics Data System (ADS)

    Clarkson, Peter A.

    2003-04-01

    The six Painlevé equations (PI-PVI) were first discovered about a hundred years ago by Painlevé and his colleagues in an investigation of nonlinear second-order ordinary differential equations. Recently, there has been considerable interest in the Painlevé equations primarily due to the fact that they arise as reductions of the soliton equations which are solvable by inverse scattering. Consequently, the Painlevé equations can be regarded as completely integrable equations and possess solutions which can be expressed in terms of solutions of linear integral equations, despite being nonlinear equations. Although first discovered from strictly mathematical considerations, the Painlevé equations have arisen in a variety of important physical applications including statistical mechanics, plasma physics, nonlinear waves, quantum gravity, quantum field theory, general relativity, nonlinear optics and fibre optics. The Painlevé equations may be thought of a nonlinear analogues of the classical special functions. They possess hierarchies of rational solutions and one-parameter families of solutions expressible in terms of the classical special functions, for special values of the parameters. Further the Painlevé equations admit symmetries under affine Weyl groups which are related to the associated Bäcklund transformations. In this paper, I discuss some of the remarkable properties which the Painlevé equations possess including connection formulae, Bäcklund transformations associated discrete equations, and hierarchies of exact solutions. In particular, the second Painlevé equation PII is used to illustrate these properties and some of the applications of PII are also discussed.

  19. An integrable shallow water equation with linear and nonlinear dispersion.

    PubMed

    Dullin, H R; Gottwald, G A; Holm, D D

    2001-11-01

    We use asymptotic analysis and a near-identity normal form transformation from water wave theory to derive a 1+1 unidirectional nonlinear wave equation that combines the linear dispersion of the Korteweg-deVries (KdV) equation with the nonlinear/nonlocal dispersion of the Camassa-Holm (CH) equation. This equation is one order more accurate in asymptotic approximation beyond KdV, yet it still preserves complete integrability via the inverse scattering transform method. Its traveling wave solutions contain both the KdV solitons and the CH peakons as limiting cases. PMID:11690414

  20. Nonlinear ordinary differential equations: A discussion on symmetries and singularities

    NASA Astrophysics Data System (ADS)

    Paliathanasis, Andronikos; Leach, P. G. L.

    2016-06-01

    Two essential methods, the symmetry analysis and the singularity analysis, for the study of the integrability of nonlinear ordinary differential equations is the purpose of this work. The main similarities and the differences of these two different methods are discussed.

  1. Oscillation theorems for second order nonlinear forced differential equations.

    PubMed

    Salhin, Ambarka A; Din, Ummul Khair Salma; Ahmad, Rokiah Rozita; Noorani, Mohd Salmi Md

    2014-01-01

    In this paper, a class of second order forced nonlinear differential equation is considered and several new oscillation theorems are obtained. Our results generalize and improve those known ones in the literature. PMID:25077054

  2. Late-time attractor for the cubic nonlinear wave equation

    SciTech Connect

    Szpak, Nikodem

    2010-08-15

    We apply our recently developed scaling technique for obtaining late-time asymptotics to the cubic nonlinear wave equation and explain the appearance and approach to the two-parameter attractor found recently by Bizon and Zenginoglu.

  3. Multivariate Padé Approximations For Solving Nonlinear Diffusion Equations

    NASA Astrophysics Data System (ADS)

    Turut, V.

    2015-11-01

    In this paper, multivariate Padé approximation is applied to power series solutions of nonlinear diffusion equations. As it is seen from tables, multivariate Padé approximation (MPA) gives reliable solutions and numerical results.

  4. Numerical methods for the Poisson-Fermi equation in electrolytes

    NASA Astrophysics Data System (ADS)

    Liu, Jinn-Liang

    2013-08-01

    The Poisson-Fermi equation proposed by Bazant, Storey, and Kornyshev [Phys. Rev. Lett. 106 (2011) 046102] for ionic liquids is applied to and numerically studied for electrolytes and biological ion channels in three-dimensional space. This is a fourth-order nonlinear PDE that deals with both steric and correlation effects of all ions and solvent molecules involved in a model system. The Fermi distribution follows from classical lattice models of configurational entropy of finite size ions and solvent molecules and hence prevents the long and outstanding problem of unphysical divergence predicted by the Gouy-Chapman model at large potentials due to the Boltzmann distribution of point charges. The equation reduces to Poisson-Boltzmann if the correlation length vanishes. A simplified matched interface and boundary method exhibiting optimal convergence is first developed for this equation by using a gramicidin A channel model that illustrates challenging issues associated with the geometric singularities of molecular surfaces of channel proteins in realistic 3D simulations. Various numerical methods then follow to tackle a range of numerical problems concerning the fourth-order term, nonlinearity, stability, efficiency, and effectiveness. The most significant feature of the Poisson-Fermi equation, namely, its inclusion of steric and correlation effects, is demonstrated by showing good agreement with Monte Carlo simulation data for a charged wall model and an L type calcium channel model.

  5. Kinetic effects on Alfven wave nonlinearity. II - The modified nonlinear wave equation

    NASA Technical Reports Server (NTRS)

    Spangler, Steven R.

    1990-01-01

    A previously developed Vlasov theory is used here to study the role of resonant particle and other kinetic effects on Alfven wave nonlinearity. A hybrid fluid-Vlasov equation approach is used to obtain a modified version of the derivative nonlinear Schroedinger equation. The differences between a scalar model for the plasma pressure and a tensor model are discussed. The susceptibilty of the modified nonlinear wave equation to modulational instability is studied. The modulational instability normally associated with the derivative nonlinear Schroedinger equation will, under most circumstances, be restricted to left circularly polarized waves. The nonlocal term in the modified nonlinear wave equation engenders a new modulational instability that is independent of beta and the sense of circular polarization. This new instability may explain the occurrence of wave packet steepening for all values of the plasma beta in the vicinity of the earth's bow shock.

  6. Invariant tori for a class of nonlinear evolution equations

    SciTech Connect

    Kolesov, A Yu; Rozov, N Kh

    2013-06-30

    The paper looks at quite a wide class of nonlinear evolution equations in a Banach space, including the typical boundary value problems for the main wave equations in mathematical physics (the telegraph equation, the equation of a vibrating beam, various equations from the elastic stability and so on). For this class of equations a unified approach to the bifurcation of invariant tori of arbitrary finite dimension is put forward. Namely, the problem of the birth of such tori from the zero equilibrium is investigated under the assumption that in the stability problem for this equilibrium the situation arises close to an infinite-dimensional degeneracy. Bibliography: 28 titles.

  7. Lattice Boltzmann model for generalized nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Lai, Huilin; Ma, Changfeng

    2011-10-01

    In this paper, a lattice Boltzmann model is developed to solve a class of the nonlinear wave equations. Through selecting equilibrium distribution function and an amending function properly, the governing evolution equation can be recovered correctly according to our proposed scheme, in which the Chapman-Enskog expansion is employed. We validate the algorithm on some problems where analytic solutions are available, including the second-order telegraph equation, the nonlinear Klein-Gordon equation, and the damped, driven sine-Gordon equation. It is found that the numerical results agree well with the analytic solutions, which indicates that the present algorithm is very effective and can be used to solve more general nonlinear problems.

  8. Nonlinear Kramers equation associated with nonextensive statistical mechanics.

    PubMed

    Mendes, G A; Ribeiro, M S; Mendes, R S; Lenzi, E K; Nobre, F D

    2015-05-01

    Stationary and time-dependent solutions of a nonlinear Kramers equation, as well as its associated nonlinear Fokker-Planck equations, are investigated within the context of Tsallis nonextensive statistical mechanics. Since no general analytical time-dependent solutions are found for such a nonlinear Kramers equation, an ansatz is considered and the corresponding asymptotic behavior is studied and compared with those known for the standard linear Kramers equation. The H-theorem is analyzed for this equation and its connection with Tsallis entropy is investigated. An application is discussed, namely the motion of Hydra cells in two-dimensional cellular aggregates, for which previous measurements have verified q-Gaussian distributions for velocity components and superdiffusion. The present analysis is in quantitative agreement with these experimental results. PMID:26066118

  9. Solutions to Class of Linear and Nonlinear Fractional Differential Equations

    NASA Astrophysics Data System (ADS)

    Abdel-Salam, Emad A.-B.; Hassan, Gamal F.

    2016-02-01

    In this paper, the fractional auxiliary sub-equation expansion method is proposed to solve nonlinear fractional differential equations. To illustrate the effectiveness of the method, we discuss the space-time fractional KdV equation, the space-time fractional RLW equation, the space-time fractional Boussinesq equation, and the (3+1)-space-time fractional ZK equation. The solutions are expressed in terms of fractional hyperbolic and fractional trigonometric functions. These solutions are useful to understand the mechanisms of the complicated nonlinear physical phenomena and fractional differential equations. Among these solutions, some are found for the first time. The analytical solution of homogenous linear FDEs with constant coefficients are obtained by using the series and the Mittag–Leffler function methods. The obtained results recover the well-know solutions when α = 1.

  10. Solutions to Class of Linear and Nonlinear Fractional Differential Equations

    NASA Astrophysics Data System (ADS)

    Emad A-B., Abdel-Salam; Gamal, F. Hassan

    2016-02-01

    In this paper, the fractional auxiliary sub-equation expansion method is proposed to solve nonlinear fractional differential equations. To illustrate the effectiveness of the method, we discuss the space-time fractional KdV equation, the space-time fractional RLW equation, the space-time fractional Boussinesq equation, and the (3+1)-space-time fractional ZK equation. The solutions are expressed in terms of fractional hyperbolic and fractional trigonometric functions. These solutions are useful to understand the mechanisms of the complicated nonlinear physical phenomena and fractional differential equations. Among these solutions, some are found for the first time. The analytical solution of homogenous linear FDEs with constant coefficients are obtained by using the series and the Mittag-Leffler function methods. The obtained results recover the well-know solutions when α = 1.

  11. Derivation of an Applied Nonlinear Schroedinger Equation.

    SciTech Connect

    Pitts, Todd Alan; Laine, Mark Richard; Schwarz, Jens; Rambo, Patrick K.; Karelitz, David B.

    2015-01-01

    We derive from first principles a mathematical physics model useful for understanding nonlinear optical propagation (including filamentation). All assumptions necessary for the development are clearly explained. We include the Kerr effect, Raman scattering, and ionization (as well as linear and nonlinear shock, diffraction and dispersion). We explain the phenomenological sub-models and each assumption required to arrive at a complete and consistent theoretical description. The development includes the relationship between shock and ionization and demonstrates why inclusion of Drude model impedance effects alters the nature of the shock operator. Unclassified Unlimited Release

  12. Nonlinear flap-lag axial equations of a rotating beam

    NASA Technical Reports Server (NTRS)

    Kaza, K. R. V.; Kvaternik, R. G.

    1977-01-01

    It is possible to identify essentially four approaches by which analysts have established either the linear or nonlinear governing equations of motion for a particular problem related to the dynamics of rotating elastic bodies. The approaches include the effective applied load artifice in combination with a variational principle and the use of Newton's second law, written as D'Alembert's principle, applied to the deformed configuration. A third approach is a variational method in which nonlinear strain-displacement relations and a first-degree displacement field are used. The method introduced by Vigneron (1975) for deriving the linear flap-lag equations of a rotating beam constitutes the fourth approach. The reported investigation shows that all four approaches make use of the geometric nonlinear theory of elasticity. An alternative method for deriving the nonlinear coupled flap-lag-axial equations of motion is also discussed.

  13. Entropy and convexity for nonlinear partial differential equations

    PubMed Central

    Ball, John M.; Chen, Gui-Qiang G.

    2013-01-01

    Partial differential equations are ubiquitous in almost all applications of mathematics, where they provide a natural mathematical description of many phenomena involving change in physical, chemical, biological and social processes. The concept of entropy originated in thermodynamics and statistical physics during the nineteenth century to describe the heat exchanges that occur in the thermal processes in a thermodynamic system, while the original notion of convexity is for sets and functions in mathematics. Since then, entropy and convexity have become two of the most important concepts in mathematics. In particular, nonlinear methods via entropy and convexity have been playing an increasingly important role in the analysis of nonlinear partial differential equations in recent decades. This opening article of the Theme Issue is intended to provide an introduction to entropy, convexity and related nonlinear methods for the analysis of nonlinear partial differential equations. We also provide a brief discussion about the content and contributions of the papers that make up this Theme Issue. PMID:24249768

  14. The numerical dynamic for highly nonlinear partial differential equations

    NASA Technical Reports Server (NTRS)

    Lafon, A.; Yee, H. C.

    1992-01-01

    Problems associated with the numerical computation of highly nonlinear equations in computational fluid dynamics are set forth and analyzed in terms of the potential ranges of spurious behaviors. A reaction-convection equation with a nonlinear source term is employed to evaluate the effects related to spatial and temporal discretizations. The discretization of the source term is described according to several methods, and the various techniques are shown to have a significant effect on the stability of the spurious solutions. Traditional linearized stability analyses cannot provide the level of confidence required for accurate fluid dynamics computations, and the incorporation of nonlinear analysis is proposed. Nonlinear analysis based on nonlinear dynamical systems complements the conventional linear approach and is valuable in the analysis of hypersonic aerodynamics and combustion phenomena.

  15. The Jeffcott equations in nonlinear rotordynamics

    NASA Technical Reports Server (NTRS)

    Zalik, R. A.

    1987-01-01

    The Jeffcott equations are a system of coupled differential equations representing the behavior of a rotating shaft. This is a simple model which allows investigation of the basic dynamic behavior of rotating machinery. Nolinearities can be introduced by taking into consideration deadband, side force, and rubbing, among others. The properties of the solutions of the Jeffcott equations with deadband are studied. In particular, it is shown how bounds for the solution of these equations can be obtained from bounds for the solutions of the linearized equations. By studying the behavior of the Fourier transforms of the solutions, we are also able to predict the onset of destructive vibrations. These conclusions are verified by means of numerical solutions of the equations, and of power spectrum density (PSD) plots. This study offers insight into a possible detection method to determine pump stability margins during flight and hot fire tests, and was motivated by the need to explain a phenomenon observed in the development phase of the cryogenic pumps of the Space Shuttle, during hot fire ground testing; namely, the appearance of vibrations at frequencies that could not be accounted for by means of linear models.

