Science.gov

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 new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation.

    PubMed

    Boschitsch, Alexander H; Fenley, Marcia O

    2007-04-15

    The nonlinear Poisson-Boltzmann equation (PBE) has been successfully used for the prediction of numerous electrostatic properties of highly charged biopolyelectrolytes immersed in aqueous salt solutions. While numerous numerical solvers for the 3D PBE have been developed, the formulation of the outer boundary treatments used in these methods has only been loosely addressed, especially in the nonlinear case. The de facto standard in current nonlinear PBE implementations is to either set the potential at the outer boundaries to zero or estimate it using the (linear) Debye-Hückel (DH) approximation. However, an assessment of how these outer boundary treatments affect the overall solution accuracy does not appear to have been previously made. As will be demonstrated here, both approximations can, under certain conditions, produce completely erroneous estimates of the potential and energy salt dependencies. A related concern for calculations carried out on grids of finite extent (e.g., all current finite difference and finite element implementations) is the contribution to the energy and salt dependence from the exterior region outside the computational grid. This too is shown to be significant, especially at low salt concentration where essentially all of the contributions to the excess osmotic pressure and ion stress energies originate from this exterior region. In this paper the authors introduce a new outer boundary treatment that is valid for both the linear and nonlinear PBE. The authors also formulate energy corrections to account for contributions from outside the computational domain. Finally, the authors also consider the effects of general ion exclusion layers upon biomolecular electrostatics. It is shown that while these layers tend to increase the surface electrostatic potential, under physiological salt conditions and high net charges their effect on the excess osmotic pressure term, which is a measure of the salt dependence of the total electrostatic

  4. 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.

  5. 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

  6. Using pseudo transient continuation and the finite element method to solve the nonlinear Poisson-Boltzmann equation

    SciTech Connect

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

    2000-12-27

    The nonlinear Poisson-Boltzmann (PB) equation is solved using Pseudo Transient Continuation. The PB solver is constructed by modifying the nonlinear diffusion module of a 3D, massively parallel, unstructured-grid, finite element, radiation-hydrodynamics code. The solver also computes the electrostatic energy and evaluates the force on a user-specified contour. Either Dirichlet or mixed boundary conditions are allowed. The latter specifies surface charges, approximates far-field conditions, or linearizes conditions ''regulating'' the surface charge. The code may be run in either Cartesian, cylindrical, or spherical coordinates. The potential and force due to a conical probe interacting with a flat plate is computed and the result compared with direct force measurements by chemical force microscopy.

  7. Comparing the Predictions of the Nonlinear Poisson-Boltzmann Equation and the Ion Size-Modified Poisson-Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an Aqueous Salt Solution

    PubMed Central

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

    2011-01-01

    The ion size-modified Poisson Boltzmann equation (SMPBE) is applied to the simple model problem of a low-dielectric spherical cavity containing a central charge, in an aqueous salt solution to investigate the finite ion size effect upon the electrostatic free energy and its sensitivity to changes in salt concentration. The SMPBE is shown to predict a very different electrostatic free energy than the nonlinear Poisson-Boltzmann equation (NLPBE) due to the additional entropic cost of placing ions in solution. Although the energy predictions of the SMPBE can be reproduced by fitting an appropriatelysized Stern layer, or ion-exclusion layer to the NLPBE calculations, the size of the Stern layer is difficult to estimate a priori. The SMPBE also produces a saturation layer when the central charge becomes sufficiently large. Ion-competition effects on various integrated quantities such the total number of ions predicted by the SMPBE are qualitatively similar to those given by the NLPBE and those found in available experimental results. PMID:22723750

  8. The Numerical Solution of the Nonlinear Poisson-Boltzmann Equation Under the Anisotropic Boundary Condition for Colloidal Plasmas

    NASA Astrophysics Data System (ADS)

    Cai, Huanqing; Ye, Qizheng

    2010-04-01

    Based on the model of the Wigner-Seitz cell, the surface potential of the spherical macroparticle (radius a) expands in terms of the monopole (q). A dipole (p) model is assumed for an anisotropic boundary condition of the nonlinear Poisson-Boltzmann equation. Using the finite element method implemented by the FlexPDE software, the potential distribution around the macroparticle is obtained for different ratios p/qa. The calculated results for the potential show that there is an attractive region in the vicinity of the macroparticle when |p/qa|>1.1, and noticeably there is a potential well behind the macroparticle when |p/qa| = 1.1, i.e., there exists both an attractive region and a repulsive region simultaneously. This means that the attractive interaction between macroparticles may arise from the anisotropic distribution of the surrounding plasmas, which well explains some experimental observations.

  9. 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.

  10. Non-linear Poisson-Boltzmann theory for swollen clays

    NASA Astrophysics Data System (ADS)

    Leote de Carvalho, R. J. F.; Trizac, E.; Hansen, J.-P.

    1998-08-01

    The non-linear Poisson-Boltzmann (PB) equation for a circular, uniformly char ged platelet, confined together with co- and counter-ions to a cylindrical cell, is solved semi-analytically by transforming it into an integral equation and solving the latter iteratively. This method proves efficient and robust, and can be readily generalized to other problems based on cell models, treated within non-linear Poisson-like theory. The solution to the PB equation is computed over a wide range of physical conditions, and the resulting osmotic equation of state is shown to be in semi-quantitative agreement with recent experimental data for Laponite clay suspensions, in the concentrated gel phase.

  11. On removal of charge singularity in Poisson-Boltzmann equation.

    PubMed

    Cai, Qin; Wang, Jun; Zhao, Hong-Kai; Luo, Ray

    2009-04-14

    The Poisson-Boltzmann theory has become widely accepted in modeling electrostatic solvation interactions in biomolecular calculations. However the standard practice of atomic point charges in molecular mechanics force fields introduces singularity into the Poisson-Boltzmann equation. The finite-difference/finite-volume discretization approach to the Poisson-Boltzmann equation alleviates the numerical difficulty associated with the charge singularity but introduces discretization error into the electrostatic potential. Decomposition of the electrostatic potential has been explored to remove the charge singularity explicitly to achieve higher numerical accuracy in the solution of the electrostatic potential. In this study, we propose an efficient method to overcome the charge singularity problem. In our framework, two separate equations for two different potentials in two different regions are solved simultaneously, i.e., the reaction field potential in the solute region and the total potential in the solvent region. The proposed method can be readily implemented with typical finite-difference Poisson-Boltzmann solvers and return the singularity-free reaction field potential with a single run. Test runs on 42 small molecules and 4 large proteins show a very high agreement between the reaction field energies computed by the proposed method and those by the classical finite-difference Poisson-Boltzmann method. It is also interesting to note that the proposed method converges faster than the classical method, though additional time is needed to compute Coulombic potential on the dielectric boundary. The higher precision, accuracy, and efficiency of the proposed method will allow for more robust electrostatic calculations in molecular mechanics simulations of complex biomolecular systems.

  12. Diffusiophoresis of concentrated suspensions of spherical particles with charge-regulated surface: polarization effect with nonlinear poisson-Boltzmann equation.

    PubMed

    Lou, James; Shih, Chun-Yu; Lee, Eric

    2010-01-05

    Diffusiophoresis in concentrated suspensions of spherical colloids with charge-regulated surface is investigated theoretically. The charge-regulated surface considered here is the generalization of conventional constant surface potential and constant surface charge density situations. Kuwabara's unit cell model is adopted to describe the system and a pseudospectral method based on Chebyshev polynomial is employed to solve the governing general electrokinetic equations. Excellent agreements with experimental data available in literature were obtained for the limiting case of constant surface potential and very dilute suspension. It is found, among other things, that in general the larger the number of dissociated functional groups on particle surface is, the higher the particle surface potential, hence the larger the magnitude of the particle mobility. The electric potential on particle surface depends on both the concentration of dissociated hydrogen ions and the concentration of electrolyte in the solution. The electric potential on particle surface turns out to be the dominant factor in the determination of the eventual particle diffusiophoretic mobility. Local maximum of diffusiophoretic mobility as a function of double layer thickness is observed. Its reason and influence is discussed. Corresponding behavior for the constant potential situation, however, may yield a monotonously increasing profile.

  13. Analytical solutions of the Poisson-Boltzmann equation: biological applications

    NASA Astrophysics Data System (ADS)

    Fenley, Andrew; Gordon, John; Onufriev, Alexey

    2006-03-01

    Electrostatic interactions are a key factor for determining many properties of bio-molecules. The ability to compute the electrostatic potential generated by a molecule is often essential in understanding the mechanism behind its biological function such as catalytic activity, ligand binding, and macromolecular association. We propose an approximate analytical solution to the (linearized) Poisson-Boltzmann (PB) equation that is suitable for computing electrostatic potential around realistic biomolecules. The approximation is tested against the numerical solutions of the PB equation on a test set of 600 representative structures including proteins, DNA, and macromolecular complexes. The approach allows one to generate, with the power of a desktop PC, electrostatic potential maps of virtually any molecule of interest, from single proteins to large protein complexes such as viral capsids. The new approach is orders of magnitude less computationally intense than its numerical counterpart, yet is almost equal in accuracy. When studying very large molecular systems, our method is a practical and inexpensive way of computing bio- molecular potential at atomic resolution. We demonstrate the usefullnes of the new approach by exploring the details of electrostatic potentials generated by two of such systems: the nucleosome core particle (25,000 atoms) and tobacco ring spot virus (500,000 atoms). Biologically relevant insights are generated.

  14. Surface Tension of Acid Solutions: Fluctuations beyond the Nonlinear Poisson-Boltzmann Theory.

    PubMed

    Markovich, Tomer; Andelman, David; Podgornik, Rudi

    2017-01-10

    We extend our previous study of surface tension of ionic solutions and apply it to acids (and salts) with strong ion-surface interactions, as described by a single adhesivity parameter for the ionic species interacting with the interface. We derive the appropriate nonlinear boundary condition with an effective surface charge due to the adsorption of ions from the bulk onto the interface. The calculation is done using the loop-expansion technique, where the zero loop (mean field) corresponds of the full nonlinear Poisson-Boltzmann equation. The surface tension is obtained analytically to one-loop order, where the mean-field contribution is a modification of the Poisson-Boltzmann surface tension and the one-loop contribution gives a generalization of the Onsager-Samaras result. Adhesivity significantly affects both contributions to the surface tension, as can be seen from the dependence of surface tension on salt concentration for strongly absorbing ions. Comparison with available experimental data on a wide range of different acids and salts allows the fitting of the adhesivity parameter. In addition, it identifies the regime(s) where the hypotheses on which the theory is based are outside their range of validity.

  15. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:24559370

  17. Structural interactions in ionic liquids linked to higher-order Poisson-Boltzmann equations.

    PubMed

    Blossey, R; Maggs, A C; Podgornik, R

    2017-06-01

    We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation introduced by Bazant et al. [Phys. Rev. Lett. 106, 046102 (2011)]PRLTAO0031-900710.1103/PhysRevLett.106.046102, whereby the structuring near the surface is determined by bulk coefficients.

  18. 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.

  19. 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

  20. 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.

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

    PubMed

    Holst, Michael; McCammon, James Andrew; Yu, Zeyun; Zhou, Youngcheng; Zhu, Yunrong

    2012-01-01

    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

  2. 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

  3. A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules

    NASA Astrophysics Data System (ADS)

    Xie, Dexuan; Jiang, Yi

    2016-10-01

    The nonlocal dielectric approach has been studied for more than forty years but only limited to water solvent until the recent work of Xie et al. (2013) [20]. As the development of this recent work, in this paper, a nonlocal modified Poisson-Boltzmann equation (NMPBE) is proposed to incorporate nonlocal dielectric effects into the classic Poisson-Boltzmann equation (PBE) for protein in ionic solvent. The focus of this paper is to present an efficient finite element algorithm and a related software package for solving NMPBE. Numerical results are reported to validate this new software package and demonstrate its high performance for protein molecules. They also show the potential of NMPBE as a better predictor of electrostatic solvation and binding free energies than PBE.

  4. Asymptotic analysis of the Poisson-Boltzmann equation describing electrokinetics in porous media

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    We consider the Poisson-Boltzmann equation in a periodic cell, representative of a porous medium. It is a model for the electrostatic distribution of N chemical species diluted in a liquid at rest, occupying the pore space with charged solid boundaries. We study the asymptotic behaviour of its solution depending on a parameter β, which is the square of the ratio between a characteristic pore length and the Debye length. For small β we identify the limit problem which is still a nonlinear Poisson equation involving only one species with maximal valence, opposite to the average of the given surface charge density. This result justifies the Donnan effect, observing that the ions for which the charge is that of the solid phase are expelled from the pores. For large β we prove that the solution behaves like a boundary layer near the pore walls and is constant far away in the bulk. Our analysis is valid for Neumann boundary conditions (namely for imposed surface charge densities) and establishes rigorously that solid interfaces are uncoupled from the bulk fluid so that simplified additive theories, such as the popular Derjaguin, Landau, Verwey and Overbeek approach, can be used. We show that the asymptotic behaviour is completely different in the case of Dirichlet boundary conditions (namely for imposed surface potential).

  5. Nonlinear Poisson-Boltzmann model of charged lipid membranes: Accounting for the presence of zwitterionic lipids

    NASA Astrophysics Data System (ADS)

    Mengistu, Demmelash H.; May, Sylvio

    2008-09-01

    The nonlinear Poisson-Boltzmann model is used to derive analytical expressions for the free energies of both mixed anionic-zwitterionic and mixed cationic-zwitterionic lipid membranes as function of the mole fraction of charged lipids. Accounting explicitly for the electrostatic properties of the zwitterionic lipid species affects the free energy of anionic and cationic membranes in a qualitatively different way: That of an anionic membrane changes monotonously as a function of the mole fraction of charged lipids, whereas it passes through a pronounced minimum for a cationic membrane.

  6. Numerical Difficulties Computing Electrostatic Potentials Near Interfaces with the Poisson-Boltzmann Equation.

    PubMed

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

    2017-08-08

    Many researchers compute surface maps of the electrostatic potential (φ) with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of φ, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of φ) at the surface. The Cartesian Poisson-Boltzmann solver contains several features that reduce the numerical noise in surface maps of φ: First, CPB introduces additional mesh points at the Cartesian grid/surface intersections where the PB equation is solved. This procedure ensures that the solution for interior mesh points only references nodes on the interior or on the surfaces; similarly for exterior points. Second, for added points on the surface, a second order least-squares reconstruction (LSR) is implemented that analytically incorporates the discontinuities at the surface. LSR is used both during the solution phase to compute φ at the surface and during postprocessing to obtain φ, induced charges, and ionic pressures. Third, it uses an adaptive grid where the finest grid cells are located near the molecular surface.

  7. 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.

  8. 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

  9. 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(+).

  10. pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements.

    PubMed

    Sakalli, Ilkay; Knapp, Ernst-Walter

    2015-11-05

    Knowledge on pK(A) values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson-Boltzmann equation (lPBE) can successfully be used to compute pK(A) values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK(A) values. This work focuses on a comparison between pK(A) computations obtained with the well-established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK(A) values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK(A) values and we show for the FE method how different parameters influence the accuracy of computed pK(A) values.

  11. Ion strength limit of computed excess functions based on the linearized Poisson-Boltzmann equation.

    PubMed

    Fraenkel, Dan

    2015-12-05

    The linearized Poisson-Boltzmann (L-PB) equation is examined for its κ-range of validity (κ, Debye reciprocal length). This is done for the Debye-Hückel (DH) theory, i.e., using a single ion size, and for the SiS treatment (D. Fraenkel, Mol. Phys. 2010, 108, 1435), which extends the DH theory to the case of ion-size dissimilarity (therefore dubbed DH-SiS). The linearization of the PB equation has been claimed responsible for the DH theory's failure to fit with experiment at > 0.1 m; but DH-SiS fits with data of the mean ionic activity coefficient, γ± (molal), against m, even at m > 1 (κ > 0.33 Å(-1) ). The SiS expressions combine the overall extra-electrostatic potential energy of the smaller ion, as central ion-Ψa>b (κ), with that of the larger ion, as central ion-Ψb>a (κ); a and b are, respectively, the counterion and co-ion distances of closest approach. Ψa>b and Ψb>a are derived from the L-PB equation, which appears to conflict with their being effective up to moderate electrolyte concentrations (≈1 m). However, the L-PB equation can be valid up to κ ≥ 1.3 Å(-1) if one abandons the 1/κ criterion for its effectiveness and, instead, use, as criterion, the mean-field electrostatic interaction potential of the central ion with its ion cloud, at a radial distance dividing the cloud charge into two equal parts. The DH theory's failure is, thus, not because of using the L-PB equation; the lethal approximation is assigning a single size to the positive and negative ions. © 2015 Wiley Periodicals, Inc.

  12. SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

    PubMed

    Xie, Yang; Ying, Jinyong; Xie, Dexuan

    2017-03-30

    SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc.

  13. Electrostatic forces in the Poisson-Boltzmann systems.

    PubMed

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

    2013-09-07

    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.

  14. 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.

  15. Polarizable Poisson-Boltzmann equation: the study of polarizability effects on the structure of a double layer.

    PubMed

    Frydel, Derek

    2011-06-21

    We incorporate ion polarizabilities into the Poisson-Boltzmann equation by modifying the effective dielectric constant and the Boltzmann distribution of ions. The extent of the polarizability effects is controlled by two parameters, γ(1) and γ(2); γ(1) determines the polarization effects in a dilute system and γ(2) regulates the dependence of the polarizability effects on the concentration of ions. For a polarizable ion in an aqueous solution γ(1) ≈ 0.01 and the polarizability effects are negligible. The conditions where γ(1) and/or γ(2) are large and the polarizability is relevant involve the low dielectric constant media, high surface charge, and/or large ionic concentrations. © 2011 American Institute of Physics

  16. Simplifications of the Poisson-Boltzmann Equation for the Electrostatic Interaction of Close Hydrophilic Surfaces in Water.

    PubMed

    Biesheuvel, P. Maarten

    2001-06-15

    Simple solutions of the Poisson-Boltzmann (PB) equation for the electrostatic double-layer interaction of close, planar hydrophilic surfaces in water are evaluated. Four routes, being the weak overlap approximation, the Debye-Hückel linearization based on low electrostatic potentials, the Ettelaie-Buscall linearization based on small variations in the potential, and a new approach based on the fact that concentrations are virtually constant in the gap between close surfaces, are discussed. The Ettelaie-Buscall and constant-concentration approach become increasingly accurate for closer surfaces and are exact for touching surfaces, while the weak overlap approximation is exact for an isolated surface. The Debye-Hückel linearization is valid as long as potentials remain low, independent of separation. In contrast to the Ettelaie-Buscall approach and the weak overlap approximation, the Debye-Hückel linearization and constant-concentration approach can also be used for systems containing multivalent ions. Simulations in which the four approaches are compared with the PB equation for the constant-charge model, the constant-potential model, as being used in the DLVO theory, and the charge-regulation model are presented. Copyright 2001 Academic Press.

  17. Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions

    NASA Astrophysics Data System (ADS)

    Hwang, Feng-Nan; Cai, Shang-Rong; Shao, Yun-Long; Wu, Jong-Shinn

    2010-09-01

    We investigate fully parallel Newton-Krylov-Schwarz (NKS) algorithms for solving the large sparse nonlinear systems of equations arising from the finite element discretization of the three-dimensional Poisson-Boltzmann equation (PBE), which is often used to describe the colloidal phenomena of an electric double layer around charged objects in colloidal and interfacial science. The NKS algorithm employs an inexact Newton method with backtracking (INB) as the nonlinear solver in conjunction with a Krylov subspace method as the linear solver for the corresponding Jacobian system. An overlapping Schwarz method as a preconditioner to accelerate the convergence of the linear solver. Two test cases including two isolated charged particles and two colloidal particles in a cylindrical pore are used as benchmark problems to validate the correctness of our parallel NKS-based PBE solver. In addition, a truly three-dimensional case, which models the interaction between two charged spherical particles within a rough charged micro-capillary, is simulated to demonstrate the applicability of our PBE solver to handle a problem with complex geometry. Finally, based on the result obtained from a PC cluster of parallel machines, we show numerically that NKS is quite suitable for the numerical simulation of interaction between colloidal particles, since NKS is robust in the sense that INB is able to converge within a small number of iterations regardless of the geometry, the mesh size, the number of processors. With help of an additive preconditioned Krylov subspace method NKS achieves parallel efficiency of 71% or better on up to a hundred processors for a 3D problem with 5 million unknowns.

  18. Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes.

    PubMed

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2015-04-05

    The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson-Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev-Bashford-Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson-Boltzmann model.

  19. The Poisson-Boltzmann theory for the two-plates problem: some exact results.

    PubMed

    Xing, Xiang-Jun

    2011-12-01

    The general solution to the nonlinear Poisson-Boltzmann equation for two parallel charged plates, either inside a symmetric electrolyte, or inside a 2q:-q asymmetric electrolyte, is found in terms of Weierstrass elliptic functions. From this we derive some exact asymptotic results for the interaction between charged plates, as well as the exact form of the renormalized surface charge density.

  20. Poisson-Boltzmann theory for two parallel uniformly charged plates

    SciTech Connect

    Xing Xiangjun

    2011-04-15

    We solve the nonlinear Poisson-Boltzmann equation for two parallel and like-charged plates both inside a symmetric electrolyte, and inside a 2:1 asymmetric electrolyte, in terms of Weierstrass elliptic functions. From these solutions we derive the functional relation between the surface charge density, the plate separation, and the pressure between plates. For the one plate problem, we obtain exact expressions for the electrostatic potential and for the renormalized surface charge density, both in symmetric and in asymmetric electrolytes. For the two plate problems, we obtain new exact asymptotic results in various regimes.

  1. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.

    PubMed

    Wang, Nuo; Zhou, Shenggao; Kekenes-Huskey, Peter M; Li, Bo; McCammon, J Andrew

    2014-12-26

    Mean-field methods, such as the Poisson-Boltzmann equation (PBE), are often used to calculate the electrostatic properties of molecular systems. In the past two decades, an enhancement of the PBE, the size-modified Poisson-Boltzmann equation (SMPBE), has been reported. Here, the PBE and the SMPBE are reevaluated for realistic molecular systems, namely, lipid bilayers, under eight different sets of input parameters. The SMPBE appears to reproduce the molecular dynamics simulation results better than the PBE only under specific parameter sets, but in general, it performs no better than the Stern layer correction of the PBE. These results emphasize the need for careful discussions of the accuracy of mean-field calculations on realistic systems with respect to the choice of parameters and call for reconsideration of the cost-efficiency and the significance of the current SMPBE formulation.

  2. Ion-conserving Poisson-Boltzmann theory.

    PubMed

    Sugioka, Hideyuki

    2012-07-01

    It is well known that the Poisson-Nernst-Planck (PNP) theory and the classical Gouy-Chapman theory are inconsistent at a high applied voltage. For solving this problem, we propose an ion-conserving Poisson-Boltzmann theory, which shows remarkable agreement with the numerical PNP solutions, even at a high applied voltage. In other words, we have found the exact analytical solutions for steady PNP equations; we believe that this finding greatly contributes to understanding surface science between solids and liquids.

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

    NASA Astrophysics Data System (ADS)

    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.

  4. 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.

  5. Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements.

    PubMed

    Altman, Michael D; Bardhan, Jaydeep P; White, Jacob K; Tidor, Bruce

    2009-01-15

    We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson-Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Fourth, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as nonrigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as

  6. Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson-Boltzmann Equation Over a Broad Range of Salt Concentration.

    PubMed

    Fenley, Marcia O; Mascagni, Michael; McClain, James; Silalahi, Alexander R J; Simonov, Nikolai A

    2010-01-01

    Dielectric continuum or implicit solvent models provide a significant reduction in computational cost when accounting for the salt-mediated electrostatic interactions of biomolecules immersed in an ionic environment. These models, in which the solvent and ions are replaced by a dielectric continuum, seek to capture the average statistical effects of the ionic solvent, while the solute is treated at the atomic level of detail. For decades, the solution of the three-dimensional Poisson-Boltzmann equation (PBE), which has become a standard implicit-solvent tool for assessing electrostatic effects in biomolecular systems, has been based on various deterministic numerical methods. Some deterministic PBE algorithms have drawbacks, which include a lack of properly assessing their accuracy, geometrical difficulties caused by discretization, and for some problems their cost in both memory and computation time. Our original stochastic method resolves some of these difficulties by solving the PBE using the Monte Carlo method (MCM). This new approach to the PBE is capable of efficiently solving complex, multi-domain and salt-dependent problems in biomolecular continuum electrostatics to high precision. Here we improve upon our novel stochastic approach by simultaneouly computating of electrostatic potential and solvation free energies at different ionic concentrations through correlated Monte Carlo (MC) sampling. By using carefully constructed correlated random walks in our algorithm, we can actually compute the solution to a standard system including the linearized PBE (LPBE) at all salt concentrations of interest, simultaneously. This approach not only accelerates our MCPBE algorithm, but seems to have cost and accuracy advantages over deterministic methods as well. We verify the effectiveness of this technique by applying it to two common electrostatic computations: the electrostatic potential and polar solvation free energy for calcium binding proteins that are compared

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

    SciTech Connect

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

    2016-01-07

    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.

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

    PubMed

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

    2016-01-07

    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.

  9. Counterion condensation and shape within Poisson-Boltzmann theory.

    PubMed

    Lamm, Gene; Pack, George R

    2010-07-01

    An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes. Analytical high-charge/low-salt and low-charge/high-salt limits are shown to be similar to results obtained by others based on PB or counterion condensation theory. Several important general observations concerning polyelectrolytes treated within the context of PB theory can be made including: (1) all charged surfaces display some counterion condensation for finite electrolyte concentration, (2) the effect of surface geometry is described primarily by the sum of the Debye constant and the mean curvature of the surface, (3) two surfaces with the same surface charge density and mean curvature condense approximately identical fractions of counterions, (4) the amount of condensation is not determined by a predefined "condensation distance" although such a distance can be determined uniquely from it, and (5) substantial condensation occurs if the Debye constant of the electrolyte is much less than the mean curvature of a highly charged polyelectrolyte.

  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. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.

    PubMed

    Bertonati, Claudia; Honig, Barry; Alexov, Emil

    2007-03-15

    The salt dependence of the binding free energy of five protein-protein hetero-dimers and two homo-dimers/tetramers was calculated from numerical solutions to the Poisson-Boltzmann equation. Overall, the agreement with experimental values is very good. In all cases except one involving the highly charged lactoglobulin homo-dimer, increasing the salt concentration is found both experimentally and theoretically to decrease the binding affinity. To clarify the source of salt effects, the salt-dependent free energy of binding is partitioned into screening terms and to self-energy terms that involve the interaction of the charge distribution of a monomer with its own ion atmosphere. In six of the seven complexes studied, screening makes the largest contribution but self-energy effects can also be significant. The calculated salt effects are found to be insensitive to force-field parameters and to the internal dielectric constant assigned to the monomers. Nonlinearities due to high charge densities, which are extremely important in the binding of proteins to negatively charged membrane surfaces and to nucleic acids, make much smaller contributions to the protein-protein complexes studied here, with the exception of highly charged lactoglobulin dimers. Our results indicate that the Poisson-Boltzmann equation captures much of the physical basis of the nonspecific salt dependence of protein-protein complexation.

  12. 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

  13. 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

  14. 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

  15. Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution.

    PubMed

    Bathe, M; Grodzinsky, A J; Tidor, B; Rutledge, G C

    2004-10-22

    Optimal linearized Poisson-Boltzmann (OLPB) theory is applied to the simulation of flexible polyelectrolytes in solution. As previously demonstrated in the contexts of the cell model [H. H. von Grunberg, R. van Roij, and G. Klein, Europhys. Lett. 55, 580 (2001)] and a particle-based model [B. Beresfordsmith, D. Y. C. Chan, and D. J. Mitchell, J. Colloid Interface Sci. 105, 216 (1985)] of charged colloids, OLPB theory is applicable to thermodynamic states at which conventional, Debye-Huckel (DH) linearization of the Poisson-Boltzmann equation is rendered invalid by violation of the condition that the electrostatic coupling energy of a mobile ion be much smaller than its thermal energy throughout space, |nu(alpha)e psi(r)|nonlinear theory where conventional DH theory fails, namely at large ratios of mean counterion density to reservoir salt density, when the Donnan potential is large. (c) 2004 American Institute of Physics.

  16. Comparison of the Nernst-Planck model and the Poisson-Boltzmann model for electroosmotic flows in microchannels.

    PubMed

    Park, H M; Lee, J S; Kim, T W

    2007-11-15

    In the analysis of electroosmotic flows, the internal electric potential is usually modeled by the Poisson-Boltzmann equation. The Poisson-Boltzmann equation is derived from the assumption of thermodynamic equilibrium where the ionic distributions are not affected by fluid flows. Although this is a reasonable assumption for steady electroosmotic flows through straight microchannels, there are some important cases where convective transport of ions has nontrivial effects. In these cases, it is necessary to adopt the Nernst-Planck equation instead of the Poisson-Boltzmann equation to model the internal electric field. In the present work, the predictions of the Nernst-Planck equation are compared with those of the Poisson-Boltzmann equation for electroosmotic flows in various microchannels where the convective transport of ions is not negligible.

  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.

  18. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

    SciTech Connect

    Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A.; Head-Gordon, Teresa

    2016-11-02

    We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.

  19. Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver

    SciTech Connect

    Zhang, Bo; Lu, Benzhuo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; McCammon, J. Andrew

    2013-01-01

    This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. Lastly, the potential of the solver is demonstrated with preliminary numerical results.

  20. Protein-ion binding process on finite macromolecular concentration. A Poisson-Boltzmann and Monte Carlo study.

    PubMed

    de Carvalho, Sidney Jurado; Fenley, Márcia O; da Silva, Fernando Luís Barroso

    2008-12-25

    Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.

  1. Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

    PubMed Central

    Pang, Xiaodong; Zhou, Huan-Xiang

    2012-01-01

    The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent. PMID:23293674

  2. Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

    PubMed

    Pang, Xiaodong; Zhou, Huan-Xiang

    2013-01-01

    The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.

  3. Ionic size effects on the Poisson-Boltzmann theory

    NASA Astrophysics Data System (ADS)

    Colla, Thiago; Nunes Lopes, Lucas; dos Santos, Alexandre P.

    2017-07-01

    In this paper, we develop a simple theory to study the effects of ionic size on ionic distributions around a charged spherical particle. We include a correction to the regular Poisson-Boltzmann equation in order to take into account the size of ions in a mean-field regime. The results are compared with Monte Carlo simulations and a density functional theory based on the fundamental measure approach and a second-order bulk expansion which accounts for electrostatic correlations. The agreement is very good even for multivalent ions. Our results show that the theory can be applied with very good accuracy in the description of ions with highly effective ionic radii and low concentration, interacting with a colloid or a nanoparticle in an electrolyte solution.

  4. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

    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 [J. Am. Chem. Soc. 58, 1486 (1936)] 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. Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here the authors 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 AMOEBA 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 150mM salt lowered the electrostatic solvation energy between 2 and 13kcal /mole, depending on

  5. 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

  6. Ion-Conserving Modified Poisson-Boltzmann Theory Considering a Steric Effect in an Electrolyte

    NASA Astrophysics Data System (ADS)

    Sugioka, Hideyuki

    2016-12-01

    The modified Poisson-Nernst-Planck (MPNP) and modified Poisson-Boltzmann (MPB) equations are well known as fundamental equations that consider a steric effect, which prevents unphysical ion concentrations. However, it is unclear whether they are equivalent or not. To clarify this problem, we propose an improved free energy formulation that considers a steric limit with an ion-conserving condition and successfully derive the ion-conserving modified Poisson-Boltzmann (IC-MPB) equations that are equivalent to the MPNP equations. Furthermore, we numerically examine the equivalence by comparing between the IC-MPB solutions obtained by the Newton method and the steady MPNP solutions obtained by the finite-element finite-volume method. A surprising aspect of our finding is that the MPB solutions are much different from the MPNP (IC-MPB) solutions in a confined space. We consider that our findings will significantly contribute to understanding the surface science between solids and liquids.

  7. 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

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

    PubMed Central

    Boschitsch, Alexander H.; Fenley, Marcia O.

    2011-01-01

    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

  9. Slits, plates, and Poisson-Boltzmann theory in a local formulation of nonlocal electrostatics.

    PubMed

    Paillusson, Fabien; Blossey, Ralf

    2010-11-01

    Polar liquids like water carry a characteristic nanometric length scale, the correlation length of orientation polarizations. Continuum theories that can capture this feature commonly run under the name of "nonlocal" electrostatics since their dielectric response is characterized by a scale-dependent dielectric function ε(q), where q is the wave vector; the Poisson(-Boltzmann) equation then turns into an integro-differential equation. Recently, "local" formulations have been put forward for these theories and applied to water, solvated ions, and proteins. We review the local formalism and show how it can be applied to a structured liquid in slit and plate geometries, and solve the Poisson-Boltzmann theory for a charged plate in a structured solvent with counterions. Our results establish a coherent picture of the local version of nonlocal electrostatics and show its ease of use when compared to the original formulation.

  10. Phase coexistence in colloidal suspensions: an analytic Poisson-Boltzmann treatment.

    PubMed

    Knott, M; Ford, I J

    2001-03-01

    We solve the linearized Poisson-Boltzmann equation analytically, subject to justifiable approximations, for a suspension containing a large number of identical spherical macroions under conditions of constant surface charge and zero added salt, in order to investigate the phase behavior of charge-stabilized colloidal suspensions. Our results for the electrostatic part of the Helmholtz free energy lead to an interaction which resembles the intermolecular interaction in the theory of molecular fluids. When combined with the ideal gas free energy of the counterions, this produces a van der Waals loop in the pV diagram, indicating coexistence between phases with different densities, for certain values of the macroion radius and charge. We also derive an expression for the surface potential of the macroions, and clarify the interpretation of the Poisson-Boltzmann equation.

  11. Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations

    PubMed Central

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

    2012-01-01

    Grid dependence in numerical reaction field energies and solvation forces is a well-known limitation in the finite-difference Poisson-Boltzmann methods. In this study we have investigated several numerical strategies to overcome the limitation. Specifically, we have included trimer arc dots during analytical molecular surface generation to improve the convergence of numerical reaction field energies and solvation forces. We have also utilized the level set function to trace the molecular surface implicitly to simplify the numerical mapping of the grid-independent solvent excluded surface. We have further explored to combine the weighted harmonic averaging of boundary dielectrics with a charge-based approach to improve the convergence and stability of numerical reaction field energies and solvation forces. Our test data show that the convergence and stability in both numerical energies and forces can be improved significantly when the combined strategy is applied to either the Poisson equation or the full Poisson-Boltzmann equation. PMID:23185142

  12. The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations.

    PubMed

    Tjong, Harianto; Zhou, Huang-Xiang

    2006-11-28

    The Poisson-Boltzmann equation gives the electrostatic free energy of a solute molecule (with dielectric constant epsilon(l)) solvated in a continuum solvent (with dielectric constant epsilon(s)). Here a simple formula is presented that accurately predicts the electrostatic free energy for all combinations of epsilon(l) and epsilon(s) from the calculation on a single set of epsilon(l) and epsilon(s) values.

