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1.
    
Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.  相似文献   

2.
    
Numerous DNA biosensor platforms developed in the last decades rely on DNA electrostatics as the basis for detection. However, the overwhelming number of theoretical studies and computational models of DNA electrostatics poses a barrier to leveraging our deeper mechanistic understanding in this area for the development of new technologies that will push the field towards more sensitive, quantitative, and reliable DNA-based sensors. In this review, we will bridge the gap between the theory and applications of DNA charge and electrical surfaces to overcome this barrier. We will discuss key theories such as Manning's counterion condensation theory, the Poisson-Boltzmann equation, and the Gouy-Chapman model, and provide examples of technological applications that rely on these theories.  相似文献   

3.
    
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 (?rf) of the electrostatic potential (?), eliminating the charge‐induced singularities in ?. CPB can also use a least‐squares reconstruction method to improve estimates of ? 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 ? 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. © 2014 Wiley Periodicals, Inc.  相似文献   

4.
    
Based on extended Langmuir's method on the dressed micelles, approximate expressions for the calculation of interfacial tension and electrostatic free energy of spherical ionic micelles with high surface potentials have been presented. These expressions are derived from nonlinear Poisson‐Boltzmann equation. The present formulae for the calculation of interfacial tension and electrostatic free energy of spherical ionic micelles are in quite good agreement with Hayter's results.  相似文献   

5.
    
A simpler expression of the surface charge density/surface potential relationship for spherical reverse micelles is obtained. In order to illustrate its application the approximate solution was used to calculate the thermodynamic characteristics and adsorption excesses. The approximate solution is based on the extended Langmuir's approach to the Poisson‐Boltzmann equation. The solutions for spherical reverse micelle are quite accurate provided that their radius and surface charge density are relatively larger. It is anticipated that this solution will be much easier to use in applications.  相似文献   

6.
We propose a numerical procedure for the calculation of the electrostatic repulsion force between two identical, parallel surfaces immersed in anab electrolyte solution. These surfaces are coated with an ion-penetrable membrane carrying fixed charges. The amount of fixed charges is governed by the dissociation of the functional groups in the membrane phase. The effect of pH on the degree of dissociation of these functional groups is taken into account. The difficulty of extensive use of Jacobi elliptic function in the numerical treatment of Poisson-Boltzmann equation can be circumvented by resorting to the present algorithm.  相似文献   

7.
    
The Gauss transform of Slater‐type orbitals is used to express several types of molecular integrals involving these functions in terms of simple auxiliary functions. After reviewing this transform and the way it can be combined with the shift operator technique, a master formula for overlap integrals is derived and used to obtain multipolar moments associated to fragments of two‐center distributions and overlaps of derivatives of Slater functions. Moreover, it is proved that integrals involving two‐center distributions and irregular harmonics placed at arbitrary points (which determine the electrostatic potential, field and field gradient, as well as higher order derivatives of the potential) can be expressed in terms of auxiliary functions of the same type as those appearing in the overlap. The recurrence relations and series expansions of these functions are thoroughly studied, and algorithms for their calculation are presented. The usefulness and efficiency of this procedure are tested by developing two independent codes: one for the derivatives of the overlap integrals with respect to the centers of the functions, and another for derivatives of the potential (electrostatic field, field gradient, and so forth) at arbitrary points. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008  相似文献   

8.
    
Continuum solvent models, particularly those based on the Poisson‐Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one‐sided and two‐sided methods with both first‐order and second‐order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one‐dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface‐to‐atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second‐order methods, including the one‐dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one‐dimensional method is far more efficient than standard second‐order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc.  相似文献   

9.
    
In this article, an approximate expression for the calculation of surface potential for spherical ionic micelles has been presented. This simple analytic form overcomes the complexity of original theory. The calculated values of surface potential of spherical ionic micelles are in quite good agreement with the exact numerical values of nonlinear Poisson‐Boltzmann equation.  相似文献   

10.
多电解质溶液中带电胶体粒子的电势分布由球形Poisson-Boltzmann方程(PBE)描述.PBE是一个非线性的微分方程,且难以求得其解析解.本文采用非线性P-B积分方程,计算电势分布的数值解.首先,根据静电场和热力学系统中的物理定理,导出描述电势分布的P-B积分方程(PBIE);其次,用迭代方法求PBIE的数值解.最后,计算了在3-1型电解液中无量纲半径κa分别为0.12和0.22,无量纲表面电势ξ分别为1,2,4,6时球形胶体粒子外部的电势值.为了检验数值解的精度,计算了表面电荷密度,并与Loeb(1961)和Oshima(1995)等人的结果比较,本文结果的相对误差小于1%,优于Oshima的结果.  相似文献   

11.
    
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.  相似文献   

12.
    