  16. Relations between nonlinear Riccati equations and other equations in fundamental physics

    NASA Astrophysics Data System (ADS)

    Schuch, Dieter

    2014-10-01

    Many phenomena in the observable macroscopic world obey nonlinear evolution equations while the microscopic world is governed by quantum mechanics, a fundamental theory that is supposedly linear. In order to combine these two worlds in a common formalism, at least one of them must sacrifice one of its dogmas. Linearizing nonlinear dynamics would destroy the fundamental property of this theory, however, it can be shown that quantum mechanics can be reformulated in terms of nonlinear Riccati equations. In a first step, it will be shown that the information about the dynamics of quantum systems with analytical solutions can not only be obtainable from the time-dependent Schrödinger equation but equally-well from a complex Riccati equation. Comparison with supersymmetric quantum mechanics shows that even additional information can be obtained from the nonlinear formulation. Furthermore, the time-independent Schrödinger equation can also be rewritten as a complex Riccati equation for any potential. Extension of the Riccati formulation to include irreversible dissipative effects is straightforward. Via (real and complex) Riccati equations, other fields of physics can also be treated within the same formalism, e.g., statistical thermodynamics, nonlinear dynamical systems like those obeying a logistic equation as well as wave equations in classical optics, Bose- Einstein condensates and cosmological models. Finally, the link to abstract "quantizations" such as the Pythagorean triples and Riccati equations connected with trigonometric and hyperbolic functions will be shown.

  17. Generalized nonlinear Proca equation and its free-particle solutions

    NASA Astrophysics Data System (ADS)

    Nobre, F. D.; Plastino, A. R.

    2016-06-01

    We introduce a nonlinear extension of Proca's field theory for massive vector (spin 1) bosons. The associated relativistic nonlinear wave equation is related to recently advanced nonlinear extensions of the Schrödinger, Dirac, and Klein-Gordon equations inspired on the non-extensive generalized thermostatistics. This is a theoretical framework that has been applied in recent years to several problems in nuclear and particle physics, gravitational physics, and quantum field theory. The nonlinear Proca equation investigated here has a power-law nonlinearity characterized by a real parameter q (formally corresponding to the Tsallis entropic parameter) in such a way that the standard linear Proca wave equation is recovered in the limit q → 1. We derive the nonlinear Proca equation from a Lagrangian, which, besides the usual vectorial field Ψ ^{μ }(ěc {x},t), involves an additional field Φ ^{μ }(ěc {x},t). We obtain exact time-dependent soliton-like solutions for these fields having the form of a q-plane wave, and we show that both field equations lead to the relativistic energy-momentum relation E2 = p2c2 + m2c4 for all values of q. This suggests that the present nonlinear theory constitutes a new field theoretical representation of particle dynamics. In the limit of massless particles the present q-generalized Proca theory reduces to Maxwell electromagnetism, and the q-plane waves yield localized, transverse solutions of Maxwell equations. Physical consequences and possible applications are discussed.

  18. Optimal Variational Asymptotic Method for Nonlinear Fractional Partial Differential Equations

    PubMed Central

    Baranwal, Vipul K.; Pandey, Ram K.

    2014-01-01

    We propose optimal variational asymptotic method to solve time fractional nonlinear partial differential equations. In the proposed method, an arbitrary number of auxiliary parameters γ0, γ1, γ2,… and auxiliary functions H0(x), H1(x), H2(x),… are introduced in the correction functional of the standard variational iteration method. The optimal values of these parameters are obtained by minimizing the square residual error. To test the method, we apply it to solve two important classes of nonlinear partial differential equations: (1) the fractional advection-diffusion equation with nonlinear source term and (2) the fractional Swift-Hohenberg equation. Only few iterations are required to achieve fairly accurate solutions of both the first and second problems.

  19. An iterative method for systems of nonlinear hyperbolic equations

    NASA Technical Reports Server (NTRS)

    Scroggs, Jeffrey S.

    1989-01-01

    An iterative algorithm for the efficient solution of systems of nonlinear hyperbolic equations is presented. Parallelism is evident at several levels. In the formation of the iteration, the equations are decoupled, thereby providing large grain parallelism. Parallelism may also be exploited within the solves for each equation. Convergence of the interation is established via a bounding function argument. Experimental results in two-dimensions are presented.

  20. Liapunov functions for non-linear difference equation stability analysis.

    NASA Technical Reports Server (NTRS)

    Park, K. E.; Kinnen, E.

    1972-01-01

    Liapunov functions to determine the stability of non-linear autonomous difference equations can be developed through the use of auxiliary exact difference equations. For this purpose definitions are introduced for the gradient of an implicit function of a discrete variable, a principal sum, a definite sum and an exact difference equation, and a theorem for exactness of a difference form is proved. Examples illustrate the procedure.

  1. Nonlinear Resonance and Duffing's Spring Equation

    ERIC Educational Resources Information Center

    Fay, Temple H.

    2006-01-01

    This note discusses the boundary in the frequency--amplitude plane for boundedness of solutions to the forced spring Duffing type equation. For fixed initial conditions and fixed parameter [epsilon] results are reported of a systematic numerical investigation on the global stability of solutions to the initial value problem as the parameters F and…

  2. Nonlinear Resonance and Duffing's Spring Equation II

    ERIC Educational Resources Information Center

    Fay, T. H.; Joubert, Stephan V.

    2007-01-01

    The paper discusses the boundary in the frequency-amplitude plane for boundedness of solutions to the forced spring Duffing type equation x[umlaut] + x + [epsilon]x[cubed] = F cos[omega]t. For fixed initial conditions and for representative fixed values of the parameter [epsilon], the results are reported of a systematic numerical investigation…

  3. Non-Linear Spring Equations and Stability

    ERIC Educational Resources Information Center

    Fay, Temple H.; Joubert, Stephan V.

    2009-01-01

    We discuss the boundary in the Poincare phase plane for boundedness of solutions to spring model equations of the form [second derivative of]x + x + epsilonx[superscript 2] = Fcoswt and the [second derivative of]x + x + epsilonx[superscript 3] = Fcoswt and report the results of a systematic numerical investigation on the global stability of…

  4. A Procedure to Construct Conservation Laws of Nonlinear Evolution Equations

    NASA Astrophysics Data System (ADS)

    Yaşar, Emrullah; San, Sait

    2016-05-01

    In this article, we established abundant local conservation laws to some nonlinear evolution equations by a new combined approach, which is a union of multiplier and Ibragimov's new conservation theorem method. One can conclude that the solutions of the adjoint equations corresponding to the new conservation theorem can be obtained via multiplier functions. Many new families of conservation laws of the Pochammer-Chree (PC) equation and the Kaup-Boussinesq type of coupled KdV system are successfully obtained. The combined method presents a wider applicability for handling the conservation laws of nonlinear wave equations. The conserved vectors obtained here can be important for the explanation of some practical physical problems, reductions, and solutions of the underlying equations.

  5. An Effective Schema for Solving Some Nonlinear Partial Differential Equation Arising In Nonlinear Physics

    NASA Astrophysics Data System (ADS)

    Baskonus, Haci Mehmet; Bulut, Hasan

    2015-10-01

    In this paper, a new computational algorithm called the "Improved Bernoulli sub-equation function method" has been proposed. This algorithm is based on the Bernoulli Sub-ODE method. Firstly, the nonlinear evaluation equations used for representing various physical phenomena are converted into ordinary differential equations by using various wave transformations. In this way, nonlinearity is preserved and represent nonlinear physical problems. The nonlinearity of physical problems together with the derivations is seen as the secret key to solve the general structure of problems. The proposed analytical schema, which is newly submitted to the literature, has been expressed comprehensively in this paper. The analytical solutions, application results, and comparisons are presented by plotting the two and three dimensional surfaces of analytical solutions obtained by using the methods proposed for some important nonlinear physical problems. Finally, a conclusion has been presented by mentioning the important discoveries in this study.

  6. Evolution equation for non-linear cosmological perturbations

    SciTech Connect

    Brustein, Ram; Riotto, Antonio E-mail: Antonio.Riotto@cern.ch

    2011-11-01

    We present a novel approach, based entirely on the gravitational potential, for studying the evolution of non-linear cosmological matter perturbations. Starting from the perturbed Einstein equations, we integrate out the non-relativistic degrees of freedom of the cosmic fluid and obtain a single closed equation for the gravitational potential. We then verify the validity of the new equation by comparing its approximate solutions to known results in the theory of non-linear cosmological perturbations. First, we show explicitly that the perturbative solution of our equation matches the standard perturbative solutions. Next, using the mean field approximation to the equation, we show that its solution reproduces in a simple way the exponential suppression of the non-linear propagator on small scales due to the velocity dispersion. Our approach can therefore reproduce the main features of the renormalized perturbation theory and (time)-renormalization group approaches to the study of non-linear cosmological perturbations, with some possibly important differences. We conclude by a preliminary discussion of the nature of the full solutions of the equation and their significance.

  7. Algebraic calculation of stroboscopic maps of ordinary, nonlinear differential equations

    SciTech Connect

    Wackerbauer, R. ); Huebler, A. . Center for Complex Systems Research); Mayer-Kress, G. California Univ., Santa Cruz, CA . Dept. of Mathematics)

    1991-07-25

    The relation between the parameters of a differential equation and corresponding discrete maps are becoming increasingly important in the study of nonlinear dynamical systems. Maps are well adopted for numerical computation and several universal properties of them are known. Therefore some perturbation methods have been proposed to deduce them for physical systems, which can be modeled by an ordinary differential equation (ODE) with a small nonlinearity. A new iterative, rigorous algebraic method for the calculation of the coefficients of a Taylor expansion of a stroboscopic map from ODE's with not necessarily small nonlinearities is presented. It is shown analytically that most of the coefficients are small for a small integration time and grow slowly in the course of time if the flow vector field of the ODE is polynomial and if the ODE has fixed point in the origin. Approximations of different orders respectively of the rest term are investigated for several nonlinear systems. 31 refs., 16 figs.

  8. A Jacobi collocation approximation for nonlinear coupled viscous Burgers' equation

    NASA Astrophysics Data System (ADS)

    Doha, Eid; Bhrawy, Ali; Abdelkawy, Mohamed; Hafez, Ramy

    2014-02-01

    This article presents a numerical approximation of the initial-boundary nonlinear coupled viscous Burgers' equation based on spectral methods. A Jacobi-Gauss-Lobatto collocation (J-GL-C) scheme in combination with the implicit Runge-Kutta-Nyström (IRKN) scheme are employed to obtain highly accurate approximations to the mentioned problem. This J-GL-C method, based on Jacobi polynomials and Gauss-Lobatto quadrature integration, reduces solving the nonlinear coupled viscous Burgers' equation to a system of nonlinear ordinary differential equation which is far easier to solve. The given examples show, by selecting relatively few J-GL-C points, the accuracy of the approximations and the utility of the approach over other analytical or numerical methods. The illustrative examples demonstrate the accuracy, efficiency, and versatility of the proposed algorithm.

  9. Biological multi-rogue waves in discrete nonlinear Schrödinger equation with saturable nonlinearities

    NASA Astrophysics Data System (ADS)

    Tchinang Tchameu, J. D.; Togueu Motcheyo, A. B.; Tchawoua, C.

    2016-09-01

    The discrete multi-rogue waves (DMRW) as solution of the discrete nonlinear Schrödinger (DNLS) equation with saturable nonlinearities is studied numerically. These biological rogue waves represent the complex probability amplitude of finding an amide-I vibrational quantum at a site. We observe that the growth in the higher order saturable nonlinearity implies the formation of DMRW including an increase in the short-living DMRW and a decrease in amplitude of the long-living DMRW.

  10. Stochasticity in numerical solutions of the nonlinear Schroedinger equation

    NASA Technical Reports Server (NTRS)

    Shen, Mei-Mei; Nicholson, D. R.

    1987-01-01

    The cubically nonlinear Schroedinger equation is an important model of nonlinear phenomena in fluids and plasmas. Numerical solutions in a spatially periodic system commonly involve truncation to a finite number of Fourier modes. These solutions are found to be stochastic in the sense that the largest Liapunov exponent is positive. As the number of modes is increased, the size of this exponent appears to converge to zero, in agreement with the recent demonstration of the integrability of the spatially periodic case.

  11. The Buoyancy Budget With a Nonlinear Equation of State

    NASA Astrophysics Data System (ADS)

    Hieronymus, M. H.; Nycander, J.

    2012-12-01

    There has been a number of studies focusing on different aspects of having a nonlinear equation of state for seawater. Amongst other things it has been shown that the nonlinear equation of state has implications for the oceanic energy budget and that nonlinear processes can be a significant source of dense water production. This presentation will focus on the oceanic buoyancy budget. The nonlinear equation of state of seawater can introduce a sink or source of buoyancy when water parcels of unequal salinities and temperatures are mixed. A common example is the process known as cabbeling, which is responsible for forming a water mass that is denser than the original constituents in a mixture of two water masses with equal densities but different salinities and temperatures. This presentation will contain quantitative estimates of these nonlinear effects on the buoyancy budget of the global ocean. Because of these nonlinear effects there is a net sink of buoyancy in the oceans interior and the size of this sink can be determined from the buoyancy fluxes at the ocean boundaries. These boundary buoyancy fluxes are calculated using two surface heat flux climatologies one based on in situ measurements, the other on a reanalysis and in both cases using a nonlinear equation of state. The presentation also treats the buoyancy budget in the State of the art ocean model Nucleus for European Modelling of the Ocean (NEMO) and the results from NEMO are seen to be in good agreement with the buoyancy budgets based on the heat flux climatologies. Using the ocean model is a good complement to the surface flux climatologies, because in NEMO the buoyancy fluxes can be evaluated at all vertical model levels. This means that the vertical distribution of the buoyancy sink can be looked into. The results from NEMO shows that in large parts of the ocean the nonlinear buoyancy sink is the largest contribution to the buoyancy budget.

  12. Nonlinear generalized master equations and accounting for initial correlations

    NASA Astrophysics Data System (ADS)

    Los, V. F.