  13. The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

    PubMed Central

    Kirmizialtin, Serdal; Silalahi, Alexander R.J.; Elber, Ron; Fenley, Marcia O.

    2012-01-01

    The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 Å away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg2+ distributions are still at significant variances for shorter distances. PMID:22385854

  14. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

    PubMed

    Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

    2016-11-02

    We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc.

  15. Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver

    DOE PAGES

    Zhang, Bo; Lu, Benzhuo; Cheng, Xiaolin; ...

    2013-01-01

    This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. Lastly, the potential of the solver is demonstrated with preliminary numericalmore » results.« less

  16. Poisson-Boltzmann model of electrolytes containing uniformly charged spherical nanoparticles

    NASA Astrophysics Data System (ADS)

    Bohinc, Klemen; Volpe Bossa, Guilherme; Gavryushov, Sergei; May, Sylvio

    2016-12-01

    Like-charged macromolecules typically repel each other in aqueous solutions that contain small mobile ions. The interaction tends to turn attractive if mobile ions with spatially extended charge distributions are added. Such systems can be modeled within the mean-field Poisson-Boltzmann formalism by explicitly accounting for charge-charge correlations within the spatially extended ions. We consider an aqueous solution that contains a mixture of spherical nanoparticles with uniform surface charge density and small mobile salt ions, sandwiched between two like-charged planar surfaces. We perform the minimization of an appropriate free energy functional, which leads to a non-linear integral-differential equation for the electrostatic potential that we solve numerically and compare with predictions from Monte Carlo simulations. Nanoparticles with uniform surface charge density are contrasted with nanoparticles that have all their charges relocated at the center. Our mean-field model predicts that only the former (especially when large and highly charged particles) but not the latter are able to mediate attractive interactions between like-charged planar surfaces. We also demonstrate that at high salt concentration attractive interactions between like-charged planar surfaces turn into repulsion.

  17. Poisson-Boltzmann model of electrolytes containing uniformly charged spherical nanoparticles.

    PubMed

    Bohinc, Klemen; Volpe Bossa, Guilherme; Gavryushov, Sergei; May, Sylvio

    2016-12-21

    Like-charged macromolecules typically repel each other in aqueous solutions that contain small mobile ions. The interaction tends to turn attractive if mobile ions with spatially extended charge distributions are added. Such systems can be modeled within the mean-field Poisson-Boltzmann formalism by explicitly accounting for charge-charge correlations within the spatially extended ions. We consider an aqueous solution that contains a mixture of spherical nanoparticles with uniform surface charge density and small mobile salt ions, sandwiched between two like-charged planar surfaces. We perform the minimization of an appropriate free energy functional, which leads to a non-linear integral-differential equation for the electrostatic potential that we solve numerically and compare with predictions from Monte Carlo simulations. Nanoparticles with uniform surface charge density are contrasted with nanoparticles that have all their charges relocated at the center. Our mean-field model predicts that only the former (especially when large and highly charged particles) but not the latter are able to mediate attractive interactions between like-charged planar surfaces. We also demonstrate that at high salt concentration attractive interactions between like-charged planar surfaces turn into repulsion.

  18. Poisson-Boltzmann theory of charged colloids: limits of the cell model for salty suspensions

    NASA Astrophysics Data System (ADS)

    Denton, A. R.

    2010-09-01

    Thermodynamic properties of charge-stabilized colloidal suspensions and polyelectrolyte solutions are commonly modelled by implementing the mean-field Poisson-Boltzmann (PB) theory within a cell model. This approach models a bulk system by a single macroion, together with counterions and salt ions, confined to a symmetrically shaped, electroneutral cell. While easing numerical solution of the nonlinear PB equation, the cell model neglects microion-induced interactions and correlations between macroions, precluding modelling of macroion ordering phenomena. An alternative approach, which avoids the artificial constraints of cell geometry, exploits the mapping of a macroion-microion mixture onto a one-component model of pseudo-macroions governed by effective interparticle interactions. In practice, effective-interaction models are usually based on linear-screening approximations, which can accurately describe strong nonlinear screening only by incorporating an effective (renormalized) macroion charge. Combining charge renormalization and linearized PB theories, in both the cell model and an effective-interaction (cell-free) model, we compute osmotic pressures of highly charged colloids and monovalent microions, in Donnan equilibrium with a salt reservoir, over a range of concentrations. By comparing predictions with primitive model simulation data for salt-free suspensions, and with predictions from nonlinear PB theory for salty suspensions, we chart the limits of both the cell model and linear-screening approximations in modelling bulk thermodynamic properties. Up to moderately strong electrostatic couplings, the cell model proves accurate for predicting osmotic pressures of deionized (counterion-dominated) suspensions. With increasing salt concentration, however, the relative contribution of macroion interactions to the osmotic pressure grows, leading predictions from the cell and effective-interaction models to deviate. No evidence is found for a liquid

  19. Dipolar Poisson-Boltzmann approach to ionic solutions: a mean field and loop expansion analysis.

    PubMed

    Levy, Amir; Andelman, David; Orland, Henri

    2013-10-28

    We study the variation of the dielectric response of ionic aqueous solutions as function of their ionic strength. The effect of salt on the dielectric constant appears through the coupling between ions and dipolar water molecules. On a mean-field level, we account for any internal charge distribution of particles. The dipolar degrees of freedom are added to the ionic ones and result in a generalization of the Poisson-Boltzmann (PB) equation called the Dipolar PB (DPB). By looking at the DPB equation around a fixed point-like ion, a closed-form formula for the dielectric constant is obtained. We express the dielectric constant using the "hydration length" that characterizes the hydration shell of dipoles around ions, and thus the strength of the dielectric decrement. The DPB equation is then examined for three additional cases: mixture of solvents, polarizable medium, and ions of finite size. Employing field-theoretical methods, we expand the Gibbs free-energy to first order in a loop expansion and calculate self-consistently the dielectric constant. For pure water, the dipolar fluctuations represent an important correction to the mean-field value and good agreement with the water dielectric constant is obtained. For ionic solutions we predict analytically the dielectric decrement that depends on the ionic strength in a nonlinear way. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles. A linear dependence of the dielectric constant on the salt concentration is observed at low salinity, and a noticeable deviation from linearity can be seen for ionic strength above 1 M, in agreement with experiments.

  20. A simple algorithm for calculating electrical double layer interactions in asymmetric electrolytes-Poisson-Boltzmann theory.

    PubMed

    Chan, Derek Y C

    2002-01-15

    A simple, general, and numerically robust algorithm is presented for calculating the disjoining pressure and interaction free energy per unit area between two identically charged flat plates due to electrical double layer interactions according to the nonlinear Poisson-Boltzmann theory. The result is applicable to electrolytes with any number of ionic species having any combination of valencies as well as to constant potential, constant charge, or charge regulation boundary conditions on the plates. The algorithm is very simple to implement on commonly available numerical software environments and is therefore particularly suitable for use in data analysis.

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

    PubMed

    Sharma, P; Mišković, Z L

    2015-10-07

    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.

  2. A Poisson-Boltzmann dynamics method with nonperiodic boundary condition

    NASA Astrophysics Data System (ADS)

    Lu, Qiang; Luo, Ray

    2003-12-01

    We have developed a well-behaved and efficient finite difference Poisson-Boltzmann dynamics method with a nonperiodic boundary condition. This is made possible, in part, by a rather fine grid spacing used for the finite difference treatment of the reaction field interaction. The stability is also made possible by a new dielectric model that is smooth both over time and over space, an important issue in the application of implicit solvents. In addition, the electrostatic focusing technique facilitates the use of an accurate yet efficient nonperiodic boundary condition: boundary grid potentials computed by the sum of potentials from individual grid charges. Finally, the particle-particle particle-mesh technique is adopted in the computation of the Coulombic interaction to balance accuracy and efficiency in simulations of large biomolecules. Preliminary testing shows that the nonperiodic Poisson-Boltzmann dynamics method is numerically stable in trajectories at least 4 ns long. The new model is also fairly efficient: it is comparable to that of the pairwise generalized Born solvent model, making it a strong candidate for dynamics simulations of biomolecules in dilute aqueous solutions. Note that the current treatment of total electrostatic interactions is with no cutoff, which is important for simulations of biomolecules. Rigorous treatment of the Debye-Hückel screening is also possible within the Poisson-Boltzmann framework: its importance is demonstrated by a simulation of a highly charged protein.

  3. 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

    2015-02-05

    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.

  4. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems

    PubMed Central

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

    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://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. PMID:20532187

  5. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations.

    PubMed

    Lu, Benzhuo; McCammon, J Andrew

    2007-05-01

    A patch representation differing from the traditional treatments in the boundary element method (BEM) is presented, which we call the constant "node patch" method. Its application to solving the Poisson-Boltzmann equation (PBE) demonstrates considerable improvement in speed compared with the constant element and linear element methods. In addition, for the node-based BEMs, we propose an efficient interpolation method for the calculation of the electrostatic stress tensor and PB force on the solvated molecular surface. This force calculation is simply an O(N) algorithm (N is the number of elements). Moreover, our calculations also show that the geometric factor correction in the boundary integral equations significantly increases the accuracy of the potential solution on the boundary, and thereby the PB force calculation.

  6. 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.

  7. 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

    2010-06-01

    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://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. Program summaryProgram title: AFMPB: Adaptive fast multipole Poisson-Boltzmann solver Catalogue identifier: AEGB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 453 649 No. of bytes in distributed program, including test data, etc.: 8 764 754 Distribution format: tar.gz Programming language: Fortran Computer: Any Operating system: Any RAM: Depends on the size of the discretized biomolecular system Classification: 3 External routines: Pre- and post-processing tools are required for generating the boundary elements and for visualization. Users can use MSMS ( http://www.scripps.edu/~sanner/html/msms_home.html) for pre-processing, and VMD ( http://www.ks.uiuc.edu/Research/vmd/) for visualization. Sub-programs included: An iterative Krylov subspace solvers package from SPARSKIT by Yousef Saad ( http://www-users.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html), and the fast multipole methods subroutines from FMMSuite ( http

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Ambia-Garrido, Joaquin; Montgomery Pettitt, Bernard

    2007-10-01

    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, avoiding the DNA folding problem.

  10. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. 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

  12. 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.

  13. A Dynamic Poisson-Boltzmann Method of Simulating Polypeptides

    NASA Astrophysics Data System (ADS)

    Campbell, Victoria S.; Grayce, Christopher J.

    1998-03-01

    We present a method of performing molecular dynamics simulations of charged polymeric species in solution such as polypeptides that takes into account the instantaneous response of the ionic atmosphere to fluctuations in polymer conformation without employing explicit solvent and salt ions. Using density functional theory we write the free energy of the ionic atmosphere around the polymer as a functional of its density in the linearized Poisson-Boltzmann limit. We then add to a normal MD simulation of a charged polymer extra degrees of freedom, namely the parameters describing the instantaneous ion atomosphere density. These parameters vary dynamically under the influence of the coupled mechanical and thermodynamic forces, so that the instantaneous variations in the ionic atmosphere as the polymer conformation fluctuates are described. Using this method MD simulations were carried out on a model polypeptide system and both conformational properties as well as the electric field generated by this method were compared to results obtained by using fixed Debye-Huckel potentials.

  14. AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

    PubMed Central

    Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

    2011-01-01

    In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

  15. Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid.

    PubMed

    Sahin, Buyukdagli; Ralf, Blossey

    2014-07-16

    We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent which generalizes the point-like dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (1996 J. Phys. Chem. 100 2612) and Abrashkin et al (2007 Phys. Rev. Lett. 99 077801). We formulate a nonlocal Poisson-Boltzmann equation (NLPB) and study both linear and nonlinear dielectric response in this model for the case of a single plane geometry. Our results shed light on the relevance of nonlocal versus nonlinear effects in continuum models of material electrostatics.

  16. Free-energy functionals of the electrostatic potential for Poisson-Boltzmann theory.

    PubMed

    Jadhao, Vikram; Solis, Francisco J; de la Cruz, Monica Olvera

    2013-08-01

    In simulating charged systems, it is often useful to treat some ionic components of the system at the mean-field level and solve the Poisson-Boltzmann (PB) equation to get their respective density profiles. The numerically intensive task of solving the PB equation at each step of the simulation can be bypassed using variational methods that treat the electrostatic potential as a dynamic variable. But such approaches require the access to a true free-energy functional: a functional that not only provides the correct solution of the PB equation upon extremization, but also evaluates to the true free energy of the system at its minimum. Moreover, the numerical efficiency of such procedures is further enhanced if the free-energy functional is local and is expressed in terms of the electrostatic potential. Existing PB functionals of the electrostatic potential, while possessing the local structure, are not free-energy functionals. We present a variational formulation with a local free-energy functional of the potential. In addition, we also construct a nonlocal free-energy functional of the electrostatic potential. These functionals are suited for employment in simulation schemes based on the ideas of dynamical optimization.

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

    PubMed

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

    2009-06-09

    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.

  18. Ca/Na selectivity coefficients from the Poisson-Boltzmann theory

    NASA Astrophysics Data System (ADS)

    Hedström, Magnus; Karnland, Ola

    As a model for ion equilibrium in montmorillonite, the Poisson-Boltzmann (PB) equation was solved for two parallel charged surfaces in contact with an external NaCl/CaCl 2 mixed solution. The ion concentration profiles in the montmorillonite interlayer were obtained from the PB equation and integration of those gave the occupancy of Na + and Ca 2+ in the clay. That information together with the composition of the external electrolyte were then used for the calculation of the Gaines-Thomas selectivity coefficient K GT. The predictions from the model were compared to experimental data from batch as well as compacted conditions, and the agreement was generally good. With a surface layer-charge density of one unit charge per 145 Å 2, which is close to the value for Wyoming-type montmorillonite, the calculated selectivity coefficients were found to vary from about 4 in batch to 8 in compacted montmorillonite with dry density ∼1700 kg/m 3. From the point of view of assessing the evolution, with regard to sodium-calcium ion exchange, of the bentonite buffer in a repository for spent nuclear fuel, these results justify the use of data obtained in batch experiments.

  19. 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.

  20. 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.

  1. 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

  2. Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach.

    PubMed

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

    2010-08-04

    Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to understanding the binding of charged ligands to nucleic acids. Because the linear Poisson-Boltzmann equation (PBE) and the more approximate generalized Born approach are applied routinely to nucleic acids and their interactions with charged ligands, the reliability of these methods is examined vis-à-vis an efficient nonlinear PBE method. For moderate salt concentrations, the negative derivative, SK(pred), of the electrostatic binding free energy, DeltaG(el), with respect to the logarithm of the 1:1 salt concentration, [M(+)], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is shown to be consistently negative and virtually constant over the salt range considered (0.1-0.4 M NaCl). The magnitude of SK(pred) is approximately equal to the charge on the drug, as predicted by counterion condensation theory (CCT) and observed in thermodynamic binding studies. The linear PBE is shown to overestimate the magnitude of SK(pred), whereas the nonlinear PBE closely matches the experimental results. The PBE predictions of SK(pred) were not correlated with DeltaG(el) in the presence of a dielectric discontinuity, as would be expected from the CCT. Because this correlation does not hold, parameterizing the PBE predictions of DeltaG(el) against the reported experimental data is not possible. Moreover, the common practice of extracting the electrostatic and nonelectrostatic contributions to the binding of charged ligands to biopolyelectrolytes based on the simple relation between experimental SK values and the electrostatic binding free energy that is based on CCT is called into question by the results presented here. Although the rigid-docking nonlinear PB calculations provide reliable predictions of SK(pred), at least for the charged ligand-nucleic acid complexes studied here, accurate estimates of DeltaG(el) will require further development in theoretical and experimental

  3. 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.

  4. Comparison of a hydrogel model to the Poisson-Boltzmann cell model

    NASA Astrophysics Data System (ADS)

    Claudio, Gil C.; Kremer, Kurt; Holm, Christian

    2009-09-01

    We have investigated a single charged microgel in aqueous solution with a combined simulational model and Poisson-Boltzmann theory. In the simulations we use a coarse-grained charged bead-spring model in a dielectric continuum, with explicit counterions and full electrostatic interactions under periodic and nonperiodic boundary conditions. The Poisson-Boltzmann hydrogel model is that of a single charged colloid confined to a spherical cell where the counterions are allowed to enter the uniformly charged sphere. In order to investigate the origin of the differences these two models may give, we performed a variety of simulations of different hydrogel models which were designed to test for the influence of charge correlations, excluded volume interactions, arrangement of charges along the polymer chains, and thermal fluctuations in the chains of the gel. These intermediate models systematically allow us to connect the Poisson-Boltzmann cell model to the bead-spring model hydrogel model in a stepwise manner thereby testing various approximations. Overall, the simulational results of all these hydrogel models are in good agreement, especially for the number of confined counterions within the gel. Our results support the applicability of the Poisson-Boltzmann cell model to study ionic properties of hydrogels under dilute conditions.

  5. Comparison of a hydrogel model to the Poisson-Boltzmann cell model.

    PubMed

    Claudio, Gil C; Kremer, Kurt; Holm, Christian

    2009-09-07

    We have investigated a single charged microgel in aqueous solution with a combined simulational model and Poisson-Boltzmann theory. In the simulations we use a coarse-grained charged bead-spring model in a dielectric continuum, with explicit counterions and full electrostatic interactions under periodic and nonperiodic boundary conditions. The Poisson-Boltzmann hydrogel model is that of a single charged colloid confined to a spherical cell where the counterions are allowed to enter the uniformly charged sphere. In order to investigate the origin of the differences these two models may give, we performed a variety of simulations of different hydrogel models which were designed to test for the influence of charge correlations, excluded volume interactions, arrangement of charges along the polymer chains, and thermal fluctuations in the chains of the gel. These intermediate models systematically allow us to connect the Poisson-Boltzmann cell model to the bead-spring model hydrogel model in a stepwise manner thereby testing various approximations. Overall, the simulational results of all these hydrogel models are in good agreement, especially for the number of confined counterions within the gel. Our results support the applicability of the Poisson-Boltzmann cell model to study ionic properties of hydrogels under dilute conditions.

  6. 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.

  7. Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels.

    PubMed

    Corry, Ben; Kuyucak, Serdar; Chung, Shin-Ho

    2003-06-01

    We demonstrated previously that the two continuum theories widely used in modeling biological ion channels give unreliable results when the radius of the conduit is less than two Debye lengths. The reason for this failure is the neglect of surface charges on the protein wall induced by permeating ions. Here we attempt to improve the accuracy of the Poisson-Boltzmann and Poisson-Nernst-Planck theories, when applied to channel-like environments, by including a specific dielectric self-energy term to overcome spurious shielding effects inherent in these theories. By comparing results with Brownian dynamics simulations, we show that the inclusion of an additional term in the equations yields significant qualitative improvements. The modified theories perform well in very wide and very narrow channels, but are less successful at intermediate sizes. The situation is worse in multi-ion channels because of the inability of the continuum theories to handle the ion-to-ion interactions correctly. Thus, further work is required if these continuum theories are to be reliably salvaged for quantitative studies of biological ion channels in all situations.

  8. Dielectric Self-Energy in Poisson-Boltzmann and Poisson-Nernst-Planck Models of Ion Channels

    PubMed Central

    Corry, Ben; Kuyucak, Serdar; Chung, Shin-Ho

    2003-01-01

    We demonstrated previously that the two continuum theories widely used in modeling biological ion channels give unreliable results when the radius of the conduit is less than two Debye lengths. The reason for this failure is the neglect of surface charges on the protein wall induced by permeating ions. Here we attempt to improve the accuracy of the Poisson-Boltzmann and Poisson-Nernst-Planck theories, when applied to channel-like environments, by including a specific dielectric self-energy term to overcome spurious shielding effects inherent in these theories. By comparing results with Brownian dynamics simulations, we show that the inclusion of an additional term in the equations yields significant qualitative improvements. The modified theories perform well in very wide and very narrow channels, but are less successful at intermediate sizes. The situation is worse in multi-ion channels because of the inability of the continuum theories to handle the ion-to-ion interactions correctly. Thus, further work is required if these continuum theories are to be reliably salvaged for quantitative studies of biological ion channels in all situations. PMID:12770869

  9. How accurate is Poisson-Boltzmann theory for monovalent ions near highly charged interfaces?

    PubMed

    Bu, Wei; Vaknin, David; Travesset, Alex

    2006-06-20

    Surface sensitive synchrotron X-ray scattering studies were performed to obtain the distribution of monovalent ions next to a highly charged interface. A lipid phosphate (dihexadecyl hydrogen-phosphate) was spread as a monolayer at the air-water interface to control surface charge density. Using anomalous reflectivity off and at the L3 Cs+ resonance, we provide spatial counterion (Cs+) distributions next to the negatively charged interfaces. Five decades in bulk concentrations are investigated, demonstrating that the interfacial distribution is strongly dependent on bulk concentration. We show that this is due to the strong binding constant of hydronium H3O+ to the phosphate group, leading to proton-transfer back to the phosphate group and to a reduced surface charge. The increase of Cs+ concentration modifies the contact value potential, thereby causing proton release. This process effectively modifies surface charge density and enables exploration of ion distributions as a function of effective surface charge-density. The experimentally obtained ion distributions are compared to distributions calculated by Poisson-Boltzmann theory accounting for the variation of surface charge density due to proton release and binding. We also discuss the accuracy of our experimental results in discriminating possible deviations from Poisson-Boltzmann theory.

  10. 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.

  11. Integrable nonlinear relativistic equations

    NASA Astrophysics Data System (ADS)

    Hadad, Yaron

    This work focuses on three nonlinear relativistic equations: the symmetric Chiral field equation, Einstein's field equation for metrics with two commuting Killing vectors and Einstein's field equation for diagonal metrics that depend on three variables. The symmetric Chiral field equation is studied using the Zakharov-Mikhailov transform, with which its infinitely many local conservation laws are derived and its solitons on diagonal backgrounds are studied. It is also proven that it is equivalent to a novel equation that poses a fascinating similarity to the Sinh-Gordon equation. For the 1+1 Einstein equation the Belinski-Zakharov transformation is explored. It is used to derive explicit formula for N gravitational solitons on arbitrary diagonal background. In particular, the method is used to derive gravitational solitons on the Einstein-Rosen background. The similarities and differences between the attributes of the solitons of the symmetric Chiral field equation and those of the 1+1 Einstein equation are emphasized, and their origin is pointed out. For the 1+2 Einstein equation, new equations describing diagonal metrics are derived and their compatibility is proven. Different gravitational waves are studied that naturally extend the class of Bondi-Pirani-Robinson waves. It is further shown that the Bondi-Pirani-Robinson waves are stable with respect to perturbations of the spacetime. Their stability is closely related to the stability of the Schwarzschild black hole and the relation between the two allows to conjecture about the stability of a wide range of gravitational phenomena. Lastly, a new set of equations that describe weak gravitational waves is derived. This new system of equations is closely and fundamentally connected with the nonlinear Schrodinger equation and can be properly called the nonlinear Schrodinger-Einstein equations. A few preliminary solutions are constructed.

  12. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation.

    PubMed

    Lu, Ben Zhuo; Chen, Wei Zu; Wang, Cun Xin; Xu, Xiao-jie

    2002-08-15

    The electrostatic force including the intramolecular Coulombic interactions and the electrostatic contribution of solvation effect were entirely calculated by using the finite difference Poisson-Boltzmann method (FDPB), which was incorporated into the GROMOS96 force field to complete a new finite difference stochastic dynamics procedure (FDSD). Simulations were performed on an insulin dimer. Different relative dielectric constants were successively assigned to the protein interior; a value of 17 was selected as optimal for our system. The simulation data were analyzed and compared with those obtained from 500-ps molecular dynamics (MD) simulation with explicit water and a 500-ps conventional stochastic dynamics (SD) simulation without the mean solvent force. The results indicate that the FDSD method with GROMOS96 force field is suitable to study the dynamics and structure of proteins in solution if used with the optimal protein dielectric constant. Copyright 2002 Wiley-Liss, Inc.

  13. Incorporation of excluded-volume correlations into Poisson-Boltzmann theory.

    PubMed

    Antypov, Dmytro; Barbosa, Marcia C; Holm, Christian

    2005-06-01

    We investigate the effect of excluded-volume interactions on the electrolyte distribution around a charged macroion. First, we introduce a criterion for determining when hard-core effects should be taken into account beyond standard mean-field Poisson-Boltzmann (PB) theory. Next, we demonstrate that several commonly proposed local-density-functional approaches for excluded-volume interactions cannot be used for this purpose. Instead, we employ a nonlocal excess free energy by using a simple constant-weight approach. We compare the ion distribution and osmotic pressure predicted by this theory with Monte Carlo simulations. They agree very well for weakly developed correlations and give the correct layering effect for stronger ones. In all investigated cases our simple weighted-density theory yields more realistic results than the standard PB approach, whereas all local density theories do not improve on the PB density profiles, but on the contrary, deviate even more from the simulation results.

  14. Incorporating headgroup structure into the Poisson-Boltzmann model of charged lipid membranes

    NASA Astrophysics Data System (ADS)

    Wang, Muyang; Chen, Er-Qiang; Yang, Shuang; May, Sylvio

    2013-07-01

    Charged lipids often possess a complex headgroup structure with several spatially separated charges and internal conformational degrees of freedom. We propose a headgroup model consisting of two rod-like segments of the same length that form a flexible joint, with three charges of arbitrary sign and valence located at the joint and the two terminal positions. One terminal charge is firmly anchored at the polar-apolar interface of the lipid layer whereas the other two benefit from the orientational degrees of freedom of the two headgroup segments. This headgroup model is incorporated into the mean-field continuum Poisson-Boltzmann formalism of the electric double layer. For sufficiently small lengths of the two rod-like segments a closed-form expression of the charging free energy is calculated. For three specific examples—a zwitterionic headgroup with conformational freedom and two headgroups that carry an excess charge—we analyze and discuss conformational properties and electrostatic free energies.

  15. Perturbed nonlinear differential equations

    NASA Technical Reports Server (NTRS)

    Proctor, T. G.

    1974-01-01

    For perturbed nonlinear systems, a norm, other than the supremum norm, is introduced on some spaces of continuous functions. This makes possible the study of new types of behavior. A study is presented on a perturbed nonlinear differential equation defined on a half line, and the existence of a family of solutions with special boundedness properties is established. The ideas developed are applied to the study of integral manifolds, and examples are given.

  16. 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.

  17. 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.

  18. 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.

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

    PubMed

    Koehl, Patrice; Orland, Henri; Delarue, Marc

    2011-08-07

    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 χ(1) 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.

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

    PubMed Central

    Koehl, Patrice; Orland, Henri; Delarue, Marc

    2011-01-01

    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. PMID:21823735

  1. 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

    2013-10-03

    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.

  2. Perturbed nonlinear differential equations

    NASA Technical Reports Server (NTRS)

    Proctor, T. G.

    1972-01-01

    The existence of a solution defined for all t and possessing a type of boundedness property is established for the perturbed nonlinear system y = f(t,y) + F(t,y). The unperturbed system x = f(t,x) has a dichotomy in which some solutions exist and are well behaved as t increases to infinity, and some solution exists and are well behaved as t decreases to minus infinity. A similar study is made for a perturbed nonlinear differential equation defined on a half line, R+, and the existence of a family of solutions with special boundedness properties is established. The ideas are applied to integral manifolds.

  3. Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.

    PubMed

    Nguyen, Duc D; Wang, Bao; Wei, Guo-Wei

    2017-05-15

    Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  4. 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.

  5. Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics.

    PubMed Central

    Moy, G; Corry, B; Kuyucak, S; Chung, S H

    2000-01-01

    Continuum theories of electrolytes are widely used to describe physical processes in various biological systems. Although these are well-established theories in macroscopic situations, it is not clear from the outset that they should work in small systems whose dimensions are comparable to or smaller than the Debye length. Here, we test the validity of the mean-field approximation in Poisson-Boltzmann theory by comparing its predictions with those of Brownian dynamics simulations. For this purpose we use spherical and cylindrical boundaries and a catenary shape similar to that of the acetylcholine receptor channel. The interior region filled with electrolyte is assumed to have a high dielectric constant, and the exterior region representing protein a low one. Comparisons of the force on a test ion obtained with the two methods show that the shielding effect due to counterions is overestimated in Poisson-Boltzmann theory when the ion is within a Debye length of the boundary. As the ion gets closer to the boundary, the discrepancy in force grows rapidly. The implication for membrane channels, whose radii are typically smaller than the Debye length, is that Poisson-Boltzmann theory cannot be used to obtain reliable estimates of the electrostatic potential energy and force on an ion in the channel environment. PMID:10777732

  6. Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics.

    PubMed

    Moy, G; Corry, B; Kuyucak, S; Chung, S H

    2000-05-01

    Continuum theories of electrolytes are widely used to describe physical processes in various biological systems. Although these are well-established theories in macroscopic situations, it is not clear from the outset that they should work in small systems whose dimensions are comparable to or smaller than the Debye length. Here, we test the validity of the mean-field approximation in Poisson-Boltzmann theory by comparing its predictions with those of Brownian dynamics simulations. For this purpose we use spherical and cylindrical boundaries and a catenary shape similar to that of the acetylcholine receptor channel. The interior region filled with electrolyte is assumed to have a high dielectric constant, and the exterior region representing protein a low one. Comparisons of the force on a test ion obtained with the two methods show that the shielding effect due to counterions is overestimated in Poisson-Boltzmann theory when the ion is within a Debye length of the boundary. As the ion gets closer to the boundary, the discrepancy in force grows rapidly. The implication for membrane channels, whose radii are typically smaller than the Debye length, is that Poisson-Boltzmann theory cannot be used to obtain reliable estimates of the electrostatic potential energy and force on an ion in the channel environment.

  7. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.

    PubMed

    Wang, Jun; Tan, Chunhu; Chanco, Emmanuel; Luo, Ray

    2010-02-07

    A critical issue in the development of implicit solvent models is their quality in realistic simulations of non-trivial systems. In a previous study, we quantitatively compared the reaction field energies of static structures calculated with the Poisson-Boltzmann implicit solvent and the TIP3P explicit solvent and found an overall agreement, though a discrepancy was also observed in the electrostatic potentials of mean force for salt-bridging and hydrogen-bonding dimers (see J. Phys. Chem. B, 2006, 110, 18680). In this study, we are interested in how the implicit solvent performs in molecular dynamics simulations. To guarantee sampling convergence in simulated observables in the explicit solvent, we explored to use a high-temperature constant-volume simulation setting at 450 K but with the water density at 300 K. The relevance of the artificial simulation setting to room-temperature simulations of biomolecules was first investigated by systematic comparisons of the polar and nonpolar solvation free energies of 23 amino acid analogues at 300 K and 450 K, respectively. Assisted by the artificial simulation setting, we found the simulated secondary structure populations agree very well between the implicit and explicit solvents for tested dipeptides and peptides. In addition, the agreement in the populations of hydrophobic contacts is reasonable. However, our analysis also shows that the populations of the salt bridges are too low in the implicit solvent. The low salt-bridge population perhaps results from a combination of the atomic-centered modified van der Waals surface and the small solvent probe radius optimized to best reproduce the polar potential of mean force profiles. In addition, the lower accuracy of the electrostatic forces and the lack of water-bridged minima in the implicit solvents may also contribute to the instability of the salt bridge populations.

  8. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics.

    PubMed

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

    2008-12-15

    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 epsilon(r) in the solvent region and also in a variable solvent density rho(r) 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 rapid than that from molecular dynamics, applications of a density-profile-based solvation energy to the identification of the true structure among a set of decoys become computationally feasible. Various possible improvements of the model are discussed, as well as extensions of the formalism to treat mixtures of dipolar solvents of different sizes.

  9. 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.

  10. 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

  11. A modified Poisson-Boltzmann analysis of the capacitance behavior of the electric double layer at low temperatures.

    PubMed

    Bhuiyan, L B; Outhwaite, C W; Henderson, D

    2005-07-15

    The modified Poisson-Boltzmann theory is used to analyze the anomalous behavior of the electric double layer capacitance for small surface charge at low temperatures and densities. Good agreement is found with simulation and recent density-functional theory results. Negative adsorption is also found in line with theory and simulation. An unsatisfactory feature is the relatively poor structure in this region due to the inherent approximations in the theory. This feature is unimportant in relation to the capacitance results but has implications when calculating adsorption properties.

  12. Nonlinear equations of 'variable type'

    NASA Astrophysics Data System (ADS)

    Larkin, N. A.; Novikov, V. A.; Ianenko, N. N.

    In this monograph, new scientific results related to the theory of equations of 'variable type' are presented. Equations of 'variable type' are equations for which the original type is not preserved within the entire domain of coefficient definition. This part of the theory of differential equations with partial derivatives has been developed intensively in connection with the requirements of mechanics. The relations between equations of the considered type and the problems of mathematical physics are explored, taking into account quasi-linear equations, and models of mathematical physics which lead to equations of 'variable type'. Such models are related to transonic flows, problems involving a separation of the boundary layer, gasdynamics and the van der Waals equation, shock wave phenomena, and a combustion model with a turbulent diffusion flame. Attention is also given to nonlinear parabolic equations, and nonlinear partial differential equations of the third order.

  13. A modified Poisson-Boltzmann model including charge regulation for the adsorption of ionizable polyelectrolytes to charged interfaces, applied to lysozyme adsorption on silica.

    PubMed

    Biesheuvel, P Maarten; van der Veen, Marijn; Norde, Willem

    2005-03-10

    The equilibrium adsorption of polyelectrolytes with multiple types of ionizable groups is described using a modified Poisson-Boltzmann equation including charge regulation of both the polymer and the interface. A one-dimensional mean-field model is used in which the electrostatic potential is assumed constant in the lateral direction parallel to the surface. The electrostatic potential and ionization degrees of the different ionizable groups are calculated as function of the distance from the surface after which the electric and chemical contributions to the free energy are obtained. The various interactions between small ions, surface and polyelectrolyte are self-consistently considered in the model, such as the increase in charge of polyelectrolyte and surface upon adsorption as well as the displacement of small ions and the decrease of permittivity. These interactions may lead to complex dependencies of the adsorbed amount of polyelectrolyte on pH, ionic strength, and properties of the polymer (volume, permittivity, number, and type of ionizable groups) and of the surface (number of ionizable groups, pK, Stern capacity). For the adsorption of lysozyme on silica, the model qualitatively describes the gradual increase of adsorbed amount with pH up to a maximum value at pHc, which is below the iso-electric point, as well as the sharp decrease of adsorbed amount beyond pHc. With increasing ionic strength the adsorbed amount decreases (for pH > pHc), and pHc shifts to lower values.

  14. Energetic decomposition with the generalized-born and Poisson-Boltzmann solvent models: lessons from association of G-protein components.

