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.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074970 | PMC |
| http://dx.doi.org/10.1155/2014/560987 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Analytical Solutions for Electroosmotic Flow and Heat Transfer Characteristics of Nanofluids in Circular Cylindrical Microchannels with Slip-Dependent Zeta Potential Considering Thermal Radiative Effects.
Micromachines (Basel)
January 2025
School of Mechanical Engineering and Rail Transit, Changzhou University, Changzhou 213164, China.
This study analyzes the impact of slip-dependent zeta potential on the heat transfer characteristics of nanofluids in cylindrical microchannels with consideration of thermal radiation effects. An analytical model is developed, accounting for the coupling between surface potential and interfacial slip. The linearized Poisson-Boltzmann equation, along with the momentum and energy conservation equations, is solved analytically to obtain the electrical potential field, velocity field, temperature distribution, and Nusselt number for both slip-dependent (SD) and slip-independent (SI) zeta potentials.
View Article and Find Full Text PDFVDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model.
J Comput Chem
January 2025
Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA.
Voltage-dependent anion channel (VDAC) is the primary conduit for regulated passage of ions and metabolites into and out of a mitochondrion. Calculating the solvation free energy for VDAC is crucial for understanding its stability, function, and interactions within the cellular environment. In this article, numerical schemes for computing the total solvation free energy for VDAC-comprising electrostatic, ideal gas, and excess free energies plus the nonpolar energy-are developed based on a nonuniform size modified Poisson-Boltzmann ion channel (nuSMPBIC) finite element solver along with tetrahedral meshes for VDAC proteins.
View Article and Find Full Text PDFConstrained Heterogeneous CoFeO/ZnO/PMS Fenton-Like System for Industrial Wastewater Remediation with Recyclability and Zero Metal Loss.
Angew Chem Int Ed Engl
December 2024
Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
Although heterogeneous Fenton-like processes have attracted widespread attention in wastewater treatment, the mass leached active ions lead to secondary pollution and confuse the demarcation of reaction region. By constructing a constrained completely heterogeneous system and highlighting its reaction region concentrated within the slipping plane of particles, this work achieves efficient organic pollutants degradation without leaching of any free active metal components. Based on the Poisson-Boltzmann equation and electric double layer model, the specific existing of the constrained region is confirmed, and this neglected reaction region between solid interface and slipping plane in traditional heterogeneous Fenton-like reaction is clarified firstly.
View Article and Find Full Text PDFElectrokinetic Power-Series Solution in Narrow Cylindrical Capillaries for All Zeta Potentials.
Electrophoresis
December 2024
Department of Mechanical & Aerospace Engineering, School of Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
Work from Rice and Whitehead showed the results of electrokinetic flow in a capillary tube under the assumption of low zeta potential 25 mV, limiting the approximation's usability. Further research conducted by Philip and Wooding provided an alternative solution that assumes high zeta potentials 25 mV and relies on Rice and Whitehead's solution for lower ranges. However, this solution is presented as a piecewise function, where the functions change based on the zeta potential and the parameter, introducing infinite values for the zeta potential and discontinuities in the derived functions.
View Article and Find Full Text PDFFrom Implicit to Explicit: An Interaction-Reorganization Approach to Molecular Solvation Energy.
J Chem Theory Comput
December 2024
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
Accurate calculation of solvation energies has long fascinated researchers, but complex interactions within bulk water molecules pose significant challenges. Currently, molecular solvation energy calculations are mostly based on implicit solvent approximations in which the solvent molecules are treated as continuum dielectric media. However, the implicit solvent approach is not ideal because it lacks certain real solvation effects, such as that of the first solvation shell, etc.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!