    2009-08-01

    We develop a new method based on using a time-dependent operator (generally not a projection operator) converting a distribution function (statistical operator) of a total system into the relevant form that allows deriving new exact nonlinear generalized master equations (GMEs). The derived inhomogeneous nonlinear GME is a generalization of the linear Nakajima-Zwanzig GME and can be viewed as an alternative to the BBGKY chain. It is suitable for obtaining both nonlinear and linear evolution equations. As in the conventional linear GME, there is an inhomogeneous term comprising all multiparticle initial correlations. To include the initial correlations into consideration, we convert the obtained inhomogeneous nonlinear GME into the homogenous form by the previously suggested method. We use no conventional approximation like the random phase approximation (RPA) or the Bogoliubov principle of weakening of initial correlations. The obtained exact homogeneous nonlinear GME describes all evolution stages of the (sub)system of interest and treats initial correlations on an equal footing with collisions via the modified memory kernel. As an application, we obtain a new homogeneous nonlinear equation retaining initial correlations for a one-particle distribution function of the spatially inhomogeneous nonideal gas of classical particles. In contrast to existing approaches, this equation holds for all time scales and takes the influence of pair collisions and initial correlations on the dissipative and nondissipative characteristics of the system into account consistently with the adopted approximation (linear in the gas density). We show that on the kinetic time scale, the time-reversible terms resulting from the initial correlations vanish (if the particle dynamics are endowed with the mixing property) and this equation can be converted into the Vlasov-Landau and Boltzmann equations without any additional commonly used approximations. The entire process of transition can

  13. Decay and stability for nonlinear hyperbolic equations

    NASA Astrophysics Data System (ADS)

    Marcati, Pierangelo

    This paper deals with the asymptotic stability of the null solution of a semilinear partial differential equation. The La Salle Invariance Principle has been used to obtain the stability results. The first result is given under quite general hypotheses assuming only the precompactness of the orbits and the local existence. In the second part, under some restrictions, sufficient conditions for precompactness of the orbits and decay of solutions are given. An existence and uniqueness theorem is proved in the Appendix. Some examples are given.

  14. Cylindrical nonlinear Schroedinger equation versus cylindrical Korteweg-de Vries equation

    SciTech Connect

    Fedele, Renato; De Nicola, Sergio; Grecu, Dan; Visinescu, Anca; Shukla, Padma K.

    2008-10-15

    A correspondence between the family of cylindrical nonlinear Schroedinger (cNLS) equations and the one of cylindrical Korteweg-de Vries (cKdV) equations is constructed. It associates non stationary solutions of the first family with the ones of the second family. This is done by using a correspondence, recently found, between the families of generalized NLS equation and generalized KdV equation, and their solutions in the form of travelling waves, respectively. In particular, non-stationary soliton-like solutions of the cNLS equation can be associated with non-stationary soliton-like solutions of cKdV equation.

  15. From nonlinear Schrödinger hierarchy to some (2+1)-dimensional nonlinear pseudodifferential equations

    NASA Astrophysics Data System (ADS)

    Yang, Xiao; Du, Dianlou

    2010-08-01

    The Poisson structure on CN×RN is introduced to give the Hamiltonian system associated with a spectral problem which yields the nonlinear Schrödinger (NLS) hierarchy. The Hamiltonian system is proven to be Liouville integrable. Some (2+1)-dimensional equations including NLS equation, Kadomtesev-Petviashvili I (KPI) equation, coupled KPI equation, and modified Kadomtesev-Petviashvili (mKP) equation, are decomposed into Hamilton flows via the NLS hierarchy. The algebraic curve, Abel-Jacobi coordinates, and Riemann-Jacobi inversion are used to obtain the algebrogeometric solutions of these equations.

  16. From nonlinear Schroedinger hierarchy to some (2+1)-dimensional nonlinear pseudodifferential equations

    SciTech Connect

    Yang Xiao; Du Dianlou

    2010-08-15

    The Poisson structure on C{sup N}xR{sup N} is introduced to give the Hamiltonian system associated with a spectral problem which yields the nonlinear Schroedinger (NLS) hierarchy. The Hamiltonian system is proven to be Liouville integrable. Some (2+1)-dimensional equations including NLS equation, Kadomtesev-Petviashvili I (KPI) equation, coupled KPI equation, and modified Kadomtesev-Petviashvili (mKP) equation, are decomposed into Hamilton flows via the NLS hierarchy. The algebraic curve, Abel-Jacobi coordinates, and Riemann-Jacobi inversion are used to obtain the algebrogeometric solutions of these equations.

  17. Convergence of Galerkin approximations for operator Riccati equations: A nonlinear evolution equation approach

    NASA Technical Reports Server (NTRS)

    Rosen, I. G.

    1988-01-01

    An approximation and convergence theory was developed for Galerkin approximations to infinite dimensional operator Riccati differential equations formulated in the space of Hilbert-Schmidt operators on a separable Hilbert space. The Riccati equation was treated as a nonlinear evolution equation with dynamics described by a nonlinear monotone perturbation of a strongly coercive linear operator. A generic approximation result was proven for quasi-autonomous nonlinear evolution system involving accretive operators which was then used to demonstrate the Hilbert-Schmidt norm convergence of Galerkin approximations to the solution of the Riccati equation. The application of the results was illustrated in the context of a linear quadratic optimal control problem for a one dimensional heat equation.

  18. On the Dirichlet problem for a nonlinear elliptic equation

    NASA Astrophysics Data System (ADS)

    Egorov, Yu V.

    2015-04-01

    We prove the existence of an infinite set of solutions to the Dirichlet problem for a nonlinear elliptic equation of the second order. Such a problem for a nonlinear elliptic equation with Laplace operator was studied earlier by Krasnosel'skii, Bahri, Berestycki, Lions, Rabinowitz, Struwe and others. We study the spectrum of this problem and prove the weak convergence to 0 of the sequence of normed eigenfunctions. Moreover, we obtain some estimates for the 'Fourier coefficients' of functions in W^1p,0(Ω). This allows us to improve the preceding results. Bibliography: 8 titles.

  19. Multiply scaled constrained nonlinear equation solvers. [for nonlinear heat conduction problems

    NASA Technical Reports Server (NTRS)

    Padovan, Joe; Krishna, Lala

    1986-01-01

    To improve the numerical stability of nonlinear equation solvers, a partitioned multiply scaled constraint scheme is developed. This scheme enables hierarchical levels of control for nonlinear equation solvers. To complement the procedure, partitioned convergence checks are established along with self-adaptive partitioning schemes. Overall, such procedures greatly enhance the numerical stability of the original solvers. To demonstrate and motivate the development of the scheme, the problem of nonlinear heat conduction is considered. In this context the main emphasis is given to successive substitution-type schemes. To verify the improved numerical characteristics associated with partitioned multiply scaled solvers, results are presented for several benchmark examples.

  20. Conservation laws of inviscid Burgers equation with nonlinear damping

    NASA Astrophysics Data System (ADS)

    Abdulwahhab, Muhammad Alim

    2014-06-01

    In this paper, the new conservation theorem presented in Ibragimov (2007) [14] is used to find conservation laws of the inviscid Burgers equation with nonlinear damping ut+g(u)ux+λh(u)=0. We show that this equation is both quasi self-adjoint and self-adjoint, and use these concepts to simplify conserved quantities for various choices of g(u) and h(u).

  1. Intermittency and solitons in the driven dissipative nonlinear Schroedinger equation

    NASA Technical Reports Server (NTRS)

    Moon, H. T.; Goldman, M. V.

    1984-01-01

    The cubic nonlinear Schroedinger equation, in the presence of driving and Landau damping, is studied numerically. As the pump intensity is increased, the system exhibits a transition from intermittency to a two-torus to chaos. The laminar phase of the intermittency is also a two-torus motion which corresponds in physical space to two identical solitons of amplitude determined by a power-balance equation.

  2. Optimization of a finite difference method for nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Chen, Miaochao

    2013-07-01

    Wave equations have important fluid dynamics background, which are extensively used in many fields, such as aviation, meteorology, maritime, water conservancy, etc. This paper is devoted to the explicit difference method for nonlinear wave equations. Firstly, a three-level and explicit difference scheme is derived. It is shown that the explicit difference scheme is uniquely solvable and convergent. Moreover, a numerical experiment is conducted to illustrate the theoretical results of the presented method.

  3. Maximum Likelihood Estimation of Nonlinear Structural Equation Models.

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Zhu, Hong-Tu

    2002-01-01

    Developed an EM type algorithm for maximum likelihood estimation of a general nonlinear structural equation model in which the E-step is completed by a Metropolis-Hastings algorithm. Illustrated the methodology with results from a simulation study and two real examples using data from previous studies. (SLD)

  4. Model Comparison of Nonlinear Structural Equation Models with Fixed Covariates.

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Song, Xin-Yuan

    2003-01-01

    Proposed a new nonlinear structural equation model with fixed covariates to deal with some complicated substantive theory and developed a Bayesian path sampling procedure for model comparison. Illustrated the approach with an illustrative example using data from an international study. (SLD)

  5. Local Influence Analysis of Nonlinear Structural Equation Models

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Tang, Nian-Sheng

    2004-01-01

    By regarding the latent random vectors as hypothetical missing data and based on the conditional expectation of the complete-data log-likelihood function in the EM algorithm, we investigate assessment of local influence of various perturbation schemes in a nonlinear structural equation model. The basic building blocks of local influence analysis…

  6. Topological horseshoes in travelling waves of discretized nonlinear wave equations

    SciTech Connect

    Chen, Yi-Chiuan; Chen, Shyan-Shiou; Yuan, Juan-Ming

    2014-04-15

    Applying the concept of anti-integrable limit to coupled map lattices originated from space-time discretized nonlinear wave equations, we show that there exist topological horseshoes in the phase space formed by the initial states of travelling wave solutions. In particular, the coupled map lattices display spatio-temporal chaos on the horseshoes.

  7. Tensor methods for large sparse systems of nonlinear equations

    SciTech Connect

    Bouaricha, A.; Schnabel, R.B.

    1996-12-31

    This paper introduces censor methods for solving, large sparse systems of nonlinear equations. Tensor methods for nonlinear equations were developed in the context of solving small to medium- sized dense problems. They base each iteration on a quadratic model of the nonlinear equations. where the second-order term is selected so that the model requires no more derivative or function information per iteration than standard linear model-based methods, and hardly more storage or arithmetic operations per iteration. Computational experiments on small to medium-sized problems have shown censor methods to be considerably more efficient than standard Newton-based methods, with a particularly large advantage on singular problems. This paper considers the extension of this approach to solve large sparse problems. The key issue that must be considered is how to make efficient use of sparsity in forming and solving the censor model problem at each iteration. Accomplishing this turns out to require an entirely new way of solving the tensor model that successfully exploits the sparsity of the Jacobian, whether the Jacobian is nonsingular or singular. We develop such an approach and, based upon it, an efficient tensor method for solving large sparse systems of nonlinear equations. Test results indicate that this tensor method is significantly more efficient and robust than an efficient sparse Newton-based method. in terms of iterations, function evaluations. and execution time.

  8. Bounded and periodic solutions of nonlinear functional differential equations

    SciTech Connect

    Slyusarchuk, Vasilii E

    2012-05-31

    Conditions for the existence of bounded and periodic solutions of the nonlinear functional differential equation d{sup m}x(t)/dt{sup m} + (Fx)(t) = h(t), t element of R, are presented, involving local linear approximations to the operator F. Bibliography: 23 titles.

  9. Painleve analysis for a nonlinear Schroedinger equation in three dimensions

    SciTech Connect

    Chowdhury, A.R.; Chanda, P.K.

    1987-09-01

    A Painleve analysis is performed for the nonlinear Schroedinger equation in (2 + 1) dimensions following the methodology of Weiss et al. simplified in the sense of Kruskal. At least for one branch it is found that the required number of arbitrary functions (as demanded by the Cauchy-Kovalevskaya theorem) exists, signalling complete integrability.

  10. An Efficient Numerical Approach for Nonlinear Fokker-Planck equations

    NASA Astrophysics Data System (ADS)

    Otten, Dustin; Vedula, Prakash

    2009-03-01

    Fokker-Planck equations which are nonlinear with respect to their probability densities that occur in many nonequilibrium systems relevant to mean field interaction models, plasmas, classical fermions and bosons can be challenging to solve numerically. To address some underlying challenges in obtaining numerical solutions, we propose a quadrature based moment method for efficient and accurate determination of transient (and stationary) solutions of nonlinear Fokker-Planck equations. In this approach the distribution function is represented as a collection of Dirac delta functions with corresponding quadrature weights and locations, that are in turn determined from constraints based on evolution of generalized moments. Properties of the distribution function can be obtained by solution of transport equations for quadrature weights and locations. We will apply this computational approach to study a wide range of problems, including the Desai-Zwanzig Model (for nonlinear muscular contraction) and multivariate nonlinear Fokker-Planck equations describing classical fermions and bosons, and will also demonstrate good agreement with results obtained from Monte Carlo and other standard numerical methods.

  11. Forced oscillations of nonlinear damped equation of suspended string

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Masaru; Nagai, Tohru; Matsukane, Katsuya

    2008-06-01

    We shall study the existence of time-periodic solutions of nonlinear damped equation of suspended string to which a periodic nonlinear force works. We shall be conterned with weak, strong and classical time-periodic solutions and also the regularity of the solutions. To formulate our results, we shall take suitable weighted Sobolev-type spaces introduced by [M. Yamaguchi, Almost periodic oscillations of suspended string under quasiperiodic linear force, J. Math. Anal. Appl. 303 (2) (2005) 643-660; M. Yamaguchi, Infinitely many time-periodic solutions of nonlinear equation of suspended string, Funkcial. Ekvac., in press]. We shall study properties of the function spaces and show inequalities on the function spaces. To show our results we shall apply the Schauder fixed point theorem and the fixed point continuation theorem in the function spaces.

  12. Predicting stabilizing mutations in proteins using Poisson-Boltzmann based models: study of unfolded state ensemble models and development of a successful binary classifier based on residue interaction energies.