    PubMed

    Carrascal, Noel; Green, David F

    2010-04-22

    Continuum electrostatic models have been shown to be powerful tools in providing insight into the energetics of biomolecular processes. While the Poisson-Boltzmann (PB) equation provides a theoretically rigorous approach to computing electrostatic free energies of solution in such a model, computational cost makes its use for large ensembles of states impractical. The generalized-Born (GB) approximation provides a much faster alternative, although with a weaker theoretical framework. While much attention has been given to how GB recapitulates PB energetics for the overall stability of a biomolecule or the affinity of a complex, little attention has been given to how the contributions of individual functional groups are captured by the two methods. Accurately capturing these individual electrostatic components is essential both for the development of a mechanistic understanding of biomolecular processes and for the design of variant sequences and structures with desired properties. Here, we present a detailed comparison of the group-wise decomposition of both PB and GB electrostatic free energies of binding, using association of various components of the heterotrimeric-G-protein complex as a model. We find that, while net binding free energies are strongly correlated in the two models, the correlations of individual group contributions are highly variable; in some cases, strong correlation is seen, while in others, there is essentially none. Structurally, the GB model seems to capture the magnitude of direct, short-range electrostatic interactions quite well but performs more poorly with moderate-range "action-at-a-distance" interactions--GB has a tendency to overestimate solvent screening over moderate distances, and to underestimate the costs of desolvating charged groups somewhat removed from the binding interface. Despite this, however, GB does seem to be quite effective as a predictor of those groups that will be computed to be most significant in a PB

  15. 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.

  16. 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.

  17. DIFFUSED SOLUTE-SOLVENT INTERFACE WITH POISSON-BOLTZMANN ELECTROSTATICS: FREE-ENERGY VARIATION AND SHARP-INTERFACE LIMIT.

    PubMed

    Li, B O; Liu, Yuan

    A phase-field free-energy functional for the solvation of charged molecules (e.g., proteins) in aqueous solvent (i.e., water or salted water) is constructed. The functional consists of the solute volumetric and solute-solvent interfacial energies, the solute-solvent van der Waals interaction energy, and the continuum electrostatic free energy described by the Poisson-Boltzmann theory. All these are expressed in terms of phase fields that, for low free-energy conformations, are close to one value in the solute phase and another in the solvent phase. A key property of the model is that the phase-field interpolation of dielectric coefficient has the vanishing derivative at both solute and solvent phases. The first variation of such an effective free-energy functional is derived. Matched asymptotic analysis is carried out for the resulting relaxation dynamics of the diffused solute-solvent interface. It is shown that the sharp-interface limit is exactly the variational implicit-solvent model that has successfully captured capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states of underlying biomolecular systems as found in experiment and molecular dynamics simulations. Our phase-field approach and analysis can be used to possibly couple the description of interfacial fluctuations for efficient numerical computations of biomolecular interactions.

  18. Poisson-Boltzmann description of interaction forces and aggregation rates involving charged colloidal particles in asymmetric electrolytes.

    PubMed

    Trefalt, Gregor; Szilagyi, Istvan; Borkovec, Michal

    2013-09-15

    Forces and aggregation rates involving spherical particles are studied numerically within the theory of Derjaguin, Landau, Verwey, and Overbeek (DLVO) for asymmetric and mixed electrolytes. Thereby, the double layer interactions are treated at the Debye-Hückel (DH) and Poisson-Boltzmann (PB) levels. The DH model is applicable for weakly charged systems, and effects of ion valence enter only implicitly through the ionic strength. The PB model is necessary for more highly charged systems, and depends on the actual ionic composition. One finds that forces in asymmetric electrolytes at fixed ionic strength weaken when the valence of the counterions is increased or when the valence of the coions is decreased. In symmetric electrolytes, the effect of counterions is more important than the one of the coions. For weakly charged systems, the critical coagulation concentration (CCC) decreases with the square of the valence in symmetric electrolytes, while this decrease is weaker in asymmetric ones. With increasing charge density, the dependence of the CCC on the valence becomes stronger, but the classical Schulze-Hardy decrease with the sixths power of the valence is only recovered for unrealistically high charge densities. Mixtures of electrolytes are treated within the same framework, and one observes that already small amounts of multivalent ions affect the system considerably. An empirical mixing rule is proposed to describe the calculated CCCs. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. A perspective on streaming current in silica nanofluidic channels: Poisson-Boltzmann model versus Poisson-Nernst-Planck model.

    PubMed

    Chang, Chih-Chang; Yang, Ruey-Jen

    2009-11-15

    Choi and Kim [J. Colloid Interface Sci. 333 (2009) 672] proposed a new wall boundary condition for zeta-potential and surface charge density to describe the electrokinetic flow-induced currents in silica nanofluidic channels using the Poisson-Boltzmann (PB) model and the Poisson-Nernst-Planck (PNP) model. They showed that the results from the PNP model are in close agreement with the experimental data reported by van der Heyden et al. [Phys. Rev. Lett. 95 (2005) 116104]. In this paper, a theoretical model based on the PB model incorporating their proposed boundary condition is presented, which does not necessitate highly expensive computational effort. The results from our proposed model are shown to be in agreement with their numerical results of the PNP model. The present model also addresses the importance of the electrical resistance of reservoirs or the position of the electrodes for the measurement of the streaming current. Further, we point out that there is a misinterpretation in a comparison between their numerical results and those of van der Heyden et al.'s experiments. Finally, we conclude that the experimental data still cannot be predicted accurately by their proposed boundary condition and model, especially for the electrolyte concentration C(0)<10(-3)M.

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

    PubMed Central

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

    2011-01-01

    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

  1. Transferable ionic parameters for first-principles Poisson-Boltzmann solvation calculations: Neutral solutes in aqueous monovalent salt solutions

    NASA Astrophysics Data System (ADS)

    Ringe, Stefan; Oberhofer, Harald; Reuter, Karsten

    2017-04-01

    Implicit solvation calculations based on a Stern-layer corrected size-modified Poisson-Boltzmann (SMPB) model are an effective approach to capture electrolytic effects in first-principles electronic structure calculations. For a given salt solution, they require a range of ion-specific parameters, which describe the size of the dissolved ions as well as thickness and shape of the Stern layer. Out of this defined parameter space, we show that the Stern layer thickness expressed in terms of the solute's electron density and the resulting ionic cavity volume completely determine ion effects on the stability of neutral solutes. Using the efficient SMPB functionality of the full-potential density-functional theory package FHI-aims, we derive optimized such Stern layer parameters for neutral solutes in various aqueous monovalent electrolytes. The parametrization protocol relies on fitting to reference Setschenow coefficients that describe solvation free energy changes with ionic strength at low to medium concentrations. The availability of such data for NaCl solutions yields a highly predictive SMPB model that allows to recover the measured Setschenow coefficients with an accuracy that is comparable to prevalent quantitative regression models. Correspondingly derived SMPB parameters for other salts suffer from a much scarcer experimental data base but lead to Stern layer properties that follow a physically reasonable trend with ionic hydration numbers.

  2. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

    PubMed

    Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

    2017-06-13

    We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

  3. Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.

    PubMed

    Hsieh, Meng-Juei; Luo, Ray

    2004-08-15

    A well-behaved physics-based all-atom scoring function for protein structure prediction is analyzed with several widely used all-atom decoy sets. The scoring function, termed AMBER/Poisson-Boltzmann (PB), is based on a refined AMBER force field for intramolecular interactions and an efficient PB model for solvation interactions. Testing on the chosen decoy sets shows that the scoring function, which is designed to consider detailed chemical environments, is able to consistently discriminate all 62 native crystal structures after considering the heteroatom groups, disulfide bonds, and crystal packing effects that are not included in the decoy structures. When NMR structures are considered in the testing, the scoring function is able to discriminate 8 out of 10 targets. In the more challenging test of selecting near-native structures, the scoring function also performs very well: for the majority of the targets studied, the scoring function is able to select decoys that are close to the corresponding native structures as evaluated by ranking numbers and backbone Calpha root mean square deviations. Various important components of the scoring function are also studied to understand their discriminative contributions toward the rankings of native and near-native structures. It is found that neither the nonpolar solvation energy as modeled by the surface area model nor a higher protein dielectric constant improves its discriminative power. The terms remaining to be improved are related to 1-4 interactions. The most troublesome term is found to be the large and highly fluctuating 1-4 electrostatics term, not the dihedral-angle term. These data support ongoing efforts in the community to develop protein structure prediction methods with physics-based potentials that are competitive with knowledge-based potentials.

  4. 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.

  5. Solutions of the cylindrical nonlinear Maxwell equations.

    PubMed

    Xiong, Hao; Si, Liu-Gang; Ding, Chunling; Lü, Xin-You; Yang, Xiaoxue; Wu, Ying

    2012-01-01

    Cylindrical nonlinear optics is a burgeoning research area which describes cylindrical electromagnetic wave propagation in nonlinear media. Finding new exact solutions for different types of nonlinearity and inhomogeneity to describe cylindrical electromagnetic wave propagation is of great interest and meaningful for theory and application. This paper gives exact solutions for the cylindrical nonlinear Maxwell equations and presents an interesting connection between the exact solutions for different cylindrical nonlinear Maxwell equations. We also provide some examples and discussion to show the application of the results we obtained. Our results provide the basis for solving complex systems of nonlinearity and inhomogeneity with simple systems.

  6. Systems of Nonlinear Hyperbolic Partial Differential Equations

    DTIC Science & Technology

    1997-12-01

    McKinney) Travelling wave solutions of the modified Korteweg - deVries -Burgers Equation . J. Differential Equations , 116 (1995), 448-467. 4. (with D.G...SUBTITLE Systems of Nonlinear Hyperbolic Partial Differential Equations 6. AUTHOR’S) Michael Shearer PERFORMING ORGANIZATION NAMES(S) AND...DISTRIBUTION CODE 13. ABSTRACT (Maximum 200 words) This project concerns properties of wave propagation in partial differential equations that are nonlinear

  7. Modified Poisson-Boltzmann Equation in the Electric Double Layer Theory for an Electrolyte with Size Asymmetric Ions

    DTIC Science & Technology

    1988-09-26

    curves. The latter two features are routinely observed in experiments. Results have been published in the literature in the Journal of Chemical Physics and...accurately for 1:1 valency electrolytes and satisfactorily for higher valency systems. An article on this has been published in the Journal of Chemical Physics . We

  8. Additivity of nonlinear biomass equations

    Treesearch

    Bernard R. Parresol

    2001-01-01

    Two procedures that guarantee the property of additivity among the components of tree biomass and total tree biomass utilizing nonlinear functions are developed. Procedure 1 is a simple combination approach, and procedure 2 is based on nonlinear joint-generalized regression (nonlinear seemingly unrelated regressions) with parameter restrictions. Statistical theory is...

  9. Exact Analytic Result of Contact Value for the Density in a Modified Poisson-Boltzmann Theory of an Electrical Double Layer.

    PubMed

    Lou, Ping; Lee, Jin Yong

    2009-04-14

    For a simple modified Poisson-Boltzmann (SMPB) theory, taking into account the finite ionic size, we have derived the exact analytic expression for the contact values of the difference profile of the counterion and co-ion, as well as of the sum (density) and product profiles, near a charged planar electrode that is immersed in a binary symmetric electrolyte. In the zero ionic size or dilute limit, these contact values reduce to the contact values of the Poisson-Boltzmann (PB) theory. The analytic results of the SMPB theory, for the difference, sum, and product profiles were compared with the results of the Monte-Carlo (MC) simulations [ Bhuiyan, L. B.; Outhwaite, C. W.; Henderson, D. J. Electroanal. Chem. 2007, 607, 54 ; Bhuiyan, L. B.; Henderson, D. J. Chem. Phys. 2008, 128, 117101 ], as well as of the PB theory. In general, the analytic expression of the SMPB theory gives better agreement with the MC data than the PB theory does. For the difference profile, as the electrode charge increases, the result of the PB theory departs from the MC data, but the SMPB theory still reproduces the MC data quite well, which indicates the importance of including steric effects in modeling diffuse layer properties. As for the product profile, (i) it drops to zero as the electrode charge approaches infinity; (ii) the speed of the drop increases with the ionic size, and these behaviors are in contrast with the predictions of the PB theory, where the product is identically 1.

  10. Nonlinear Poisson Equation for Heterogeneous Media

    PubMed Central

    Hu, Langhua; Wei, Guo-Wei

    2012-01-01

    The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. PMID:22947937

  11. Nonlinear Poisson equation for heterogeneous media.

    PubMed

    Hu, Langhua; Wei, Guo-Wei

    2012-08-22

    The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects.

  12. Nonlinear gyrokinetic equations for tokamak microturbulence

    SciTech Connect

    Hahm, T.S.

    1988-05-01

    A nonlinear electrostatic gyrokinetic Vlasov equation, as well as Poisson equation, has been derived in a form suitable for particle simulation studies of tokamak microturbulence and associated anomalous transport. This work differs from the existing nonlinear gyrokinetic theories in toroidal geometry, since the present equations conserve energy while retaining the crucial linear and nonlinear polarization physics. In the derivation, the action-variational Lie perturbation method is utilized in order to preserve the Hamiltonian structure of the original Vlasov-Poisson system. Emphasis is placed on the dominant physics of the collective fluctuations in toroidal geometry, rather than on details of particle orbits. 13 refs.

  13. 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.

  14. Robust iterative method for nonlinear Helmholtz equation

    NASA Astrophysics Data System (ADS)

    Yuan, Lijun; Lu, Ya Yan

    2017-08-01

    A new iterative method is developed for solving the two-dimensional nonlinear Helmholtz equation which governs polarized light in media with the optical Kerr nonlinearity. In the strongly nonlinear regime, the nonlinear Helmholtz equation could have multiple solutions related to phenomena such as optical bistability and symmetry breaking. The new method exhibits a much more robust convergence behavior than existing iterative methods, such as frozen-nonlinearity iteration, Newton's method and damped Newton's method, and it can be used to find solutions when good initial guesses are unavailable. Numerical results are presented for the scattering of light by a nonlinear circular cylinder based on the exact nonlocal boundary condition and a pseudospectral method in the polar coordinate system.

  15. Identification for a Nonlinear Periodic Wave Equation

    SciTech Connect

    Morosanu, C.; Trenchea, C.

    2001-07-01

    This work is concerned with an approximation process for the identification of nonlinearities in the nonlinear periodic wave equation. It is based on the least-squares approach and on a splitting method. A numerical algorithm of gradient type and the numerical implementation are given.

  16. Polynomial solutions of nonlinear integral equations

    NASA Astrophysics Data System (ADS)

    Dominici, Diego

    2009-05-01

    We analyze the polynomial solutions of a nonlinear integral equation, generalizing the work of Bender and Ben-Naim (2007 J. Phys. A: Math. Theor. 40 F9, 2008 J. Nonlinear Math. Phys. 15 (Suppl. 3) 73). We show that, in some cases, an orthogonal solution exists and we give its general form in terms of kernel polynomials.

  17. Hybrid approach for nonlinear wave equation

    NASA Astrophysics Data System (ADS)

    Bogdanov, Alexander; Mareev, Vladimir

    2017-07-01

    The solution of nonintegrable nonlinear equations is very difficult even numerically and practically impossible by standard analytical technic. New view, offered by heterogeneous computational systems, gives some new possibilities, but also need novel approaches for numerical realization of pertinent algorithms. We shall give some examples of such analysis on the base of nonlinear wave's evolution study in multiphase media with chemical reaction.

  18. 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.

  19. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.

    PubMed

    Archontis, G; Simonson, T; Karplus, M

    2001-02-16

    Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to incorporate artificial amino acid residues into proteins in vivo. In a previous paper, the binding to aspartyl-tRNA synthetase of the substrate Asp and the analogue Asn were compared by molecular dynamics free energy simulations. Molecular dynamics combined with Poisson-Boltzmann free energy calculations represent a less expensive approach, suitable for examining multiple active site mutations in an engineering effort. Here, Poisson-Boltzmann free energy calculations for aspartyl-tRNA synthetase are first validated by their ability to reproduce selected molecular dynamics binding free energy differences, then used to examine the possibility of Asn binding to native and mutant aspartyl-tRNA synthetase. A component analysis of the Poisson-Boltzmann free energies is employed to identify specific interactions that determine the binding affinities. The combined use of molecular dynamics free energy simulations to study one binding process thoroughly, followed by molecular dynamics and Poisson-Boltzmann free energy calculations to study a series of related ligands or mutations is proposed as a paradigm for protein or ligand design. The binding of Asn in an alternate, "head-to-tail" orientation observed in the homologous asparagine synthetase is analyzed, and found to be more stable than the "Asp-like" orientation studied earlier. The new orientation is probably unsuitable for catalysis. A conserved active site lysine (Lys198 in Escherichia coli) that recognizes the Asp side-chain is changed to a leucine residue, found at the corresponding position in asparaginyl-tRNA synthetase. It is interesting that the binding of Asp is calculated to increase slightly (rather than to decrease), while that of Asn is calculated, as expected, to increase strongly, to

  20. Lax integrable nonlinear partial difference equations

    NASA Astrophysics Data System (ADS)

    Sahadevan, R.; Nagavigneshwari, G.

    2015-03-01

    A systematic investigation to derive nonlinear lattice equations governed by partial difference equations admitting specific Lax representation is presented. Further whether or not the identified lattice equations possess other characteristics of integrability namely Consistency Around the Cube (CAC) property and linearizability through a global transformation is analyzed. Also it is presented that how to derive higher order ordinary difference equations or mappings from the obtained lattice equations through periodic reduction and investigated whether they are measure preserving or linearizable and admit sufficient number of integrals leading to their integrability.

  1. On Coupled Rate Equations with Quadratic Nonlinearities

    PubMed Central

    Montroll, Elliott W.

    1972-01-01

    Rate equations with quadratic nonlinearities appear in many fields, such as chemical kinetics, population dynamics, transport theory, hydrodynamics, etc. Such equations, which may arise from basic principles or which may be phenomenological, are generally solved by linearization and application of perturbation theory. Here, a somewhat different strategy is emphasized. Alternative nonlinear models that can be solved exactly and whose solutions have the qualitative character expected from the original equations are first searched for. Then, the original equations are treated as perturbations of those of the solvable model. Hence, the function of the perturbation theory is to improve numerical accuracy of solutions, rather than to furnish the basic qualitative behavior of the solutions of the equations. PMID:16592013

  2. Efficient numerical methods for nonlinear Schrodinger equations

    NASA Astrophysics Data System (ADS)

    Liang, Xiao

    The nonlinear Schrodinger equations are widely used to model a number of important physical phenomena, including solitary wave propagations in optical fibers, deep water turbulence, laser beam transmissions, and the Bose-Einstein condensation, just to mention a few. In the field of optics and photonics, the systems of nonlinear Schrodinger equations can be used to model multi-component solitons and the interaction of self-focusing laser beams. In three spatial dimensions, the nonlinear Schrodinger equation is known as the Gross-Pitaevskii equation, which models the soliton in a low-cost graded-index fiber. Recently, research on nonlinear space fractional Schrodinger equations, which capture the self-similarity in the fractional environment, has become prevalent. Our study includes the systems of multi-dimensional nonlinear space fractional Schrodinger equations. To solve the systems of multi-dimensional nonlinear Schrodinger equations efficiently, several novel numerical methods are presented. The central difference and quartic spline approximation based exponential time differencing Crank-Nicolson method is introduced for solving systems of one- and two-dimensional nonlinear Schrodinger equations. A local extrapolation is employed to achieve fourth-order accuracy in time. The numerical examples include the transmission of a self-focusing laser beam. The local discontinuous Galerkin methods combined with the fourth-order exponential time differencing Runge-Kutta time discretization are studied for solving the systems of nonlinear Schrodinger equations with hyperbolic terms, which are critical in modeling optical solitons in the birefringent fibers. The local discontinuous Galerkin method is able to achieve any order of accuracy in space, thanks to the usage of piecewise polynomial spaces. The exponential time differencing methods are employed to deal with the coupled nonlinearities for the reason that there is no need to solve nonlinear systems at every time step

  3. Prolongation structures of nonlinear evolution equations

    NASA Technical Reports Server (NTRS)

    Wahlquist, H. D.; Estabrook, F. B.

    1975-01-01

    A technique is developed for systematically deriving a 'prolongation structure' - a set of interrelated potentials and pseudopotentials - for nonlinear partial differential equations in two independent variables. When this is applied to the Korteweg-de Vries equation, a new infinite set of conserved quantities is obtained. Known solution techniques are shown to result from the discovery of such a structure: related partial differential equations for the potential functions, linear 'inverse scattering' equations for auxiliary functions, Backlund transformations. Generalizations of these techniques will result from the use of irreducible matrix representations of the prolongation structure.

  4. On implicit abstract neutral nonlinear differential equations

    SciTech Connect

    Hernández, Eduardo; O’Regan, Donal

    2016-04-15

    In this paper we continue our developments in Hernández and O’Regan (J Funct Anal 261:3457–3481, 2011) on the existence of solutions for abstract neutral differential equations. In particular we extend the results in Hernández and O’Regan (J Funct Anal 261:3457–3481, 2011) for the case of implicit nonlinear neutral equations and we focus on applications to partial “nonlinear” neutral differential equations. Some applications involving partial neutral differential equations are presented.

  5. Dielectric saturation of the ion hydration shell and interaction between two double helices of DNA in mono- and multivalent electrolyte solutions: foundations of the epsilon-modified Poisson-Boltzmann theory.

    PubMed

    Gavryushov, Sergei

    2007-05-17

    Potentials of mean force between single Na+, Ca2+, and Mg2+ cations and a highly charged spherical macroion in SPC/E water have been determined using molecular dynamics simulations. Results are compared to the electrostatic energy calculations for the primitive polarization model (PPM) of hydrated cations describing the ion hydration shell as a dielectric sphere of low permittivity (Gavryushov, S.; Linse, P. J. Phys. Chem. B 2003, 107, 7135). Parameters of the ion dielectric sphere and radius of the macroion/water dielectric boundary were extracted by means of this comparison to approximate the short-range repulsion of ions near the interface. To explore the counterion distributions around a simplified model of DNA, the obtained PPM parameters for Na+ and Ca2+ have been substituted into the modified Poisson-Boltzmann (MPB) equations derived for the PPM and named the epsilon-MPB (epsilon-MPB) theory. epsilon-MPB results for DNA suggest that such polarization effects are important in the case of 2:1 electrolyte and highly charged macromolecules. The three-dimensional implementation of the epsilon-MPB theory was also applied to calculation of the energies of interaction between two parallel macromolecules of DNA in solutions of NaCl and CaCl2. Being compared to results of MPB calculations without the ion polarization effects, it suggests that the ion hydration shell polarization and inhomogeneous solvent permittivity might be essential factors in the experimentally known hydration forces acting between charged macromolecules and bilayers at separations of less than 20 A between their surfaces.

  6. The optimal modified variational iteration method for the Lane-Emden equations with Neumann and Robin boundary conditions

    NASA Astrophysics Data System (ADS)

    Singh, Randhir; Das, Nilima; Kumar, Jitendra

    2017-06-01

    An effective analytical technique is proposed for the solution of the Lane-Emden equations. The proposed technique is based on the variational iteration method (VIM) and the convergence control parameter h . In order to avoid solving a sequence of nonlinear algebraic or complicated integrals for the derivation of unknown constant, the boundary conditions are used before designing the recursive scheme for solution. The series solutions are found which converges rapidly to the exact solution. Convergence analysis and error bounds are discussed. Accuracy, applicability of the method is examined by solving three singular problems: i) nonlinear Poisson-Boltzmann equation, ii) distribution of heat sources in the human head, iii) second-kind Lane-Emden equation.

  7. 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.

  8. Exact solutions for nonlinear foam drainage equation

    NASA Astrophysics Data System (ADS)

    Zayed, E. M. E.; Al-Nowehy, Abdul-Ghani

    2017-02-01

    In this paper, the modified simple equation method, the exp-function method, the soliton ansatz method, the Riccati equation expansion method and the ( G^' }/G)-expansion method are used to construct exact solutions with parameters of the nonlinear foam drainage equation. When these parameters are taken to be special values, the solitary wave solutions and the trigonometric function solutions are derived from the exact solutions. The obtained results confirm that the proposed methods are efficient techniques for analytic treatments of a wide variety of nonlinear partial differential equations in mathematical physics. We compare our results together with each other yielding from these integration tools. Also, our results have been compared with the well-known results of others.

  9. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

    PubMed Central

    Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew

    2008-01-01

    In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946

  10. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces.

    PubMed

    Zhou, Y C; Holst, Michael; McCammon, J Andrew

    2008-04-01

    In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods.

  11. The Stochastic Nonlinear Damped Wave Equation

    SciTech Connect

    Barbu, V. Da Prato, G.

    2002-12-19

    We prove the existence of an invariant measure for the transition semigroup associated with a nonlinear damped stochastic wave equation in R{sup n} of the Klein-Gordon type. The uniqueness of the invariant measure and the structure of the corresponding Kolmogorov operator are also studied.

  12. A combination method for solving nonlinear equations

    NASA Astrophysics Data System (ADS)

    Silalahi, B. P.; Laila, R.; Sitanggang, I. S.

    2017-01-01

    This paper discusses methods for finding solutions of nonlinear equations: the Newton method, the Halley method and the combination of the Newton method, the Newton inverse method and the Halley method. Computational results in terms of the accuracy, the number of iterations and the running time for solving some given problems are presented.

  13. Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/Poisson-Boltzmann study.

    PubMed

    Bredenberg, Johan H; Russo, Cristina; Fenley, Marcia O

    2008-06-01

    The TATA-binding protein (TBP) is a key component of the archaea ternary preinitiation transcription assembly. The archaeon TBP, from the halophile/hyperthermophile organism Pyrococcus woesei, is adapted to high concentrations of salt and high-temperature environments. Although most eukaryotic TBPs are mesophilic and adapted to physiological conditions of temperature and salt, they are very similar to their halophilic counterparts in sequence and fold. However, whereas the binding affinity to DNA of halophilic TBPs increases with increasing salt concentration, the opposite is observed for mesophilic TBPs. We investigated these differences in nonspecific salt-dependent DNA-binding behavior of halophilic and mesophilic TBPs by using a combined molecular mechanics/Poisson-Boltzmann approach. Our results are qualitatively in good agreement with experimentally observed salt-dependent DNA-binding for mesophilic and halophilic TBPs, and suggest that the distribution and the total number of charged residues may be the main underlying contributor in the association process. Therefore, the difference in the salt-dependent binding behavior of mesophilic and halophilic TBPs to DNA may be due to the very unique charge and electrostatic potential distribution of these TBPs, which consequently alters the number of repulsive and attractive electrostatic interactions.

  14. Investigating the dielectric effects of channel pore water on the electrostatic barriers of the permeation ion by the finite difference Poisson-Boltzmann method.

    PubMed

    Cheng, W; Wang, C X; Chen, W Z; Xu, Y W; Shi, Y Y

    1998-01-01

    In this paper, the finite difference Poisson-Boltzmann (FDPB) method with four dielectric constants is developed to study the effect of dielectric saturation on the electrostatic barriers of the permeation ion. In this method, the inner shape of the channel pore is explicitly represented, and the fact that the dielectric constant inside the channel pore is different from that of bulk water is taken into account. A model channel system which is a righthanded twist bundle with four alpha-helical segments is provided for this study. From the FDPB calculations, it is found that the difference of the ionic electrostatic solvation energy for wider domains depends strongly on the pore radius in the vicinity of the ion when the pore dielectric constant is changed from 78 to 5. However, the electrostatic solvation energy of the permeation ion can not be significantly affected by the dielectric constant in regions with small pore radii. Our results indicate that the local electrostatic interactions inside the ion channel are of major importance for ion electrostatic solvation energies, and the effect of dielectric saturation on the electrostatic barriers is coupled to the interior channel dimensions.

  15. On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium.

    PubMed

    Teixeira, Vitor H; Cunha, Carlos A; Machuqueiro, Miguel; Oliveira, A Sofia F; Victor, Bruno L; Soares, Cláudio M; Baptista, António M

    2005-08-04

    Poisson-Boltzmann (PB) models are a fast and common tool for studying electrostatic processes in proteins, particularly their ionization equilibrium (protonation and/or reduction), often yielding quite good results when compared with more detailed models. Yet, they are conceptually very simple and necessarily approximate, their empirical character being most evident when it comes to the choice of the dielectric constant assigned to the protein region. The present study analyzes several factors affecting the ability of PB-based methods to model protein ionization equilibrium. We give particular attention to a suggestion made by Warshel and co-workers (e.g., Sham et al. J. Phys. Chem. B 1997, 101, 4458) of using different protein dielectric constants for computing the individual (site) and the pairwise (site-site) terms of the ionization free energies. Our prediction of pK(a) values for several proteins indicates that no advantage is obtained by such a procedure, even for sites that are buried and/or display large pK(a) shifts relative to the solution values. In particular, the present methodology gives the best predictions using a dielectric constant around 20, for shifted/buried and nonshifted/exposed sites alike. The similarities and differences between the PB model and Warshel's PDLD/S model are discussed, as well as the reasons behind their apparently discrepant results. The present PB model is shown to predict also good reduction potentials in redox proteins.

  16. 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.

  17. Lattice Boltzmann model for nonlinear convection-diffusion equations.

    PubMed

    Shi, Baochang; Guo, Zhaoli

    2009-01-01

    A lattice Boltzmann model for convection-diffusion equation with nonlinear convection and isotropic-diffusion terms is proposed through selecting equilibrium distribution function properly. The model can be applied to the common real and complex-valued nonlinear evolutionary equations, such as the nonlinear Schrödinger equation, complex Ginzburg-Landau equation, Burgers-Fisher equation, nonlinear heat conduction equation, and sine-Gordon equation, by using a real and complex-valued distribution function and relaxation time. Detailed simulations of these equations are performed, and it is found that the numerical results agree well with the analytical solutions and the numerical solutions reported in previous studies.

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

    SciTech Connect

    Chen, Shouxin; Gibbons, Gary W.; Yang, Yisong E-mail: gwg1@damtp.cam.ac.uk

    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.

  19. 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.

  20. The polydisperse cell model: Nonlinear screening and charge renormalization in colloidal mixtures

    NASA Astrophysics Data System (ADS)

    Torres, Aldemar; Téllez, Gabriel; van Roij, René

    2008-04-01

    We propose a model for the calculation of renormalized charges and osmotic properties of mixtures of highly charged colloidal particles. The model is a generalization of the cell model and the notion of charge renormalization as introduced by Alexander et al. [J. Chem. Phys. 80, 5776 (1984)]. The total solution is partitioned into as many different cells as components in the mixture. The radii of these cells are determined self-consistently for a given set of parameters from the solution of the nonlinear Poisson-Boltzmann equation with appropriate boundary conditions. This generalizes Alexanders's model where the (unique) Wigner-Seitz cell radius is solely fixed by the colloid packing fraction. We illustrate the technique by considering a binary mixture of the colloids with the same sign of charge. The present model can be used to calculate thermodynamic properties of highly charged colloidal mixtures at the level of linear theories, while taking the effect of nonlinear screening into account.

  1. 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.

  2. Numerical solutions of nonlinear wave equations

    SciTech Connect

    Kouri, D.J.; Zhang, D.S.; Wei, G.W.; Konshak, T.; Hoffman, D.K.

    1999-01-01

    Accurate, stable numerical solutions of the (nonlinear) sine-Gordon equation are obtained with particular consideration of initial conditions that are exponentially close to the phase space homoclinic manifolds. Earlier local, grid-based numerical studies have encountered difficulties, including numerically induced chaos for such initial conditions. The present results are obtained using the recently reported distributed approximating functional method for calculating spatial derivatives to high accuracy and a simple, explicit method for the time evolution. The numerical solutions are chaos-free for the same conditions employed in previous work that encountered chaos. Moreover, stable results that are free of homoclinic-orbit crossing are obtained even when initial conditions are within 10{sup {minus}7} of the phase space separatrix value {pi}. It also is found that the present approach yields extremely accurate solutions for the Korteweg{endash}de Vries and nonlinear Schr{umlt o}dinger equations. Our results support Ablowitz and co-workers{close_quote} conjecture that ensuring high accuracy of spatial derivatives is more important than the use of symplectic time integration schemes for solving solitary wave equations. {copyright} {ital 1999} {ital The American Physical Society}

  3. Nonlinear progressive wave equation for stratified atmospheres.

    PubMed

    Edward McDonald, B; Piacsek, Andrew A

    2011-11-01

    The nonlinear progressive wave equation (NPE) [McDonald and Kuperman, J. Acoust. Soc. Am. 81, 1406-1417 (1987)] is expressed in a form to accommodate changes in the ambient atmospheric density, pressure, and sound speed as the time-stepping computational window moves along a path possibly traversing significant altitude differences (in pressure scale heights). The modification is accomplished by the addition of a stratification term related to that derived in the 1970s for linear range-stepping calculations and later adopted into Khokhlov-Zabolotskaya-Kuznetsov-type nonlinear models. The modified NPE is shown to preserve acoustic energy in a ray tube and yields analytic similarity solutions for vertically propagating N waves in isothermal and thermally stratified atmospheres.

  4. Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

    2012-04-01

    Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

  5. 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.

  6. Ada Programming for Solving Nonlinear Equations

    NASA Astrophysics Data System (ADS)

    Wu, Trong

    This paper introduces the Ada programming for solving non-linear equations over a new class of real numbers which are based on the concepts of model numbers and rough numbers for a given computer system. We will study structures of Ada interval computation over model numbers and rough numbers. To do these, we must revise commonly interval computation from compact intervals to closed-open intervals for their initial intervals. This way, we can promise that the final resulting interval will always be a shorter than the result from the ordinary interval computation. Two examples are presented, one is use Newton method and the other is apply iterative method for solving non-line equations. The Ada programs and their the approximated solutions are given in both decimal and binary values.

  7. Invariant metrics, contractions and nonlinear matrix equations

    NASA Astrophysics Data System (ADS)

    Lee, Hosoo; Lim, Yongdo

    2008-04-01

    In this paper we consider the semigroup generated by the self-maps on the open convex cone of positive definite matrices of translations, congruence transformations and matrix inversion that includes symplectic Hamiltonians and show that every member of the semigroup contracts any invariant metric distance inherited from a symmetric gauge function. This extends the results of Bougerol for the Riemannian metric and of Liverani-Wojtkowski for the Thompson part metric. A uniform upper bound of the Lipschitz contraction constant for a member of the semigroup is given in terms of the minimum eigenvalues of its determining matrices. We apply this result to a variety of nonlinear equations including Stein and Riccati equations for uniqueness and existence of positive definite solutions and find a new convergence analysis of iterative algorithms for the positive definite solution depending only on the least contraction coefficient for the invariant metric from the spectral norm.

