scholarly journals SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Yi Jiang ◽  
Yang Xie ◽  
Jinyong Ying ◽  
Dexuan Xie ◽  
Zeyun Yu
Keyword(s):  
Continuum Model ◽  
Scientific Community ◽  
Web Server ◽  
Implicit Solvent ◽  
Poisson Boltzmann ◽  
Finite Difference Solution ◽  
Ionic Solvent ◽  
Poisson Boltzmann Equation ◽  
User Friendly ◽  
The Web

AbstractThe Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present an SDPBS web server in this paper that allows clients to visualize and manipulate the molecular structure of a biomolecule, and to calculate PBE solutions in a remote and user friendly fashion. The web server is available on the website https://lsextrnprod.uwm.edu/electrostatics/.

scholarly journals A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications

2014 ◽  
Vol 2 (1) ◽  
pp. 86-97 ◽  
Author(s):  
Dexuan Xie ◽  
Yi Jiang ◽  
Jinyong Ying
Keyword(s):  
Finite Element ◽  
Boltzmann Equation ◽  
Continuum Model ◽  
Numerical Algorithms ◽  
Implicit Solvent ◽  
Numerical Comparison ◽  
Test Model ◽  
Comparison Study ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Abstract The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.

scholarly journals Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules

2014 ◽  
Vol 2 (1) ◽  
pp. 107-127 ◽  
Author(s):  
Duan Chen
Keyword(s):  
Free Energy ◽  
Jacobian Matrix ◽  
Discontinuous Coefficients ◽  
Energy Functional ◽  
Implicit Solvent ◽  
Newton's Iteration ◽  
Solvent Model ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Dna Strand

Abstract Description of inhomogeneous dielectric properties of a solvent in the vicinity of ions has been attracting research interests in mathematical modeling for many years. From many experimental results, it has been concluded that the dielectric response of a solvent linearly depends on the ionic strength within a certain range. Based on this assumption, a new implicit solvent model is proposed in the form of total free energy functional and a quasi-linear Poisson-Boltzmann equation (QPBE) is derived. Classical Newton’s iteration can be used to solve the QPBE numerically but the corresponding Jacobian matrix is complicated due to the quasi-linear term. In the current work, a systematic formulation of the Jacobian matrix is derived. As an alternative option, an algorithm mixing the Newton’s iteration and the fixed point method is proposed to avoid the complicated Jacobian matrix, and it is a more general algorithm for equation with discontinuous coefficients. Computational efficiency and accuracy for these two methods are investigated based on a set of equation parameters. At last, the QPBE with singular charge source and piece-wisely defined dielectric functions has been applied to analyze electrostatics of macro biomolecules in a complicated solvent. A set of computational algorithms such as interface method, singular charge removal technique and the Newtonfixed- point iteration are employed to solve the QPBE. Biological applications of the proposed model and algorithms are provided, including calculation of electrostatic solvation free energy of proteins, investigation of physical properties of channel pore of an ion channel, and electrostatics analysis for the segment of a DNA strand.

scholarly journals GerminaQuant: a new tool for germination measurements

2015 ◽  
Vol 37 (3) ◽  
pp. 248-255 ◽  
Author(s):  
Felipe Rafael Ferreira Marques ◽  
Marcos Vinicius Meiado ◽  
Natália Maria Corte Real de Castro ◽  
Mariana Lins de Oliveira Campos ◽  
Keila Rêgo Mendes ◽  
...  
Keyword(s):  
Scientific Community ◽  
Seedling Emergence ◽  
Computer Software ◽  
Research Community ◽  
Ease Of Use ◽  
Output Data ◽  
C Programming Language ◽  
C Programming ◽  
User Friendly ◽  
The Web

Abstract:The seed technologies related with germination and seed research has provided unprecedented opportunities for the biologic research community. Researchers require such information to rapidly determine the speed of seedling emergence. However, an immense amount of data must be analyzed to achieve this goal. In this paper, we introduce a computer software designed for broad use to facilitate the understanding of germination processes and their analysis. GerminaQuant 1.0 was written in the C++ programming language and presents a user-friendly interface. The accuracy of the software was tested using fifty different matrices, whose output values were compared with other spreadsheets available on the web. With data analysis, we showed that the GerminaQuant is capable of generating mathematical calculations with extreme accuracy, besides have a good performance and wide ease of use in any kind of computer. In addition, the new software has been tested by at least eighty users, which compared functionality, designer and accuracy of the output data. In all variables, the GerminaQuant was evaluated as superior compared to other spreadsheets available on the web. The full GerminaQuant package (for Windows(r), Macintosh(r) and Linux(r)) is freely available to the scientific community and can be easily downloaded from the website (http://www.ufpe.br/lev).

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