    PubMed

    Estrada, Jorge; Echenique, Pablo; Sancho, Javier

    2015-12-14

    In many cases the stability of a protein has to be increased to permit its biotechnological use. Rational methods of protein stabilization based on optimizing electrostatic interactions have provided some fine successful predictions. However, the precise calculation of stabilization energies remains challenging, one reason being that the electrostatic effects on the unfolded state are often neglected. We have explored here the feasibility of incorporating Poisson-Boltzmann model electrostatic calculations performed on representations of the unfolded state as large ensembles of geometrically optimized conformations calculated using the ProtSA server. Using a data set of 80 electrostatic mutations experimentally tested in two-state proteins, the predictive performance of several such models has been compared to that of a simple one that considers an unfolded structure of non-interacting residues. The unfolded ensemble models, while showing correlation between the predicted stabilization values and the experimental ones, are worse than the simple model, suggesting that the ensembles do not capture well the energetics of the unfolded state. A more attainable goal is classifying potential mutations as either stabilizing or non-stabilizing, rather than accurately calculating their stabilization energies. To implement a fast classification method that can assist in selecting stabilizing mutations, we have used a much simpler electrostatic model based only on the native structure and have determined its precision using different stabilizing energy thresholds. The binary classifier developed finds 7 true stabilizing mutants out of every 10 proposed candidates and can be used as a robust tool to propose stabilizing mutations. PMID:26530878

  13. Optimal analytic method for the nonlinear Hasegawa-Mima equation

    NASA Astrophysics Data System (ADS)

    Baxter, Mathew; Van Gorder, Robert A.; Vajravelu, Kuppalapalle

    2014-05-01

    The Hasegawa-Mima equation is a nonlinear partial differential equation that describes the electric potential due to a drift wave in a plasma. In the present paper, we apply the method of homotopy analysis to a slightly more general Hasegawa-Mima equation, which accounts for hyper-viscous damping or viscous dissipation. First, we outline the method for the general initial/boundary value problem over a compact rectangular spatial domain. We use a two-stage method, where both the convergence control parameter and the auxiliary linear operator are optimally selected to minimize the residual error due to the approximation. To do the latter, we consider a family of operators parameterized by a constant which gives the decay rate of the solutions. After outlining the general method, we consider a number of concrete examples in order to demonstrate the utility of this approach. The results enable us to study properties of the initial/boundary value problem for the generalized Hasegawa-Mima equation. In several cases considered, we are able to obtain solutions with extremely small residual errors after relatively few iterations are computed (residual errors on the order of 10-15 are found in multiple cases after only three iterations). The results demonstrate that selecting a parameterized auxiliary linear operator can be extremely useful for minimizing residual errors when used concurrently with the optimal homotopy analysis method, suggesting that this approach can prove useful for a number of nonlinear partial differential equations arising in physics and nonlinear mechanics.

  14. Some mathematical aspects of the correspondence between the generalized nonlinear Schroedinger equation and the generalized Korteweg-de Vries equation

    SciTech Connect

    Fedele, Renato; De Nicola, Sergio; Grecu, Dan; Visinescu, Anca; Shukla, Padma K.

    2009-11-10

    A review of the recent studies on the correspondence between a wide family of the generalized nonlinear Schroedinger equations and a wide family of the generalized Korteweg-de Vries equations is presented. It was constructed some years ago within the framework of a recently-developed approach based on the Madelung's fluid representation of the generalized nonlinear Schroedinger equation. The present analysis extends the former approach, developed for nonlinear Schroedinger equation with a nonlinear term proportional to a multiplicative operator, to the cases of derivative operators and the ones corresponding to cylindrical nonlinear Schroedinger equations.

  15. Shock-wave structure using nonlinear model Boltzmann equations.

    NASA Technical Reports Server (NTRS)

    Segal, B. M.; Ferziger, J. H.

    1972-01-01

    The structure of strong plane shock waves in a perfect monatomic gas was studied using four nonlinear models of the Boltzmann equation. The models involved the use of a simplified collision operator with velocity-independent collision frequency, in place of the complicated Boltzmann collision operator. The models employed were the BGK and ellipsoidal models developed by earlier authors, and the polynomial and trimodal gain function models developed during the work. An exact set of moment equations was derived for the density, velocity, temperature, viscous stress, and heat flux within the shock. This set was reduced to a pair of coupled nonlinear integral equations and solved using specially adapted numerical techniques. A new and simple Gauss-Seidel iteration was developed during the work and found to be as efficient as the best earlier iteration methods.

  16. Transformation matrices between non-linear and linear differential equations

    NASA Technical Reports Server (NTRS)

    Sartain, R. L.

    1983-01-01

    In the linearization of systems of non-linear differential equations, those systems which can be exactly transformed into the second order linear differential equation Y"-AY'-BY=0 where Y, Y', and Y" are n x 1 vectors and A and B are constant n x n matrices of real numbers were considered. The 2n x 2n matrix was used to transform the above matrix equation into the first order matrix equation X' = MX. Specially the matrix M and the conditions which will diagonalize or triangularize M were studied. Transformation matrices P and P sub -1 were used to accomplish this diagonalization or triangularization to return to the solution of the second order matrix differential equation system from the first order system.

  17. Phase space lattices and integrable nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Tracy, Eugene; Zobin, Nahum

    2003-10-01

    Nonlinear wave equations in fluids and plasmas that are integrable by Inverse Scattering Theory (IST), such as the Korteweg-deVries and nonlinear Schrodinger equations, are known to be infinite-dimensional Hamiltonian systems [1]. These are of interest physically because they predict new phenomena not present in linear wave theories, such as solitons and rogue waves. The IST method provides solutions of these equations in terms of a special class of functions called Riemann theta functions. The usual approach to the theory of theta functions tends to obscure the underlying phase space structure. A theory due to Mumford and Igusa [2], however shows that the theta functions arise naturally in the study of phase space lattices. We will describe this theory, as well as potential applications to nonlinear signal processing and the statistical theory of nonlinear waves. 1] , S. Novikov, S. V. Manakov, L. P. Pitaevskii and V. E. Zakharov, Theory of solitons: the inverse scattering method (Consultants Bureau, New York, 1984). 2] D. Mumford, Tata lectures on theta, Vols. I-III (Birkhauser); J. Igusa, Theta functions (Springer-Verlag, New York, 1972).

  18. An adaptive grid algorithm for one-dimensional nonlinear equations

    NASA Technical Reports Server (NTRS)

    Gutierrez, William E.; Hills, Richard G.

    1990-01-01

    Richards' equation, which models the flow of liquid through unsaturated porous media, is highly nonlinear and difficult to solve. Step gradients in the field variables require the use of fine grids and small time step sizes. The numerical instabilities caused by the nonlinearities often require the use of iterative methods such as Picard or Newton interation. These difficulties result in large CPU requirements in solving Richards equation. With this in mind, adaptive and multigrid methods are investigated for use with nonlinear equations such as Richards' equation. Attention is focused on one-dimensional transient problems. To investigate the use of multigrid and adaptive grid methods, a series of problems are studied. First, a multigrid program is developed and used to solve an ordinary differential equation, demonstrating the efficiency with which low and high frequency errors are smoothed out. The multigrid algorithm and an adaptive grid algorithm is used to solve one-dimensional transient partial differential equations, such as the diffusive and convective-diffusion equations. The performance of these programs are compared to that of the Gauss-Seidel and tridiagonal methods. The adaptive and multigrid schemes outperformed the Gauss-Seidel algorithm, but were not as fast as the tridiagonal method. The adaptive grid scheme solved the problems slightly faster than the multigrid method. To solve nonlinear problems, Picard iterations are introduced into the adaptive grid and tridiagonal methods. Burgers' equation is used as a test problem for the two algorithms. Both methods obtain solutions of comparable accuracy for similar time increments. For the Burgers' equation, the adaptive grid method finds the solution approximately three times faster than the tridiagonal method. Finally, both schemes are used to solve the water content formulation of the Richards' equation. For this problem, the adaptive grid method obtains a more accurate solution in fewer work units and

  19. Travelling Waves for the Nonlinear Schrödinger Equation with General Nonlinearity in Dimension Two

    NASA Astrophysics Data System (ADS)

    Chiron, David; Scheid, Claire

    2016-02-01

    We investigate numerically the two-dimensional travelling waves of the nonlinear Schrödinger equation for a general nonlinearity and with nonzero condition at infinity. In particular, we are interested in the energy-momentum diagrams. We propose a numerical strategy based on the variational structure of the equation. The key point is to characterize the saddle points of the action as minimizers of another functional that allows us to use a gradient flow. We combine this approach with a continuation method in speed in order to obtain the full range of velocities. Through various examples, we show that even though the nonlinearity has the same behaviour as the well-known Gross-Pitaevskii nonlinearity, the qualitative properties of the travelling waves may be extremely different. For instance, we observe cusps, a modified KP-I asymptotic in the transonic limit, various multiplicity results and "one-dimensional spreading" phenomena.

  20. Dielectric Decrement Effects on Nonlinear Electrophoresis of Ideally Polarizable Particles

    NASA Astrophysics Data System (ADS)

    Moran, Jeffrey L.; Chan, Wai Hong Ronald; Buie, Cullen R.; Figliuzzi, Bruno

    2014-11-01

    We present numerical simulations of nonlinear electrophoresis of ideally polarizable particles that specifically include the effects of a spatially non-uniform dielectric permittivity near the particle surface. Models for this dielectric decrement phenomenon have been developed by several authors, including Ben-Yaakov et al. [J. Phys.: Condens. Matter 2009] Hatlo et al. [EPL 2012], and Zhao & Zhai [JFM 2013]. We extend this work to ideally polarizable particles and include the effects of surface conduction and advective transport in the electric double layer. By numerically solving for the coupled velocity field, electric potential, and ionic concentration distributions in the bulk solution surrounding the particle, we demonstrate that the dielectric decrement model predicts ionic saturation around the particle and thus physical implications that resemble those resulting from the steric model developed by Kilic et al. [PRE 2007], albeit with differences that reflect the nonlinearity of the modified Poisson-Boltzmann equation. In addition, we develop a generalized condensed layer model that approximates both the steric and dielectric decrement models in the limits of strong electric fields and negligible surface conduction to obtain more physical insights into these models. We demonstrate that the mobility in both models asymptotically scales as the square root of the electric field at high fields, recovering the result of Bazant et al. [Adv. Colloid Interface Sci. 2009].

  1. Recent extensions to the OMNI language to allow nonlinear equation and an interface to a nonlinear solver

    SciTech Connect

    Golush, W.G.

    1994-12-31

    Nonlinear equations are expressed using a new OMNI statement FORM NLE. This allows OMNI Constructs, Classes, Tables, and New Variables to be used in nonlinear equations. The interface passes the nonlinear equations and symbolic derivatives to a general nonlinear solver. After optimization, the row and column activities of the solution are written to an OMNI Standard Solution File. Reports are written from this file using the OMNI FORM LINE report writer. The interface will be illustrated with an example of a nonlinear model written in OMNI and solved using the MINOS nonlinear solver.

  2. Multi-soliton rational solutions for some nonlinear evolution equations

    NASA Astrophysics Data System (ADS)

    Osman, Mohamed S.

    2016-01-01

    The Korteweg-de Vries equation (KdV) and the (2+ 1)-dimensional Nizhnik-Novikov-Veselov system (NNV) are presented. Multi-soliton rational solutions of these equations are obtained via the generalized unified method. The analysis emphasizes the power of this method and its capability of handling completely (or partially) integrable equations. Compared with Hirota's method and the inverse scattering method, the proposed method gives more general exact multi-wave solutions without much additional effort. The results show that, by virtue of symbolic computation, the generalized unified method may provide us with a straightforward and effective mathematical tool for seeking multi-soliton rational solutions for solving many nonlinear evolution equations arising in different branches of sciences.

  3. Numerical solution of control problems governed by nonlinear differential equations

    SciTech Connect

    Heinkenschloss, M.

    1994-12-31

    In this presentation the author investigates an iterative method for the solution of optimal control problems. These problems are formulated as constrained optimization problems with constraints arising from the state equation and in the form of bound constraints on the control. The method for the solution of these problems uses the special structure of the problem arising from the bound constraint and the state equation. It is derived from SQP methods and projected Newton methods and combines the advantages of both methods. The bound constraint is satisfied by all iterates using a projection, the nonlinear state equation is satisfied in the limit. Only a linearized state equation has to be solved in every iteration. The solution of the linearized problems are done using multilevel methods and GMRES.

  4. Modified non-linear Burgers' equations and cosmic ray shocks

    NASA Technical Reports Server (NTRS)

    Zank, G. P.; Webb, G. M.; Mckenzie, J. F.

    1988-01-01

    A reductive perturbation scheme is used to derive a generalized non-linear Burgers' equation, which includes the effects of dispersion, in the long wavelength regime for the two-fluid hydrodynamical model used to describe cosmic ray acceleration by the first-order Fermi process in astrophysical shocks. The generalized Burger's equation is derived for both relativistic and non-relativistic cosmic ray shocks, and describes the time evolution of weak shocks in the theory of diffusive shock acceleration. The inclusion of dispersive effects modifies the phase velocity of the shock obtained from the lower order non-linear Burger's equation through the introduction of higher order terms from the long wavelength dispersion equation. The travelling wave solution of the generalized Burgers' equation for a single shock shows that larger cosmic ray pressures result in broader shock transitions. The results for relativistic shocks show a steepening of the shock as the shock speed approaches the relativistic cosmic ray sound speed. The dependence of the shock speed on the cosmic ray pressure is also discussed.

  5. Solving nonlinear evolution equation system using two different methods

    NASA Astrophysics Data System (ADS)

    Kaplan, Melike; Bekir, Ahmet; Ozer, Mehmet N.

    2015-12-01

    This paper deals with constructing more general exact solutions of the coupled Higgs equation by using the (G0/G, 1/G)-expansion and (1/G0)-expansion methods. The obtained solutions are expressed by three types of functions: hyperbolic, trigonometric and rational functions with free parameters. It has been shown that the suggested methods are productive and will be used to solve nonlinear partial differential equations in applied mathematics and engineering. Throughout the paper, all the calculations are made with the aid of the Maple software.

  6. Numerical study of fractional nonlinear Schrödinger equations.

    PubMed

    Klein, Christian; Sparber, Christof; Markowich, Peter

    2014-12-01

    Using a Fourier spectral method, we provide a detailed numerical investigation of dispersive Schrödinger-type equations involving a fractional Laplacian in an one-dimensional case. By an appropriate choice of the dispersive exponent, both mass and energy sub- and supercritical regimes can be identified. This allows us to study the possibility of finite time blow-up versus global existence, the nature of the blow-up, the stability and instability of nonlinear ground states and the long-time dynamics of solutions. The latter is also studied in a semiclassical setting. Moreover, we numerically construct ground state solutions of the fractional nonlinear Schrödinger equation. PMID:25484604

  7. Quadratic nonlinear Klein-Gordon equation in one dimension

    NASA Astrophysics Data System (ADS)

    Hayashi, Nakao; Naumkin, Pavel I.

    2012-10-01

    We study the initial value problem for the quadratic nonlinear Klein-Gordon equation vtt + v - vxx = λv2, t ∈ R, x ∈ R, with initial conditions v(0, x) = v0(x), vt(0, x) = v1(x), x ∈ R, where v0 and v1 are real-valued functions, λ ∈ R. Using the method of normal forms of Shatah ["Normal forms and quadratic nonlinear Klein-Gordon equations," Commun. Pure Appl. Math. 38, 685-696 (1985)], we obtain a sharp asymptotic behavior of small solutions without the condition of a compact support on the initial data, which was assumed in the previous work of J.-M. Delort ["Existence globale et comportement asymptotique pour l'équation de Klein-Gordon quasi-linéaire á données petites en dimension 1," Ann. Sci. Ec. Normale Super. 34(4), 1-61 (2001)].