  8. Galerkin Methods for Nonlinear Elliptic Equations.

    NASA Astrophysics Data System (ADS)

    Murdoch, Thomas

    Available from UMI in association with The British Library. Requires signed TDF. This thesis exploits in the nonlinear situation the optimal approximation property of the finite element method for linear, elliptic problems. Of particular interest are the steady state semiconductor equations in one and two dimensions. Instead of discretising the differential equations by the finite element method and solving the nonlinear algebraic equations by Newton's method, a Newton linearisation of the continuous problem is preferred and a sequence of linear problems solved until some convergence criterion is achieved. For nonlinear Poisson equations, this approach reduces to solving a sequence of linear, elliptic, self -adjoint problems, their approximation by the finite element being optimal in a suitably defined energy norm. Consequently, there is the potential to recover a smoother representation of the underlying solution at each step of the Newton iteration. When this approach is applied to the continuity equations for semiconductor devices, a sequence of linear problems of the form -_{nabla }(anabla u - bu) = f must be solved. The Galerkin method in its crude form does not adequately represent the true solution: however, generalising the framework to permit Petrov-Galerkin approximations remedies the situation. For one dimensional problems, the work of Barrett and Morton allows an optimal test space to be chosen at each step of the Newton iteration so that the resulting approximation is near optimal in a norm closely related to the standard L^2 norm. More detailed information about the underlying solution can then be obtained by recovering a solution of an appropriate form. For two-dimensional problems, since the optimal test functions are difficult to find in practice, an upwinding method due to Heinrich et.al. is used at each step of the Newton iteration. Also, a framework is presented in which various upwind methods may be compared. The thesis also addresses the

  9. Equating TIMSS Mathematics Subtests with Nonlinear Equating Methods Using NEAT Design: Circle-Arc Equating Approaches

    ERIC Educational Resources Information Center

    Ozdemir, Burhanettin

    2017-01-01

    The purpose of this study is to equate Trends in International Mathematics and Science Study (TIMSS) mathematics subtest scores obtained from TIMSS 2011 to scores obtained from TIMSS 2007 form with different nonlinear observed score equating methods under Non-Equivalent Anchor Test (NEAT) design where common items are used to link two or more test…

  10. Strongly Nonlinear Integral Equations of Hammerstein Type

    PubMed Central

    Browder, Felix E.

    1975-01-01

    This paper studies the solution of the nonlinear Hammerstein equation u(x) + ʃ k(x,y)f[y,u(y)]μ(dy) = h(x) in the singular case, i.e., where the linear operator K with kernel k(x,y) is not defined for all the range of the nonlinear mapping F given by Fu(y) = f[y,u(y)] over the whole class X of functions u which are potential solutions of the equation. An existence theorem is derived under relatively minimal assumptions upon k and f, namely that (Ku,u) ≥ 0, that K maps L1 into L1loc and is compact from L1 [unk] L∞ into L1loc, that f(y,s) has the same sign as s for ǀsǀ ≥ R, and that for each constant r > 0, ǀf(y,s)ǀ ≤ gr(y) for ǀsǀ ≤ r where g is bounded and summable. The proof is obtained by combining a priori bounds, a truncation procedure, and a convergence argument using the Dunford-Pettis theorem. PMID:16578727

  11. Notes on the Modified Nonlinear Schrodinger Equation

    NASA Astrophysics Data System (ADS)

    Pizzo, N. E.; Melville, W. K.

    2011-12-01

    In this study, we present the derivation of a modified Nonlinear Schrodinger equation (MNLSE) based on variational calculus. Using weakly nonlinear theory we derive an averaged Lagrangian, which in turn yields a slightly modified version of the MNLSE that conserves wave action. We also explore ramifications of the MNLSE with respect to the coupling between mean currents and non-uniform radiation stresses. We present this in the context of breaking waves and the free long waves they generate (Kristian Dysthe, personal communication). It has been noted in laboratory experiments (Meza et al, 1999) that breaking waves transfer some energy to modes far below the peak frequency of the spectrum. The transfer mechanism is widely believed to be the result of nonlinear four wave resonant interactions; however, the coupling between breaking-induced non-uniform radiation stresses and long wave radiation suggests a potential alternative explanation. Through direct numerical simulations, along with the theory, we test the feasibility of this mechanism by comparing it to data from wave tank experiments (Drazen et al., 2008).

  12. Nonlinear Dynamics of the Leggett Equation

    NASA Astrophysics Data System (ADS)

    Ragan, Robert J.

    1995-01-01

    We study the nonlinear dynamics of spin-polarized Fermi liquids. Our starting point is the equation of motion for the magnetization derived by Leggett and Rice, which accounts for spin-rotation effects in the limit of small polarization. We also include later modifications to the theory by Meyerovich, and Jeon and Mullin, which account for polarization dependences of the transport coefficients. In the analysis of NMR experiments the methods of current research can be summarized as follows: (a) to linearize the Leggett equation by considering small amplitude oscillations (small tip angles), (b) to use perturbation theory to account for small spin-rotation effects, (c) to exploit the simple helical solution which describes spin-echo experiments. In this thesis, we report progress in several directions: (1) We extend the linear theory to describe bounded spin diffusion with spin-rotation and finite-polarization effects. The analysis is valid for arbitrary tip angles and arbitrary degree of nonlinearity. (2) We show that because of the spin-rotation effect, the helical solution exhibits a Castiang instability for large tip angles. In the limit of small damping, we use the inverse scattering theory developed by Levy to display the full nonlinear evolution of the instabilities. (3) We use perturbation theory to show that anisotropy in the spin diffusion coefficients gives rise to multiple spin echoes, even in the absence of spin -rotation effects. This description applies to experiments on ^3He-^4He solutions at ^3He concentrations of 3-5%. This experiment provides a unique means of verifying the theory of Jeon and Mullin. We also report some exact results in the theory of anisotropic spin diffusion.

  13. Nonlinear integral equations for the sausage model

    NASA Astrophysics Data System (ADS)

    Ahn, Changrim; Balog, Janos; Ravanini, Francesco

    2017-08-01

    The sausage model, first proposed by Fateev, Onofri, and Zamolodchikov, is a deformation of the O(3) sigma model preserving integrability. The target space is deformed from the sphere to ‘sausage’ shape by a deformation parameter ν. This model is defined by a factorizable S-matrix which is obtained by deforming that of the O(3) sigma model by a parameter λ. Clues for the deformed sigma model are provided by various UV and IR information through the thermodynamic Bethe ansatz (TBA) analysis based on the S-matrix. Application of TBA to the sausage model is, however, limited to the case of 1/λ integer where the coupled integral equations can be truncated to a finite number. In this paper, we propose a finite set of nonlinear integral equations (NLIEs), which are applicable to generic value of λ. Our derivation is based on T-Q relations extracted from the truncated TBA equations. For a consistency check, we compute next-leading order corrections of the vacuum energy and extract the S-matrix information in the IR limit. We also solved the NLIE both analytically and numerically in the UV limit to get the effective central charge and compared with that of the zero-mode dynamics to obtain exact relation between ν and λ. Dedicated to the memory of Petr Petrovich Kulish.

  14. Nonlinear scalar field equations involving the fractional Laplacian

    NASA Astrophysics Data System (ADS)

    Byeon, Jaeyoung; Kwon, Ohsang; Seok, Jinmyoung

    2017-04-01

    In this paper we study the existence, regularity, radial symmetry and decay property of a mountain pass solution for nonlinear scalar field equations involving the fractional Laplacian under an almost optimal class of continuous nonlinearities.

  15. Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.

    PubMed

    Aldeghi, Matteo; Bodkin, Michael J; Knapp, Stefan; Biggin, Philip C

    2017-09-25

    Binding free energy calculations that make use of alchemical pathways are becoming increasingly feasible thanks to advances in hardware and algorithms. Although relative binding free energy (RBFE) calculations are starting to find widespread use, absolute binding free energy (ABFE) calculations are still being explored mainly in academic settings due to the high computational requirements and still uncertain predictive value. However, in some drug design scenarios, RBFE calculations are not applicable and ABFE calculations could provide an alternative. Computationally cheaper end-point calculations in implicit solvent, such as molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations, could too be used if one is primarily interested in a relative ranking of affinities. Here, we compare MMPBSA calculations to previously performed absolute alchemical free energy calculations in their ability to correlate with experimental binding free energies for three sets of bromodomain-inhibitor pairs. Different MMPBSA approaches have been considered, including a standard single-trajectory protocol, a protocol that includes a binding entropy estimate, and protocols that take into account the ligand hydration shell. Despite the improvements observed with the latter two MMPBSA approaches, ABFE calculations were found to be overall superior in obtaining correlation with experimental affinities for the test cases considered. A difference in weighted average Pearson ([Formula: see text]) and Spearman ([Formula: see text]) correlations of 0.25 and 0.31 was observed when using a standard single-trajectory MMPBSA setup ([Formula: see text] = 0.64 and [Formula: see text] = 0.66 for ABFE; [Formula: see text] = 0.39 and [Formula: see text] = 0.35 for MMPBSA). The best performing MMPBSA protocols returned weighted average Pearson and Spearman correlations that were about 0.1 inferior to ABFE calculations: [Formula: see text] = 0.55 and [Formula: see text] = 0.56 when including

  16. Some new solutions of nonlinear evolution equations with variable coefficients

    NASA Astrophysics Data System (ADS)

    Virdi, Jasvinder Singh

    2016-05-01

    We construct the traveling wave solutions of nonlinear evolution equations (NLEEs) with variable coefficients arising in physics. Some interesting nonlinear evolution equations are investigated by traveling wave solutions which are expressed by the hyperbolic functions, the trigonometric functions and rational functions. The applied method will be used in further works to establish more entirely new solutions for other kinds of such nonlinear evolution equations with variable coefficients arising in physics.

  17. Nonlinear Parabolic Equations Involving Measures as Initial Conditions.

    DTIC Science & Technology

    1981-09-01

    CHART N N N Afl4Uf’t 1N II Il MRC Technical Summary Report # 2277 0 NONLINEAR PARABOLIC EQUATIONS INVOLVING MEASURES AS INITIAL CONDITIONS I Haim Brezis ...NONLINEAR PARABOLIC EQUATIONS INVOLVING MEASURES AS INITIAL CONDITIONS Haim Brezis and Avner Friedman Technical Summary Report #2277 September 1981...with NRC, and not with the authors of this report. * 𔃾s ’a * ’ 4| NONLINEAR PARABOLIC EQUATIONS INVOLVING MEASURES AS INITIAL CONDITIONS Haim Brezis

  18. 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.

  19. Bifurcation and stability for a nonlinear parabolic partial differential equation

    NASA Technical Reports Server (NTRS)

    Chafee, N.

    1973-01-01

    Theorems are developed to support bifurcation and stability of nonlinear parabolic partial differential equations in the solution of the asymptotic behavior of functions with certain specified properties.

  20. Exact solutions to nonlinear delay differential equations of hyperbolic type

    NASA Astrophysics Data System (ADS)

    Vyazmin, Andrei V.; Sorokin, Vsevolod G.

    2017-01-01

    We consider nonlinear delay differential equations of hyperbolic type, including equations with varying transfer coefficients and varying delays. The equations contain one or two arbitrary functions of a single argument. We present new classes of exact generalized and functional separable solutions. All the solutions involve free parameters and can be suitable for solving certain model problems as well as testing numerical and approximate analytical methods for similar and more complex nonlinear differential-difference equations.

  1. Transient finite element analysis of electric double layer using Nernst-Planck-Poisson equations with a modified Stern layer.

    PubMed

    Lim, Jongil; Whitcomb, John; Boyd, James; Varghese, Julian

    2007-01-01

    A finite element implementation of the transient nonlinear Nernst-Planck-Poisson (NPP) and Nernst-Planck-Poisson-modified Stern (NPPMS) models is presented. The NPPMS model uses multipoint constraints to account for finite ion size, resulting in realistic ion concentrations even at high surface potential. The Poisson-Boltzmann equation is used to provide a limited check of the transient models for low surface potential and dilute bulk solutions. The effects of the surface potential and bulk molarity on the electric potential and ion concentrations as functions of space and time are studied. The ability of the models to predict realistic energy storage capacity is investigated. The predicted energy is much more sensitive to surface potential than to bulk solution molarity.

  2. 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.

  3. Nonlinear Schrödinger equation with complex supersymmetric potentials

    NASA Astrophysics Data System (ADS)

    Nath, D.; Roy, P.

    2017-03-01

    Using the concept of supersymmetry we obtain exact analytical solutions of nonlinear Schrödinger equation with a number of complex supersymmetric potentials and power law nonlinearity. Linear stability of these solutions for self-focusing as well as de-focusing nonlinearity has also been examined.

  4. Nonlinear equation for Farley–Buneman waves in multispecies plasma

    SciTech Connect

    Litt, S. K.; Smolyakov, A. I. Bains, A. S.; Pokhotelov, O. A.; Onishchenko, O. G.; Horton, W.

    2016-05-15

    The nonlinear equation describing the Farley–Buneman (FB) waves in multispecies collisional plasmas is derived by employing the multiple-scale reduction analysis. It is shown that the presence of several ion species with different collisionalities and different ion masses removes the degeneracy of the nonlinear equation and generates the nonlinear terms resulting in wave steepening and wave breaking. This effect may be responsible for formation of one-dimensional coherent FB waves of a finite amplitude.

  5. Exploring the nonlinear cloud and rain equation.

    PubMed

    Koren, Ilan; Tziperman, Eli; Feingold, Graham

    2017-01-01

    Marine stratocumulus cloud decks are regarded as the reflectors of the climate system, returning back to space a significant part of the income solar radiation, thus cooling the atmosphere. Such clouds can exist in two stable modes, open and closed cells, for a wide range of environmental conditions. This emergent behavior of the system, and its sensitivity to aerosol and environmental properties, is captured by a set of nonlinear equations. Here, using linear stability analysis, we express the transition from steady to a limit-cycle state analytically, showing how it depends on the model parameters. We show that the control of the droplet concentration (N), the environmental carrying-capacity (H0), and the cloud recovery parameter (τ) can be linked by a single nondimensional parameter (μ=N/(ατH0)), suggesting that for deeper clouds the transition from open (oscillating) to closed (stable fixed point) cells will occur for higher droplet concentration (i.e., higher aerosol loading). The analytical calculations of the possible states, and how they are affected by changes in aerosol and the environmental variables, provide an enhanced understanding of the complex interactions of clouds and rain.

  6. Exploring the nonlinear cloud and rain equation

    NASA Astrophysics Data System (ADS)

    Koren, Ilan; Tziperman, Eli; Feingold, Graham

    2017-01-01

    Marine stratocumulus cloud decks are regarded as the reflectors of the climate system, returning back to space a significant part of the income solar radiation, thus cooling the atmosphere. Such clouds can exist in two stable modes, open and closed cells, for a wide range of environmental conditions. This emergent behavior of the system, and its sensitivity to aerosol and environmental properties, is captured by a set of nonlinear equations. Here, using linear stability analysis, we express the transition from steady to a limit-cycle state analytically, showing how it depends on the model parameters. We show that the control of the droplet concentration (N), the environmental carrying-capacity (H0), and the cloud recovery parameter (τ) can be linked by a single nondimensional parameter (μ=√{N }/(ατH0) ) , suggesting that for deeper clouds the transition from open (oscillating) to closed (stable fixed point) cells will occur for higher droplet concentration (i.e., higher aerosol loading). The analytical calculations of the possible states, and how they are affected by changes in aerosol and the environmental variables, provide an enhanced understanding of the complex interactions of clouds and rain.

  7. 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.

  8. 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.

  9. Nonlinearizations of spectral problems of the nonlinear Schroedinger equation and the real-valued modified Korteweg-de Vries equation

    SciTech Connect

    Zhou Ruguang

    2007-01-15

    A procedure of nonlinearization of spectral problem that allows to impose reality conditions or restriction conditions on potentials is presented. As applications, integrable decompositions of the nonlinear Schroedinger equation and the real-valued modified Korteweg-de Vries equation are obtained.

  10. 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.

  11. Nonlinear Evolution Equations in Banach Spaces.

    DTIC Science & Technology

    relationship to the evolution equation is studied. The results obtained extend several known existence theorems and provide generalized solutions of the evolution equation in more general cases. (Author)

  12. The effect of nonlinearity on unstable zones of Mathieu equation

    NASA Astrophysics Data System (ADS)

    Saryazdi, M. Gh

    2017-03-01

    Mathieu equation is a well-known ordinary differential equation in which the excitation term appears as the non-constant coefficient. The mathematical modelling of many dynamic systems leads to Mathieu equation. The determination of the locus of unstable zone is important for the control of dynamic systems. In this paper, the stable and unstable regions of Mathieu equation are determined for three cases of linear and nonlinear equations using the homotopy perturbation method. The effect of nonlinearity is examined in the unstable zone. The results show that the transition curves of linear Mathieu equation depend on the frequency of the excitation term. However, for nonlinear equations, the curves depend also on initial conditions. In addition, increasing the amplitude of response leads to an increase in the unstable zone.

  13. On a generalized Kirchhoff equation with sublinear nonlinearities

    NASA Astrophysics Data System (ADS)

    Santos Júnior, João R.; Siciliano, Gaetano

    2017-07-01

    In this paper we consider a generalized Kirchhoff? equation in a bounded domain under the effect of a sublinear nonlinearity. Under suitable assumptions on the data of the problem we show that, with a simple change of variable, the equation can be reduced to a classical semilinear equation and then studied with standard tools.

  14. Additive nonlinear biomass equations: A likelihood-based approach

    Treesearch

    David L. R. Affleck; Ulises Dieguez-Aranda

    2016-01-01

    Since Parresol’s (Can. J. For. Res. 31:865-878, 2001) seminal article on the topic, it has become standard to develop nonlinear tree biomass equations to ensure compatibility among total and component predictions and to fit these equations using multistep generalized least-squares methods. In particular, many studies have specified equations for total tree...

  15. Lump-type solutions to nonlinear differential equations derived from generalized bilinear equations

    NASA Astrophysics Data System (ADS)

    Ma, Wen-Xiu; Zhou, Yuan; Dougherty, Rachael

    2016-08-01

    Lump-type solutions, rationally localized in many directions in the space, are analyzed for nonlinear differential equations derived from generalized bilinear differential equations. By symbolic computations with Maple, positive quadratic and quartic polynomial solutions to two classes of generalized bilinear differential equations on f are computed, and thus, lump-type solutions are presented to the corresponding nonlinear differential equations on u, generated from taking a transformation of dependent variables u = 2(ln f)x.

  16. A numerical scheme for nonlinear Helmholtz equations with strong nonlinear optical effects.

    PubMed

    Xu, Zhengfu; Bao, Gang

    2010-11-01

    A numerical scheme is presented to solve the nonlinear Helmholtz (NLH) equation modeling second-harmonic generation (SHG) in photonic bandgap material doped with a nonlinear χ((2)) effect and the NLH equation modeling wave propagation in Kerr type gratings with a nonlinear χ((3)) effect in the one-dimensional case. Both of these nonlinear phenomena arise as a result of the combination of high electromagnetic mode density and nonlinear reaction from the medium. When the mode intensity of the incident wave is significantly strong, which makes the nonlinear effect non-negligible, numerical methods based on the linearization of the essentially nonlinear problem will become inadequate. In this work, a robust, stable numerical scheme is designed to simulate the NLH equations with strong nonlinearity.

  17. 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.

  18. 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.

  19. Linearized oscillation theory for a nonlinear delay impulsive equation

    NASA Astrophysics Data System (ADS)

    Berezansky, Leonid; Braverman, Elena

    2003-12-01

    For a scalar nonlinear impulsive delay differential equationwith rk(t)≥0,hk(t)≤t, limj-->∞ τj=∞, such an auxiliary linear impulsive delay differential equationis constructed that oscillation (nonoscillation) of the nonlinear equation can be deduced from the corresponding properties of the linear equation. Coefficients rk(t) and delays are not assumed to be continuous. Explicit oscillation and nonoscillation conditions are established for some nonlinear impulsive models of population dynamics, such as the impulsive logistic equation and the impulsive generalized Lasota-Wazewska equation which describes the survival of red blood cells. It is noted that unlike nonimpulsive delay logistic equations a solution of a delay impulsive logistic equation may become negative.

  20. Variable-coefficient extended mapping method for nonlinear evolution equations

    NASA Astrophysics Data System (ADS)

    Zhang, Sheng; Xia, Tiecheng

    2008-03-01

    In this Letter, a variable-coefficient extended mapping method is proposed to seek new and more general exact solutions of nonlinear evolution equations. Being concise and straightforward, this method is applied to the mKdV equation with variable coefficients and ( 2+1)-dimensional Nizhnik-Novikov-Veselov equations. As a result, many new and more general exact solutions are obtained including Jacobi elliptic function solutions, hyperbolic function solutions and trigonometric function solutions. It is shown that the proposed method provides a very effective and powerful mathematical tool for solving a great many nonlinear evolution equations in mathematical physics.

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

    PubMed

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

    2001-11-05

    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.

  2. Asymptotic Behavior for a Strongly Damped Nonlinear Wave Equation.

    DTIC Science & Technology

    1980-06-01

    Equation (1) may also be considered as an ordinary differential equation on a Banach space. This is the setting I prefer, as it usually seems much more... NONLINEAR WAVE EQUATION ~0 by gc~ Paul Massatt Lefschetz Center for Dynamical Systems Division of Applied Mathematics Brown University Providence, Rhode...Interim -) DAMPED NONLINEAR WAVE EQUATION . 6. PERFORMING 0G. RMRT UMBER 7. AUTHOR(a) S. CONTRACT OR GRANT NUMBER(O) PAUL!MASSATT 47 -Xo AFdSR-76-3,992 / 9

  3. 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.

  4. Differentiability at lateral boundary for fully nonlinear parabolic equations

    NASA Astrophysics Data System (ADS)

    Ma, Feiyao; Moreira, Diego R.; Wang, Lihe

    2017-09-01

    For fully nonlinear uniformly parabolic equations, the first derivatives regularity of viscosity solutions at lateral boundary is studied under new Dini type conditions for the boundary, which is called Reifenberg Dini conditions and is weaker than usual Dini conditions.

  5. Lipschitz regularity results for nonlinear strictly elliptic equations and applications

    NASA Astrophysics Data System (ADS)

    Ley, Olivier; Nguyen, Vinh Duc

    2017-10-01

    Most of Lipschitz regularity results for nonlinear strictly elliptic equations are obtained for a suitable growth power of the nonlinearity with respect to the gradient variable (subquadratic for instance). For equations with superquadratic growth power in gradient, one usually uses weak Bernstein-type arguments which require regularity and/or convex-type assumptions on the gradient nonlinearity. In this article, we obtain new Lipschitz regularity results for a large class of nonlinear strictly elliptic equations with possibly arbitrary growth power of the Hamiltonian with respect to the gradient variable using some ideas coming from Ishii-Lions' method. We use these bounds to solve an ergodic problem and to study the regularity and the large time behavior of the solution of the evolution equation.

  6. Comparative study of homotopy continuation methods for nonlinear algebraic equations

    NASA Astrophysics Data System (ADS)

    Nor, Hafizudin Mohamad; Ismail, Ahmad Izani Md.; Majid, Ahmad Abd.

    2014-07-01

    We compare some recent homotopy continuation methods to see which method has greater applicability and greater accuracy. We test the methods on systems of nonlinear algebraic equations. The results obtained indicate the superior accuracy of Newton Homotopy Continuation Method (NHCM).

  7. A Nonlinear Hyperbolic Volterra Equation in Viscoelasticity.

    DTIC Science & Technology

    1980-06-01

    35L55, 35L67, 47H10, 47H15 Key Words: nonlinear viscoelastic motion, materials with memory, stress- strain relaxation functions, nonlinear Volterra...homogeneous body. Here the dissipation mechanism which is induced by memory effects of the viscoelastic materials (stress-strain relaxation function - the...GREENBERG, J. M., A priori estimates for flows in dissipative materials , J. Math. Anal. Appl. 60 (1977), 617-630. CMD/JAN/scr Ii -31- SECURITY

  8. Integrable nonlocal nonlinear Schrödinger equation.

    PubMed

    Ablowitz, Mark J; Musslimani, Ziad H

    2013-02-08

    A new integrable nonlocal nonlinear Schrödinger equation is introduced. It possesses a Lax pair and an infinite number of conservation laws and is PT symmetric. The inverse scattering transform and scattering data with suitable symmetries are discussed. A method to find pure soliton solutions is given. An explicit breathing one soliton solution is found. Key properties are discussed and contrasted with the classical nonlinear Schrödinger equation.

  9. The Fluid Dynamic Limit of the Nonlinear Boltzmann Equation,

    DTIC Science & Technology

    1980-02-01

    dynamics is ’ . strongly nonlinear. Previously, Glikson [4] and Kaniel and Shinbrot [10 showed existence locally in time. Global existence of solutions... Glikson , A., On the existence of general solutions of the initial-value problem for the nonlinear Boltzmann equation with a cut-off, Arch. Rational

  10. 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.

  11. Nonlinear acoustic wave equations with fractional loss operators.

    PubMed

    Prieur, Fabrice; Holm, Sverre

    2011-09-01

    Fractional derivatives are well suited to describe wave propagation in complex media. When introduced in classical wave equations, they allow a modeling of attenuation and dispersion that better describes sound propagation in biological tissues. Traditional constitutive equations from solid mechanics and heat conduction are modified using fractional derivatives. They are used to derive a nonlinear wave equation which describes attenuation and dispersion laws that match observations. This wave equation is a generalization of the Westervelt equation, and also leads to a fractional version of the Khokhlov-Zabolotskaya-Kuznetsov and Burgers' equations.

  12. The nonlinear modified equation approach to analyzing finite difference schemes

    NASA Technical Reports Server (NTRS)

    Klopfer, G. H.; Mcrae, D. S.

    1981-01-01

    The nonlinear modified equation approach is taken in this paper to analyze the generalized Lax-Wendroff explicit scheme approximation to the unsteady one- and two-dimensional equations of gas dynamics. Three important applications of the method are demonstrated. The nonlinear modified equation analysis is used to (1) generate higher order accurate schemes, (2) obtain more accurate estimates of the discretization error for nonlinear systems of partial differential equations, and (3) generate an adaptive mesh procedure for the unsteady gas dynamic equations. Results are obtained for all three areas. For the adaptive mesh procedure, mesh point requirements for equal resolution of discontinuities were reduced by a factor of five for a 1-D shock tube problem solved by the explicit MacCormack scheme.

  13. 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.

  14. Super-rogue waves in simulations based on weakly nonlinear and fully nonlinear hydrodynamic equations.

    PubMed

    Slunyaev, A; Pelinovsky, E; Sergeeva, A; Chabchoub, A; Hoffmann, N; Onorato, M; Akhmediev, N

    2013-07-01

    The rogue wave solutions (rational multibreathers) of the nonlinear Schrödinger equation (NLS) are tested in numerical simulations of weakly nonlinear and fully nonlinear hydrodynamic equations. Only the lowest order solutions from 1 to 5 are considered. A higher accuracy of wave propagation in space is reached using the modified NLS equation, also known as the Dysthe equation. This numerical modeling allowed us to directly compare simulations with recent results of laboratory measurements in Chabchoub et al. [Phys. Rev. E 86, 056601 (2012)]. In order to achieve even higher physical accuracy, we employed fully nonlinear simulations of potential Euler equations. These simulations provided us with basic characteristics of long time evolution of rational solutions of the NLS equation in the case of near-breaking conditions. The analytic NLS solutions are found to describe the actual wave dynamics of steep waves reasonably well.

  15. Generation of Nonlinear Evolution Equations by Reductions of the Self-Dual Yang—Mills Equations

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-Feng; Hon-Wah, Tam

    2014-02-01

    With the help of some reductions of the self-dual Yang Mills (briefly written as sdYM) equations, we introduce a Lax pair whose compatibility condition leads to a set of (2 + 1)-dimensional equations. Its first reduction gives rise to a generalized variable-coefficient Burgers equation with a forced term. Furthermore, the Burgers equation again reduces to a forced Burgers equation with constant coefficients, the standard Burgers equation, the heat equation, the Fisher equation, and the Huxley equation, respectively. The second reduction generates a few new (2 + 1)-dimensional nonlinear integrable systems, in particular, obtains a kind of (2 + 1)-dimensional integrable couplings of a new (2 + 1)-dimensional integrable nonlinear equation.

  16. GHM method for obtaining rationalsolutions of nonlinear differential equations.

    PubMed

    Vazquez-Leal, Hector; Sarmiento-Reyes, Arturo

    2015-01-01

    In this paper, we propose the application of the general homotopy method (GHM) to obtain rational solutions of nonlinear differential equations. It delivers a high precision representation of the nonlinear differential equation using a few linear algebraic terms. In order to assess the benefits of this proposal, three nonlinear problems are solved and compared against other semi-analytic methods or numerical methods. The obtained results show that GHM is a powerful tool, capable to generate highly accurate rational solutions. AMS subject classification 34L30.

  17. 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

  18. Nonlinear partial differential equations: Integrability, geometry and related topics

    NASA Astrophysics Data System (ADS)

    Krasil'shchik, Joseph; Rubtsov, Volodya

    2017-03-01

    Geometry and Differential Equations became inextricably entwined during the last one hundred fifty years after S. Lie and F. Klein's fundamental insights. The two subjects go hand in hand and they mutually enrich each other, especially after the "Soliton Revolution" and the glorious streak of Symplectic and Poisson Geometry methods in the context of Integrability and Solvability problems for Non-linear Differential Equations.

  19. 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.

  20. Entropy and convexity for nonlinear partial differential equations.

    PubMed

    Ball, John M; Chen, Gui-Qiang G

    2013-12-28

    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.

  1. 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

  2. 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.

  3. 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.

  4. Model Predictive Control for Nonlinear Parabolic Partial Differential Equations

    NASA Astrophysics Data System (ADS)

    Hashimoto, Tomoaki; Yoshioka, Yusuke; Ohtsuka, Toshiyuki

    In this study, the optimal control problem of nonlinear parabolic partial differential equations (PDEs) is investigated. Optimal control of nonlinear PDEs is an open problem with applications that include fluid, thermal, biological, and chemically-reacting systems. Model predictive control with a fast numerical solution method has been well established to solve the optimal control problem of nonlinear systems described by ordinary differential equations. In this study, we develop a design method of the model predictive control for nonlinear systems described by parabolic PDEs. Our approach is a direct infinite dimensional extension of the model predictive control method for finite-dimensional systems. The objective of this paper is to develop an efficient algorithm for numerically solving the model predictive control problem of nonlinear parabolic PDEs. The effectiveness of the proposed method is verified by numerical simulations.

  5. 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.

  6. 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.

  7. 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.

  8. Nonlinear equations of dynamics for spinning paraboloidal antennas

    NASA Technical Reports Server (NTRS)

    Utku, S.; Shoemaker, W. L.; Salama, M.

    1983-01-01

    The nonlinear strain-displacement and velocity-displacement relations of spinning imperfect rotational paraboloidal thin shell antennas are derived for nonaxisymmetrical deformations. Using these relations with the admissible trial functions in the principle functional of dynamics, the nonlinear equations of stress inducing motion are expressed in the form of a set of quasi-linear ordinary differential equations of the undetermined functions by means of the Rayleigh-Ritz procedure. These equations include all nonlinear terms up to and including the third degree. Explicit expressions are given for the coefficient matrices appearing in these equations. Both translational and rotational off-sets of the axis of revolution (and also the apex point of the paraboloid) with respect to the spin axis are considered. Although the material of the antenna is assumed linearly elastic, it can be anisotropic.

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

    PubMed

    Baranwal, Vipul K; Pandey, Ram K; Singh, Om P

    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 γ 0, γ 1, γ 2,… and auxiliary functions H 0(x), H 1(x), H 2(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.

  10. A general non-linear multilevel structural equation mixture model

    PubMed Central

    Kelava, Augustin; Brandt, Holger

    2014-01-01

    In the past 2 decades latent variable modeling has become a standard tool in the social sciences. In the same time period, traditional linear structural equation models have been extended to include non-linear interaction and quadratic effects (e.g., Klein and Moosbrugger, 2000), and multilevel modeling (Rabe-Hesketh et al., 2004). We present a general non-linear multilevel structural equation mixture model (GNM-SEMM) that combines recent semiparametric non-linear structural equation models (Kelava and Nagengast, 2012; Kelava et al., 2014) with multilevel structural equation mixture models (Muthén and Asparouhov, 2009) for clustered and non-normally distributed data. The proposed approach allows for semiparametric relationships at the within and at the between levels. We present examples from the educational science to illustrate different submodels from the general framework. PMID:25101022

  11. Nonlinear waves described by the generalized Swift-Hohenberg equation

    NASA Astrophysics Data System (ADS)

    Ryabov, P. N.; Kudryashov, N. A.

    2017-01-01

    We study the wave processes described by the generalized Swift-Hohenberg equation. We show that the traveling wave reduction of this equation does not pass the Kovalevskaya test. Some solitary wave solutions and kink solutions of the generalized Swift-Hohenberg equation are found. We use the pseudo-spectral algorithm to perform the numerical simulation of the wave processes described by the mixed boundary value problem for the generalized Swift-Hohenberg equation. This algorithm was tested on the obtained solutions. Some features of the nonlinear waves evolution described by the generalized Swift-Hohenberg equation are studied.

  12. Approximating a nonlinear advanced-delayed equation from acoustics

    NASA Astrophysics Data System (ADS)

    Teodoro, M. Filomena

    2016-10-01

    We approximate the solution of a particular non-linear mixed type functional differential equation from physiology, the mucosal wave model of the vocal oscillation during phonation. The mathematical equation models a superficial wave propagating through the tissues. The numerical scheme is adapted from the work presented in [1, 2, 3], using homotopy analysis method (HAM) to solve the non linear mixed type equation under study.

  13. 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.

  14. Cylindrical Pulsons in Nonlinear Relativistic Wave Equations

    NASA Astrophysics Data System (ADS)

    Geicke, J.

    1984-05-01

    Numerical results to the Higgs scalar equation and the sine-Gordon equation with cylindrical symmetry are reported. Two separated energy regions are found where a Higgs kink develops into pulsons when reaching the origin r = 0, while only for higher energies a reflection is observed. The pulsons to both equations are studied in detail by modifying the initial kink shapes. In comparison with the spherical pulsons the cylindrical ones are extremely long-lived. For amplitudes slightly below half the distance between two (neighboured) vacua of the theories no decrease of the amplitudes and no perceivable radiation have been obtained by the numerical solution, examined during a time of order 1000. On the other hand, "heavy" sine-Gordon pulsons (with amplitudes 3π ~ 4π) are found to decay fast during a time t approx 100 in cylindrical symmetry.

  15. The Jeffcott equations in nonlinear rotordynamics

    NASA Technical Reports Server (NTRS)

    Zalik, R. A.

    1989-01-01

    The solutions of the Jeffcott equations describing the behavior of a rotating shaft are investigated analytically, with a focus on the case where deadband is taken into account. Bounds on the solutions are obtained from those for the linearized equations, and the onset of destructive vibrations is predicted by analyzing the Fourier transforms of the solutions; good agreement with numerical solutions and power-spectrum density plots is demonstrated. It is suggested that the present analytical approach could be applied to determine cryogenic-pump stability margins in flight and hot-fire ground testing of launch vehicles such as the Space Shuttle.

  16. 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…

  17. 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…

  18. 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…

  19. Multi-diffusive nonlinear Fokker-Planck equation

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauricio S.; Casas, Gabriela A.; Nobre, Fernando D.

    2017-02-01

    Nonlinear Fokker-Planck equations, characterized by more than one diffusion term, have appeared recently in literature. Here, it is shown that these equations may be derived either from approximations in a master equation, or from a Langevin-type approach. An H-theorem is proven, relating these Fokker-Planck equations to an entropy composed by a sum of contributions, each of them associated with a given diffusion term. Moreover, the stationary state of the Fokker-Planck equation is shown to coincide with the equilibrium state, obtained by extremization of the entropy, in the sense that both procedures yield precisely the same equation. Due to the nonlinear character of this equation, the equilibrium probability may be obtained, in most cases, only by means of numerical approaches. Some examples are worked out, where the equilibrium probability distribution is computed for nonlinear Fokker-Planck equations presenting two diffusion terms, corresponding to an entropy characterized by a sum of two contributions. It is shown that the resulting equilibrium distribution, in general, presents a form that differs from a sum of the equilibrium distributions that maximizes each entropic contribution separately, although in some cases one may construct such a linear combination as a good approximation for the equilibrium distribution.