Efficient quantum chemical calculations of electrostatic properties, namely, the electron density (EDN), electrostatic potential (ESP), and electric field (EFL), were performed using the fragment molecular orbital (FMO) method. The numerical errors associated with the FMO scheme were examined at the HF, MP2, and RI‐MP2 levels of theory using 4 small peptides. As a result, the FMO errors in the EDN, ESP, and EFL were significantly smaller than the magnitude of the electron correlation effects, which indicated that the FMO method provides sufficiently accurate values of electrostatic properties. In addition, an attempt to reduce the computational effort was proposed by combining the FMO scheme and a point charge approximation. The error due to this approximation was examined using 2 proteins, prion protein and human immunodeficiency virus type 1 protease. As illustrative examples, the ESP values at the molecular surface of these proteins were calculated at the MP2 level of theory.  相似文献   

13.
    
Many types of molecular integrals involving Slater functions can be expressed, with the ζ‐function method in terms of sets of one‐dimensional auxiliary integrals whose integrands contain two‐range functions. After reviewing the properties of these functions (including recurrence relations, derivatives, integral representations, and series expansions), we carry out a detailed study of the auxiliary integrals aimed to facilitate both the formal and computational applications of the ζ‐function method. The usefulness of this study in formal applications is illustrated with an example. The high performance in numerical applications is proved by the development of a very efficient program for the calculation of two‐center integrals with Slater functions corresponding to electrostatic potential, electric field, and electric field gradient. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006  相似文献   

14.
    
CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery.  相似文献   

15.
    
Determining the position and magnitude of Surface Site Interaction Points (SSIP) is a useful technique for understanding intermolecular interactions. SSIPs have been used for the prediction of solvation properties and for virtual co‐crystal screening. To determine the SSIPs for a molecule, the Molecular Electrostatic Potential Surface (MEPS) is first calculated using ab initio methods such as Density Functional Theory. This leads to a high cost in terms of computation time and is not compatible with the analysis of huge molecular databases. Herein, we present a method for the fast estimation of SSIPs, which is based on the MEPS calculated from MMFF94 atomic partial charges. The results show that this method can be used to calculate SSIPs for large molecular databases with a much higher speed than the original ab initio methodology. © 2017 Wiley Periodicals, Inc.  相似文献   

16.
    
Calibration method of atomic multipole moments (AMMs) is presented with respect to geometries of all-siliceous zeolite models obtained with X-ray diffraction (XRD) methods. Mulliken atomic charges and AMMs are calculated for all-siliceous types possessing small size elementary unit cells at the hybrid density functional theory (DFT) (B3LYP) and general gradient approximation (GGA) Perdew-Burke-Ernzerhof (PBE) levels and then used to fit the dependences versus geometry variables for the Mulliken charges and versus special coordinate for the AMMs. Fitted and exact charges and AMMs are used to compute electrostatic potential (EP) and electric field (EF) for all-siliceous zeolites with CRYSTAL. A possibility of application of the point AMMs to quantum mechanical/molecular mechanics computations or classic simulation of physical adsorption is evaluated. The considered models expand over wide range of structural parameters and could be applied even to amorphous all-siliceous systems.  相似文献   

17.
Recently, great progress has been achieved in development of a wide variety of formulations for gene delivery in vitro and in vivo, which include lipids, peptides and DNA (LPD). Additionally, application of natural histone–DNA complexes (chromatin) in combination with transfection lipids has been suggested as a potential route for gene delivery (chromofection). However, the thermodynamic mechanisms responsible for formation of the ternary lipid–peptide–DNA supramolecular structures have rarely been analyzed. Using recent experimental studies on LPD complexes (including mixtures of chromatin with cationic lipids) and general polyelectrolyte theory, we review and analyze the major determinants defining the internal structure, particle composition and size, surface charge and ultimately, transfection properties of the LPD formulations.  相似文献   

18.
A molecular thermodynamic model for polyelectrolyte systems—called pePC-SAFT—is proposed. The effect of charged monomers within the polyelectrolyte chain is explicitly taken into account in the reference term by replacing the hard-chain contribution of the PC-SAFT model by a charged-hard-chain contribution. Moreover, counterion condensation is accounted for to determine the effective number of charges along the polyion as well as of free counterions. The electrostatic contribution of the free counterions is described by a Debye–Hückel term.  相似文献   

19.
More than one century ago, Lippmann found that capillary forces can be effectively controlled by external electrostatic forces. As a simple example, by applying a voltage between a conducting liquid droplet and the surface it is sitting on we are able to adjust the wetting angle of the drop. Since Lippmann's findings, electrocapillary phenomena – or electrowetting – have developed into a series of tools for manipulating microdroplets on solid surfaces, or small amounts of liquids in capillaries for microfluidic applications. In this article, we briefly review some recent progress of fundamental understanding of electrowetting and address some still unsolved issues. Specifically, we focus on static and dynamic electrowetting. In static electrowetting, we discuss some basic phenomena found in DC and AC electrowetting, and some theories about the origin of contact angle saturation. In dynamic electrowetting, we introduce some studies about this rather recent area. At last, we address some other capillary phenomena governed by electrostatics and we give an outlook that might stimulate further investigations on electrowetting.  相似文献   

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