  8. Numerical study of fractional nonlinear Schrödinger equations

    PubMed Central

    Klein, Christian; Sparber, Christof; Markowich, Peter

    2014-01-01

    Using a Fourier spectral method, we provide a detailed numerical investigation of dispersive Schrödinger-type equations involving a fractional Laplacian in an one-dimensional case. By an appropriate choice of the dispersive exponent, both mass and energy sub- and supercritical regimes can be identified. This allows us to study the possibility of finite time blow-up versus global existence, the nature of the blow-up, the stability and instability of nonlinear ground states and the long-time dynamics of solutions. The latter is also studied in a semiclassical setting. Moreover, we numerically construct ground state solutions of the fractional nonlinear Schrödinger equation. PMID:25484604

  9. Unitary qubit extremely parallelized algorithms for coupled nonlinear Schrodinger equations

    NASA Astrophysics Data System (ADS)

    Oganesov, Armen; Flint, Chris; Vahala, George; Vahala, Linda; Yepez, Jeffrey; Soe, Min

    2015-11-01

    The nonlinear Schrodinger equation (NLS) is a ubiquitous equation occurring in plasma physics, nonlinear optics and in Bose Einstein condensates. Viewed from the BEC standpoint of phase transitions, the wave function is the order parameter and topological defects in that manifold are simply the vortices, which for a scalar NLS have quantized circulation. In multi-species NLS the topological nature of the vortices are radically different with some classes of vortices no longer having quantized circulation as in classical turbulence. Moreover, some of the vortex equivalence classes need no longer be Abelian. This strongly effects the permitted vortex reconnections. The effect of these structures on the spectral properties of the ensuing turbulence will be investigated. Our 3D algorithm is based on a novel unitary qubit lattice scheme that is ideally parallelized - tested up to 780 000 cores on Mira. This scheme is mesoscopic (like lattice Boltzmann), but fully unitary (unlike LB). Supported by NSF, DoD.

  10. Parallel iterative methods for sparse linear and nonlinear equations

    NASA Technical Reports Server (NTRS)

    Saad, Youcef

    1989-01-01

    As three-dimensional models are gaining importance, iterative methods will become almost mandatory. Among these, preconditioned Krylov subspace methods have been viewed as the most efficient and reliable, when solving linear as well as nonlinear systems of equations. There has been several different approaches taken to adapt iterative methods for supercomputers. Some of these approaches are discussed and the methods that deal more specifically with general unstructured sparse matrices, such as those arising from finite element methods, are emphasized.

  11. Fast neural solution of a nonlinear wave equation

    NASA Technical Reports Server (NTRS)

    Toomarian, Nikzad; Barhen, Jacob

    1992-01-01

    A neural algorithm for rapidly simulating a certain class of nonlinear wave phenomena using analog VLSI neural hardware is presented and applied to the Korteweg-de Vries partial differential equation. The corresponding neural architecture is obtained from a pseudospectral representation of the spatial dependence, along with a leap-frog scheme for the temporal evolution. Numerical simulations demonstrated the robustness of the proposed approach.

  12. Approximate solutions for non-linear iterative fractional differential equations

    NASA Astrophysics Data System (ADS)

    Damag, Faten H.; Kiliçman, Adem; Ibrahim, Rabha W.

    2016-06-01

    This paper establishes approximate solution for non-linear iterative fractional differential equations: d/γv (s ) d sγ =ℵ (s ,v ,v (v )), where γ ∈ (0, 1], s ∈ I := [0, 1]. Our method is based on some convergence tools for analytic solution in a connected region. We show that the suggested solution is unique and convergent by some well known geometric functions.

  13. Inhomogeneous critical nonlinear Schroedinger equations with a harmonic potential

    SciTech Connect

    Cao Daomin; Han Pigong

    2010-04-15

    In this paper, we study the Cauchy problem of the inhomogeneous nonlinear Schroedinger equation with a harmonic potential: i{partial_derivative}{sub t}u=-div(f(x){nabla}u)+|x|{sup 2}u-k(x)|u|{sup 4/N}u, x is an element of R{sup N}, N{>=}1, which models the remarkable Bose-Einstein condensation. We discuss the existence and nonexistence results and investigate the limiting profile of blow-up solutions with critical mass.

  14. Nonlinear Generalized Hydrodynamic Wave Equations in Strongly Coupled Dusty Plasmas

    SciTech Connect

    Veeresha, B. M.; Sen, A.; Kaw, P. K.

    2008-09-07

    A set of nonlinear equations for the study of low frequency waves in a strongly coupled dusty plasma medium is derived using the phenomenological generalized hydrodynamic (GH) model and is used to study the modulational stability of dust acoustic waves to parallel perturbations. Dust compressibility contributions arising from strong Coulomb coupling effects are found to introduce significant modifications in the threshold and range of the instability domain.

  15. Symmetries and reductions of order for certain nonlinear third- and second-order differential equations with arbitrary nonlinearity

    NASA Astrophysics Data System (ADS)

    Tamizhmani, K. M.; Krishnakumar, K.; Leach, P. G. L.

    2015-11-01

    We examine the reductions of the order of certain third- and second-order nonlinear equations with arbitrary nonlinearity through their symmetries and some appropriate transformations. We use the folding transformation which enables one to change from a nonlinearity with an arbitrary exponent to a nonlinearity with a specific numerical exponent.

  16. Improved algorithm for solving nonlinear parabolized stability equations

    NASA Astrophysics Data System (ADS)

    Zhao, Lei; Zhang, Cun-bo; Liu, Jian-xin; Luo, Ji-sheng

    2016-08-01

    Due to its high computational efficiency and ability to consider nonparallel and nonlinear effects, nonlinear parabolized stability equations (NPSE) approach has been widely used to study the stability and transition mechanisms. However, it often diverges in hypersonic boundary layers when the amplitude of disturbance reaches a certain level. In this study, an improved algorithm for solving NPSE is developed. In this algorithm, the mean flow distortion is included into the linear operator instead of into the nonlinear forcing terms in NPSE. An under-relaxation factor for computing the nonlinear terms is introduced during the iteration process to guarantee the robustness of the algorithm. Two case studies, the nonlinear development of stationary crossflow vortices and the fundamental resonance of the second mode disturbance in hypersonic boundary layers, are presented to validate the proposed algorithm for NPSE. Results from direct numerical simulation (DNS) are regarded as the baseline for comparison. Good agreement can be found between the proposed algorithm and DNS, which indicates the great potential of the proposed method on studying the crossflow and streamwise instability in hypersonic boundary layers. Project supported by the National Natural Science Foundation of China (Grant Nos. 11332007 and 11402167).

  17. Rogue wave solutions for a generalized nonautonomous nonlinear equation in a nonlinear inhomogeneous fiber

    NASA Astrophysics Data System (ADS)

    Xie, Xi-Yang; Tian, Bo; Wang, Yu-Feng; Sun, Ya; Jiang, Yan

    2015-11-01

    In this paper, we investigate a generalized nonautonomous nonlinear equation which describes the ultrashort optical pulse propagating in a nonlinear inhomogeneous fiber. By virtue of the generalized Darboux transformation, the first- and second-order rogue-wave solutions for the generalized nonautonomous nonlinear equation are obtained, under some variable-coefficient constraints. Properties of the first- and second-order rogue waves are graphically presented and analyzed: When the coefficients are all chosen as the constants, we can observe the some functions, the shapes of wave crests and troughs for the first- and second-order rogue waves change. Oscillating behaviors of the first- and second-order rogue waves are observed when the coefficients are the trigonometric functions.

  18. Nonlinear electromagnetic gyrokinetic equations for rotating axisymmetric plasmas

    SciTech Connect

    Artun, M.; Tang, W.M.

    1994-03-01

    The influence of sheared equilibrium flows on the confinement properties of tokamak plasmas is a topic of much current interest. A proper theoretical foundation for the systematic kinetic analysis of this important problem has been provided here by presented the derivation of a set of nonlinear electromagnetic gyrokinetic equations applicable to low frequency microinstabilities in a rotating axisymmetric plasma. The subsonic rotation velocity considered is in the direction of symmetry with the angular rotation frequency being a function of the equilibrium magnetic flux surface. In accordance with experimental observations, the rotation profile is chosen to scale with the ion temperature. The results obtained represent the shear flow generalization of the earlier analysis by Frieman and Chen where such flows were not taken into account. In order to make it readily applicable to gyrokinetic particle simulations, this set of equations is cast in a phase-space-conserving continuity equation form.

  19. Equations for Nonlinear MHD Convection in Shearless Magnetic Systems

    SciTech Connect

    Pastukhov, V.P.

    2005-07-15

    A closed set of reduced dynamic equations is derived that describe nonlinear low-frequency flute MHD convection and resulting nondiffusive transport processes in weakly dissipative plasmas with closed or open magnetic field lines. The equations obtained make it possible to self-consistently simulate transport processes and the establishment of the self-consistent plasma temperature and density profiles for a large class of axisymmetric nonparaxial shearless magnetic devices: levitated dipole configurations, mirror systems, compact tori, etc. Reduced equations that are suitable for modeling the long-term evolution of the plasma on time scales comparable to the plasma lifetime are derived by the method of the adiabatic separation of fast and slow motions.

  20. Multipulses of Nonlinearly Coupled Schrödinger Equations

    NASA Astrophysics Data System (ADS)

    Yew, Alice C.

    2001-06-01

    The capacity of coupled nonlinear Schrödinger (NLS) equations to support multipulse solutions (multibump solitary-waves) is investigated. A detailed analysis is undertaken for a system of quadratically coupled equations that describe the phenomena of second harmonic generation and parametric wave interaction in non-centrosymmetric optical materials. Utilising the framework of homoclinic bifurcation theory, and employing a Lyapunov-Schmidt reduction method developed by Hale, Lin, and Sandstede, a novel mechanism for the generation of multipulses is identified, which arises from a resonant semi-simple eigenvalue configuration of the linearised steady-state equations. Conditions for the existence of multipulses, as well as a description of their geometry, are derived from the analysis.

  1. Simulation of nonlinear Westervelt equation for the investigation of acoustic streaming and nonlinear propagation effects.

    PubMed

    Solovchuk, Maxim; Sheu, Tony W H; Thiriet, Marc

    2013-11-01

    This study investigates the influence of blood flow on temperature distribution during high-intensity focused ultrasound (HIFU) ablation of liver tumors. A three-dimensional acoustic-thermal-hydrodynamic coupling model is developed to compute the temperature field in the hepatic cancerous region. The model is based on the nonlinear Westervelt equation, bioheat equations for the perfused tissue and blood flow domains. The nonlinear Navier-Stokes equations are employed to describe the flow in large blood vessels. The effect of acoustic streaming is also taken into account in the present HIFU simulation study. A simulation of the Westervelt equation requires a prohibitively large amount of computer resources. Therefore a sixth-order accurate acoustic scheme in three-point stencil was developed for effectively solving the nonlinear wave equation. Results show that focused ultrasound beam with the peak intensity 2470 W/cm(2) can induce acoustic streaming velocities up to 75 cm/s in the vessel with a diameter of 3 mm. The predicted temperature difference for the cases considered with and without acoustic streaming effect is 13.5 °C or 81% on the blood vessel wall for the vein. Tumor necrosis was studied in a region close to major vessels. The theoretical feasibility to safely necrotize the tumors close to major hepatic arteries and veins was shown. PMID:24180802

  2. The method of patches for solving stiff nonlinear differential equations

    NASA Astrophysics Data System (ADS)

    Brydon, David Van George, Jr.

    1998-12-01

    This dissertation describes a new method for solving very stiff sets of ordinary differential equations. The basic idea is to replace the original nonlinear equations with a set of equally stiff equations that are piecewise linear, and therefore can be solved exactly. We demonstrate the value of the method on small systems of equations for which some other methods are inefficient or produce spurious solutions, estimate error bounds, and discuss extensions of the method to larger systems of equations and to partial differential equations. Putzer's method is developed in a novel way for efficient and accurate solution of dx/dt = Ax+b. The physical problem of interest is spatial pattern formation in open reaction-diffusion chemical systems, as studied in the experiments of Kyoung Lee, Harry Swinney, et al. I develop a new experiment model that agrees reasonably well with experimental results. I solve the model, applying the new method to the two-variable Gaspar- Showalter chemical kinetics in two space dimensions. Because of time and computer limitations, only preliminary pattern-formation results are achieved and reported.

  3. The truncation model of the derivative nonlinear Schroedinger equation

    SciTech Connect

    Sanchez-Arriaga, G.; Hada, T.; Nariyuki, Y.

    2009-04-15

    The derivative nonlinear Schroedinger (DNLS) equation is explored using a truncation model with three resonant traveling waves. In the conservative case, the system derives from a time-independent Hamiltonian function with only one degree of freedom and the solutions can be written using elliptic functions. In spite of its low dimensional order, the truncation model preserves some features from the DNLS equation. In particular, the modulational instability criterion fits with the existence of two hyperbolic fixed points joined by a heteroclinic orbit that forces the exchange of energy between the three waves. On the other hand, numerical integrations of the DNLS equation show that the truncation model fails when wave energy is increased or left-hand polarized modulational unstable modes are present. When dissipative and growth terms are added the system exhibits a very complex dynamics including appearance of several attractors, period doubling bifurcations leading to chaos as well as other nonlinear phenomenon. In this case, the validity of the truncation model depends on the strength of the dissipation and the kind of attractor investigated.

  4. Theoretical and numerical studies of nonlinear shell equations

    NASA Astrophysics Data System (ADS)

    Hermann, M.; Kaiser, D.; Schröder, M.

    1999-07-01

    We study the solution field M of a parameter dependent nonlinear two-point boundary value problem presented by Troger and Steindl [H. Troger, A. Steindl, Nonlinear Stability and Bifurcation Theory, Springer, Wien, New York, 1991]. This problem models the buckling of a thin-walled spherical shell under a uniform external static pressure. The boundary value problem is formulated as an abstract operator equation T( x, λ)=0 in appropriate Banach spaces. By exploiting the equivariance of T, we obtain detailed informations about the structure of M. These theoretical results are used to compute efficiently interesting parts of M with numerical standard techniques. Bifurcation diagrams, a stability diagram and pictures of deformed shells are presented.