  20. 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.

  1. 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.

  2. Localized Nonlinear Waves in Nonlinear Schr¨odinger Equation with Nonlinearities Modulated in Space and Time

    NASA Astrophysics Data System (ADS)

    Chen, Junchao; Li, Biao

    2011-12-01

    In this paper, the generalized sub-equation method is extended to investigate localized nonlinear waves of the one-dimensional nonlinear Schrödinger equation (NLSE) with potentials and nonlinearities depending on time and on spatial coordinates. With the help of symbolic computation, three families of analytical solutions of this NLS-type equation are presented. Based on these solutions, periodically and quasiperiodically oscillating solitons (dark and bright) and moving solitons are observed. Some implications to Bose-Einstein condensates are also discussed

  3. Transport equations for subdiffusion with nonlinear particle interaction.

    PubMed

    Straka, P; Fedotov, S

    2015-02-07

    We show how the nonlinear interaction effects 'volume filling' and 'adhesion' can be incorporated into the fractional subdiffusive transport of cells and individual organisms. To this end, we use microscopic random walk models with anomalous trapping and systematically derive generic non-Markovian and nonlinear governing equations for the mean concentrations of the subdiffusive cells or organisms. We uncover an interesting interaction between the nonlinearities and the non-Markovian nature of the transport. In the subdiffusive case, this interaction manifests itself in a nontrivial combination of nonlinear terms with fractional derivatives. In the long time limit, however, these equations simplify to a form without fractional operators. This provides an easy method for the study of aggregation phenomena. In particular, this enables us to show that volume filling can prevent "anomalous aggregation," which occurs in subdiffusive systems with a spatially varying anomalous exponent.

  4. Periodic orbits in nonlinear wave equations on networks

    NASA Astrophysics Data System (ADS)

    Caputo, J. G.; Khames, I.; Knippel, A.; Panayotaros, P.

    2017-09-01

    We consider a cubic nonlinear wave equation on a network and show that inspecting the normal modes of the graph, we can immediately identify which ones extend into nonlinear periodic orbits. Two main classes of nonlinear periodic orbits exist: modes without soft nodes and others. For the former which are the Goldstone and the bivalent modes, the linearized equations decouple. A Floquet analysis was conducted systematically for chains; it indicates that the Goldstone mode is usually stable and the bivalent mode is always unstable. The linearized equations for the second type of modes are coupled, they indicate which modes will be excited when the orbit destabilizes. Numerical results for the second class show that modes with a single eigenvalue are unstable below a threshold amplitude. Conversely, modes with multiple eigenvalues always seem unstable. This study could be applied to coupled mechanical systems.

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

    NASA Astrophysics Data System (ADS)

    Doha, Eid H.; Bhrawy, Ali H.; Abdelkawy, Mohamed A.; Hafez, Ramy M.

    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.

  6. 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.

  7. An Efficient Numerical Solution of Nonlinear Hunter-Saxton Equation

    NASA Astrophysics Data System (ADS)

    Parand, Kourosh; Delkhosh, Mehdi

    2017-05-01

    In this paper, the nonlinear Hunter-Saxton equation, which is a famous partial differential equation, is solved by using a hybrid numerical method based on the quasilinearization method and the bivariate generalized fractional order of the Chebyshev functions (B-GFCF) collocation method. First, using the quasilinearization method, the equation is converted into a sequence of linear partial differential equations (LPD), and then these LPDs are solved using the B-GFCF collocation method. A very good approximation of solutions is obtained, and comparisons show that the obtained results are more accurate than the results of other researchers.

  8. 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.

  9. 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.

  10. 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.

  11. Numerical study of fractional nonlinear Schrödinger equations.

    PubMed

    Klein, Christian; Sparber, Christof; Markowich, Peter

    2014-12-08

    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.

  12. Burgers' equation and the evolution of nonlinear second sound

    NASA Astrophysics Data System (ADS)

    Davidowitz, Hananel; L'vov, Yuri; Steinberg, Victor

    A systematic, experimental and numerical search for subharmonic generation and/or amplification was conducted at intermediate times and moderate Reynolds numbers in nonlinear second sound near the superfluid transition. We found that the nonlinear acoustic waves are dynamically monotonic in the sense that only energy cascades to smaller and smaller scales (until the dissipation scale) exist. There is no indication of a decay of monochromatic waves to waves of lower wave numbers. This precludes the existence of a decay instability in Burgers' equation as has been discussed in the literature. We thus extend the theoretical proof of Sinai concerning the absence of subharmonics in the solutions of Burger's equation to intermediate times.

  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. 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.

  15. 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).

  16. 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.

  17. Existence of stationary states for nonlinear Dirac equations

    NASA Astrophysics Data System (ADS)

    Merle, F.

    We generalize the previous result of Cazenave and Vasquez on the existence of stationary states for nonlinear Dirac equations of the form i∑ μ3 = 0 γμ∂μΨ - mΨ + L( ΨΨ) Ψ = 0. We seek solutions which are separable in spherical coordinates and we then make use of a shooting method to solve the associated problem for ordinary differential equations.

  18. 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.

  19. Case-Deletion Diagnostics for Nonlinear Structural Equation Models

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Lu, Bin

    2003-01-01

    In this article, a case-deletion procedure is proposed to detect influential observations in a nonlinear structural equation model. The key idea is to develop the diagnostic measures based on the conditional expectation of the complete-data log-likelihood function in the EM algorithm. An one-step pseudo approximation is proposed to reduce the…

  20. 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.

  1. A new perturbative approach to nonlinear partial differential equations

    SciTech Connect

    Bender, C.M.; Boettcher, S. ); Milton, K.A. )

    1991-11-01

    This paper shows how to solve some nonlinear wave equations as perturbation expansions in powers of a parameter that expresses the degree of nonlinearity. For the case of the Burgers equation {ital u}{sub {ital t}}+{ital uu}{sub {ital x}}={ital u}{sub {ital xx}}, the general nonlinear equation {ital u}{sub {ital t}}+{ital u}{sup {delta}}{ital u}{sub {ital x}}={ital u}{sub {ital xx}} is considered and expanded in powers of {delta}. The coefficients of the {delta} series to sixth order in powers of {delta} is determined and Pade summation is used to evaluate the perturbation series for large values of {delta}. The numerical results are accurate and the method is very general; it applies to other well-studied partial differential equations such as the Korteweg--de Vries equation, {ital u}{sub {ital t}}+{ital uu}{sub {ital x}} ={ital u}{sub {ital xxx}}.

  2. Long-time relaxation processes in the nonlinear Schroedinger equation

    SciTech Connect

    Ovchinnikov, Yu. N.; Sigal, I. M.

    2011-03-15

    The nonlinear Schroedinger equation, known in low-temperature physics as the Gross-Pitaevskii equation, has a large family of excitations of different kinds. They include sound excitations, vortices, and solitons. The dynamics of vortices strictly depends on the separation between them. For large separations, some kind of adiabatic approximation can be used. We consider the case where an adiabatic approximation can be used (large separation between vortices) and the opposite case of a decay of the initial state, which is close to the double vortex solution. In the last problem, no adiabatic parameter exists (the interaction is strong). Nevertheless, a small numerical parameter arises in the problem of the decay rate, connected with an existence of a large centrifugal potential, which leads to a small value of the increment. The properties of the nonlinear wave equation are briefly considered in the Appendix A.

  3. Traveling wavefront solutions to nonlinear reaction-diffusion-convection equations

    NASA Astrophysics Data System (ADS)

    Indekeu, Joseph O.; Smets, Ruben

    2017-08-01

    Physically motivated modified Fisher equations are studied in which nonlinear convection and nonlinear diffusion is allowed for besides the usual growth and spread of a population. It is pointed out that in a large variety of cases separable functions in the form of exponentially decaying sharp wavefronts solve the differential equation exactly provided a co-moving point source or sink is active at the wavefront. The velocity dispersion and front steepness may differ from those of some previously studied exact smooth traveling wave solutions. For an extension of the reaction-diffusion-convection equation, featuring a memory effect in the form of a maturity delay for growth and spread, also smooth exact wavefront solutions are obtained. The stability of the solutions is verified analytically and numerically.

  4. Embedded eigenvalues and the nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Asad, R.; Simpson, G.

    2011-03-01

    A common challenge in proving asymptotic stability of solitary waves is understanding the spectrum of the operator associated with the linearized flow. The existence of eigenvalues can inhibit the dispersive estimates key to proving stability. Following the work of Marzuola and Simpson [Nonlinearity 52, 389 (2011)], 10.1088/0951-7715/24/2/003, we prove the absence of embedded eigenvalues for a collection of nonlinear Schrödinger equations, including some one and three dimensional supercritical equations, and the three dimensional cubic-quintic equation. Our results also rule out nonzero eigenvalues within the spectral gap and end point resonances. The proof is computer assisted as it depends on the signs of certain inner products which do not readily admit analytic representations. Our source code is available for verification at http://hdl.handle.net/1807/26121.

  5. 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.

  6. 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.

  7. Curl forces and the nonlinear Fokker-Planck equation

    NASA Astrophysics Data System (ADS)

    Wedemann, R. S.; Plastino, A. R.; Tsallis, C.

    2016-12-01

    Nonlinear Fokker-Planck equations endowed with curl drift forces are investigated. The conditions under which these evolution equations admit stationary solutions, which are q exponentials of an appropriate potential function, are determined. It is proved that when these stationary solutions exist, the nonlinear Fokker-Planck equations satisfy an H theorem in terms of a free-energy-like quantity involving the Sq entropy. A particular two-dimensional model admitting analytical, time-dependent q -Gaussian solutions is discussed in detail. This model describes a system of particles with short-range interactions, performing overdamped motion under drag effects due to a rotating resisting medium. It is related to models that have been recently applied to the study of type-II superconductors. The relevance of the present developments to the study of complex systems in physics, astronomy, and biology is discussed.

  8. 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.

  9. 1/f noise from nonlinear stochastic differential equations

    NASA Astrophysics Data System (ADS)

    Ruseckas, J.; Kaulakys, B.

    2010-03-01

    We consider a class of nonlinear stochastic differential equations, giving the power-law behavior of the power spectral density in any desirably wide range of frequency. Such equations were obtained starting from the point process models of 1/fβ noise. In this article the power-law behavior of spectrum is derived directly from the stochastic differential equations, without using the point process models. The analysis reveals that the power spectrum may be represented as a sum of the Lorentzian spectra. Such a derivation provides additional justification of equations, expands the class of equations generating 1/fβ noise, and provides further insights into the origin of 1/fβ noise.

  10. 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

  11. 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.

  12. Modulational instability in fractional nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Zhang, Lifu; He, Zenghui; Conti, Claudio; Wang, Zhiteng; Hu, Yonghua; Lei, Dajun; Li, Ying; Fan, Dianyuan

    2017-07-01

    Fractional calculus is entering the field of nonlinear optics to describe unconventional regimes, as disorder biological media and soft-matter. Here we investigate spatiotemporal modulational instability (MI) in a fractional nonlinear Schrödinger equation. We derive the MI gain spectrum in terms of the Lévy indexes and a varying number of spatial dimensions. We show theoretically and numerically that the Lévy indexes affect fastest growth frequencies and MI bandwidth and gain. Our results unveil a very rich scenario that may occur in the propagation of ultrashort pulses in random media and metamaterials, and may sustain novel kinds of propagation invariant optical bullets.

  13. Integrable equations of the infinite nonlinear Schrödinger equation hierarchy with time variable coefficients.

    PubMed

    Kedziora, D J; Ankiewicz, A; Chowdury, A; Akhmediev, N

    2015-10-01

    We present an infinite nonlinear Schrödinger equation hierarchy of integrable equations, together with the recurrence relations defining it. To demonstrate integrability, we present the Lax pairs for the whole hierarchy, specify its Darboux transformations and provide several examples of solutions. These resulting wavefunctions are given in exact analytical form. We then show that the Lax pair and Darboux transformation formalisms still apply in this scheme when the coefficients in the hierarchy depend on the propagation variable (e.g., time). This extension thus allows for the construction of complicated solutions within a greatly diversified domain of generalised nonlinear systems.

  14. Nonlinear Smoluchowski velocity for electroosmosis of Power-law fluids over a surface with arbitrary zeta potentials.

    PubMed

    Zhao, Cunlu; Yang, Chun

    2010-03-01

    Electroosmotic flow of Power-law fluids over a surface with arbitrary zeta potentials is analyzed. The governing equations including the nonlinear Poisson-Boltzmann equation, the Cauchy momentum equation and the continuity equation are solved to seek exact solutions for the electroosmotic velocity, shear stress, and dynamic viscosity distributions inside the electric double layer. Specifically, an expression for the general Smoluchowski velocity is obtained for electroosmosis of Power-law fluids in a fashion similar to the classic Smoluchowski velocity for Newtonian fluids. The existing Smoluchowski slip velocities under two special cases, (i) for Newtonian fluids with arbitrary zeta potentials and (ii) for Power-law fluids with small zeta potentials, can be recovered from our derived formula. It is interesting to note that the general Smoluchowski velocity for non-Newtonian Power-law fluids is a nonlinear function of the electric field strength and surface zeta potentials; this is due to the coupling electrostatics and non-Newtonian fluid behavior, which is different from its counterpart for Newtonian fluids. This general Smoluchowski velocity is of practical significance in determining the flow rates in microfluidic devices involving non-Newtonian Power-law fluids.

  15. Nonlinearity, PT Symmetry, Twist, and Disorder in Discrete Nonlinear Schroedinger Equation

    NASA Astrophysics Data System (ADS)

    Castro-Castro, Claudia K.

    The study of optical fiber arrays has drawn a great deal of attention in the field of nonlinear physics during the past few years since they provide spatially inhomogeneous structures for guiding light signals. We analyze the management and control of light transfer in nonlinear multi-core fibers. We utilize mathematical modeling and numerical simulations to specifically show how nonlinearity, coupling, geometric twist, and balanced gain/loss relate to existence and stability of nonlinear optical modes modeled by the Discrete Nonlinear Schrodinger Equation (DNLS). In addition, we explore the effects of the inherent variability on the fiber core diameter (disorder) by building a statistical understanding of the formation of low or high-amplitude (localized/breather) states, and the long-time asymptotics of DNLS with low-amplitude initial conditions.

  16. Unleashing Empirical Equations with "Nonlinear Fitting" and "GUM Tree Calculator"

    NASA Astrophysics Data System (ADS)

    Lovell-Smith, J. W.; Saunders, P.; Feistel, R.

    2017-10-01

    Empirical equations having large numbers of fitted parameters, such as the international standard reference equations published by the International Association for the Properties of Water and Steam (IAPWS), which form the basis of the "Thermodynamic Equation of Seawater—2010" (TEOS-10), provide the means to calculate many quantities very accurately. The parameters of these equations are found by least-squares fitting to large bodies of measurement data. However, the usefulness of these equations is limited since uncertainties are not readily available for most of the quantities able to be calculated, the covariance of the measurement data is not considered, and further propagation of the uncertainty in the calculated result is restricted since the covariance of calculated quantities is unknown. In this paper, we present two tools developed at MSL that are particularly useful in unleashing the full power of such empirical equations. "Nonlinear Fitting" enables propagation of the covariance of the measurement data into the parameters using generalized least-squares methods. The parameter covariance then may be published along with the equations. Then, when using these large, complex equations, "GUM Tree Calculator" enables the simultaneous calculation of any derived quantity and its uncertainty, by automatic propagation of the parameter covariance into the calculated quantity. We demonstrate these tools in exploratory work to determine and propagate uncertainties associated with the IAPWS-95 parameters.

  17. 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.

  18. Physical dynamics of quasi-particles in nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Christov, Ivan; Christov, C. I.

    2008-02-01

    By treating the centers of solitons as point particles and studying their discrete dynamics, we demonstrate a new approach to the quantization of the soliton solutions of the sine-Gordon equation, one of the first model nonlinear field equations. In particular, we show that a linear superposition of the non-interacting shapes of two solitons offers a qualitative (and to a good approximation quantitative) description of the true two-soliton solution, provided that the trajectories of the centers of the superimposed solitons are considered unknown. Via variational calculus, we establish that the dynamics of the quasi-particles obey a pseudo-Newtonian law, which includes cross-mass terms. The successful identification of the governing equations of the (discrete) quasi-particles from the (continuous) field equation shows that the proposed approach provides a basis for the passage from the continuous to a discrete description of the field.

  19. On the Amplitude Equations for Weakly Nonlinear Surface Waves

    NASA Astrophysics Data System (ADS)

    Benzoni-Gavage, Sylvie; Coulombel, Jean-François

    2012-09-01

    Nonlocal generalizations of Burgers' equation were derived in earlier work by Hunter (Contemp Math, vol 100, pp 185-202. AMS, 1989), and more recently by Benzoni-Gavage and Rosini (Comput Math Appl 57(3-4):1463-1484, 2009), as weakly nonlinear amplitude equations for hyperbolic boundary value problems admitting linear surface waves. The local-in-time well-posedness of such equations in Sobolev spaces was proved by Benzoni-Gavage (Differ Integr Equ 22(3-4):303-320, 2009) under an appropriate stability condition originally pointed out by Hunter. The same stability condition has also been shown to be necessary for well-posedness in Sobolev spaces in a previous work of the authors in collaboration with Tzvetkov (Benzoni-Gavage et al. in Adv Math 227(6):2220-2240, 2011). In this article, we show how the verification of Hunter's stability condition follows from natural stability assumptions on the original hyperbolic boundary value problem, thus avoiding lengthy computations in each particular situation. We also show that the resulting amplitude equation has a Hamiltonian structure when the original boundary value problem has a variational origin. Our analysis encompasses previous equations derived for nonlinear Rayleigh waves in elasticity.

  20. 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.

  1. Numerical Solution of a Nonlinear Integro-Differential Equation

    NASA Astrophysics Data System (ADS)

    Buša, Ján; Hnatič, Michal; Honkonen, Juha; Lučivjanský, Tomáš

    2016-02-01

    A discretization algorithm for the numerical solution of a nonlinear integrodifferential equation modeling the temporal variation of the mean number density a(t) in the single-species annihilation reaction A + A → 0 is discussed. The proposed solution for the two-dimensional case (where the integral entering the equation is divergent) uses regularization and then finite differences for the approximation of the differential operator together with a piecewise linear approximation of a(t) under the integral. The presented numerical results point to basic features of the behavior of the number density function a(t) and suggest further improvement of the proposed algorithm.

  2. Nonzero solutions of nonlinear integral equations modeling infectious disease

    SciTech Connect

    Williams, L.R.; Leggett, R.W.

    1982-01-01

    Sufficient conditions to insure the existence of periodic solutions to the nonlinear integral equation, x(t) = ..integral../sup t//sub t-tau/f(s,x(s))ds, are given in terms of simple product and product integral inequalities. The equation can be interpreted as a model for the spread of infectious diseases (e.g., gonorrhea or any of the rhinovirus viruses) if x(t) is the proportion of infectives at time t and f(t,x(t)) is the proportion of new infectives per unit time.

  3. Connecting orbits for nonlinear differential equations at resonance

    NASA Astrophysics Data System (ADS)

    Kokocki, Piotr

    We study the existence of orbits connecting stationary points for the first order differential equations being at resonance at infinity, where the right hand side is the perturbations of a sectorial operator. Our aim is to prove an index formula expressing the Conley index of associated semiflow with respect to appropriately large ball, in terms of special geometrical assumptions imposed on the nonlinearity. We also prove that the geometrical assumptions are generalization of the well-known in literature Landesman-Lazer and strong resonance conditions. Obtained index formula will be used to derive the criteria determining the existence of orbits connecting stationary points for the heat equation being at resonance at infinity.

  4. Inverse Problem of Variational Calculus for Nonlinear Evolution Equations

    NASA Astrophysics Data System (ADS)

    Ali, Sk. Golam; Talukdar, B.; Das, U.

    2007-06-01

    We couple a nonlinear evolution equation with an associated one and derive the action principle. This allows us to write the Lagrangian density of the system in terms of the original field variables rather than Casimir potentials. We find that the corresponding Hamiltonian density provides a natural basis to recast the pair of equations in the canonical form. Amongst the case studies presented the KdV and modified KdV pairs exhibit bi-Hamiltonian structure and allow one to realize the associated fields in physical terms.

  5. Singular Solutions of Fully Nonlinear Elliptic Equations and Applications

    NASA Astrophysics Data System (ADS)

    Armstrong, Scott N.; Sirakov, Boyan; Smart, Charles K.

    2012-08-01

    We study the properties of solutions of fully nonlinear, positively homogeneous elliptic equations near boundary points of Lipschitz domains at which the solution may be singular. We show that these equations have two positive solutions in each cone of {R^n} , and the solutions are unique in an appropriate sense. We introduce a new method for analyzing the behavior of solutions near certain Lipschitz boundary points, which permits us to classify isolated boundary singularities of solutions which are bounded from either above or below. We also obtain a sharp Phragmén-Lindelöf result as well as a principle of positive singularities in certain Lipschitz domains.

  6. 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

  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. The exotic conformal Galilei algebra and nonlinear partial differential equations

    NASA Astrophysics Data System (ADS)

    Cherniha, Roman; Henkel, Malte

    2010-09-01

    The conformal Galilei algebra (CGA) and the exotic conformal Galilei algebra (ECGA) are applied to construct partial differential equations (PDEs) and systems of PDEs, which admit these algebras. We show that there are no single second-order PDEs invariant under the CGA but systems of PDEs can admit this algebra. Moreover, a wide class of nonlinear PDEs exists, which are conditionally invariant under CGA. It is further shown that there are systems of non-linear PDEs admitting ECGA with the realisation obtained very recently in [D. Martelli and Y. Tachikawa, arXiv:0903.5184v2 [hep-th] (2009)]. Moreover, wide classes of non-linear systems, invariant under two different 10-dimensional subalgebras of ECGA are explicitly constructed and an example with possible physical interpretation is presented.

  9. Loss of Energy Concentration in Nonlinear Evolution Beam Equations

    NASA Astrophysics Data System (ADS)

    Garrione, Maurizio; Gazzola, Filippo

    2017-05-01

    Motivated by the oscillations that were seen at the Tacoma Narrows Bridge, we introduce the notion of solutions with a prevailing mode for the nonlinear evolution beam equation u_{tt} + u_{xxxx} + f(u)= g(x, t) in bounded space-time intervals. We give a new definition of instability for these particular solutions, based on the loss of energy concentration on their prevailing mode. We distinguish between two different forms of energy transfer, one physiological (unavoidable and depending on the nonlinearity) and one due to the insurgence of instability. We then prove a theoretical result allowing to reduce the study of this kind of infinite-dimensional stability to that of a finite-dimensional approximation. With this background, we study the occurrence of instability for three different kinds of nonlinearities f and for some forcing terms g, highlighting some of their structural properties and performing some numerical simulations.

  10. Chaoticons described by nonlocal nonlinear Schrödinger equation.

    PubMed

    Zhong, Lanhua; Li, Yuqi; Chen, Yong; Hong, Weiyi; Hu, Wei; Guo, Qi

    2017-01-30

    It is shown that the unstable evolutions of the Hermite-Gauss-type stationary solutions for the nonlocal nonlinear Schrödinger equation with the exponential-decay response function can evolve into chaotic states. This new kind of entities are referred to as chaoticons because they exhibit not only chaotic properties (with positive Lyapunov exponents and spatial decoherence) but also soliton-like properties (with invariant statistic width and interaction of quasi-elastic collisions).

  11. Chaoticons described by nonlocal nonlinear Schrödinger equation

    PubMed Central

    Zhong, Lanhua; Li, Yuqi; Chen, Yong; Hong, Weiyi; Hu, Wei; Guo, Qi

    2017-01-01

    It is shown that the unstable evolutions of the Hermite-Gauss-type stationary solutions for the nonlocal nonlinear Schrödinger equation with the exponential-decay response function can evolve into chaotic states. This new kind of entities are referred to as chaoticons because they exhibit not only chaotic properties (with positive Lyapunov exponents and spatial decoherence) but also soliton-like properties (with invariant statistic width and interaction of quasi-elastic collisions). PMID:28134268

  12. 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.

  13. 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.

  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. Stabilisation of second-order nonlinear equations with variable delay

    NASA Astrophysics Data System (ADS)

    Berezansky, Leonid; Braverman, Elena; Idels, Lev

    2015-08-01

    For a wide class of second-order nonlinear non-autonomous models, we illustrate that combining proportional state control with the feedback that is proportional to the derivative of the chaotic signal allows to stabilise unstable motions of the system. The delays are variable, which leads to more flexible controls permitting delay perturbations; only delay bounds are significant for stabilisation by a delayed control. The results are applied to the sunflower equation which has an infinite number of equilibrium points.

  16. Solution behaviors in coupled Schrödinger equations with full-modulated nonlinearities

    NASA Astrophysics Data System (ADS)

    Pınar, Zehra; Deliktaş, Ekin

    2017-02-01

    The nonlinear partial differential equations have an important role in real life problems. To obtain the exact solutions of the nonlinear partial differential equations, a number of approximate methods are known in the literature. In this work, a time- space modulated nonlinearities of coupled Schrödinger equations are considered. We provide a large class of Jacobi-elliptic solutions via the auxiliary equation method with sixth order nonlinearity and the Chebyshev approximation.

  17. Derivation of the Biot-Savart equation from the nonlinear Schrödinger equation.

    PubMed

    Bustamante, Miguel D; Nazarenko, Sergey

    2015-11-01

    We present a systematic derivation of the Biot-Savart equation from the nonlinear Schrödinger equation, in the limit when the curvature radius of vortex lines and the intervortex distance are much greater than the vortex healing length, or core radius. We derive the Biot-Savart equations in Hamiltonian form with Hamiltonian expressed in terms of vortex lines,H=κ(2)/8π∫(|s-s'|>ξ(*))(ds·ds')/|s-s'|,with cutoff length ξ(*)≈0.3416293/√(ρ(0)), where ρ(0) is the background condensate density far from the vortex lines and κ is the quantum of circulation.

  18. Nonlinear Optical Wave Equation for Micro- and Nano-Structured Media and Its Application

    DTIC Science & Technology

    2013-03-01

    AFRL-AFOSR-UK-TR-2013-0012 Nonlinear Optical Wave Equation for Micro - and Nano - Structured Media and Its Application Dr...September 2012 4. TITLE AND SUBTITLE Nonlinear Optical Wave Equation for Micro - and Nano - Structured Media and Its...Equation, Nano -structed Media, Nonlinear Fiber Lasers 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT SAR 18, NUMBER OF PAGES 12

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

    SciTech Connect

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

    2015-11-15

    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.

  20. 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.

  1. Complete integrability of nonlocal nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Gerdjikov, V. S.; Saxena, A.

    2017-01-01

    Based on the completeness relation for the squared solutions of the Lax operator L, we show that a subset of nonlocal equations from the hierarchy of nonlocal nonlinear Schrödinger equations (NLS) is a completely integrable system. The spectral properties of the Lax operator indicate that there are two types of soliton solutions. The relevant action-angle variables are parametrized by the scattering data of the Lax operator. The notion of the symplectic basis, which directly maps the variations of the potential of L to the variations of the action-angle variables has been generalized to the nonlocal case. We also show that the inverse scattering method can be viewed as a generalized Fourier transform. Using the trace identities and the symplectic basis, we construct the hierarchy Hamiltonian structures for the nonlocal NLS equations.

  2. 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.

  3. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.

    PubMed

    Hou, Tingjun; Wang, Junmei; Li, Youyong; Wang, Wei

    2011-04-15

    In molecular docking, it is challenging to develop a scoring function that is accurate to conduct high-throughput screenings. Most scoring functions implemented in popular docking software packages were developed with many approximations for computational efficiency, which sacrifices the accuracy of prediction. With advanced technology and powerful computational hardware nowadays, it is feasible to use rigorous scoring functions, such as molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) in molecular docking studies. Here, we systematically investigated the performance of MM/PBSA and MM/GBSA to identify the correct binding conformations and predict the binding free energies for 98 protein-ligand complexes. Comparison studies showed that MM/GBSA (69.4%) outperformed MM/PBSA (45.5%) and many popular scoring functions to identify the correct binding conformations. Moreover, we found that molecular dynamics simulations are necessary for some systems to identify the correct binding conformations. Based on our results, we proposed the guideline for MM/GBSA to predict the binding conformations. We then tested the performance of MM/GBSA and MM/PBSA to reproduce the binding free energies of the 98 protein-ligand complexes. The best prediction of MM/GBSA model with internal dielectric constant 2.0, produced a Spearman's correlation coefficient of 0.66, which is better than MM/PBSA (0.49) and almost all scoring functions used in molecular docking. In summary, MM/GBSA performs well for both binding pose predictions and binding free-energy estimations and is efficient to re-score the top-hit poses produced by other less-accurate scoring functions. Copyright © 2010 Wiley Periodicals, Inc.

  4. Evaluation of model fit in nonlinear multilevel structural equation modeling

    PubMed Central

    Schermelleh-Engel, Karin; Kerwer, Martin; Klein, Andreas G.

    2013-01-01

    Evaluating model fit in nonlinear multilevel structural equation models (MSEM) presents a challenge as no adequate test statistic is available. Nevertheless, using a product indicator approach a likelihood ratio test for linear models is provided which may also be useful for nonlinear MSEM. The main problem with nonlinear models is that product variables are non-normally distributed. Although robust test statistics have been developed for linear SEM to ensure valid results under the condition of non-normality, they have not yet been investigated for nonlinear MSEM. In a Monte Carlo study, the performance of the robust likelihood ratio test was investigated for models with single-level latent interaction effects using the unconstrained product indicator approach. As overall model fit evaluation has a potential limitation in detecting the lack of fit at a single level even for linear models, level-specific model fit evaluation was also investigated using partially saturated models. Four population models were considered: a model with interaction effects at both levels, an interaction effect at the within-group level, an interaction effect at the between-group level, and a model with no interaction effects at both levels. For these models the number of groups, predictor correlation, and model misspecification was varied. The results indicate that the robust test statistic performed sufficiently well. Advantages of level-specific model fit evaluation for the detection of model misfit are demonstrated. PMID:24624110

  5. Approximate analytic solutions to coupled nonlinear Dirac equations

    NASA Astrophysics Data System (ADS)

    Khare, Avinash; Cooper, Fred; Saxena, Avadh

    2017-03-01

    We consider the coupled nonlinear Dirac equations (NLDEs) in 1 + 1 dimensions with scalar-scalar self-interactions g12 / 2 (ψ bar ψ) 2 + g22/2 (ϕ bar ϕ) 2 + g32 (ψ bar ψ) (ϕ bar ϕ) as well as vector-vector interactions of the form g1/22 (ψ bar γμ ψ) (ψ bar γμ ψ) + g22/2 (ϕ bar γμ ϕ) (ϕ bar γμ ϕ) + g32 (ψ bar γμ ψ) (ϕ bar γμ ϕ). Writing the two components of the assumed rest frame solution of the coupled NLDE equations in the form ψ =e - iω1 t {R1 cos ⁡ θ ,R1 sin ⁡ θ }, ϕ =e - iω2 t {R2 cos ⁡ η ,R2 sin ⁡ η }, and assuming that θ (x) , η (x) have the same functional form they had when g3 = 0, which is an approximation consistent with the conservation laws, we then find approximate analytic solutions for Ri (x) which are valid for small values of g32 / g22 and g32 / g12. In the nonrelativistic limit we show that both of these coupled models go over to the same coupled nonlinear Schrödinger equation for which we obtain two exact pulse solutions vanishing at x → ± ∞.

  6. Coupled equations of electromagnetic waves in nonlinear metamaterial waveguides.

    PubMed

    Azari, Mina; Hatami, Mohsen; Meygoli, Vahid; Yousefi, Elham

    2016-11-01

    Over the past decades, scientists have presented ways to manipulate the macroscopic properties of a material at levels unachieved before, and called them metamaterials. This research can be considered an important step forward in electromagnetics and optics. In this study, higher-order nonlinear coupled equations in a special kind of metamaterial waveguides (a planar waveguide with metamaterial core) will be derived from both electric and magnetic components of the transverse electric mode of electromagnetic pulse propagation. On the other hand, achieving the refractive index in this research is worthwhile. It is also shown that the coupled equations are not symmetric with respect to the electric and magnetic fields, unlike these kinds of equations in fiber optics and dielectric waveguides. Simulations on the propagation of a fundamental soliton pulse in a nonlinear metamaterial waveguide near the resonance frequency (a little lower than the magnetic resonant frequency) are performed to study its behavior. These pulses are recommended to practice in optical communications in controlled switching by external voltage, even in low power.

  7. Approximate analytic solutions to coupled nonlinear Dirac equations

    DOE PAGES

    Khare, Avinash; Cooper, Fred; Saxena, Avadh

    2017-01-30

    Here, we consider the coupled nonlinear Dirac equations (NLDEs) in 1+11+1 dimensions with scalar–scalar self-interactions g12/2(more » $$\\bar{ψ}$$ψ)2 + g22/2($$\\bar{Φ}$$Φ)2 + g23($$\\bar{ψ}$$ψ)($$\\bar{Φ}$$Φ) as well as vector–vector interactions g12/2($$\\bar{ψ}$$γμψ)($$\\bar{ψ}$$γμψ) + g22/2($$\\bar{Φ}$$γμΦ)($$\\bar{Φ}$$γμΦ) + g23($$\\bar{ψ}$$γμψ)($$\\bar{Φ}$$γμΦ). Writing the two components of the assumed rest frame solution of the coupled NLDE equations in the form ψ=e–iω1tR1cosθ,R1sinθΦ=e–iω2tR2cosη,R2sinη, and assuming that θ(x),η(x) have the same functional form they had when g3 = 0, which is an approximation consistent with the conservation laws, we then find approximate analytic solutions for Ri(x) which are valid for small values of g32/g22 and g32/g12. In the nonrelativistic limit we show that both of these coupled models go over to the same coupled nonlinear Schrödinger equation for which we obtain two exact pulse solutions vanishing at x → ±∞.« less

  8. Robust fast controller design via nonlinear fractional differential equations.

    PubMed

    Zhou, Xi; Wei, Yiheng; Liang, Shu; Wang, Yong

    2017-07-01

    A new method for linear system controller design is proposed whereby the closed-loop system achieves both robustness and fast response. The robustness performance considered here means the damping ratio of closed-loop system can keep its desired value under system parameter perturbation, while the fast response, represented by rise time of system output, can be improved by tuning the controller parameter. We exploit techniques from both the nonlinear systems control and the fractional order systems control to derive a novel nonlinear fractional order controller. For theoretical analysis of the closed-loop system performance, two comparison theorems are developed for a class of fractional differential equations. Moreover, the rise time of the closed-loop system can be estimated, which facilitates our controller design to satisfy the fast response performance and maintain the robustness. Finally, numerical examples are given to illustrate the effectiveness of our methods. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  9. 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

  10. Continuous symmetries of certain nonlinear partial difference equations and their reductions

    NASA Astrophysics Data System (ADS)

    Sahadevan, R.; Nagavigneshwari, G.

    2014-09-01

    In this article, Quispel, Roberts and Thompson type of nonlinear partial difference equation with two independent variables is considered and identified five distinct nonlinear partial difference equations admitting continuous point symmetries quadratic in the dependent variable. Using the degree growth of iterates the integrability nature of the obtained nonlinear partial difference equations is discussed. It is also shown how to derive higher order ordinary difference equations from the periodic reduction of the identified nonlinear partial difference equations. The integrability nature of the obtained ordinary difference equations is investigated wherever possible.

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

    NASA Astrophysics Data System (ADS)

    Khare, Avinash; Saxena, Avadh

    2014-03-01

    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, λϕ4, 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 dn2(x, m), it also admits solutions in terms of dn^2(x,m) ± sqrt{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.

  12. 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.

  13. New Analytical Solution for Nonlinear Shallow Water-Wave Equations

    NASA Astrophysics Data System (ADS)

    Aydin, Baran; Kânoğlu, Utku

    2017-03-01

    We solve the nonlinear shallow water-wave equations over a linearly sloping beach as an initial-boundary value problem under general initial conditions, i.e., an initial wave profile with and without initial velocity. The methodology presented here is extremely simple and allows a solution in terms of eigenfunction expansion, avoiding integral transform techniques, which sometimes result in singular integrals. We estimate parameters, such as the temporal variations of the shoreline position and the depth-averaged velocity, compare with existing solutions, and observe perfect agreement with substantially less computational effort.

  14. New Analytical Solution for Nonlinear Shallow Water-Wave Equations

    NASA Astrophysics Data System (ADS)

    Aydin, Baran; Kânoğlu, Utku

    2017-08-01

    We solve the nonlinear shallow water-wave equations over a linearly sloping beach as an initial-boundary value problem under general initial conditions, i.e., an initial wave profile with and without initial velocity. The methodology presented here is extremely simple and allows a solution in terms of eigenfunction expansion, avoiding integral transform techniques, which sometimes result in singular integrals. We estimate parameters, such as the temporal variations of the shoreline position and the depth-averaged velocity, compare with existing solutions, and observe perfect agreement with substantially less computational effort.

  15. Fourth order wave equations with nonlinear strain and source terms

    NASA Astrophysics Data System (ADS)

    Liu, Yacheng; Xu, Runzhang

    2007-07-01

    In this paper we study the initial boundary value problem for fourth order wave equations with nonlinear strain and source terms. First we introduce a family of potential wells and prove the invariance of some sets and vacuum isolating of solutions. Then we obtain a threshold result of global existence and nonexistence. Finally we discuss the global existence of solutions for the problem with critical initial condition I(u0)[greater-or-equal, slanted]0, E(0)=d. So the Esquivel-Avila's results are generalized and improved.

  16. Some existence results on nonlinear fractional differential equations.

    PubMed

    Baleanu, Dumitru; Rezapour, Shahram; Mohammadi, Hakimeh

    2013-05-13

    In this paper, by using fixed-point methods, we study the existence and uniqueness of a solution for the nonlinear fractional differential equation boundary-value problem D(α)u(t)=f(t,u(t)) with a Riemann-Liouville fractional derivative via the different boundary-value problems u(0)=u(T), and the three-point boundary condition u(0)=β(1)u(η) and u(T)=β(2)u(η), where T>0, t∈I=[0,T], 0<α<1, 0<η

  17. 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.

  18. Numerical solution of nonlinear Hammerstein fuzzy functional integral equations

    NASA Astrophysics Data System (ADS)

    Enkov, Svetoslav; Georgieva, Atanaska; Nikolla, Renato

    2016-12-01

    In this work we investigate nonlinear Hammerstein fuzzy functional integral equation. Our aim is to provide an efficient iterative method of successive approximations by optimal quadrature formula for classes of fuzzy number-valued functions of Lipschitz type to approximate the solution. We prove the convergence of the method by Banach's fixed point theorem and investigate the numerical stability of the presented method with respect to the choice of the first iteration. Finally, illustrative numerical experiment demonstrate the accuracy and the convergence of the proposed method.

  19. 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.

  20. Multiple scales analysis and travelling wave solutions for KdV type nonlinear evolution equations

    NASA Astrophysics Data System (ADS)

    Ayhan, Burcu; Ozer, M. Naci; Bekir, Ahmet

    2017-01-01

    Nonlinear evolution equations are the mathematical models of problems that arise in many field of science. These equations has become an important field of study in applied mathematics in recent years. We apply exact solution methods and multiple scale method which is known as a perturbation method to nonlinear evolution equations. Using exact solution methods we get travelling wave solutions expressed by hyperbolic functions, trigonometric functions and rational functions. Also we derive Nonlinear Schrödinger (NLS) type equations from Korteweg-de Vries (KdV) type nonlinear evolution equations and we get approximate solutions for KdV type equations using multiple scale method. The proposed methods are direct and effective and can be used for many nonlinear evolution equations. It is shown that these methods provide a powerful mathematical tool to solve nonlinear evolution equations in mathematical physics.

  1. 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

  2. A procedure to construct exact solutions of nonlinear fractional differential equations.

    PubMed

    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.

  3. On invariant analysis of some time fractional nonlinear systems of partial differential equations. I

    NASA Astrophysics Data System (ADS)

    Singla, Komal; Gupta, R. K.

    2016-10-01

    An investigation of Lie point symmetries for systems of time fractional partial differential equations including Ito system, coupled Burgers equations, coupled Korteweg de Vries equations, Hirota-Satsuma coupled KdV equations, and coupled nonlinear Hirota equations has been done. Using the obtained symmetries, each one of the systems is reduced to the nonlinear system of fractional ordinary differential equations involving Erdélyi-Kober fractional differential operator depending on a parameter α.

  4. 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).

  5. 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

  6. 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.

  7. Self-focusing and modulational analysis for nonlinear Schroedinger equations

    SciTech Connect

    Weinsten, M.I.

    1982-01-01

    For the initial-value problem (IVP) for the nonlinear Schroedinger equation, a sufficient condition for the existence of a unique global solution of the IVP is found. The condition is derived by solving a variational problem to obtain the best constant for a classical interpolation estimate of Nirenberg and Gagliardo. A systematic analysis of the singular structure is presented here for the first time. Methods apply to the general critical case. Linear modulational stability of the ground state relative to small perturbations in NLS and/or the initial data is established in the subcritical case. A sufficient condition for the existence of a unique global solution of a generalized Korteweg-de Vries equation is obtained in terms of the solitary (traveling) wave solution.

  8. Ergodicity for Nonlinear Stochastic Equations in Variational Formulation

    SciTech Connect

    Barbu, Viorel Da Prato, Giuseppe

    2006-03-15

    This paper is concerned with nonlinear partial differential equations of the calculus of variation (see [13]) perturbed by noise. Well-posedness of the problem was proved by Pardoux in the seventies (see [14]), using monotonicity methods.The aim of the present work is to investigate the asymptotic behaviour of the corresponding transition semigroup P{sub t}. We show existence and, under suitable assumptions, uniqueness of an ergodic invariant measure {nu}. Moreover, we solve the Kolmogorov equation and prove the so-called 'identite du carre du champs'. This will be used to study the Sobolev space W{sup 1,2}(H,{nu}) and to obtain information on the domain of the infinitesimal generator of P{sub t}.

  9. 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

  10. Exact solutions and maximal dimension of invariant subspaces of time fractional coupled nonlinear partial differential equations

    NASA Astrophysics Data System (ADS)

    Sahadevan, R.; Prakash, P.

    2017-01-01

    We show how invariant subspace method can be extended to time fractional coupled nonlinear partial differential equations and construct their exact solutions. Effectiveness of the method has been illustrated through time fractional Hunter-Saxton equation, time fractional coupled nonlinear diffusion system, time fractional coupled Boussinesq equation and time fractional Whitman-Broer-Kaup system. Also we explain how maximal dimension of the time fractional coupled nonlinear partial differential equations can be estimated.

  11. Approximate symmetry and solutions of the nonlinear Klein-Gordon equation with a small parameter

    NASA Astrophysics Data System (ADS)

    Rahimian, Mohammad; Toomanian, Megerdich; Nadjafikhah, Mehdi

    In this paper, the Lie approximate symmetry analysis is applied to investigate new solutions of the nonlinear Klein-Gordon equation with a small parameter. The nonlinear Klein-Gordon equation is used to model many nonlinear phenomena. The hyperbolic function method and Riccati equation method are employed to solve some of the obtained reduced ordinary differential equations. We construct new analytical solutions with a small parameter which is effectively obtained by the proposed method.

  12. 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.

  13. 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.

  14. 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.

  15. An Improved Closure of the Born-Green-Yvon Equation for the Electric Double Layer.

    DTIC Science & Technology

    1985-10-15

    are those of the MPB5 and the HNC, MSA It is noteworthy to say chat the MPB5 ,ses a Debye - Huckel like bulk correlation functions, while the good...Carlo simulation and other theories , such as the modified Poisson Boltzmann (version: 5) (MPB5) and the Hypernetted chain/mean spherical approximation...HNC,MSA), and its recent improvements. In contrast to these theories the BGY equation satisfies the contact theorem always. Furthermore the bulk pair

  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. An effective analytic approach for solving nonlinear fractional partial differential equations

    NASA Astrophysics Data System (ADS)

    Ma, Junchi; Zhang, Xiaolong; Liang, Songxin

    2016-08-01

    Nonlinear fractional differential equations are widely used for modelling problems in applied mathematics. A new analytic approach with two parameters c1 and c2 is first proposed for solving nonlinear fractional partial differential equations. These parameters are used to improve the accuracy of the resulting series approximations. It turns out that much more accurate series approximations are obtained by choosing proper values of c1 and c2. To demonstrate the applicability and effectiveness of the new method, two typical fractional partial differential equations, the nonlinear gas dynamics equation and the nonlinear KdV-Burgers equation, are solved.

  18. Evans functions and bifurcations of nonlinear waves of some nonlinear reaction diffusion equations

    NASA Astrophysics Data System (ADS)

    Zhang, Linghai

    2017-10-01

    The main purposes of this paper are to accomplish the existence, stability, instability and bifurcation of the nonlinear waves of the nonlinear system of reaction diffusion equations ut =uxx + α [ βH (u - θ) - u ] - w, wt = ε (u - γw) and to establish the existence, stability, instability and bifurcation of the nonlinear waves of the nonlinear scalar reaction diffusion equation ut =uxx + α [ βH (u - θ) - u ], under different conditions on the model constants. To establish the bifurcation for the system, we will study the existence and instability of a standing pulse solution if 0 < 2 (1 + αγ) θ < αβγ; the existence and stability of two standing wave fronts if 2 (1 + αγ) θ = αβγ and γ2 ε > 1; the existence and instability of two standing wave fronts if 2 (1 + αγ) θ = αβγ and 0 <γ2 ε < 1; the existence and instability of an upside down standing pulse solution if 0 < (1 + αγ) θ < αβγ < 2 (1 + αγ) θ. To establish the bifurcation for the scalar equation, we will study the existence and stability of a traveling wave front as well as the existence and instability of a standing pulse solution if 0 < 2 θ < β; the existence and stability of two standing wave fronts if 2 θ = β; the existence and stability of a traveling wave front as well as the existence and instability of an upside down standing pulse solution if 0 < θ < β < 2 θ. By the way, we will also study the existence and stability of a traveling wave back of the nonlinear scalar reaction diffusion equation ut =uxx + α [ βH (u - θ) - u ] -w0, where w0 = α (β - 2 θ) > 0 is a positive constant, if 0 < 2 θ < β. To achieve the main goals, we will make complete use of the special structures of the model equations and we will construct Evans functions and apply them to study the eigenvalues and eigenfunctions of several eigenvalue problems associated with several linear differential operators. It turns out that a complex number λ0 is an eigenvalue of the linear

  19. 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.

  20. Chaos in the fractional order nonlinear Bloch equation with delay

    NASA Astrophysics Data System (ADS)

    Baleanu, Dumitru; Magin, Richard L.; Bhalekar, Sachin; Daftardar-Gejji, Varsha

    2015-08-01

    The Bloch equation describes the dynamics of nuclear magnetization in the presence of static and time-varying magnetic fields. In this paper we extend a nonlinear model of the Bloch equation to include both fractional derivatives and time delays. The Caputo fractional time derivative (α) in the range from 0.85 to 1.00 is introduced on the left side of the Bloch equation in a commensurate manner in increments of 0.01 to provide an adjustable degree of system memory. Time delays for the z component of magnetization are inserted on the right side of the Bloch equation with values of 0, 10 and 100 ms to balance the fractional derivative with delay terms that also express the history of an earlier state. In the absence of delay, τ = 0 , we obtained results consistent with the previously published bifurcation diagram, with two cycles appearing at α = 0.8548 with subsequent period doubling that leads to chaos at α = 0.9436 . A periodic window is observed for the range 0.962 < α < 0.9858 , with chaos arising again as α nears 1.00. The bifurcation diagram for the case with a 10 ms delay is similar: two cycles appear at the value α = 0.8532 , and the transition from two to four cycles at α = 0.9259 . With further increases in the fractional order, period doubling continues until at α = 0.9449 chaos ensues. In the case of a 100 millisecond delay the transitions from one cycle to two cycles and two cycles to four cycles are observed at α = 0.8441 , and α = 0.8635 , respectively. However, the system exhibits chaos at much lower values of α (α = 0.8635). A periodic window is observed in the interval 0.897 < α < 0.9341 , with chaos again appearing for larger values of α . In general, as the value of α decreased the system showed transitions from chaos to transient chaos, and then to stability. Delays naturally appear in many NMR systems, and pulse programming allows the user control over the process. By including both the fractional derivative and time delays in

  1. 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…

  2. Exact multisoliton solutions of general nonlinear Schrödinger equation with derivative.

    PubMed

    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.

  3. Nonlinearity Domination in Hassellmann Equation as a Reason for Alternative Framework of its Numerical Simulation

    DTIC Science & Technology

    2014-09-30

    nonlinear Schrodinger equation. It is well known that dark solitons are exact solutions of such equation. In the present paper it has been shown that gray...in numerical computations of Nonlinear Schrodinger equation, and in the optical fibers experiments. In particular it has been shown that the

  4. 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

  5. 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…

  6. Nonlinear SCHRÖDINGER Equations on Super Symmetric Spaces Related to Orthogonal-Symplectic Lie Superalgebras

    NASA Astrophysics Data System (ADS)

    Canoglu, Ahmet; Güldogan, Bahri; Salihoglu, Selâmi

    We obtain new integrable coupled nonlinear partial differential equations by assuming the soliton connection having values in orthogonal-symplectic Lie superalgebras [B(m, n), C(n), D(m, n)]. These equations are coupled Nonlinear Schrödinger equations on various super symmetric spaces.

  7. 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.

  8. An almost symmetric Strang splitting scheme for nonlinear evolution equations.

    PubMed

    Einkemmer, Lukas; Ostermann, Alexander

    2014-07-01

    In this paper we consider splitting methods for the time integration of parabolic and certain classes of hyperbolic partial differential equations, where one partial flow cannot be computed exactly. Instead, we use a numerical approximation based on the linearization of the vector field. This is of interest in applications as it allows us to apply splitting methods to a wider class of problems from the sciences. However, in the situation described, the classic Strang splitting scheme, while still being a method of second order, is not longer symmetric. This, in turn, implies that the construction of higher order methods by composition is limited to order three only. To remedy this situation, based on previous work in the context of ordinary differential equations, we construct a class of Strang splitting schemes that are symmetric up to a desired order. We show rigorously that, under suitable assumptions on the nonlinearity, these methods are of second order and can then be used to construct higher order methods by composition. In addition, we illustrate the theoretical results by conducting numerical experiments for the Brusselator system and the KdV equation.

  9. 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.

  10. Implementation of nonreflecting boundary conditions for the nonlinear Euler equations

    NASA Astrophysics Data System (ADS)

    Atassi, Oliver V.; Galán, José M.

    2008-01-01

    Computationally efficient nonreflecting boundary conditions are derived for the Euler equations with acoustic, entropic and vortical inflow disturbances. The formulation linearizes the Euler equations near the inlet/outlet boundaries and expands the solution in terms of Fourier-Bessel modes. This leads to an 'exact' nonreflecting boundary condition, local in space but nonlocal in time, for each Fourier-Bessel mode of the perturbation pressure. The perturbation velocity and density are then calculated using acoustic, entropic and vortical mode splitting. Extension of the boundary conditions to nonuniform swirling flows is presented for the narrow annulus limit which is relevant to many aeroacoustic problems. The boundary conditions are implemented for the nonlinear Euler equations which are solved in space using the finite volume approximation and integrated in time using a MacCormack scheme. Two test problems are carried out: propagation of acoustic waves in an annular duct and the scattering of a vortical wave by a cascade. Comparison between the present exact conditions and commonly used approximate local boundary conditions is made. Results show that, unlike the local boundary conditions whose accuracy depends on the group velocity of the scattered waves, the present conditions give accurate solutions for a range of problems that have a wide array of group velocities. Results also show that this approach leads to a significant savings in computational time and memory by obviating the need to store the pressure field and calculate the nonlocal convolution integral at each point in the inlet and exit boundaries.

  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. 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.

  14. Nonlinear dirac and diffusion equations in 1+1 dimensions from stochastic considerations

    PubMed

    Maharana

    2000-08-01

    We generalize the method of obtaining fundamental linear partial differential equations such as the diffusion and Schrodinger equation, the Dirac, and the telegrapher's equation from a simple stochastic consideration to arrive at a certain nonlinear form of these equations. A group classification through a one-parameter group of transformations for two of these equations is also carried out.

  15. Soliton solutions to coupled nonlinear wave equations in (2 + 1)-dimensions

    NASA Astrophysics Data System (ADS)

    Jawad, A. J. M.; Johnson, S.; Yildirim, A.; Kumar, S.; Biswas, A.

    2013-03-01

    This paper implemented the tanh method to solve a few coupled nonlinear wave equations in (2 + 1)-dimensions. They are the Konopelchenko-Dubrovsky equation, dispersive long wave equation and the Riemann wave equation. Additionally, the traveling wave hypothesis is used to extract a few more solutons to some of these equations. Finally, the numerical simulations supplement these analytical results.

  16. 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

  17. 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.

  18. The nonlinear Schrödinger equation with generalized nonlinearities and PT-symmetric potentials: Stable solitons, interactions, and excitations.

    PubMed

    Yan, Zhenya; Chen, Yong

    2017-07-01

    We investigate the nonlinear Schrödinger (NLS) equation with generalized nonlinearities and complex non-Hermitian potentials and present the novel parity-time-( PT-) symmetric potentials for the NLS equation with power-law nonlinearities supporting some bright solitons. For distinct types of PT-symmetric potentials including Scarf-II, Hermite-Gaussian, and asymptotically periodic potentials, we, respectively, explore the phase transitions for the linear Hamiltonian operators. Moreover, we analytically find stable bright solitons in the generalized NLS equations with several types of PT-symmetric potentials, and their stability is corroborated by the linear stability spectrum and direct wave-propagation simulations. Interactions of two solitons are also explored. More interestingly, we find that the nonlinearity can excite the unstable linear modes (i.e., possessing broken linear PT-symmetric phase) to stable nonlinear modes. The results may excite potential applications in nonlinear optics, Bose-Einstein condensates, and relevant fields.

  19. The nonlinear Schrödinger equation with generalized nonlinearities and P T -symmetric potentials: Stable solitons, interactions, and excitations

    NASA Astrophysics Data System (ADS)

    Yan, Zhenya; Chen, Yong

    2017-07-01

    We investigate the nonlinear Schrödinger (NLS) equation with generalized nonlinearities and complex non-Hermitian potentials and present the novel parity-time-( P T -) symmetric potentials for the NLS equation with power-law nonlinearities supporting some bright solitons. For distinct types of P T -symmetric potentials including Scarf-II, Hermite-Gaussian, and asymptotically periodic potentials, we, respectively, explore the phase transitions for the linear Hamiltonian operators. Moreover, we analytically find stable bright solitons in the generalized NLS equations with several types of P T -symmetric potentials, and their stability is corroborated by the linear stability spectrum and direct wave-propagation simulations. Interactions of two solitons are also explored. More interestingly, we find that the nonlinearity can excite the unstable linear modes (i.e., possessing broken linear P T -symmetric phase) to stable nonlinear modes. The results may excite potential applications in nonlinear optics, Bose-Einstein condensates, and relevant fields.

  20. 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.

  1. Self-similar solutions for a nonlinear radiation diffusion equation

    SciTech Connect

    Garnier, Josselin; Malinie, Guy; Saillard, Yves; Cherfils-Clerouin, Catherine

    2006-09-15

    This paper considers the hydrodynamic equations with nonlinear conduction when the internal energy and the opacity have power-law dependences in the density and in the temperature. This system models the situation in which a dense solid is brought into contact with a thermal bath. It supports self-similar solutions that depend on the surface temperature. The self-similar solution can exhibit a shock wave followed by an ablation front if the surface temperature does not increase too fast in time, but it can exhibit a heat front followed by an isothermal shock otherwise. These flows are carefully studied in order to clarify the role of the initial solid density in the energy absorption and the ablation process. Comparisons with numerical simulations show excellent agreement.

  2. Rogue waves of a (3 + 1) -dimensional nonlinear evolution equation

    NASA Astrophysics Data System (ADS)

    Shi, Yu-bin; Zhang, Yi

    2017-03-01

    General high-order rogue waves of a (3 + 1) -dimensional Nonlinear Evolution Equation ((3+1)-d NEE) are obtained by the Hirota bilinear method, which are given in terms of determinants, whose matrix elements possess plain algebraic expressions. It is shown that the simplest (fundamental) rogue waves are line rogue waves which arise from the constant background with a line profile and then disappear into the constant background again. Two subclass of nonfundamental rogue waves are analyzed in details. By proper means of the regulations of free parameters, the dynamics of multi-rogue waves and high-order rogue waves have been illustrated in (x,t) plane and (y,z) plane by three dimensional figures.

  3. Nonequilibrium discrete nonlinear Schrödinger equation.

    PubMed

    Iubini, Stefano; Lepri, Stefano; Politi, Antonio

    2012-07-01

    We study nonequilibrium steady states of the one-dimensional discrete nonlinear Schrödinger equation. This system can be regarded as a minimal model for the stationary transport of bosonic particles such as photons in layered media or cold atoms in deep optical traps. Due to the presence of two conserved quantities, namely, energy and norm (or number of particles), the model displays coupled transport in the sense of linear irreversible thermodynamics. Monte Carlo thermostats are implemented to impose a given temperature and chemical potential at the chain ends. As a result, we find that the Onsager coefficients are finite in the thermodynamic limit, i.e., transport is normal. Depending on the position in the parameter space, the "Seebeck coefficient" may be either positive or negative. For large differences between the thermostat parameters, density and temperature profiles may display an unusual nonmonotonic shape. This is due to the strong dependence of the Onsager coefficients on the state variables.

  4. Bifurcations in a Mathieu equation with cubic nonlinearities: Part II

    NASA Astrophysics Data System (ADS)

    Ng, Leslie; Rand, Richard

    2002-09-01

    In a previous paper [Chaos Solitons Fract. 14(2) (2002) 173], the authors investigated the dynamics of the equation: d2x /dt 2+(δ+ɛ cost)x+ɛ Ax 3+Bx 2dx /dt +Cx dx /dt 2+D dx /dt 3=0 We used the method of averaging in the neighborhood of the 2:1 resonance in the limit of small forcing and small nonlinearity. We found that a degenerate bifurcation point occurs in the resulting slow flow and some of the bifurcations near this point were looked at. In this work we present additional results concerning the bifurcations around this point using analytic techniques and AUTO. An analytic approximation for a heteroclinic bifurcation curve is obtained. Additional results on the bifurcations of periodic orbits in the slow flow are also presented.

  5. 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.

  6. Solitons and other solutions to the coupled nonlinear Schrödinger type equations

    NASA Astrophysics Data System (ADS)

    El-Borai, M. M.; El-Owaidy, H. M.; Ahmed, Hamdy M.; Arnous, A. H.; Mirzazadeh, M.

    2017-06-01

    Nonlinear Schrödinger type equations arise from a wide variety of fields, such as fluids, nonlinear optics, the theory of deep water waves, plasma physics, and so on. In this paper, two integration schemes are employed to obtain solitons, periodic waves and other forms of solutions of the coupled nonlinear Schrödinger type equations. The two schemes that are studied in this paper are the Bäcklund transformation of Riccati equation and the trial solution method.

  7. Estimation of Delays and Other Parameters in Nonlinear Functional Differential Equations.

    DTIC Science & Technology

    1981-12-01

    FSTIMATION OF DELAYS AND OTHER PARAMETERS IN NONLINEAR FUNCTIONAL DIFFERENTIAL EQUATIONS by K. T. Banks and P. L. Daniel December 1981 LCDS Report #82...ESTIMATION OF DELAYS AND OTHER PARAMETERS IN NONLINEAR FUNCTIONAL DIFFERENTIAL EQUATIONS H. T. Banks and P. L. Daniel ABSTRACT We discuss a spline...based approximation scheme for nonlinear nonautonomous delay differential equations . Convergence results (using dissipative type estimates on the

  8. 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.

  9. 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.

  10. Chaos control in the nonlinear Schrödinger equation with Kerr law nonlinearity

    NASA Astrophysics Data System (ADS)

    Yin, Jiu-Li; Zhao, Liu-Wei; Tian, Li-Xin

    2014-02-01

    The nonlinear Schrödinger equation with Kerr law nonlinearity in the two-frequency interference is studied by the numerical method. Chaos occurs easily due to the absence of damping. This phenomenon will cause the distortion in the process of information transmission. We find that fiber-optic transmit signals still present chaotic phenomena if the control intensity is smaller. With the increase of intensity, the fiber-optic signal can stay in a stable state in some regions. When the strength is suppressed to a certain value, an unstable phenomenon of the fiber-optic signal occurs. Moreover we discuss the sensitivities of the parameters to be controlled. The results show that the linear term coefficient and the environment of two quite different frequences have less effects on the fiber-optic transmission. Meanwhile the phenomena of vibration, attenuation and escape occur in some regions.

  11. Lax Pairs and Integrability Conditions of Higher-Order Nonlinear Schrödinger Equations

    NASA Astrophysics Data System (ADS)

    Asad-uz-zaman, M.; Chachou Samet, H.; Khawaja, U. Al

    2016-08-01

    We derive the Lax pairs and integrability conditions of the nonlinear Schrödinger equation with higher-order terms, complex potentials, and time-dependent coefficients. Cubic and quintic nonlinearities together with derivative terms are considered. The Lax pairs and integrability conditions for some of the well-known nonlinear Schrödinger equations, including a new equation which was not considered previously in the literature, are then derived as special cases. We show most clearly with a similarity transformation that the higher-order terms restrict the integrability to linear potential in contrast with quadratic potential for the standard nonlinear Schrödinger equation.

  12. 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.

  13. Nonlinear Schrödinger equation with spatiotemporal perturbations.

    PubMed

    Mertens, Franz G; Quintero, Niurka R; Bishop, A R

    2010-01-01

    We investigate the dynamics of solitons of the cubic nonlinear Schrödinger equation (NLSE) with the following perturbations: nonparametric spatiotemporal driving of the form f(x,t)=a exp[iK(t)x], damping, and a linear term which serves to stabilize the driven soliton. Using the time evolution of norm, momentum and energy, or, alternatively, a Lagrangian approach, we develop a collective-coordinate-theory which yields a set of ordinary differential equations (ODEs) for our four collective coordinates. These ODEs are solved analytically and numerically for the case of a constant, spatially periodic force f(x). The soliton position exhibits oscillations around a mean trajectory with constant velocity. This means that the soliton performs, on the average, a unidirectional motion although the spatial average of the force vanishes. The amplitude of the oscillations is much smaller than the period of f(x). In order to find out for which regions the above solutions are stable, we calculate the time evolution of the soliton momentum P(t) and the soliton velocity V(t): This is a parameter representation of a curve P(V) which is visited by the soliton while time evolves. Our conjecture is that the soliton becomes unstable, if this curve has a branch with negative slope. This conjecture is fully confirmed by our simulations for the perturbed NLSE. Moreover, this curve also yields a good estimate for the soliton lifetime: the soliton lives longer, the shorter the branch with negative slope is.

  14. ON NONLINEAR EQUATIONS OF THE FORM F(x,\\, u,\\, Du,\\, \\Delta u) = 0

    NASA Astrophysics Data System (ADS)

    Soltanov, K. N.

    1995-02-01

    The Dirichlet problem for equations of the form F(x,\\, u,\\, Du,\\, \\Delta u) = 0 and also the initial boundary value problem for a parabolic equation with a nonlinearity are studied.Bibliography: 11 titles.

  15. 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].

  16. Rational Legendre pseudospectral approach for solving nonlinear differential equations of Lane-Emden type

    NASA Astrophysics Data System (ADS)

    Parand, K.; Shahini, M.; Dehghan, Mehdi

    2009-12-01

    Lane-Emden equation is a nonlinear singular equation in the astrophysics that corresponds to the polytropic models. In this paper, a pseudospectral technique is proposed to solve the Lane-Emden type equations on a semi-infinite domain. The method is based on rational Legendre functions and Gauss-Radau integration. The method reduces solving the nonlinear ordinary differential equation to solve a system of nonlinear algebraic equations. The comparison of the results with the other numerical methods shows the efficiency and accuracy of this method.

  17. 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

  18. Analytic study of solutions for the Born-Infeld equation in nonlinear electrodynamics

    NASA Astrophysics Data System (ADS)

    Gao, Hui; Xu, Tianzhou; Fan, Tianyou; Wang, Gangwei

    2017-03-01

    The Born-Infeld equation is an important nonlinear partial differential equation in theoretical and mathematical physics. The Lie group method is used for simplifying the nonlinear partial differential equation, which is partly solved, in which there are some difficulties; to overcome the difficulties, we develop a power series method, and find the solutions in analytic form. In the mean time, a wave propagation (traveling wave) method is developed for solving the equation, and analytic solutions are also constructed.

  19. Spatiotemporal soliton clusters in the (3+1)-dimensional nonlinear Schrödinger equation with spatially modulated nonlinearity

    NASA Astrophysics Data System (ADS)

    Wu, Hong-Yu; Jiang, Li-Hong

    2017-09-01

    From a generic transformation, a (3+1)-dimensional nonlinear Schrödinger equation with spatially modulated nonlinearity is studied and exact spatiotemporal soliton cluster solutions are derived. When the azimuthal parameter m = 0, Gaussian solitons are constructed. For the modulation depth q = 1 and the azimuthal parameter m\

  20. Higher-order nonlinear Schrodinger equations for simulations of surface wavetrains

    NASA Astrophysics Data System (ADS)

    Slunyaev, Alexey

    2016-04-01

    Numerous recent results of numerical and laboratory simulations of waves on the water surface claim that solutions of the weakly nonlinear theory for weakly modulated waves in many cases allow a smooth generalization to the conditions of strong nonlinearity and dispersion, even when the 'envelope' is difficult to determine. The conditionally 'strongly nonlinear' high-order asymptotic equations still imply the smallness of the parameter employed in the asymptotic series. Thus at some (unknown a priori) level of nonlinearity and / or dispersion the asymptotic theory breaks down; then the higher-order corrections become useless and may even make the description worse. In this paper we use the higher-order nonlinear Schrodinger (NLS) equation, derived in [1] (the fifth-order NLS equation, or next-order beyond the classic Dysthe equation [2]), for simulations of modulated deep-water wave trains, which attain very large steepness (below or beyond the breaking limit) due to the Benjamin - Feir instability. The results are compared with fully nonlinear simulations of the potential Euler equations as well as with the weakly nonlinear theories represented by the nonlinear Schrodinger equation and the classic Dysthe equation with full linear dispersion [2]. We show that the next-order Dysthe equation can significantly improve the description of strongly nonlinear wave dynamics compared with the lower-order asymptotic models. [1] A.V. Slunyaev, A high-order nonlinear envelope equation for gravity waves in finite-depth water. JETP 101, 926-941 (2005). [2] K. Trulsen, K.B. Dysthe, A modified nonlinear Schrödinger equation for broader bandwidth gravity waves on deep water. Wave Motion 24, 281-289 (1996).

  1. New Traveling Wave Solutions for a Class of Nonlinear Evolution Equations

    NASA Astrophysics Data System (ADS)

    Bai, Cheng-Jie; Zhao, Hong; Xu, Heng-Ying; Zhang, Xia

    The deformation mapping method is extended to solve a class of nonlinear evolution equations (NLEEs). Many types of explicit and exact traveling wave solutions, which contain solitary wave solutions, trigonometric function solutions, and Jacobian elliptic function solutions, are obtained by a simple algebraic transformation relation between the solutions of the NLEEs and those of the cubic nonlinear Klein-Gordon (NKG) equation.

  2. Maximum Likelihood Analysis of Nonlinear Structural Equation Models with Dichotomous Variables

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Lee, Sik-Yum

    2005-01-01

    In this article, a maximum likelihood approach is developed to analyze structural equation models with dichotomous variables that are common in behavioral, psychological and social research. To assess nonlinear causal effects among the latent variables, the structural equation in the model is defined by a nonlinear function. The basic idea of the…

  3. Breather and rogue wave solutions of a generalized nonlinear Schrödinger equation.

    PubMed

    Wang, L H; Porsezian, K; He, J S

    2013-05-01

    In this paper, using the Darboux transformation, we demonstrate the generation of first-order breather and higher-order rogue waves from a generalized nonlinear Schrödinger equation with several higher-order nonlinear effects representing femtosecond pulse propagation through nonlinear silica fiber. The same nonlinear evolution equation can also describe the soliton-type nonlinear excitations in classical Heisenberg spin chain. Such solutions have a parameter γ(1), denoting the strength of the higher-order effects. From the numerical plots of the rational solutions, the compression effects of the breather and rogue waves produced by γ(1) are discussed in detail.

  4. Localized solutions of extended discrete nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Umarov, B. A.; Ismail, Nazmi Hakim Bin; Hadi, Muhammad Salihi Abdul; Hassan, T. H.

    2017-09-01

    We consider the extended discrete nonlinear Schrödinger (EDNLSE) equation which includes the nearest neighbor nonlinear interaction in addition to the on-site cubic and quintic nonlinearities. This equation describes nonlinear excitations in dipolar Bose-Einstein condensate in a periodic optical lattice. We are particularly interested with the existence and stability conditions of localized nonlinear excitations of different types. The problem is tackled numerically, by application of Newton methods and by solving the eigenvalue problem for linearized system near the exact solution. Also the modulational instability of plane wave solution is discussed.