  5. On the nonlinear Schrodinger equation with nonzero boundary conditions

    NASA Astrophysics Data System (ADS)

    Fagerstrom, Emily

    This thesis is concerned with the study of the nonlinear Schrodinger (NLS) equation, which is important both from a physical and a mathematical point of view. In physics, it is a universal model for the evolutions of weakly nonlinear dispersive wave trains. As such it appears in many physical contexts, such as optics, acoustics, plasmas, biology, etc. Mathematically, it is a completely integrable, infinite-dimensional Hamiltonian system, and possesses a surprisingly rich structure. This equation has been extensively studied in the last 50 years, but many important questions are still open. In particular, this thesis contains the following original contributions: NLS with real spectral singularities. First, the focusing NLS equation is considered with decaying initial conditions. This situation has been studied extensively before, but the assumption is almost always made that the scattering coefficients have no real zeros, and thus the scattering data had no poles on the real axis. However, it is easy to produce example potentials with this behavior. For example, by modifying parameters in Satsuma-Yajima's sech potential, or by choosing a "box" potential with a particular area, one can obtain corresponding scattering entries with real zeros. The inverse scattering transform can be implemented by formulating the modified Jost eigenfunctions and the scattering data as a Riemann Hilbert problem. But it can also be formulated by using integral kernels. Doing so produces the Gelf'and-Levitan-Marchenko (GLM) equations. Solving these integral equations requires integrating an expression containing the reflection coefficient over the real axis. Under the usual assumption, the reflection coefficient has no poles on the real axis. In general, the integration contour cannot be deformed to avoid poles, because the reflection coefficient may not admit analytic extension off the real axis. Here it is shown that the GLM equations may be (uniquely) solved using a principal value

  6. Pseudorecurrence and chaos of cubic-quintic nonlinear Schroedinger equation

    SciTech Connect

    Zhou, C.; Lai, C.H.

    1996-12-01

    Recurrence, pseudorecurrence, and chaotic solutions for a continuum Hamiltonian system in which there exist spatial patterns of solitary wave structures are investigated using the nonlinear Schrodinger equation (NSE) with cubic and quintic terms. The theoretical analyses indicate that there may exist Birkhoff`s recurrence for the arbitrary parameter values. The numerical experiments show that there may be Fermi-Pasta-Ulam (FPU) recurrence, pseudorecurrence, and chaos when different initial conditions are chosen. The fact that the system energy is effectively shared by finite Fourier modes suggests that it may be possible to describe the continuum system in terms of some effective degrees of freedom.

  7. Vortex Solutions of the Defocusing Discrete Nonlinear Schroedinger Equation

    SciTech Connect

    Cuevas, J.; Kevrekidis, P. G.; Law, K. J. H.

    2009-09-09

    We consider the existence, stability and dynamical evolution of dark vortex states in the two-dimensional defocusing DNLS equation, a model of interest both to atomic physics and to nonlinear optics. Our considerations are chiefly based on initializing such vortex configurations at the anti-continuum limit of zero coupling between adjacent sites, and continuing them to finite values of the coupling. Discrete defocusing vortices become unstable past a critical coupling strength and, subsequently feature a cascade of alternating stabilization-destabilization windows for any finite lattice.

  8. Superposition of elliptic functions as solutions for a large number of nonlinear equations

    SciTech Connect

    Khare, Avinash; Saxena, Avadh

    2014-03-15

    For a large number of nonlinear equations, both discrete and continuum, we demonstrate a kind of linear superposition. We show that whenever a nonlinear equation admits solutions in terms of both Jacobi elliptic functions cn(x, m) and dn(x, m) with modulus m, then it also admits solutions in terms of their sum as well as difference. We have checked this in the case of several nonlinear equations such as the nonlinear Schrödinger equation, MKdV, a mixed KdV-MKdV system, a mixed quadratic-cubic nonlinear Schrödinger equation, the Ablowitz-Ladik equation, the saturable nonlinear Schrödinger equation, λϕ{sup 4}, the discrete MKdV as well as for several coupled field equations. Further, for a large number of nonlinear equations, we show that whenever a nonlinear equation admits a periodic solution in terms of dn{sup 2}(x, m), it also admits solutions in terms of dn {sup 2}(x,m)±√(m) cn (x,m) dn (x,m), even though cn(x, m)dn(x, m) is not a solution of these nonlinear equations. Finally, we also obtain superposed solutions of various forms for several coupled nonlinear equations.

  9. Stochastic Computational Approach for Complex Nonlinear Ordinary Differential Equations

    NASA Astrophysics Data System (ADS)

    Junaid, Ali Khan; Muhammad, Asif Zahoor Raja; Ijaz Mansoor, Qureshi

    2011-02-01

    We present an evolutionary computational approach for the solution of nonlinear ordinary differential equations (NLODEs). The mathematical modeling is performed by a feed-forward artificial neural network that defines an unsupervised error. The training of these networks is achieved by a hybrid intelligent algorithm, a combination of global search with genetic algorithm and local search by pattern search technique. The applicability of this approach ranges from single order NLODEs, to systems of coupled differential equations. We illustrate the method by solving a variety of model problems and present comparisons with solutions obtained by exact methods and classical numerical methods. The solution is provided on a continuous finite time interval unlike the other numerical techniques with comparable accuracy. With the advent of neuroprocessors and digital signal processors the method becomes particularly interesting due to the expected essential gains in the execution speed.

  10. Difference equation state approximations for nonlinear hereditary control problems

    NASA Technical Reports Server (NTRS)

    Rosen, I. G.

    1984-01-01

    Discrete approximation schemes for the solution of nonlinear hereditary control problems are constructed. The methods involve approximation by a sequence of optimal control problems in which the original infinite dimensional state equation has been approximated by a finite dimensional discrete difference equation. Convergence of the state approximations is argued using linear semigroup theory and is then used to demonstrate that solutions to the approximating optimal control problems in some sense approximate solutions to the original control problem. Two schemes, one based upon piecewise constant approximation, and the other involving spline functions are discussed. Numerical results are presented, analyzed and used to compare the schemes to other available approximation methods for the solution of hereditary control problems. Previously announced in STAR as N83-33589

  11. Difference equation state approximations for nonlinear hereditary control problems

    NASA Technical Reports Server (NTRS)

    Rosen, I. G.

    1982-01-01

    Discrete approximation schemes for the solution of nonlinear hereditary control problems are constructed. The methods involve approximation by a sequence of optimal control problems in which the original infinite dimensional state equation has been approximated by a finite dimensional discrete difference equation. Convergence of the state approximations is argued using linear semigroup theory and is then used to demonstrate that solutions to the approximating optimal control problems in some sense approximate solutions to the original control problem. Two schemes, one based upon piecewise constant approximation, and the other involving spline functions are discussed. Numerical results are presented, analyzed and used to compare the schemes to other available approximation methods for the solution of hereditary control problems.

  12. New variable separation solutions for the generalized nonlinear diffusion equations

    NASA Astrophysics Data System (ADS)

    Fei-Yu, Ji; Shun-Li, Zhang

    2016-03-01

    The functionally generalized variable separation of the generalized nonlinear diffusion equations ut = A(u,ux)uxx + B(u,ux) is studied by using the conditional Lie-Bäcklund symmetry method. The variant forms of the considered equations, which admit the corresponding conditional Lie-Bäcklund symmetries, are characterized. To construct functionally generalized separable solutions, several concrete examples defined on the exponential and trigonometric invariant subspaces are provided. Project supported by the National Natural Science Foundation of China (Grant Nos. 11371293, 11401458, and 11501438), the National Natural Science Foundation of China, Tian Yuan Special Foundation (Grant No. 11426169), and the Natural Science Basic Research Plan in Shaanxi Province of China (Grant No. 2015JQ1014).

  13. Nonlinear stability of oscillatory pulses in the parametric nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Chang, Paul A. C.; Promislow, Keith

    2007-03-01

    We extend the renormalization group method, developed for the study of pulse interaction in damped wave equations, to the study of oscillatory motion of supercritical pulses in the parametrically forced nonlinear Schrödinger equation (PNLS). We construct a global manifold which asymptotically attracts the flow into an {\\cal O}(r^4) neighbourhood in the H1 norm, where r is the amplitude of the internal oscillations. The oscillatory and translational dynamics of the pulses are rigorously recovered as a finite-dimensional flow on the manifold. The normal form for the projected dynamics of the oscillatory pulse shows that it is created in a supercritical Poincaré-Hopf bifurcation.

  14. A Procedure to Construct Exact Solutions of Nonlinear Fractional Differential Equations

    PubMed Central

    Güner, Özkan; Cevikel, Adem C.

    2014-01-01

    We use the fractional transformation to convert the nonlinear partial fractional differential equations with the nonlinear ordinary differential equations. The Exp-function method is extended to solve fractional partial differential equations in the sense of the modified Riemann-Liouville derivative. We apply the Exp-function method to the time fractional Sharma-Tasso-Olver equation, the space fractional Burgers equation, and the time fractional fmKdV equation. As a result, we obtain some new exact solutions. PMID:24737972

  15. Nonlinear periodic waves solutions of the nonlinear self-dual network equations

    SciTech Connect

    Laptev, Denis V. Bogdan, Mikhail M.

    2014-04-15

    The new classes of periodic solutions of nonlinear self-dual network equations describing the breather and soliton lattices, expressed in terms of the Jacobi elliptic functions have been obtained. The dependences of the frequencies on energy have been found. Numerical simulations of soliton lattice demonstrate their stability in the ideal lattice and the breather lattice instability in the dissipative lattice. However, the lifetime of such structures in the dissipative lattice can be extended through the application of ac driving terms.

  16. Charged anisotropic matter with linear or nonlinear equation of state

    SciTech Connect

    Varela, Victor; Rahaman, Farook; Ray, Saibal; Chakraborty, Koushik; Kalam, Mehedi

    2010-08-15

    Ivanov pointed out substantial analytical difficulties associated with self-gravitating, static, isotropic fluid spheres when pressure explicitly depends on matter density. Simplifications achieved with the introduction of electric charge were noticed as well. We deal with self-gravitating, charged, anisotropic fluids and get even more flexibility in solving the Einstein-Maxwell equations. In order to discuss analytical solutions we extend Krori and Barua's method to include pressure anisotropy and linear or nonlinear equations of state. The field equations are reduced to a system of three algebraic equations for the anisotropic pressures as well as matter and electrostatic energy densities. Attention is paid to compact sources characterized by positive matter density and positive radial pressure. Arising solutions satisfy the energy conditions of general relativity. Spheres with vanishing net charge contain fluid elements with unbounded proper charge density located at the fluid-vacuum interface. Notably the electric force acting on these fluid elements is finite, although the acting electric field is zero. Net charges can be huge (10{sup 19}C) and maximum electric field intensities are very large (10{sup 23}-10{sup 24} statvolt/cm) even in the case of zero net charge. Inward-directed fluid forces caused by pressure anisotropy may allow equilibrium configurations with larger net charges and electric field intensities than those found in studies of charged isotropic fluids. Links of these results with charged strange quark stars as well as models of dark matter including massive charged particles are highlighted. The van der Waals equation of state leading to matter densities constrained by cubic polynomial equations is briefly considered. The fundamental question of stability is left open.

  17. New Solutions of Three Nonlinear Space- and Time-Fractional Partial Differential Equations in Mathematical Physics

    NASA Astrophysics Data System (ADS)

    Yao, Ruo-Xia; Wang, Wei; Chen, Ting-Hua

    2014-11-01

    Motivated by the widely used ansätz method and starting from the modified Riemann—Liouville derivative together with a fractional complex transformation that can be utilized to transform nonlinear fractional partial differential equations to nonlinear ordinary differential equations, new types of exact traveling wave solutions to three important nonlinear space- and time-fractional partial differential equations are obtained simultaneously in terms of solutions of a Riccati equation. The results are new and first reported in this paper.

  18. Existence of dark solitons in a class of stationary nonlinear Schroedinger equations with periodically modulated nonlinearity and periodic asymptotics

    SciTech Connect

    Belmonte-Beitia, J.; Cuevas, J.

    2011-03-15

    In this paper, we give a proof of the existence of stationary dark soliton solutions or heteroclinic orbits of nonlinear equations of Schroedinger type with periodic inhomogeneous nonlinearity. The result is illustrated with examples of dark solitons for cubic and photorefractive nonlinearities.

  19. Nonlinear Dirac equation in two-spinor form: Separation in static RW space-time. Nonlinear Dirac equation in RW space-time

    NASA Astrophysics Data System (ADS)

    Zecca, Antonio

    2016-02-01

    The Dirac equation with nonlinear terms induced by torsion is studied in Robertson-Walker (RW) space-time. An extension of a separation method of the equation, based on the Newman-Penrose formalism and previously applied to the nonlinear case, is considered. Accordingly the angular dependence of the Dirac spinor solution is separated, under a special assumption, in the general time-dependent RW metric. In the case of static RW metric the time dependence of the Dirac spinor factors out and one is left with a pair of two coupled nonlinear radial equations. The radial equations are disentangled by a suitable substitution of the spinor solution. The problem amounts then to the solution of a single second-order highly nonlinear differential equation. Some elementary considerations are done on the asymptotic behavior of the solution of the equation.

  20. Numerical solution of the nonlinear Helmholtz equation using nonorthogonal expansions

    SciTech Connect

    Fibich, G. . E-mail: fibich@math.tau.ac.il; Tsynkov, S. . E-mail: tsynkov@math.ncsu.edu

    2005-11-20

    In [J. Comput. Phys. 171 (2001) 632-677] we developed a fourth-order numerical method for solving the nonlinear Helmholtz equation which governs the propagation of time-harmonic laser beams in media with a Kerr-type nonlinearity. A key element of the algorithm was a new nonlocal two-way artificial boundary condition (ABC), set in the direction of beam propagation. This two-way ABC provided for reflectionless propagation of the outgoing waves while also fully transmitting the given incoming beam at the boundaries of the computational domain. Altogether, the algorithm of [J. Comput. Phys. 171 (2001) 632-677] has allowed for a direct simulation of nonlinear self-focusing without neglecting nonparaxial effects and backscattering. To the best of our knowledge, this capacity has never been achieved previously in nonlinear optics. In the current paper, we propose an improved version of the algorithm. The principal innovation is that instead of using the Dirichlet boundary conditions in the direction orthogonal to that of the laser beam propagation, we now introduce Sommerfeld-type local radiation boundary conditions, which are constructed directly in the discrete framework. Numerically, implementation of the Sommerfeld conditions requires evaluation of eigenvalues and eigenvectors for a non-Hermitian matrix. Subsequently, the separation of variables, which is a key building block of the aforementioned nonlocal ABC, is implemented through an expansion with respect to the nonorthogonal basis of the eigenvectors. Numerical simulations show that the new algorithm offers a considerable improvement in its numerical performance, as well as in the range of physical phenomena that it is capable of simulating.