  5. Modulational instability in the cubic quintic nonlinear Schrödinger equation through the variational approach

    NASA Astrophysics Data System (ADS)

    Ndzana, Fabien, II; Mohamadou, Alidou; Kofané, Timoléon Crépin

    2007-07-01

    The dynamics of nonlinear pulse propagation in an average dispersion-managed soliton system is governed by a constant coefficient nonlinear Schrödinger (NLS) equation. For a special set of parameters the constant coefficient NLS equation is completely integrable. The same constant coefficient NLS equation is also applicable to optical fiber systems with phase modulation or pulse compression. We also investigate MI arising in the cubic-quintic nonlinear Schrödinger equation for ultrashort pulse propagation. Within this framework, we derive ordinary differential equations (ODE's) for the time evolution of the amplitude and phase of modulation perturbations. Analyzing the ensuing ODE's, we derive the classical modulational instability criterion and identify it numerically. We show that the quintic nonlinearity can be essential for the stability of solutions. The evolutions of modulational instability are numerically investigated and the effects of the quintic nonlinearity on the evolutions are examined. Numerical simulations demonstrate the validity of the analytical predictions.

  6. Linear homotopy solution of nonlinear systems of equations in geodesy

    NASA Astrophysics Data System (ADS)

    Paláncz, Béla; Awange, Joseph L.; Zaletnyik, Piroska; Lewis, Robert H.

    2010-01-01

    A fundamental task in geodesy is solving systems of equations. Many geodetic problems are represented as systems of multivariate polynomials. A common problem in solving such systems is improper initial starting values for iterative methods, leading to convergence to solutions with no physical meaning, or to convergence that requires global methods. Though symbolic methods such as Groebner bases or resultants have been shown to be very efficient, i.e., providing solutions for determined systems such as 3-point problem of 3D affine transformation, the symbolic algebra can be very time consuming, even with special Computer Algebra Systems (CAS). This study proposes the Linear Homotopy method that can be implemented easily in high-level computer languages like C++ and Fortran that are faster than CAS by at least two orders of magnitude. Using Mathematica, the power of Homotopy is demonstrated in solving three nonlinear geodetic problems: resection, GPS positioning, and affine transformation. The method enlarging the domain of convergence is found to be efficient, less sensitive to rounding of numbers, and has lower complexity compared to other local methods like Newton-Raphson.

  7. Bursting processes in plasmas and relevant nonlinear model equations

    SciTech Connect

    Basu, B.; Coppi, B.

    1995-01-01

    Important intrinsic plasma instabilities manifest themselves in the form of periodic bursts of fluctuations rather than as a state of stationary fluctuations, which a conventional application of quasilinear theory would lead to expect. A set of coupled nonlinear equations for the time evolution of the fluctuation amplitude and of the driving factor of the relevant instability is shown to have the features necessary to reproduce the variety of bursts that are observed experimentally. These are the periodicity, the duration, and the shape of the bursts, special consideration being given to the excitation of modes by high-energy particle populations in thermalized plasmas and to a model for the transition from a bursting state to one of stationary fluctuations. A model is introduced that is relevant to the case where the spatial dependence of the mode amplitude is important. The application of the given analysis to the bursty wave emissions observed in space is discussed. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  8. Analytical approximate solution for nonlinear space—time fractional Klein—Gordon equation

    NASA Astrophysics Data System (ADS)

    Khaled, A. Gepreel; Mohamed, S. Mohamed

    2013-01-01

    The fractional derivatives in the sense of Caputo and the homotopy analysis method are used to construct an approximate solution for the nonlinear space—time fractional derivatives Klein—Gordon equation. The numerical results show that the approaches are easy to implement and accurate when applied to the nonlinear space—time fractional derivatives Klein—Gordon equation. This method introduces a promising tool for solving many space—time fractional partial differential equations. This method is efficient and powerful in solving wide classes of nonlinear evolution fractional order equations.

  9. Nonlinear grid error effects on numerical solution of partial differential equations

    NASA Technical Reports Server (NTRS)

    Dey, S. K.

    1980-01-01

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

  10. A new solution procedure for a nonlinear infinite beam equation of motion

    NASA Astrophysics Data System (ADS)

    Jang, T. S.

    2016-10-01

    Our goal of this paper is of a purely theoretical question, however which would be fundamental in computational partial differential equations: Can a linear solution-structure for the equation of motion for an infinite nonlinear beam be directly manipulated for constructing its nonlinear solution? Here, the equation of motion is modeled as mathematically a fourth-order nonlinear partial differential equation. To answer the question, a pseudo-parameter is firstly introduced to modify the equation of motion. And then, an integral formalism for the modified equation is found here, being taken as a linear solution-structure. It enables us to formulate a nonlinear integral equation of second kind, equivalent to the original equation of motion. The fixed point approach, applied to the integral equation, results in proposing a new iterative solution procedure for constructing the nonlinear solution of the original beam equation of motion, which consists luckily of just the simple regular numerical integration for its iterative process; i.e., it appears to be fairly simple as well as straightforward to apply. A mathematical analysis is carried out on both natures of convergence and uniqueness of the iterative procedure by proving a contractive character of a nonlinear operator. It follows conclusively,therefore, that it would be one of the useful nonlinear strategies for integrating the equation of motion for a nonlinear infinite beam, whereby the preceding question may be answered. In addition, it may be worth noticing that the pseudo-parameter introduced here has double roles; firstly, it connects the original beam equation of motion with the integral equation, second, it is related with the convergence of the iterative method proposed here.

  11. A bivariate Chebyshev spectral collocation quasilinearization method for nonlinear evolution parabolic equations.

    PubMed

    Motsa, S S; Magagula, V M; Sibanda, P

    2014-01-01

    This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

  12. A Bivariate Chebyshev Spectral Collocation Quasilinearization Method for Nonlinear Evolution Parabolic Equations

    PubMed Central

    Motsa, S. S.; Magagula, V. M.; Sibanda, P.

    2014-01-01

    This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature. PMID:25254252

  13. The Riccati equation with variable coefficients expansion algorithm to find more exact solutions of nonlinear differential equations

    NASA Astrophysics Data System (ADS)

    Yan, Zhenya

    2003-04-01

    In this paper based on a system of Riccati equations with variable coefficients, we present a new Riccati equation with variable coefficients expansion method and its algorithm, which are direct and more powerful than the tanh-function method, sine-cosine method, the generalized hyperbolic-function method and the generalized Riccati equation with constant coefficient expansion method to construct more new exact solutions of nonlinear differential equations in mathematical physics. A pair of generalized Hamiltonian equations is chosen to illustrate our algorithm such that more families of new exact solutions are obtained which contain soliton-like solution and periodic solutions. This algorithm can also be applied to other nonlinear differential equations.

  14. Collapse of Solutions of the Nonlinear Schroedinger Equation with a Time-Dependent Nonlinearity: Application to Bose-Einstein Condensates

    SciTech Connect

    Konotop, V.V.; Pacciani, P.

    2005-06-24

    It is proven that periodically varying and sign definite nonlinearity in a general case does not prevent collapse in two-dimensional and three-dimensional nonlinear Schroedinger equations: at any oscillation frequency of the nonlinearity blowing up solutions exist. Contrary to the results known for a sign-alternating nonlinearity, an increase of the frequency of oscillations accelerates collapse. The effect is discussed from the viewpoint of scaling arguments. For the three-dimensional case a sufficient condition for the existence of collapse is rigorously established. The results are discussed in the context of the mean field theory of Bose-Einstein condensates with time-dependent scattering length.

  15. A family of nonlinear Schrödinger equations admitting q-plane wave solutions

    NASA Astrophysics Data System (ADS)

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

    2017-08-01

    Nonlinear Schrödinger equations with power-law nonlinearities have attracted considerable attention recently. Two previous proposals for these types of equations, corresponding respectively to the Gross-Pitaievsky equation and to the one associated with nonextensive statistical mechanics, are here unified into a single, parameterized family of nonlinear Schrödinger equations. Power-law nonlinear terms characterized by exponents depending on a real index q, typical of nonextensive statistical mechanics, are considered in such a way that the Gross-Pitaievsky equation is recovered in the limit q → 1. A classical field theory shows that, due to these nonlinearities, an extra field Φ (x → , t) (besides the usual one Ψ (x → , t)) must be introduced for consistency. The new field can be identified with Ψ* (x → , t) only when q → 1. For q ≠ 1 one has a pair of coupled nonlinear wave equations governing the joint evolution of the complex valued fields Ψ (x → , t) and Φ (x → , t). These equations reduce to the usual pair of complex-conjugate ones only in the q → 1 limit. Interestingly, the nonlinear equations obeyed by Ψ (x → , t) and Φ (x → , t) exhibit a common, soliton-like, traveling solution, which is expressible in terms of the q-exponential function that naturally emerges within nonextensive statistical mechanics.

  16. A simple and direct method for generating travelling wave solutions for nonlinear equations

    SciTech Connect

    Bazeia, D. Das, Ashok; Silva, A.

    2008-05-15

    We propose a simple and direct method for generating travelling wave solutions for nonlinear integrable equations. We illustrate how nontrivial solutions for the KdV, the mKdV and the Boussinesq equations can be obtained from simple solutions of linear equations. We describe how using this method, a soliton solution of the KdV equation can yield soliton solutions for the mKdV as well as the Boussinesq equations. Similarly, starting with cnoidal solutions of the KdV equation, we can obtain the corresponding solutions for the mKdV as well as the Boussinesq equations. Simple solutions of linear equations can also lead to cnoidal solutions of nonlinear systems. Finally, we propose and solve some new families of KdV equations and show how soliton solutions are also obtained for the higher order equations of the KdV hierarchy using this method.

  17. Exact finite difference schemes for the non-linear unidirectional wave equation

    NASA Technical Reports Server (NTRS)

    Mickens, R. E.

    1985-01-01

    Attention is given to the construction of exact finite difference schemes for the nonlinear unidirectional wave equation that describes the nonlinear propagation of a wave motion in the positive x-direction. The schemes constructed for these equations are compared with those obtained by using the usual procedures of numerical analysis. It is noted that the order of the exact finite difference models is equal to the order of the differential equation.

  18. Nonlinear Schrödinger equation: generalized Darboux transformation and rogue wave solutions.

    PubMed

    Guo, Boling; Ling, Liming; Liu, Q P

    2012-02-01

    In this paper, we construct a generalized Darboux transformation for the nonlinear Schrödinger equation. The associated N-fold Darboux transformation is given in terms of both a summation formula and determinants. As applications, we obtain compact representations for the Nth-order rogue wave solutions of the focusing nonlinear Schrödinger equation and Hirota equation. In particular, the dynamics of the general third-order rogue wave is discussed and shown to exhibit interesting structures.

  19. Analytical solutions with the improved (G’/G)-expansion method for nonlinear evolution equations

    NASA Astrophysics Data System (ADS)

    Kaplan, Melike; Bekir, Ahmet; Akbulut, Arzu

    2016-10-01

    To seek the exact solutions of nonlinear partial differential equations (NPDEs), the improved (G'/G)-expansion method is proposed in the present work. With the aid of symbolic computation, this effective method is applied to construct exact solutions of the (1+1)-dimensional nonlinear dispersive modified Benjamin-Bona-Mahony equation and (3+1)- dimensional Kudryashov-Sinelshchikov equation. As a result, new types of exact solutions are obtained.

  20. Bright solitons for a generalized nonautonomous nonlinear equation in a nonlinear inhomogeneous fiber

    NASA Astrophysics Data System (ADS)

    Xie, Xi-Yang; Tian, Bo; Liu, Lei; Guan, Yue-Yang; Jiang, Yan

    2017-06-01

    In this paper, we investigate a generalized nonautonomous nonlinear equation, which describes the ultrashort optical pulse propagating in a nonlinear inhomogeneous fiber. Under certain integrable constraints, bilinear forms, bright one- and two-soliton solutions are obtained. Via certain transformation, we investigate the properties of the solitons with the first-order dispersion parameter σ1(x, t), second-order dispersion parameter σ2(x, t), third-order dispersion parameter σ3(x, t), phase modulation and gain (loss) v(x, t). Soliton propagation and collision are graphically presented and analyzed: One soliton is shown to maintain its amplitude and width during the propagation. When we choose σ1(x, t), σ2(x, t) and σ3(x, t) differently, travelling direction of the soliton is found to alter. v(x, t) is observed to affect the amplitude of the soliton. Head-on collision between the two solitons is presented with σ1(x, t), σ2(x, t), σ3(x, t) and v(x, t) as the constants, and solitons' amplitudes are the same before and after the collision. When σ1(x, t), σ2(x, t) and σ3(x, t) are chosen as certain functions, the solitons' traveling directions change during the collision. v(x, t) can influence the amplitudes of the two solitons.

  1. Soliton solutions to a few fractional nonlinear evolution equations in shallow water wave dynamics

    NASA Astrophysics Data System (ADS)

    Mirzazadeh, Mohammad; Ekici, Mehmet; Sonmezoglu, Abdullah; Ortakaya, Sami; Eslami, Mostafa; Biswas, Anjan

    2016-05-01

    This paper studies a few nonlinear evolution equations that appear with fractional temporal evolution and fractional spatial derivatives. These are Benjamin-Bona-Mahoney equation, dispersive long wave equation and Nizhnik-Novikov-Veselov equation. The extended Jacobi's elliptic function expansion method is implemented to obtain soliton and other periodic singular solutions to these equations. In the limiting case, when the modulus of ellipticity approaches zero or unity, these doubly periodic functions approach solitary waves or shock waves or periodic singular solutions emerge.

  2. Hierarchies of nonlinear integrable equations and their symmetries in 2 + 1 dimensions

    NASA Astrophysics Data System (ADS)

    Cheng, Yi

    1990-11-01

    For a given nonlinear integrable equation in 2 + 1 dimensions, an approach is described to construct the hierarchies of equations and relevant Lie algebraic properties. The commutability and noncommutability of equations of the flow, their symmetries and mastersymmetries are then derived as direct results of these algebraic properties. The details for the modified Kadomtsev-Petviashvilli equation are shown as an example and the main results for the (2 + 1)-dimensional Caudrey-Dodd-Gibbon-Katera-Sawada equation are given.

  3. Perfectly matched layer absorbing boundary condition for nonlinear two-fluid plasma equations

    NASA Astrophysics Data System (ADS)

    Sun, X. F.; Jiang, Z. H.; Hu, X. W.; Zhuang, G.; Jiang, J. F.; Guo, W. X.

    2015-04-01

    Numerical instability occurs when coupled Maxwell equations and nonlinear two-fluid plasma equations are solved using finite difference method through parallel algorithm. Thus, a perfectly matched layer (PML) boundary condition is set to avoid the instability caused by velocity and density gradients between vacuum and plasma. A splitting method is used to first decompose governing equations to time-dependent nonlinear and linear equations. Then, a proper complex variable is used for the spatial derivative terms of the time-dependent nonlinear equation. Finally, with several auxiliary function equations, the governing equations of the absorbing boundary condition are derived by rewriting the frequency domain PML in the original physical space and time coordinates. Numerical examples in one- and two-dimensional domains show that the PML boundary condition is valid and effective. PML stability depends on the absorbing coefficient and thickness of absorbing layers.

  4. Identification of continuous-time nonlinear systems: The nonlinear difference equation with moving average noise (NDEMA) framework

    NASA Astrophysics Data System (ADS)

    Zhang, B.; Billings, S. A.

    2015-08-01

    Although a vast number of techniques for the identification of nonlinear discrete-time systems have been introduced, the identification of continuous-time nonlinear systems is still extremely difficult. In this paper, the Nonlinear Difference Equation with Moving Average noise (NDEMA) model which is a general representation of nonlinear systems and contains, as special cases, both continuous-time and discrete-time models, is first proposed. Then based on this new representation, a systematic framework for the identification of nonlinear continuous-time models is developed. The new approach can not only detect the model structure and estimate the model parameters, but also work for noisy nonlinear systems. Both simulation and experimental examples are provided to illustrate how the new approach can be applied in practice.

  5. On a hierarchy of nonlinearly dispersive generalized Korteweg - de Vries evolution equations

    DOE PAGES

    Christov, Ivan C.

    2015-08-20

    We propose a hierarchy of nonlinearly dispersive generalized Korteweg–de Vries (KdV) evolution equations based on a modification of the Lagrangian density whose induced action functional the KdV equation extremizes. Two recent nonlinear evolution equations describing wave propagation in certain generalized continua with an inherent material length scale are members of the proposed hierarchy. Like KdV, the equations from the proposed hierarchy possess Hamiltonian structure. Unlike KdV, the solutions to these equations can be compact (i.e., they vanish outside of some open interval) and, in addition, peaked. Implicit solutions for these peaked, compact traveling waves (“peakompactons”) are presented.

  6. A nonlinear Klein–Gordon equation for relativistic superfluidity

    NASA Astrophysics Data System (ADS)

    Waldron, Oliver; Van Gorder, Robert A.

    2017-10-01

    Many neutron star features can be accurately modeled only if one assumes that a significant portion of the neutron star interior is in a superfluid state and if relativitic effects are considered, and possible solutions to the underlying mathematical models include vortex solutions. It was recently shown that vorticity in relativistic superfluids can be studied under the framework of a nonlinear Klein–Gordon (NLKG) model in general curvilinear coordinates where the phase dynamics of solutions to this equation give rise to superfluidity (Xiong et al 2014 Phys. Rev. D 90 125019), and some numerical solutions were obtained. The aim of this paper will be to extract asymptotic solutions to obtain a better qualitative understanding of the possible relativistic superfluid dynamics possible under the NLKG model. We obtain asymptotic results for both spherically symmetric and cylindrically symmetric solutions, demonstrating that the solutions actually appear more regular in the relativistic regime compared to the non-relativistic limit. In fact, the asymptotic and numerical solutions actually show the best agreement in the relativistic case. We demonstrate that the relativistic effects actually tend to regularize or stabilize the solutions, relative to the non-relativistic solutions, which is an interesting finding. We then obtain a Thomas–Fermi-like perturbation result in the very large-mass limit where the kinetics become negligible relative to the self-interaction term (at leading order). We finally extend the NLKG model by assuming a curved spacetime with a metric generally used to model the space surrounding a neutron star, which is a novel generalization of the NLKG model to curved spacetime. We again obtain solutions in the large-mass limit for this case, and find that for such a spacetime non-stationary states (rather than simply stationary states) are possible in the large-mass limit.

  7. A note on the generation of phase plane plots on a digital computer. [for solution of nonlinear differential equations

    NASA Technical Reports Server (NTRS)

    Simon, M. K.

    1980-01-01

    A technique is presented for generating phase plane plots on a digital computer which circumvents the difficulties associated with more traditional methods of numerical solving nonlinear differential equations. In particular, the nonlinear differential equation of operation is formulated.

  8. Equations for description of nonlinear standing waves in constant-cross-sectioned resonators.

    PubMed

    Bednarik, Michal; Cervenka, Milan

    2014-03-01

    This work is focused on investigation of applicability of two widely used model equations for description of nonlinear standing waves in constant-cross-sectioned resonators. The investigation is based on the comparison of numerical solutions of these model equations with solutions of more accurate model equations whose validity has been verified experimentally in a number of published papers.

  9. Integrable pair-transition-coupled nonlinear Schrödinger equations.

    PubMed

    Ling, Liming; Zhao, Li-Chen

    2015-08-01

    We study integrable coupled nonlinear Schrödinger equations with pair particle transition between components. Based on exact solutions of the coupled model with attractive or repulsive interaction, we predict that some new dynamics of nonlinear excitations can exist, such as the striking transition dynamics of breathers, new excitation patterns for rogue waves, topological kink excitations, and other new stable excitation structures. In particular, we find that nonlinear wave solutions of this coupled system can be written as a linear superposition of solutions for the simplest scalar nonlinear Schrödinger equation. Possibilities to observe them are discussed in a cigar-shaped Bose-Einstein condensate with two hyperfine states. The results would enrich our knowledge on nonlinear excitations in many coupled nonlinear systems with transition coupling effects, such as multimode nonlinear fibers, coupled waveguides, and a multicomponent Bose-Einstein condensate system.

  10. A stable and accurate scheme for nonlinear diffusion equations: Application to atmospheric boundary layer

    NASA Astrophysics Data System (ADS)

    Nazari, Farshid; Mohammadian, Abdolmajid; Zadra, Ayrton; Charron, Martin

    2013-03-01

    Stability concerns are always a factor in the numerical solution of nonlinear diffusion equations, which are a class of equations widely applicable in different fields of science and engineering. In this study, a modified extended backward differentiation formulae (ME BDF) scheme is adapted for the solution of nonlinear diffusion equations, with a special focus on the atmospheric boundary layer diffusion process. The scheme is first implemented and examined for a widely used nonlinear ordinary differential equation, and then extended to a system of two nonlinear diffusion equations. A new temporal filter which leads to significant improvement of numerical results is proposed, and the impact of the filter on the stability and accuracy of the results is investigated. Noteworthy improvements are obtained as compared to other commonly used numerical schemes. Linear stability analysis of the proposed scheme is performed for both systems, and analytical stability limits are presented.

  11. Nonexistence of small, odd breathers for a class of nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Michał; Martel, Yvan; Muñoz, Claudio

    2016-11-01

    In this note, we show that for a large class of nonlinear wave equations with odd nonlinearities, any globally defined odd solution which is small in the energy space decays to 0 in the local energy norm. In particular, this result shows nonexistence of small, odd breathers for some classical nonlinear Klein Gordon equations, such as the sine-Gordon equation and φ ^4 and φ ^6 models. It also partially answers a question of Soffer and Weinstein (Invent Math 136(1): 9-74, p 19 1999) about nonexistence of breathers for the cubic NLKG in dimension one.

  12. Eigenvalue cutoff in the cubic-quintic nonlinear Schrödinger equation.

    PubMed

    Prytula, Vladyslav; Vekslerchik, Vadym; Pérez-García, Víctor M

    2008-08-01

    Using theoretical arguments, we prove the numerically well-known fact that the eigenvalues of all localized stationary solutions of the cubic-quintic (2+1) -dimensional nonlinear Schrödinger equation exhibit an upper cutoff value. The existence of the cutoff is inferred using Gagliardo-Nirenberg and Hölder inequalities together with Pohozaev identities. We also show that, in the limit of eigenvalues close to zero, the eigenstates of the cubic-quintic nonlinear Schrödinger equation behave similarly to those of the cubic nonlinear Schrödinger equation.

  13. Finding all solutions of nonlinear equations using the dual simplex method

    NASA Astrophysics Data System (ADS)

    Yamamura, Kiyotaka; Fujioka, Tsuyoshi

    2003-03-01

    Recently, an efficient algorithm has been proposed for finding all solutions of systems of nonlinear equations using linear programming. This algorithm is based on a simple test (termed the LP test) for nonexistence of a solution to a system of nonlinear equations using the dual simplex method. In this letter, an improved version of the LP test algorithm is proposed. By numerical examples, it is shown that the proposed algorithm could find all solutions of a system of 300 nonlinear equations in practical computation time.

  14. Nonexistence of small, odd breathers for a class of nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Michał; Martel, Yvan; Muñoz, Claudio

    2017-05-01

    In this note, we show that for a large class of nonlinear wave equations with odd nonlinearities, any globally defined odd solution which is small in the energy space decays to 0 in the local energy norm. In particular, this result shows nonexistence of small, odd breathers for some classical nonlinear Klein Gordon equations, such as the sine-Gordon equation and φ ^4 and φ ^6 models. It also partially answers a question of Soffer and Weinstein (Invent Math 136(1): 9-74, p 19 1999) about nonexistence of breathers for the cubic NLKG in dimension one.

  15. Numerical Simulations of Self-Focused Pulses Using the 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. Abstract of a proposed paper for presentation at the meeting NONLINEAR OPTICS: Materials, Fundamentals, and Applications, Hyatt Regency Waikaloa, Waikaloa, Hawaii, July 24-29, 1994, Cosponsored by IEEE/Lasers and Electro-Optics Society and Optical Society of America

  16. The study of nonlinear almost periodic differential equations without recourse to the H-classes of these equations

    SciTech Connect

    Slyusarchuk, V. E. E-mail: V.Ye.Slyusarchuk@NUWM.rv.ua

    2014-06-01

    The well-known theorems of Favard and Amerio on the existence of almost periodic solutions to linear and nonlinear almost periodic differential equations depend to a large extent on the H-classes and the requirement that the bounded solutions of these equations be separated. The present paper provides different conditions for the existence of almost periodic solutions. These conditions, which do not depend on the H-classes of the equations, are formulated in terms of a special functional on the set of bounded solutions of the equations under consideration. This functional is used, in particular, to test whether solutions are separated. Bibliography: 24 titles. (paper)

  17. New analytical method for solving Burgers' and nonlinear heat transfer equations and comparison with HAM

    NASA Astrophysics Data System (ADS)

    Rashidi, M. M.; Erfani, E.

    2009-09-01

    In this study, we present a numerical comparison between the differential transform method (DTM) and the homotopy analysis method (HAM) for solving Burgers' and nonlinear heat transfer problems. The first differential equation is the Burgers' equation serves as a useful model for many interesting problems in applied mathematics. The second one is the modeling equation of a straight fin with a temperature dependent thermal conductivity. In order to show the effectiveness of the DTM, the results obtained from the DTM is compared with available solutions obtained using the HAM [M.M. Rashidi, G. Domairry, S. Dinarvand, Commun. Nonlinear Sci. Numer. Simul. 14 (2009) 708-717; G. Domairry, M. Fazeli, Commun. Nonlinear Sci. Numer. Simul. 14 (2009) 489-499] and whit exact solutions. The method can easily be applied to many linear and nonlinear problems. It illustrates the validity and the great potential of the differential transform method in solving nonlinear partial differential equations. The obtained results reveal that the technique introduced here is very effective and convenient for solving nonlinear partial differential equations and nonlinear ordinary differential equations that we are found to be in good agreement with the exact solutions.

  18. Modulational instability in a purely nonlinear coupled complex Ginzburg-Landau equations through a nonlinear discrete transmission line.

    PubMed

    Ndzana, Fabien; Mohamadou, Alidou; Kofané, Timoléon C

    2008-12-01

    We study wave propagation in a nonlinear transmission line with dissipative elements. We show analytically that the telegraphers' equations of the electrical transmission line can be modeled by a pair of continuous coupled complex Ginzburg-Landau equations, coupled by purely nonlinear terms. Based on this system, we investigated both analytically and numerically the modulational instability (MI). We produce characteristics of the MI in the form of typical dependence of the instability growth rate on the wavenumbers and system parameters. Generic outcomes of the nonlinear development of the MI are investigated by dint of direct simulations of the underlying equations. We find that the initial modulated plane wave disintegrates into waves train. An apparently turbulent state takes place in the system during the propagation.

  19. Stationary states of extended nonlinear Schrödinger equation with a source

    NASA Astrophysics Data System (ADS)

    Borich, M. A.; Smagin, V. V.; Tankeev, A. P.

    2007-02-01

    Structure of nonlinear stationary states of the extended nonlinear Schrödinger equation (ENSE) with a source has been analyzed with allowance for both third-order and nonlinearity dispersion. A new class of particular solutions (solitary waves) of the ENSe has been obtained. The scenario of the destruction of these states under the effect of an external perturbation has been investigated analytically and numerically. The results obtained can be used to interpret experimental data on the weakly nonlinear dynamics of the magnetostatic envelope in heterophase ferromagnet-insulator-metal, metal-insulator-ferromagnet-insulator-metal, and other similar structures and upon the simulation of nonlinear processes in optical systems.

  20. Adaptive and iterative methods for simulations of nanopores with the PNP-Stokes equations

    NASA Astrophysics Data System (ADS)

    Mitscha-Baude, Gregor; Buttinger-Kreuzhuber, Andreas; Tulzer, Gerhard; Heitzinger, Clemens

    2017-06-01

    We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule dynamics inside nanopore sensors. The source code is released online at http://github.com/mitschabaude/nanopores. We add to existing numerical approaches by deploying goal-oriented adaptive mesh refinement. To reduce the computation overhead of mesh adaptivity, our error estimator uses the much cheaper Poisson-Boltzmann equation as a simplified model, which is justified on heuristic grounds but shown to work well in practice. To address the nonlinearity in the full PNP-Stokes system, three different linearization schemes are proposed and investigated, with two segregated iterative approaches both outperforming a naive application of Newton's method. Numerical experiments are reported on a real-world nanopore sensor geometry. We also investigate two different models for the interaction of target molecules with the nanopore sensor through the PNP-Stokes equations. In one model, the molecule is of finite size and is explicitly built into the geometry; while in the other, the molecule is located at a single point and only modeled implicitly - after solution of the system - which is computationally favorable. We compare the resulting force profiles of the electric and velocity fields acting on the molecule, and conclude that the point-size model fails to capture important physical effects such as the dependence of charge selectivity of the sensor on the molecule radius.

  1. Some exact solutions of a system of nonlinear Schroedinger equations in three-dimensional space

    SciTech Connect

    Moskalyuk, S.S.

    1988-02-01

    Interactions that break the symmetry of systems of nonrelativistic Schroedinger equations but preserve their symmetry with respect to one-parameter subgroups of the Schroedinger group are described. Ansatzes for invariant solutions and the corresponding systems of reduced equations in invariant variables for Galileo-invariant Schroedinger equations are found. Exact solutions for the system of nonlinear Schroedinger equations in three-dimensional space for the generalized Hubbard model are obtained.

  2. Traveling wave solution of fractional KdV-Burger-Kuramoto equation describing nonlinear physical phenomena

    NASA Astrophysics Data System (ADS)

    Gupta, A. K.; Ray, S. Saha

    2014-09-01

    In this paper, KdV-Burger-Kuramoto equation involving instability, dissipation, and dispersion parameters is solved numerically. The numerical solution for the fractional order KdV-Burger-Kuramoto (KBK) equation has been presented using two-dimensional Legendre wavelet method. The approximate solutions of nonlinear fractional KBK equation thus obtained by Legendre wavelet method are compared with the exact solutions. The present scheme is very simple, effective and convenient for obtaining numerical solution of the KBK equation.

  3. The (G'/G)-expansion method for the nonlinear time fractional differential equations

    NASA Astrophysics Data System (ADS)

    Unsal, Omer; Guner, Ozkan; Bekir, Ahmet; Cevikel, Adem C.

    2017-01-01

    In this paper, we obtain exact solutions of two time fractional differential equations using Jumarie's modified Riemann-Liouville derivative which is encountered in mathematical physics and applied mathematics; namely (3 + 1)-dimensional time fractional KdV-ZK equation and time fractional ADR equation by using fractional complex transform and (G/'G )-expansion method. It is shown that the considered transform and method are very useful in solving nonlinear fractional differential equations.

  4. Stable parity-time-symmetric nonlinear modes and excitations in a derivative nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Chen, Yong; Yan, Zhenya

    2017-01-01

    The effect of derivative nonlinearity and parity-time-symmetric (PT -symmetric) potentials on the wave propagation dynamics is explored in the derivative nonlinear Schrödinger equation, where the physically interesting Scarf-II and harmonic-Hermite-Gaussian potentials are chosen. We study numerically the regions of unbroken and broken linear PT -symmetric phases and find some stable bright solitons of this model in a wide range of potential parameters even though the corresponding linear PT -symmetric phases are broken. The semielastic interactions between particular bright solitons and exotic incident waves are illustrated such that we find that particular nonlinear modes almost keep their shapes after interactions even if the exotic incident waves have evidently been changed. Moreover, we exert the adiabatic switching on PT -symmetric potential parameters such that a stable nonlinear mode with the unbroken linear PT -symmetric phase can be excited to another stable nonlinear mode belonging to the broken linear PT -symmetric phase.

  5. Exact soliton solutions and their stability control in the nonlinear Schrödinger equation with spatiotemporally modulated nonlinearity.

    PubMed

    Tian, Qing; Wu, Lei; Zhang, Jie-Fang; Malomed, Boris A; Mihalache, D; Liu, W M

    2011-01-01

    We put forward a generic transformation which helps to find exact soliton solutions of the nonlinear Schrödinger equation with a spatiotemporal modulation of the nonlinearity and external potentials. As an example, we construct exact solitons for the defocusing nonlinearity and harmonic potential. When the soliton's eigenvalue is fixed, the number of exact solutions is determined by energy levels of the linear harmonic oscillator. In addition to the stable fundamental solitons, stable higher-order modes, describing array of dark solitons nested in a finite-width background, are constructed too. We also show how to control the instability domain of the nonstationary solitons.

  6. Breather solutions of the integrable quintic nonlinear Schrödinger equation and their interactions.

    PubMed

    Chowdury, A; Kedziora, D J; Ankiewicz, A; Akhmediev, N

    2015-02-01

    We present breather solutions of the quintic integrable equation of the Schrödinger hierarchy. This equation has terms describing fifth-order dispersion and matching nonlinear terms. Using a Darboux transformation, we derive first-order and second-order breather solutions. These include first- and second-order rogue-wave solutions. To some extent, these solutions are analogous with the corresponding nonlinear Schrödinger equation (NLSE) solutions. However, the presence of a free parameter in the equation results in specific solutions that have no analogues in the NLSE case. We analyze new features of these solutions.

  7. Equations of state and bump Cepheids. II - Non-linear results

    NASA Astrophysics Data System (ADS)

    Kanbur, Shashi M.

    1992-06-01

    The Hummer-Mihalas-Dappen (MHD, 1988) and a simple Saha type equation of state are used to obtain nonlinear pulsation characteristics of a grid of models spanning the Hertzsprung sequence (Cox, 1974). The grid of models is taken from Simon and Davis (1983) who used the Los Alamos equation of state in their computations. The result is a sensitivity analysis of theoretical nonlinear bump Cepheid models to the equation of state employed in the calculation. The results obtained with these equations of state are different, though not enough to resolve the Cepheid bump mass discrepancy (Stobie 1969; Simon and Schmidt, 1976; Simon, 1986).

  8. Analytical-numerical solution of a nonlinear integrodifferential equation in econometrics

    NASA Astrophysics Data System (ADS)

    Kakhktsyan, V. M.; Khachatryan, A. Kh.

    2013-07-01

    A mixed problem for a nonlinear integrodifferential equation arising in econometrics is considered. An analytical-numerical method is proposed for solving the problem. Some numerical results are presented.

  9. Longtime dynamics of the quasi-linear wave equations with structural damping and supercritical nonlinearities

    NASA Astrophysics Data System (ADS)

    Yang, Zhijian; Liu, Zhiming

    2017-03-01

    The paper investigates the well-posedness and the longtime dynamics of the quasilinear wave equations with structural damping and supercritical nonlinearities: {{u}tt}- Δ u+{{≤ft(- Δ \\right)}α}{{u}t}-\

  10. Hessian estimates in weighted Lebesgue spaces for fully nonlinear elliptic equations

    NASA Astrophysics Data System (ADS)

    Byun, Sun-Sig; Lee, Mikyoung; Palagachev, Dian K.

    2016-03-01

    We prove global regularity in weighted Lebesgue spaces for the viscosity solutions to the Dirichlet problem for fully nonlinear elliptic equations. As a consequence, regularity in Morrey spaces of the Hessian is derived as well.

  11. An Optimal System of One-dimensional Symmetry Lie Algebras of Coupled Nonlinear Schroedinger Equations

    SciTech Connect

    Pulov, Vladimir I.

    2011-04-07

    This paper is devoted to finding an optimal system of one-dimensional subalgebras of an eight-dimensional Lie algebra of point symmetry transformations, admitted by a system of two coupled nonlinear Schroedinger equations.

  12. Analytic solutions for time-dependent Schrödinger equations with linear of nonlinear Hamiltonians

    NASA Astrophysics Data System (ADS)

    Adomian, G.; Efinger, H. J.

    1994-10-01

    The decomposition method is applied to the time-dependent Schrödinger equation for linear or nonlinear Hamiltonian operators, without linearization, perturbation, or numerical methods, to obtain a rapidly converging analytic solution

  13. Evolution of higher order nonlinear equation for the dust ion-acoustic waves in nonextensive plasma

    SciTech Connect

    Yasmin, S.; Asaduzzaman, M.; Mamun, A. A.

    2012-10-15

    There are three different types of nonlinear equations, namely, Korteweg-de Vries (K-dV), modified K-dV (mK-dV), and mixed modified K-dV (mixed mK-dV) equations, for the nonlinear propagation of the dust ion-acoustic (DIA) waves. The effects of electron nonextensivity on DIA solitary waves propagating in a dusty plasma (containing negatively charged stationary dust, inertial ions, and nonextensive q distributed electrons) are examined by solving these nonlinear equations. The basic features of mixed mK-dV (higher order nonlinear equation) solitons are found to exist beyond the K-dV limit. The properties of mK-dV solitons are compared with those of mixed mK-dV solitons. It is found that both positive and negative solitons are obtained depending on the q (nonextensive parameter).

  14. Coding of nonlinear states for the Gross-Pitaevskii equation with periodic potential

    NASA Astrophysics Data System (ADS)

    Alfimov, G. L.; Avramenko, A. I.

    2013-07-01

    We study nonlinear states for the NLS-type equation with additional periodic potential U(x), also called the Gross-Pitaevskii equation, GPE, in theory of Bose-Einstein Condensate, BEC. We prove that if the nonlinearity is defocusing (repulsive, in the BEC context) then under some conditions there exists a homeomorphism between the set of all nonlinear states for GPE (i.e. real bounded solutions of some nonlinear ODE) and the set of bi-infinite sequences of numbers from 1 to N for some integer N. These sequences can be viewed as codes of the nonlinear states. We present numerical arguments that for GPE with cosine potential these conditions hold in certain areas of the plane of the external parameters. This implies that for these values of parameters all the nonlinear states can be described in terms of the coding sequences.

  15. On the structure of nonlinear constitutive equations for fiber reinforced composites

    NASA Technical Reports Server (NTRS)

    Jansson, Stefan

    1992-01-01

    The structure of constitutive equations for nonlinear multiaxial behavior of transversely isotropic fiber reinforced metal matrix composites subject to proportional loading was investigated. Results from an experimental program were combined with numerical simulations of the composite behavior for complex stress to reveal the full structure of the equations. It was found that the nonlinear response can be described by a quadratic flow-potential, based on the polynomial stress invariants, together with a hardening rule that is dominated by two different hardening mechanisms.

  16. On the problem of convergence of series solution of non-linear fractional partial differential equation

    NASA Astrophysics Data System (ADS)

    Singh, Prince; Sharma, Dinkar

    2017-07-01

    Series solution is obtained on solving non-linear fractional partial differential equation using homotopy perturbation transformation method. First of all, we apply homotopy perturbation transformation method to obtain the series solution of non-linear fractional partial differential equation. In this case, the fractional derivative is described in Caputo sense. Then, we present the facts obtained by analyzing the convergence of this series solution. Finally, the established fact is supported by an example.

  17. H[alpha]-stability of modified Runge-Kutta methods for nonlinear neutral pantograph equations

    NASA Astrophysics Data System (ADS)

    Ma, S. F.; Yang, Z. W.; Liu, M. Z.

    2007-11-01

    In this paper, we investigate H[alpha]-stability of algebraically stable Runge-Kutta methods with a variable stepsize for nonlinear neutral pantograph equations. As a result, the Radau IA, Radau IIA, Lobatto IIIC method, the odd-stage Gauss-Legendre methods and the one-leg [theta]-method with are H[alpha]-stable for nonlinear neutral pantograph equations. Some experiments are given.

  18. Solving nonlinear or stiff differential equations by Laplace homotopy analysis method(LHAM)

    NASA Astrophysics Data System (ADS)

    Chong, Fook Seng; Lem, Kong Hoong; Wong, Hui Lin

    2015-10-01

    The initial value problems of nonlinear or stiff ordinary differential equation appear in many fields of engineering science, particularly in the studies of electrical circuits, chemical reactions, wave vibration and so on. In this research, the standard homotopy analysis method hybrids with Laplace transform method to solve nonlinear and stiff differential equations. Using this modification, the problems solved by LHAM successfully yield good solutions. Some examples are examined to highlight the convenience and effectiveness of LHAM.

  19. Nonlinear System Of Equations For Multicomponent Analysis Of Artificial Food Coloring

    NASA Astrophysics Data System (ADS)

    Santosa, I. E.; Budiasih, L. K.

    2010-12-01

    In multicomponent analysis of artificial food coloring (AFC), nonlinear relation of the absorbance and the concentration forms a nonlinear system of equations. The Newton's method based algorithm has been used to calculate individual AFC concentration in the mixture of two AFCs. The absorbance was measured using a spectrophotometer at two different wavelengths.

  20. Implementation guide for MINPACK-1. [Package of Fortran subprograms for solution of systems of nonlinear equations

    SciTech Connect

    Garbow, B.S.; Hillstrom, K.E.; More, J.J.

    1980-07-01

    MINPACK-1 is a package of Fortran subprograms for the numerical solution of systems of nonlinear equations and nonlinear least-squares problems. This report describes how to implement the package from the tape on which it is transmitted. 3 tables.

  1. Exact solutions of a generalized nonlinear Schrödinger equation.

    PubMed

    Zhang, Shaowu; Yi, Lin

    2008-08-01

    Exact chirped soliton solutions of a generalized nonlinear Schrödinger equation with the cubic-quintic nonlinearities as well as the self-steeping were obtained using a variable parametric method. It was found that the formation of solutions is determined by the sign of a joint parameter solely. By performing numerical simulations, the chirped solutions are stable under perturbations.

  2. Infinite hierarchy of nonlinear Schrödinger equations and their solutions.

    PubMed

    Ankiewicz, A; Kedziora, D J; Chowdury, A; Bandelow, U; Akhmediev, N

    2016-01-01

    We study the infinite integrable nonlinear Schrödinger equation hierarchy beyond the Lakshmanan-Porsezian-Daniel equation which is a particular (fourth-order) case of the hierarchy. In particular, we present the generalized Lax pair and generalized soliton solutions, plane wave solutions, Akhmediev breathers, Kuznetsov-Ma breathers, periodic solutions, and rogue wave solutions for this infinite-order hierarchy. We find that "even- order" equations in the set affect phase and "stretching factors" in the solutions, while "odd-order" equations affect the velocities. Hence odd-order equation solutions can be real functions, while even-order equation solutions are always complex.

  3. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks.

    PubMed

    Smadbeck, Patrick; Kaznessis, Yiannis N

    2014-08-01

    Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized.

  4. An Evolution Operator Solution for a Nonlinear Beam Equation

    DTIC Science & Technology

    1990-12-01

    uniqueness for the parabolic problem Ug + (-A) m u+ I I- u = f (14) on RN X (0, 1). Again, certain restrictions apply. The Schr ~ dinger equation , [68:pg 823...evolution equation because of the time dependence in the definition of the operator A. He identifies conditions for the existence of a unique solution. In...The arguments for the adjoint and dissipativity are not repeated. Because of the explicit time dependence , (71) is called an evolution equation . For

  5. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

    PubMed Central

    Smadbeck, Patrick; Kaznessis, Yiannis N.

    2014-01-01

    Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized. PMID:25215268

  6. Nonlinear equations of motion for the elastic bending and torsion of twisted nonuniform rotor blades

    NASA Technical Reports Server (NTRS)

    Hodges, D. H.; Dowell, E. H.

    1974-01-01

    The equations of motion are developed by two complementary methods, Hamilton's principle and the Newtonian method. The resulting equations are valid to second order for long, straight, slender, homogeneous, isotropic beams undergoing moderate displacements. The ordering scheme is based on the restriction that squares of the bending slopes, the torsion deformation, and the chord/radius and thickness/radius ratios are negligible with respect to unity. All remaining nonlinear terms are retained. The equations are valid for beams with mass centroid axis and area centroid (tension) axis offsets from the elastic axis, nonuniform mass and stiffness section properties, variable pretwist, and a small precone angle. The strain-displacement relations are developed from an exact transformation between the deformed and undeformed coordinate systems. These nonlinear relations form an important contribution to the final equations. Several nonlinear structural and inertial terms in the final equations are identified that can substantially influence the aeroelastic stability and response of hingeless helicopter rotor blades.

  7. Multi-symplectic Runge-Kutta methods for nonlinear Dirac equations

    SciTech Connect

    Hong Jialin . E-mail: lichun@lsec.cc.ac.cn

    2006-01-20

    In this paper, we consider the multi-symplectic Runge-Kutta (MSRK) methods applied to the nonlinear Dirac equation in relativistic quantum physics, based on a discovery of the multi-symplecticity of the equation. In particular, the conservation of energy, momentum and charge under MSRK discretizations is investigated by means of numerical experiments and numerical comparisons with non-MSRK methods. Numerical experiments presented reveal that MSRK methods applied to the nonlinear Dirac equation preserve exactly conservation laws of charge and momentum, and conserve the energy conservation in the corresponding numerical accuracy to the method utilized. It is verified numerically that MSRK methods are stable and convergent with respect to the conservation laws of energy, momentum and charge, and MSRK methods preserve not only the inner geometric structure of the equation, but also some crucial conservative properties in quantum physics. A remarkable advantage of MSRK methods applied to the nonlinear Dirac equation is the precise preservation of charge conservation law.

  8. Existence of global decaying solutions to the exterior problem for the Klein-Gordon equation with a nonlinear localized dissipation and a derivative nonlinearity

    NASA Astrophysics Data System (ADS)

    Nakao, Mitsuhiro

    We prove the existence of global decaying solutions to the exterior problem for the Klein-Gordon equation with a nonlinear localized dissipation and a derivative nonlinearity. To derive the required estimates of solutions we employ a 'loan' method.

  9. Differential geometry techniques for sets of nonlinear partial differential equations

    NASA Technical Reports Server (NTRS)

    Estabrook, Frank B.

    1990-01-01

    An attempt is made to show that the Cartan theory of partial differential equations can be a useful technique for applied mathematics. Techniques for finding consistent subfamilies of solutions that are generically rich and well-posed and for introducing potentials or other usefully consistent auxiliary fields are introduced. An extended sample calculation involving the Korteweg-de Vries equation is given.

  10. Differential geometry techniques for sets of nonlinear partial differential equations

    NASA Technical Reports Server (NTRS)

    Estabrook, Frank B.

    1990-01-01

    An attempt is made to show that the Cartan theory of partial differential equations can be a useful technique for applied mathematics. Techniques for finding consistent subfamilies of solutions that are generically rich and well-posed and for introducing potentials or other usefully consistent auxiliary fields are introduced. An extended sample calculation involving the Korteweg-de Vries equation is given.

  11. Solitons in coupled nonlinear Schrödinger equations with variable coefficients

    NASA Astrophysics Data System (ADS)

    Han, Lijia; Huang, Yehui; Liu, Hui

    2014-09-01

    We study the coupled nonlinear Schrodinger equation with variable coefficients (VCNLS), which can be used to describe the interaction among the modes in nonlinear optics and Bose-Einstein condensation. By constructing an explicit transformation, which maps VCNLS to the classical coupled nonlinear Schrödinger equations (CNLS), we obtain Bright-Dark and Bright-Bright solitons for VCNLS. Furthermore, the optical super-lattice potentials (or periodic potentials) and hyperbolic cosine potentials with parameters are designed, which are two kinds of important potentials in physics. This method can be used to design a large variety of external potentials in VCNLS, which could be meaningful for manipulating solitons experimentally.

  12. Galerkin/Runge-Kutta discretizations of nonlinear parabolic equations

    NASA Astrophysics Data System (ADS)

    Hansen, Eskil

    2007-08-01

    Global error bounds are derived for full Galerkin/Runge-Kutta discretizations of nonlinear parabolic problems, including the evolution governed by the p-Laplacian with p[greater-or-equal, slanted]2. The analysis presented here is not based on linearization procedures, but on the fully nonlinear framework of logarithmic Lipschitz constants and an extended B-convergence theory. The global error is bounded in L2 by [Delta]xr/2+[Delta]tq, where r is the convergence order of the Galerkin method applied to the underlying stationary problem and q is the stiff order of the algebraically stable Runge-Kutta method.

  13. Painlevé analysis and exact solutions of the fourth-order equation for description of nonlinear waves

    NASA Astrophysics Data System (ADS)

    Kudryashov, Nikolay A.

    2015-11-01

    The fourth-order equation for description of nonlinear waves is considered. A few variants of this equation are studied. Painlevé test is applied to investigate integrability of these equations. We show that all these equations are not integrable, but some exact solutions of these equations exist. Analytic solutions in closed-form of the equations are found.

  14. Electrokinetic and electrostatic properties of bilayers containing gangliosides GM1, GD1a, or GT1. Comparison with a nonlinear theory.

    PubMed Central

    McDaniel, R V; Sharp, K; Brooks, D; McLaughlin, A C; Winiski, A P; Cafiso, D; McLaughlin, S

    1986-01-01

    We formed vesicles from mixtures of egg phosphatidylcholine (PC) and the gangliosides GM1, GD1a, or GT1 to model the electrokinetic properties of biological membranes. The electrophoretic mobilities of the vesicles are similar in NaCl, CsCl, and TMACl solutions, suggesting that monovalent cations do not bind significantly to these gangliosides. If we assume the sialic acid groups on the gangliosides are located some distance from the surface of the vesicle and the sugar moieties exert hydrodynamic drag, we can describe the mobility data in 1, 10, and 100 mM monovalent salt solutions with a combination of the Navier-Stokes and nonlinear Poisson-Boltzmann equations. The values we assume for the thickness of the ganglioside head group and the location of the charge affect the theoretical predictions markedly, but the Stokes radius of each sugar and the location of the hydrodynamic shear plane do not. We obtain a reasonable fit to the mobility data by assuming that all ganglioside head groups project 2.5 nm from the bilayer and all fixed charges are in a plane 1 nm from the bilayer surface. We tested the latter assumption by estimating the surface potentials of PC/ganglioside bilayers using four techniques: we made 31P nuclear magnetic resonance, fluorescence, electron spin resonance, and conductance measurements. The results are qualitatively consistent with our assumption. PMID:3697476

  15. On the solution of the fractional nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Rida, S. Z.; El-Sherbiny, H. M.; Arafa, A. A. M.

    2008-01-01

    We present the nonlinear Schrödinger (NLS) equation of fractional order. The fractional derivatives are described in the Caputo sense. The Adomian decomposition method (ADM) in applied mathematics can be used as alternative methods for obtaining analytic and approximate solutions for different types of fractional differential equations. In these schemes, the solution constructed in power series with easily computable components.

  16. The Poincaré-Bendixson Theorem and the non-linear Cauchy-Riemann equations

    NASA Astrophysics Data System (ADS)

    van den Berg, J. B.; Munaò, S.; Vandervorst, R. C. A. M.

    2016-11-01

    Fiedler and Mallet-Paret (1989) prove a version of the classical Poincaré-Bendixson Theorem for scalar parabolic equations. We prove that a similar result holds for bounded solutions of the non-linear Cauchy-Riemann equations. The latter is an application of an abstract theorem for flows with a(n) (unbounded) discrete Lyapunov function.

  17. New solutions for two integrable cases of a generalized fifth-order nonlinear equation

    NASA Astrophysics Data System (ADS)

    Wazwaz, Abdul-Majid

    2015-05-01

    Multiple-complexiton solutions for a new generalized fifth-order nonlinear integrable equation are constructed with the help of the Hirota's method and the simplified Hirota's method. By extending the real parameters into complex parameters, nonsingular complexiton solutions are obtained for two specific coefficients of the new generalized equation.

  18. Similarity solution to fractional nonlinear space-time diffusion-wave equation

    NASA Astrophysics Data System (ADS)

    Costa, F. Silva; Marão, J. A. P. F.; Soares, J. C. Alves; de Oliveira, E. Capelas

    2015-03-01

    In this article, the so-called fractional nonlinear space-time wave-diffusion equation is presented and discussed. This equation is solved by the similarity method using fractional derivatives in the Caputo, Riesz-Feller, and Riesz senses. Some particular cases are presented and the corresponding solutions are shown by means of 2-D and 3-D plots.

  19. On invariant analysis of space-time fractional nonlinear systems of partial differential equations. II

    NASA Astrophysics Data System (ADS)

    Singla, Komal; Gupta, R. K.

    2017-05-01

    In Paper I [Singla, K. and Gupta, R. K., J. Math. Phys. 57, 101504 (2016)], Lie symmetry method is developed for time fractional systems of partial differential equations. In this article, the Lie symmetry approach is proposed for space-time fractional systems of partial differential equations and applied to study some well-known physically significant space-time fractional nonlinear systems successfully.

  20. State-Dependent Riccati Equation Regulation of Systems with State and Control Nonlinearities

    NASA Technical Reports Server (NTRS)

    Beeler, Scott C.; Cox, David E. (Technical Monitor)

    2004-01-01

    The state-dependent Riccati equations (SDRE) is the basis of a technique for suboptimal feedback control of a nonlinear quadratic regulator (NQR) problem. It is an extension of the Riccati equation used for feedback control of linear problems, with the addition of nonlinearities in the state dynamics of the system resulting in a state-dependent gain matrix as the solution of the equation. In this paper several variations on the SDRE-based method will be considered for the feedback control problem with control nonlinearities. The control nonlinearities may result in complications in the numerical implementation of the control, which the different versions of the SDRE method must try to overcome. The control methods will be applied to three test problems and their resulting performance analyzed.

  1. Forward-backward equations for nonlinear propagation in axially invariant optical systems.

    PubMed

    Ferrando, Albert; Zacarés, Mario; Fernández de Córdoba, Pedro; Binosi, Daniele; Montero, Alvaro

    2005-01-01

    We present a general framework to deal with forward and backward components of the electromagnetic field in axially invariant nonlinear optical systems, which include those having any type of linear or nonlinear transverse inhomogeneities. With a minimum amount of approximations, we obtain a system of two first-order equations for forward and backward components, explicitly showing the nonlinear couplings among them. The modal approach used allows for an effective reduction of the dimensionality of the original problem from 3 + 1 (three spatial dimensions plus one time dimension) to 1 + 1 (one spatial dimension plus one frequency dimension). The new equations can be written in a spinor Dirac-like form, out of which conserved quantities can be calculated in an elegant manner. Finally, these equations inherently incorporate spatiotemporal couplings, so that they can be easily particularized to deal with purely temporal or purely spatial effects. Nonlinear forward pulse propagation and nonparaxial evolution of spatial structures are analyzed as examples.

  2. A comparison between the propagators method and the decomposition method for nonlinear equations

    SciTech Connect

    Azmy, Y.Y.; Protopopescu, V. ); Cacuci, D.G. . Dept. of Chemical and Nuclear Engineering)

    1990-01-01

    Recently, a new formalism for solving nonlinear problems has been formulated. The formalism is based on the construction of advanced and retarded propagators that generalize the customary Green's functions in linear theory. One of the main advantages of this formalism is the possibility of transforming nonlinear differential equations into nonlinear integral equations that are usually easier to handle theoretically and computationally. The aim of this paper is to compare, on an example, the performances of the propagator method with other methods used for nonlinear equations, in particular, the decomposition method. The propagator method is stable, accurate, and efficient for all initial values and time intervals considered, while the decomposition method is unstable at large time intervals, even for very conveniently chosen initial conditions. 5 refs., 4 tabs.

  3. Nonlinear tunneling of optical soliton in 3 coupled NLS equation with symbolic computation

    NASA Astrophysics Data System (ADS)

    Mani Rajan, M. S.; Mahalingam, A.; Uthayakumar, A.

    2014-07-01

    We investigated the soliton solution for N coupled nonlinear Schrödinger (CNLS) equations. These equations are coupled due to the cross-phase-modulation (CPM). Lax pair of this system is obtained via the Ablowitz-Kaup-Newell-Segur (AKNS) scheme and the corresponding Darboux transformation is constructed to derive the soliton solution. One and two soliton solutions are generated. Using two soliton solutions of 3 CNLS equation, nonlinear tunneling of soliton for both with and without exponential background has been discussed. Finally cascade compression of optical soliton through multi-nonlinear barrier has been discussed. The obtained results may have promising applications in all-optical devices based on optical solitons, study of soliton propagation in birefringence fiber systems and optical soliton with distributed dispersion and nonlinearity management.

  4. Parametric autoresonant excitation of the nonlinear Schrödinger equation.

    PubMed

    Friedland, L; Shagalov, A G

    2016-10-01

    Parametric excitation of autoresonant solutions of the nonlinear Schrodinger (NLS) equation by a chirped frequency traveling wave is discussed. Fully nonlinear theory of the process is developed based on Whitham's averaged variational principle and its predictions verified in numerical simulations. The weakly nonlinear limit of the theory is used to find the threshold on the amplitude of the driving wave for entering the autoresonant regime. It is shown that above the threshold, a flat (spatially independent) NLS solution can be fully converted into a traveling wave. A simplified, few spatial harmonics expansion approach is also developed for studying this nonlinear mode conversion process, allowing interpretation as autoresonant interaction within triads of spatial harmonics.

  5. Proposal for detection of QED vacuum nonlinearities in Maxwell's equations by the use of waveguides.

    PubMed

    Brodin, G; Marklund, M; Stenflo, L

    2001-10-22

    We present a novel method for detecting nonlinearities, due to quantum electrodynamics through photon-photon scattering, in Maxwell's equation. The photon-photon scattering gives rise to self-interaction terms which are similar to the nonlinearities due to the polarization in nonlinear optics. These self-interaction terms vanish in the limit of parallel propagating waves, but if, instead of parallel propagating waves, the modes generated in waveguides are used, there will be a nonzero total effect. Based on this idea, we calculate the nonlinear excitation of new modes and estimate the strength of this effect. Furthermore, we suggest a principal experimental setup.

  6. Exact Solutions of Atmospheric (2+1)-Dimensional Nonlinear Incompressible Non-hydrostatic Boussinesq Equations

    NASA Astrophysics Data System (ADS)

    Liu, Ping; Wang, Ya-Xiong; Ren, Bo; Li, Jin-Hua

    2016-12-01

    Exact solutions of the atmospheric (2+1)-dimensional nonlinear incompressible non-hydrostatic Boussinesq (INHB) equations are researched by Combining function expansion and symmetry method. By function expansion, several expansion coefficient equations are derived. Symmetries and similarity solutions are researched in order to obtain exact solutions of the INHB equations. Three types of symmetry reduction equations and similarity solutions for the expansion coefficient equations are proposed. Non-traveling wave solutions for the INHB equations are obtained by symmetries of the expansion coefficient equations. Making traveling wave transformations on expansion coefficient equations, we demonstrate some traveling wave solutions of the INHB equations. The evolutions on the wind velocities, temperature perturbation and pressure perturbation are demonstrated by figures, which demonstrate the periodic evolutions with time and space. Supported by the National Natural Science Foundation of China under Grant Nos. 11305031 and 11305106, and Training Programme Foundation for Outstanding Young Teachers in Higher Education Institutions of Guangdong Province under Grant No. Yq2013205

  7. Exact solutions to three-dimensional generalized nonlinear Schrödinger equations with varying potential and nonlinearities.

    PubMed

    Yan, Zhenya; Konotop, V V

    2009-09-01

    It is shown that using the similarity transformations, a set of three-dimensional p-q nonlinear Schrödinger (NLS) equations with inhomogeneous coefficients can be reduced to one-dimensional stationary NLS equation with constant or varying coefficients, thus allowing for obtaining exact localized and periodic wave solutions. In the suggested reduction the original coordinates in the (1+3) space are mapped into a set of one-parametric coordinate surfaces, whose parameter plays the role of the coordinate of the one-dimensional equation. We describe the algorithm of finding solutions and concentrate on power (linear and nonlinear) potentials presenting a number of case examples. Generalizations of the method are also discussed.

  8. Integrable nonlinear evolution partial differential equations in 4 + 2 and 3 + 1 dimensions.

    PubMed

    Fokas, A S

    2006-05-19

    The derivation and solution of integrable nonlinear evolution partial differential equations in three spatial dimensions has been the holy grail in the field of integrability since the late 1970s. The celebrated Korteweg-de Vries and nonlinear Schrödinger equations, as well as the Kadomtsev-Petviashvili (KP) and Davey-Stewartson (DS) equations, are prototypical examples of integrable evolution equations in one and two spatial dimensions, respectively. Do there exist integrable analogs of these equations in three spatial dimensions? In what follows, I present a positive answer to this question. In particular, I first present integrable generalizations of the KP and DS equations, which are formulated in four spatial dimensions and which have the novelty that they involve complex time. I then impose the requirement of real time, which implies a reduction to three spatial dimensions. I also present a method of solution.

  9. Finite-difference schemes for nonlinear wave equation that inherit energy conservation property

    NASA Astrophysics Data System (ADS)

    Furihata, Daisuke

    2001-09-01

    We propose two general finite-difference schemes that inherit energy conservation property from nonlinear wave equations, such as the nonlinear Klein-Gordon equation (NLKGE). One of proposed schemes is implicit and another is explicit. Many studies exist on FDSs that inherit energy conservation property from NLKGE and we can derive all of their schemes from the proposed general schemes in this paper. The most important feature of our procedure is a rigorous discretization of variational derivatives using summation by parts, which implies that the inherited properties are satisfied exactly. Because of this the derived schemes are expected to be numerically stable and yield solutions converging to PDE solutions. We make new FDSs for Fermi-Pasta-Ulam equation, string vibration equation, Shimoji-Kawai equation (SKE) and Ebihara equation and verify numerically the inheritance of the energy conservation property for NLKGE and SKE.

  10. Construction of the wave operator for non-linear dispersive equations

    NASA Astrophysics Data System (ADS)

    Tsuruta, Kai Erik

    In this thesis, we will study non-linear dispersive equations. The primary focus will be on the construction of the positive-time wave operator for such equations. The positive-time wave operator problem arises in the study of the asymptotics of a partial differential equation. It is a map from a space of initial data X into itself, and is loosely defined as follows: Suppose that for a solution ψlin to the dispersive equation with no non-linearity and initial data ψ +, there exists a unique solution ψ to the non-linear equation with initial data ψ0 such that ψ behaves as ψ lin as t → infinity. Then the wave operator is the map W+ that takes ψ + to ψ0. By its definition, W+ is injective. An important additional question is whether or not the map is also surjective. If so, then every non-linear solution emanating from X behaves, in some sense, linearly as it evolves (this is known as asymptotic completeness). Thus, there is some justification for treating these solutions as their much simpler linear counterparts. The main results presented in this thesis revolve around the construction of the wave operator(s) at critical non-linearities. We will study the "semi-relativistic" Schrodinger equation as well as the Klein-Gordon-Schrodinger system on R2 . In both cases, we will impose fairly general quadratic non-linearities for which conservation laws cannot be relied upon. These non-linearities fall below the scaling required to employ such tools as the Strichartz estimates. We instead adapt the "first iteration method" of Jang, Li, and Zhang to our setting which depends crucially on the critical decay of the non-linear interaction of the linear evolution. To see the critical decay in our problem, careful analysis is needed to treat the regime where one has spatial and/or time resonance.

  11. Nonlinear Instability of the Incoherent State for the Kuramoto-Sakaguchi-Fokker-Plank Equation

    NASA Astrophysics Data System (ADS)

    Ha, Seung-Yeal; Xiao, Qinghua

    2015-07-01

    We study the nonlinear instability of the incoherent solution to the Kuramoto-Sakaguchi-Fokker-Plank (KSFP) equation in a large coupling strength regime. For our instability analysis, we construct an approximate, exponentially growing perturbation mode using an elementary energy method. This method does not require spectral information from the linearized KSFP equation or an explicit growing solution for the corresponding linear equation. When the distribution function of oscillator's natural frequencies is either a Dirac measure or a bounded function with a compact support (in a small interval around the origin), the incoherent solution is nonlinearly unstable depending on the relative sizes of the coupling strength and diffusion coefficient.

  12. Non-linear generalization of the relativistic Schrödinger equations.

    NASA Astrophysics Data System (ADS)

    Ochs, U.; Sorg, M.

    1996-09-01

    The theory of the relativistic Schrödinger equations is further developped and extended to non-linear field equations. The technical advantage of the relativistic Schroedinger approach is demonstrated explicitly by solving the coupled Einstein-Klein-Gordon equations including a non-linear Higgs potential in case of a Robertson-Walker universe. The numerical results yield the effect of dynamical self-diagonalization of the Hamiltonian which corresponds to a kind of quantum de-coherence being enabled by the inflation of the universe.

  13. Integrability of an inhomogeneous nonlinear Schroedinger equation in Bose-Einstein condensates and fiber optics

    SciTech Connect

    Brugarino, Tommaso; Sciacca, Michele

    2010-09-15

    In this paper, we investigate the integrability of an inhomogeneous nonlinear Schroedinger equation, which has several applications in many branches of physics, as in Bose-Einstein condensates and fiber optics. The main issue deals with Painleve property (PP) and Liouville integrability for a nonlinear Schroedinger-type equation. Solutions of the integrable equation are obtained by means of the Darboux transformation. Finally, some applications on fiber optics and Bose-Einstein condensates are proposed (including Bose-Einstein condensates in three-dimensional in cylindrical symmetry).

  14. Cavity equations for a positive- or negative-refraction-index material with electric and magnetic nonlinearities.

    PubMed

    Mártin, Daniel A; Hoyuelos, Miguel

    2009-11-01

    We study evolution equations for electric and magnetic field amplitudes in a ring cavity with plane mirrors. The cavity is filled with a positive or negative-refraction-index material with third-order effective electric and magnetic nonlinearities. Two coupled nonlinear equations for the electric and magnetic amplitudes are obtained. We prove that the description can be reduced to one Lugiato-Lefever equation with generalized coefficients. A stability analysis of the homogeneous solution, complemented with numerical integration, shows that any combination of the parameters should correspond to one of three characteristic behaviors.

  15. Cavity equations for a positive- or negative-refraction-index material with electric and magnetic nonlinearities

    NASA Astrophysics Data System (ADS)

    Mártin, Daniel A.; Hoyuelos, Miguel

    2009-11-01

    We study evolution equations for electric and magnetic field amplitudes in a ring cavity with plane mirrors. The cavity is filled with a positive or negative-refraction-index material with third-order effective electric and magnetic nonlinearities. Two coupled nonlinear equations for the electric and magnetic amplitudes are obtained. We prove that the description can be reduced to one Lugiato-Lefever equation with generalized coefficients. A stability analysis of the homogeneous solution, complemented with numerical integration, shows that any combination of the parameters should correspond to one of three characteristic behaviors.

  16. Continuous Dependence on Modeling in the Cauchy Problem for Nonlinear Elliptic Equations.

    DTIC Science & Technology

    1987-04-01

    parameter 4. AMON INTRODUCTION A problem in ordinary or partial differential equations is said to properly posed if it has a unique solution in the...problem for second-order nonlinear partial differential equations , Doctoral thesis, Cornell University, Ithaca, N.Y., 1986. [6] J. Conlan and G. N. Trytten...IModeling in the Cauchy Problem for Nonlinear Elliptic Equations by Allan Bennett DT1C A z1t17n m (It C ltd n Inttt " CENTER.FOR.NAVAL.ANALYSFS 4401

  17. Analytical Approach for Nonlinear Partial Differential Equations of Fractional Order

    NASA Astrophysics Data System (ADS)

    Pradip, Roul

    2013-09-01

    The purpose of the paper is to present analytical and numerical solutions of a degenerate parabolic equation with time-fractional derivatives arising in the spatial diffusion of biological populations. The homotopy—perturbation method is employed for solving this class of equations, and the time-fractional derivatives are described in the sense of Caputo. Comparisons are made with those derived by Adomian's decomposition method, revealing that the homotopy perturbation method is more accurate and convenient than the Adomian's decomposition method. Furthermore, the results reveal that the approximate solution continuously depends on the time-fractional derivative and the proposed method incorporating the Caputo derivatives is a powerful and efficient technique for solving the fractional differential equations without requiring linearization or restrictive assumptions. The basis ideas presented in the paper can be further applied to solve other similar fractional partial differential equations.

  18. Multi-symplectic variational integrators for nonlinear Schrödinger equations with variable coefficients

    NASA Astrophysics Data System (ADS)

    Cui-Cui, Liao; Jin-Chao, Cui; Jiu-Zhen, Liang; Xiao-Hua, Ding

    2016-01-01

    In this paper, we propose a variational integrator for nonlinear Schrödinger equations with variable coefficients. It is shown that our variational integrator is naturally multi-symplectic. The discrete multi-symplectic structure of the integrator is presented by a multi-symplectic form formula that can be derived from the discrete Lagrangian boundary function. As two examples of nonlinear Schrödinger equations with variable coefficients, cubic nonlinear Schrödinger equations and Gross-Pitaevskii equations are extensively studied by the proposed integrator. Our numerical simulations demonstrate that the integrator is capable of preserving the mass, momentum, and energy conservation during time evolutions. Convergence tests are presented to verify that our integrator has second-order accuracy both in time and space. Project supported by the National Natural Science Foundation of China (Grant No. 11401259) and the Fundamental Research Funds for the Central Universities, China (Grant No. JUSRR11407).

  19. Bright and dark soliton solutions for some nonlinear fractional differential equations

    NASA Astrophysics Data System (ADS)

    Ozkan, Guner; Ahmet, Bekir

    2016-03-01

    In this work, we propose a new approach, namely ansatz method, for solving fractional differential equations based on a fractional complex transform and apply it to the nonlinear partial space-time fractional modified Benjamin-Bona-Mahoney (mBBM) equation, the time fractional mKdV equation and the nonlinear fractional Zoomeron equation which gives rise to some new exact solutions. The physical parameters in the soliton solutions: amplitude, inverse width, free parameters and velocity are obtained as functions of the dependent model coefficients. This method is suitable and more powerful for solving other kinds of nonlinear fractional PDEs arising in mathematical physics. Since the fractional derivatives are described in the modified Riemann-Liouville sense.

  20. Nonlinear heat conduction equations with memory: Physical meaning and analytical results

    NASA Astrophysics Data System (ADS)

    Artale Harris, Pietro; Garra, Roberto

    2017-06-01

    We study nonlinear heat conduction equations with memory effects within the framework of the fractional calculus approach to the generalized Maxwell-Cattaneo law. Our main aim is to derive the governing equations of heat propagation, considering both the empirical temperature-dependence of the thermal conductivity coefficient (which introduces nonlinearity) and memory effects, according to the general theory of Gurtin and Pipkin of finite velocity thermal propagation with memory. In this framework, we consider in detail two different approaches to the generalized Maxwell-Cattaneo law, based on the application of long-tail Mittag-Leffler memory function and power law relaxation functions, leading to nonlinear time-fractional telegraph and wave-type equations. We also discuss some explicit analytical results to the model equations based on the generalized separating variable method and discuss their meaning in relation to some well-known results of the ordinary case.