  1. Numerical solution of the nonlinear Schrödinger equation with wave operator on unbounded domains.

    PubMed

    Li, Hongwei; Wu, Xiaonan; Zhang, Jiwei

    2014-09-01

    In this paper, we generalize the unified approach proposed in Zhang et al. [J. Zhang, Z. Xu, and X. Wu, Phys. Rev. E 78, 026709 (2008)] to design the nonlinear local absorbing boundary conditions (LABCs) for the nonlinear Schrödinger equation with wave operator on unbounded domains. In fact, based on the methodology underlying the unified approach, we first split the original equation into two parts-the linear equation and the nonlinear equation-then achieve a one-way operator to approximate the linear equation to make the wave outgoing, and finally combine the one-way operator with the nonlinear equation to achieve the nonlinear LABCs. The stability of the equation with the nonlinear LABCs is also analyzed by introducing some auxiliary variables, and some numerical examples are presented to verify the accuracy and effectiveness of our proposed method. PMID:25314566

  2. On the dynamics of approximating schemes for dissipative nonlinear equations

    NASA Technical Reports Server (NTRS)

    Jones, Donald A.

    1993-01-01

    Since one can rarely write down the analytical solutions to nonlinear dissipative partial differential equations (PDE's), it is important to understand whether, and in what sense, the behavior of approximating schemes to these equations reflects the true dynamics of the original equations. Further, because standard error estimates between approximations of the true solutions coming from spectral methods - finite difference or finite element schemes, for example - and the exact solutions grow exponentially in time, this analysis provides little value in understanding the infinite time behavior of a given approximating scheme. The notion of the global attractor has been useful in quantifying the infinite time behavior of dissipative PDEs, such as the Navier-Stokes equations. Loosely speaking, the global attractor is all that remains of a sufficiently large bounded set in phase space mapped infinitely forward in time under the evolution of the PDE. Though the attractor has been shown to have some nice properties - it is compact, connected, and finite dimensional, for example - it is in general quite complicated. Nevertheless, the global attractor gives a way to understand how the infinite time behavior of approximating schemes such as the ones coming from a finite difference, finite element, or spectral method relates to that of the original PDE. Indeed, one can often show that such approximations also have a global attractor. We therefore only need to understand how the structure of the attractor for the PDE behaves under approximation. This is by no means a trivial task. Several interesting results have been obtained in this direction. However, we will not go into the details. We mention here that approximations generally lose information about the system no matter how accurate they are. There are examples that show certain parts of the attractor may be lost by arbitrary small perturbations of the original equations.

  3. Symmetry analysis and exact solutions for nonlinear equations in mathematical physics

    NASA Astrophysics Data System (ADS)

    Fushchich, Vil'gel'm. I.; Shtelen', Vladimir M.; Serov, Nikolai I.

    The book provides an overview of the current status of theoretical-algebraic methods in relation to linear and nonlinear multidimensional equations in mathematical and theoretical physics that are invariant with respect to the Poincare and Galilean groups and the wider Lie groups. Particular attention is given to the construction, in explicit form, of wide classes of accurate solutions to specific nonlinear partial differential equations, such as nonlinear wave equations for scalar, spinor, and vector fields, Young-Mills equations, and nonlinear quantum electrodynamic equations. A group-theory approach is used to analyze the classical three-body problem.

  4. Fully Electromagnetic Nonlinear Gyrokinetic Equations for Tokamak Edge Turbulence

    SciTech Connect

    Hahm, T. S.; Wang, Lu; Madsen, J.

    2008-08-01

    An energy conserving set of the fully electromagnetic nonlinear gyrokinetic Vlasov equation and Maxwell's equations, which is applicable to both L-mode turbulence with large amplitude and H-mode turbulence in the presence of high E Χ B shear has been derived. The phase-space action variational Lie perturbation method ensures the preservation of the conservation laws of the underlying Vlasov-Maxwell system. Our generalized ordering takes ρi<< ρθ¡ ~ LE ~ Lp << R (here ρi is the thermal ion Larmor radius and ρθ¡ = B/Bθ] ρi), as typically observed in the tokamak H-mode edge, with LE and Lp being the radial electric field and pressure gradient lengths. We take κ perpendicular to ρi ~ 1 for generality, and keep the relative fluctuation amplitudes eδφ /Τi ~ δΒ / Β up to the second order. Extending the electrostatic theory in the presence of high E Χ B shear [Hahm, Phys. Plasmas 3, 4658 (1996)], contributions of electromagnetic fluctuations to the particle charge density and current are explicitly evaluated via pull-back transformation from the gyrocenter distribution function in the gyrokinetic Maxwell's equation.

  5. A new method for parameter estimation in nonlinear dynamical equations

    NASA Astrophysics Data System (ADS)

    Wang, Liu; He, Wen-Ping; Liao, Le-Jian; Wan, Shi-Quan; He, Tao

    2015-01-01

    Parameter estimation is an important scientific problem in various fields such as chaos control, chaos synchronization and other mathematical models. In this paper, a new method for parameter estimation in nonlinear dynamical equations is proposed based on evolutionary modelling (EM). This will be achieved by utilizing the following characteristics of EM which includes self-organizing, adaptive and self-learning features which are inspired by biological natural selection, and mutation and genetic inheritance. The performance of the new method is demonstrated by using various numerical tests on the classic chaos model—Lorenz equation (Lorenz 1963). The results indicate that the new method can be used for fast and effective parameter estimation irrespective of whether partial parameters or all parameters are unknown in the Lorenz equation. Moreover, the new method has a good convergence rate. Noises are inevitable in observational data. The influence of observational noises on the performance of the presented method has been investigated. The results indicate that the strong noises, such as signal noise ratio (SNR) of 10 dB, have a larger influence on parameter estimation than the relatively weak noises. However, it is found that the precision of the parameter estimation remains acceptable for the relatively weak noises, e.g. SNR is 20 or 30 dB. It indicates that the presented method also has some anti-noise performance.

  6. Bayesian Analysis of Structural Equation Models with Nonlinear Covariates and Latent Variables

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Lee, Sik-Yum

    2006-01-01

    In this article, we formulate a nonlinear structural equation model (SEM) that can accommodate covariates in the measurement equation and nonlinear terms of covariates and exogenous latent variables in the structural equation. The covariates can come from continuous or discrete distributions. A Bayesian approach is developed to analyze the…

  7. Exact Multisoliton Solutions of General Nonlinear Schrödinger Equation with Derivative

    PubMed Central

    Li, Qi; Duan, Qiu-yuan; Zhang, Jian-bing

    2014-01-01

    Multisoliton solutions are derived for a general nonlinear Schrödinger equation with derivative by using Hirota's approach. The dynamics of one-soliton solution and two-soliton interactions are also illustrated. The considered equation can reduce to nonlinear Schrödinger equation with derivative as well as the solutions. PMID:25013858

  8. Stability of solitary waves in the nonlinear Dirac equation with arbitrary nonlinearity.

    PubMed

    Shao, Sihong; Quintero, Niurka R; Mertens, Franz G; Cooper, Fred; Khare, Avinash; Saxena, Avadh

    2014-09-01

    We consider the nonlinear Dirac equation in 1 + 1 dimension with scalar-scalar self interaction g(2)/κ+1(̅ΨΨ)(κ+1) and with mass m. Using the exact analytic form for rest frame solitary waves of the form Ψ(x,t)=ψ(x)e(-iωt) for arbitrary κ, we discuss the validity of various approaches to understanding stability that were successful for the nonlinear Schrödinger equation. In particular we study the validity of a version of Derrick's theorem and the criterion of Bogolubsky as well as the Vakhitov-Kolokolov criterion, and find that these criteria yield inconsistent results. Therefore, we study the stability by numerical simulations using a recently developed fourth-order operator splitting integration method. For different ranges of κ we map out the stability regimes in ω. We find that all stable nonlinear Dirac solitary waves have a one-hump profile, but not all one-hump waves are stable, while all waves with two humps are unstable. We also find that the time t(c), it takes for the instability to set in, is an exponentially increasing function of ω and t(c) decreases monotonically with increasing κ. PMID:25314512

  9. Code System for Solving Nonlinear Systems of Equations via the Gauss-Newton Method.

    Energy Science and Technology Software Center (ESTSC)

    1981-08-31

    Version 00 REGN solves nonlinear systems of numerical equations in difficult cases: high nonlinearity, poor initial approximations, a large number of unknowns, ill condition or degeneracy of a problem.

  10. Numerical Simulations of Light Bullets, Using The Full Vector, Time Dependent, Nonlinear Maxwell Equations

    NASA Technical Reports Server (NTRS)

    Goorjian, Peter M.; Silberberg, Yaron; Kwak, Dochan (Technical Monitor)

    1995-01-01

    This paper will present results in computational nonlinear optics. An algorithm will be described that solves the full vector nonlinear Maxwell's equations exactly without the approximations that we currently made. Present methods solve a reduced scalar wave equation, namely the nonlinear Schrodinger equation, and neglect the optical carrier. Also, results will be shown of calculations of 2-D electromagnetic nonlinear waves computed by directly integrating in time the nonlinear vector Maxwell's equations. The results will include simulations of 'light bullet' like pulses. Here diffraction and dispersion will be counteracted by nonlinear effects. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization, and can take into account such quantum effects as Karr and Raman interactions. The present approach is robust and should permit modeling 2-D and 3-D optical soliton propagation, scattering, and switching directly from the full-vector Maxwell's equations.

  11. Numerical Simulations of Light Bullets, Using the Full Vector, Time Dependent, Nonlinear Maxwell Equations

    NASA Technical Reports Server (NTRS)

    Goorjian, Peter M.; Silberberg, Yaron; Kwak, Dochan (Technical Monitor)

    1994-01-01

    This paper will present results in computational nonlinear optics. An algorithm will be described that solves the full vector nonlinear Maxwell's equations exactly without the approximations that are currently made. Present methods solve a reduced scalar wave equation, namely the nonlinear Schrodinger equation, and neglect the optical carrier. Also, results will be shown of calculations of 2-D electromagnetic nonlinear waves computed by directly integrating in time the nonlinear vector Maxwell's equations. The results will include simulations of 'light bullet' like pulses. Here diffraction and dispersion will be counteracted by nonlinear effects. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization, and can take into account such quantum effects as Kerr and Raman interactions. The present approach is robust and should permit modeling 2-D and 3-D optical soliton propagation, scattering, and switching directly from the full-vector Maxwell's equations.

  12. Numerical Simulations of Light Bullets, Using The Full Vector, Time Dependent, Nonlinear Maxwell Equations

    NASA Technical Reports Server (NTRS)

    Goorjian, Peter M.; Silberberg, Yaron; Kwak, Dochan (Technical Monitor)

    1994-01-01

    This paper will present results in computational nonlinear optics. An algorithm will be described that solves the full vector nonlinear Maxwell's equations exactly without the approximations that are currently made. Present methods solve a reduced scalar wave equation, namely the nonlinear Schrodinger equation, and neglect the optical carrier. Also, results will be shown of calculations of 2-D electromagnetic nonlinear waves computed by directly integrating in time the nonlinear vector Maxwell's equations. The results will include simulations of 'light bullet' like pulses. Here diffraction and dispersion will be counteracted by nonlinear effects. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization, and can take into account such quantum effects as Kerr and Raman interactions. The present approach is robust and should permit modeling 2-D and 3-D optical soliton propagation, scattering, and switching directly from the full-vector Maxwell's equations.

  13. Nongauge bright soliton of the nonlinear Schrödinger (NLS) equation and a family of generalized NLS equations

    NASA Astrophysics Data System (ADS)

    Reyes, M. A.; Gutiérrez-Ruiz, D.; Mancas, S. C.; Rosu, H. C.

    2016-01-01

    We present an approach to the bright soliton solution of the nonlinear Schrödinger (NLS) equation from the standpoint of introducing a constant potential term in the equation. We discuss a “nongauge” bright soliton for which both the envelope and the phase depend only on the traveling variable. We also construct a family of generalized NLS equations with solitonic sechp solutions in the traveling variable and find an exact equivalence with other nonlinear equations, such as the Korteveg-de Vries (KdV) and Benjamin-Bona-Mahony (BBM) equations when p = 2.

  14. A note on improved F-expansion method combined with Riccati equation applied to nonlinear evolution equations

    PubMed Central

    Islam, Md. Shafiqul; Khan, Kamruzzaman; Akbar, M. Ali; Mastroberardino, Antonio

    2014-01-01

    The purpose of this article is to present an analytical method, namely the improved F-expansion method combined with the Riccati equation, for finding exact solutions of nonlinear evolution equations. The present method is capable of calculating all branches of solutions simultaneously, even if multiple solutions are very close and thus difficult to distinguish with numerical techniques. To verify the computational efficiency, we consider the modified Benjamin–Bona–Mahony equation and the modified Korteweg-de Vries equation. Our results reveal that the method is a very effective and straightforward way of formulating the exact travelling wave solutions of nonlinear wave equations arising in mathematical physics and engineering. PMID:26064530

  15. A globalization procedure for solving nonlinear systems of equations

    NASA Astrophysics Data System (ADS)

    Shi, Yixun

    1996-09-01

    A new globalization procedure for solving a nonlinear system of equationsF(x)D0 is proposed based on the idea of combining Newton step and the steepest descent step WITHIN each iteration. Starting with an arbitrary initial point, the procedure converges either to a solution of the system or to a local minimizer off(x)D1/2F(x)TF(x). Each iteration is chosen to be as close to a Newton step as possible and could be the Newton step itself. Asymptotically the Newton step will be taken in each iteration and thus the convergence is quadratic. Numerical experiments yield positive results. Further generalizations of this procedure are also discussed in this paper.

  16. Canonical equations of Hamilton for the nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Liang, Guo; Guo, Qi; Ren, Zhanmei

    2015-09-01

    We define two different systems of mathematical physics: the second order differential system (SODS) and the first order differential system (FODS). The Newton's second law of motion and the nonlinear Schrödinger equation (NLSE) are the exemplary SODS and FODS, respectively. We obtain a new kind of canonical equations of Hamilton (CEH), which exhibit some kind of symmetry in form and are formally different from the conventional CEH without symmetry [H. Goldstein, C. Poole, J. Safko, Classical Mechanics, third ed., Addison- Wesley, 2001]. We also prove that the number of the CEHs is equal to the number of the generalized coordinates for the FODS, but twice the number of the generalized coordinates for the SODS. We show that the FODS can only be expressed by the new CEH, but not introduced by the conventional CEH, while the SODS can be done by both the new and the conventional CEHs. As an example, we prove that the nonlinear Schrödinger equation can be expressed with the new CEH in a consistent way.

  17. Green functions and Langevin equations for nonlinear diffusion equations: A comment on ‘Markov processes, Hurst exponents, and nonlinear diffusion equations’ by Bassler et al.

    NASA Astrophysics Data System (ADS)

    Frank, T. D.

    2008-02-01

    We discuss two central claims made in the study by Bassler et al. [K.E. Bassler, G.H. Gunaratne, J.L. McCauley, Physica A 369 (2006) 343]. Bassler et al. claimed that Green functions and Langevin equations cannot be defined for nonlinear diffusion equations. In addition, they claimed that nonlinear diffusion equations are linear partial differential equations disguised as nonlinear ones. We review bottom-up and top-down approaches that have been used in the literature to derive Green functions for nonlinear diffusion equations and, in doing so, show that the first claim needs to be revised. We show that the second claim as well needs to be revised. To this end, we point out similarities and differences between non-autonomous linear Fokker-Planck equations and autonomous nonlinear Fokker-Planck equations. In this context, we raise the question whether Bassler et al.’s approach to financial markets is physically plausible because it necessitates the introduction of external traders and causes. Such external entities can easily be eliminated when taking self-organization principles and concepts of nonextensive thermostatistics into account and modeling financial processes by means of nonlinear Fokker-Planck equations.

  18. Controlled Nonlinear Stochastic Delay Equations: Part I: Modeling and Approximations

    SciTech Connect

    Kushner, Harold J.

    2012-08-15

    This two-part paper deals with 'foundational' issues that have not been previously considered in the modeling and numerical optimization of nonlinear stochastic delay systems. There are new classes of models, such as those with nonlinear functions of several controls (such as products), each with is own delay, controlled random Poisson measure driving terms, admissions control with delayed retrials, and others. There are two basic and interconnected themes for these models. The first, dealt with in this part, concerns the definition of admissible control. The classical definition of an admissible control as a nonanticipative relaxed control is inadequate for these models and needs to be extended. This is needed for the convergence proofs of numerical approximations for optimal controls as well as to have a well-defined model. It is shown that the new classes of admissible controls do not enlarge the range of the value functions, is closed (together with the associated paths) under weak convergence, and is approximatable by ordinary controls. The second theme, dealt with in Part II, concerns transportation equation representations, and their role in the development of numerical algorithms with much reduced memory and computational requirements.

  19. Hyperbolicity of the Nonlinear Models of Maxwell's Equations

    NASA Astrophysics Data System (ADS)

    Serre, Denis

    . We consider the class of nonlinear models of electromagnetism that has been described by Coleman & Dill [7]. A model is completely determined by its energy density W(B,D). Viewing the electromagnetic field (B,D) as a 3×2 matrix, we show that polyconvexity of W implies the local well-posedness of the Cauchy problem within smooth functions of class Hs with s>1+d/2. The method follows that designed by Dafermos in his book [9] in the context of nonlinear elasticity. We use the fact that B×D is a (vectorial, non-convex) entropy, and we enlarge the system from 6 to 9 equations. The resulting system admits an entropy (actually the energy) that is convex. Since the energy conservation law does not derive from the system of conservation laws itself (Faraday's and Ampère's laws), but also needs the compatibility relations divB=divD=0 (the latter may be relaxed in order to take into account electric charges), the energy density is not an entropy in the classical sense. Thus the system cannot be symmetrized, strictly speaking. However, we show that the structure is close enough to symmetrizability, so that the standard estimates still hold true.

  20. Statistical mechanics of the nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Lebowitz, Joel L.; Rose, Harvey A.; Speer, Eugene R.

    1988-02-01

    We investigate the statistical mechanics of a complex field ø whose dynamics is governed by the nonlinear Schrödinger equation. Such fields describe, in suitable idealizations, Langmuir waves in a plasma, a propagating laser field in a nonlinear medium, and other phenomena. Their Hamiltonian H(φ ) = int_Ω {[1/2|nabla φ |^2 - (1/p) |φ |^p ] dx} is unbounded below and the system will, under certain conditions, develop (self-focusing) singularities in a finite time. We show that, when Ω is the circle and the L 2 norm of the field (which is conserved by the dynamics) is bounded by N, the Gibbs measure υ obtained is absolutely continuous with respect to Wiener measure and normalizable if and only if p and N are such that classical solutions exist for all time—no collapse of the solitons. This measure is essentially the same as that of a one-dimensional version of the more realisitc Zakharov model of coupled Langmuir and ion acoustic waves in a plasma. We also obtain some properties of the Gibbs state, by both analytic and numerical methods, as N and the temperature are varied.

  1. Local error estimates for discontinuous solutions of nonlinear hyperbolic equations

    NASA Technical Reports Server (NTRS)

    Tadmor, Eitan

    1989-01-01

    Let u(x,t) be the possibly discontinuous entropy solution of a nonlinear scalar conservation law with smooth initial data. Suppose u sub epsilon(x,t) is the solution of an approximate viscosity regularization, where epsilon greater than 0 is the small viscosity amplitude. It is shown that by post-processing the small viscosity approximation u sub epsilon, pointwise values of u and its derivatives can be recovered with an error as close to epsilon as desired. The analysis relies on the adjoint problem of the forward error equation, which in this case amounts to a backward linear transport with discontinuous coefficients. The novelty of this approach is to use a (generalized) E-condition of the forward problem in order to deduce a W(exp 1,infinity) energy estimate for the discontinuous backward transport equation; this, in turn, leads one to an epsilon-uniform estimate on moments of the error u(sub epsilon) - u. This approach does not follow the characteristics and, therefore, applies mutatis mutandis to other approximate solutions such as E-difference schemes.

  2. Nonlinear Dirac equation solitary waves in external fields.

    PubMed

    Mertens, Franz G; Quintero, Niurka R; Cooper, Fred; Khare, Avinash; Saxena, Avadh

    2012-10-01

    We consider nonlinear Dirac equations (NLDE's) in the 1+1 dimension with scalar-scalar self-interaction g2/κ+1(Ψ[over ¯]Ψ)κ+1 in the presence of various external electromagnetic fields. We find exact solutions for special external fields and we study the behavior of solitary-wave solutions to the NLDE in the presence of a wide variety of fields in a variational approximation depending on collective coordinates which allows the position, width, and phase of these waves to vary in time. We find that in this approximation the position q(t) of the center of the solitary wave obeys the usual behavior of a relativistic point particle in an external field. For time-independent external fields, we find that the energy of the solitary wave is conserved but not the momentum, which becomes a function of time. We postulate that, similarly to the nonlinear Schrödinger equation (NLSE), a sufficient dynamical condition for instability to arise is that dP(t)/dq[over ̇](t)<0. Here P(t) is the momentum of the solitary wave, and q[over ̇] is the velocity of the center of the wave in the collective coordinate approximation. We found for our choices of external potentials that we always have dP(t)/dq[over ̇](t)>0, so, when instabilities do occur, they are due to a different source. We investigate the accuracy of our variational approximation using numerical simulations of the NLDE and find that, when the forcing term is small and we are in a regime where the solitary wave is stable, that the behavior of the solutions of the collective coordinate equations agrees very well with the numerical simulations. We found that the time evolution of the collective coordinates of the solitary wave in our numerical simulations, namely the position of the average charge density and the momentum of the solitary wave, provide good indicators for when the solitary wave first becomes unstable. When these variables stop being smooth functions of time (t), then the solitary wave starts to distort

  3. Nonlinear response of the surface electrostatic potential formed at metal oxide/electrolyte interfaces. A Monte Carlo simulation study

    SciTech Connect

    Zarzycki, Piotr P.; Rosso, Kevin M.

    2010-01-01

    An analysis of surface potential nonlinearity at metal oxide/electrolyte interfaces is presented. By using Grand Canonical Monte Carlo simulations of a simple lattice model of an interface, we show a correlation exists between ionic strength as well as surface site densities and the non-Nernstian response of a metal oxide electrode. We propose two approaches to deal with the 0-nonlinearity: one based on perturbative expansion of the Gibbs free energy and another based on assumption of the pH-dependence of surface potential slope. The theoretical anal ysis based on our new potential form gives excellent performance at extreme pH regions, where classical formulae based on the Poisson-Boltzmann equation fail. The new formula is general and independent of any underlying assumptions. For this reason, it can be directly applied to experimental surface potential measurements, including those for individual surfaces of single crystals, as we present for data reported by Kallay and Preocanin [Kallay, Preocanin J. Colloid and Interface20 Sci. 318 (2008) 290].

  4. Finite time blowup of solutions to the nonlinear Schrödinger equation without gauge invariance

    NASA Astrophysics Data System (ADS)

    Fujiwara, Kazumasa; Ozawa, Tohru

    2016-08-01

    A lifespan estimate and a condition of the initial data for finite time blowup for the nonlinear Schrödinger equation are presented from a view point of ordinary differential equation (ODE) mechanism.

  5. Hazardous Continuation Backward in Time in Nonlinear Parabolic Equations, and an Experiment in Deblurring Nonlinearly Blurred Imagery

    PubMed Central

    Carasso, Alfred S

    2013-01-01

    Identifying sources of ground water pollution, and deblurring nanoscale imagery as well as astronomical galaxy images, are two important applications involving numerical computation of parabolic equations backward in time. Surprisingly, very little is known about backward continuation in nonlinear parabolic equations. In this paper, an iterative procedure originating in spectroscopy in the 1930’s, is adapted into a useful tool for solving a wide class of 2D nonlinear backward parabolic equations. In addition, previously unsuspected difficulties are uncovered that may preclude useful backward continuation in parabolic equations deviating too strongly from the linear, autonomous, self adjoint, canonical model. This paper explores backward continuation in selected 2D nonlinear equations, by creating fictitious blurred images obtained by using several sharp images as initial data in these equations, and capturing the corresponding solutions at some positive time T. Successful backward continuation from t=T to t = 0, would recover the original sharp image. Visual recognition provides meaningful evaluation of the degree of success or failure in the reconstructed solutions. Instructive examples are developed, illustrating the unexpected influence of certain types of nonlinearities. Visually and statistically indistinguishable blurred images are presented, with vastly different deblurring results. These examples indicate that how an image is nonlinearly blurred is critical, in addition to the amount of blur. The equations studied represent nonlinear generalizations of Brownian motion, and the blurred images may be interpreted as visually expressing the results of novel stochastic processes. PMID:26401430

  6. Nonlinear diffusion equations as asymptotic limits of Cahn-Hilliard systems

    NASA Astrophysics Data System (ADS)

    Colli, Pierluigi; Fukao, Takeshi

    2016-05-01

    An asymptotic limit of a class of Cahn-Hilliard systems is investigated to obtain a general nonlinear diffusion equation. The target diffusion equation may reproduce a number of well-known model equations: Stefan problem, porous media equation, Hele-Shaw profile, nonlinear diffusion of singular logarithmic type, nonlinear diffusion of Penrose-Fife type, fast diffusion equation and so on. Namely, by setting the suitable potential of the Cahn-Hilliard systems, all these problems can be obtained as limits of the Cahn-Hilliard related problems. Convergence results and error estimates are proved.

  7. Exact solutions to a class of nonlinear Schrödinger-type equations

    NASA Astrophysics Data System (ADS)

    Zhang, Jin-Liang; Wang, Ming-Liang

    2006-12-01

    A class of nonlinear Schrödinger-type equations, including the Rangwal--Rao equation, the Gerdjikov--Ivanov equation, the Chen--Lee--Lin equation and the Ablowitz--Ramani--Segur equation are investigated, and the exact solutions are derived with the aid of the homogeneous balance principle, and a set of subsidiary higher order ordinary differential equations (sub-ODEs for short).

  8. Analytical Solution of the Space-Time Fractional Nonlinear Schrödinger Equation

    NASA Astrophysics Data System (ADS)

    Abdel-Salam, Emad A.-B.; Yousif, Eltayeb A.; El-Aasser, Mostafa A.

    2016-02-01

    The space-time fractional nonlinear Schrödinger equation is solved by mean of on the fractional Riccati expansion method. These solutions include generalized trigonometric and hyperbolic functions which could be useful for further understanding of mechanisms of the complicated nonlinear physical phenomena and fractional differential equations. Among these solutions, some are found for the first time.

  9. Soliton Theory of Two-Dimensional Lattices: The Discrete Nonlinear Schroedinger Equation

    SciTech Connect

    Arevalo, Edward

    2009-06-05

    We theoretically investigate the motion of collective excitations in the two-dimensional nonlinear Schroedinger equation with cubic nonlinearity. The form of these excitations for a broad range of parameters is derived. Their evolution and interaction is numerically studied and the modulation instability is discussed. The case of saturable nonlinearity is revisited.

  10. Functional constraints method for constructing exact solutions to delay reaction-diffusion equations and more complex nonlinear equations

    NASA Astrophysics Data System (ADS)

    Polyanin, Andrei D.; Zhurov, Alexei I.

    2014-03-01

    We propose a new method for constructing exact solutions to nonlinear delay reaction-diffusion equations of the form ut=kuxx+F(u,w), where u=u(x,t),w=u(x,t-τ), and τ is the delay time. The method is based on searching for solutions in the form u=∑n=1Nξn(x)ηn(t), where the functions ξn(x) and ηn(t) are determined from additional functional constraints (which are difference or functional equations) and the original delay partial differential equation. All of the equations considered contain one or two arbitrary functions of a single argument. We describe a considerable number of new exact generalized separable solutions and a few more complex solutions representing a nonlinear superposition of generalized separable and traveling wave solutions. All solutions involve free parameters (in some cases, infinitely many parameters) and so can be suitable for solving certain problems and testing approximate analytical and numerical methods for nonlinear delay PDEs. The results are extended to a wide class of nonlinear partial differential-difference equations involving arbitrary linear differential operators of any order with respect to the independent variables x and t (in particular, this class includes the nonlinear delay Klein-Gordon equation) as well as to some partial functional differential equations with time-varying delay.