Grid‐based algorithm to search critical points,in the electron density,accelerated by graphics processing units

Using a grid‐based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for high‐performance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single‐precision is used. © 2014 Wiley Periodicals, Inc.     

Conformational Preferences of trans-1,2- and cis-1,3-Cyclohexanedicarboxylic Acids in Water and Dimethyl Sulfoxide as a Function of the Ionization State As Determined from NMR Spectroscopy and Density Functional Theory Quantum Mechanical Calculations

The populations of diaxial (aa) and diequatorial (ee) conformers of trans-1,2- and cis-1,3-cyclohexanedicarboxylic acids (CDCAs; 1 and 2, respectively) and their salts were determined in water and dimethyl sulfoxide (DMSO) solutions from vicinal proton-proton NMR J couplings ((3)J(HH)). Optimized geometries and free energies for these compounds were obtained at the M06-2X/cc-pVTZ(-f)++ level. Although carboxylic acid groups in cyclohexane rings are generally believed to be far more stable (～2 kcal/mol) in equatorial than axial positions, this investigation demonstrated that an aa conformation (normally assumed to be completely insignificant for these compounds) can be favored depending on the medium and ionization state: strong ee preferences (>90%) were observed in water and DMSO for both diacids and their salts, except for the dianion of 1 in DMSO, which was found to be substantially aa (～57%). The possibility of intramolecular hydrogen bonding (H-bonding) was also investigated; the ratios of the ionization constants (K(1)/K(2)) indicated an absence of intramolecular H-bonding because K(1)/K(2) ? 10(4) (a standard criterion for non-H-bonding in dicarboxylic acids) for both 1 and 2 in water and also for 2 in DMSO. For 1, K(1)/K(2) increased drastically in DMSO (K(1)/K(2) = 4 × 10(6)), where (3)J(HH) and the ratio K(1)/K(E) = 10, K(E) being the acidity constant of the monomethyl ester of 1, indicated the formation of an intramolecular H-bond for the monoanion in this solvent. An explanation for the observation of compact dianions in solution in terms of the generalized Born equation is also provided.     

Chemical hardness and the discontinuity of the Kohn-Sham exchange-correlation potential

Chemical hardness, identified as the difference between the vertical first ionization potential I and the vertical electron affinity A, is analyzed in the context of the ionization theorems to derive expressions for its evaluation at different levels of approximation that arise as a direct consequence of the derivative discontinuity of the exchange-correlation potential. The quantities involved in these expressions incorporate indirectly the effects of the discontinuity, but their values may be calculated with any functional of the local density approximation, generalized gradient approximation, or optimized effective potential type, with or without derivative discontinuity, and with or without the correct asymptotic behavior. By comparison with the vertical energy difference values of I and A, which requires the calculation of the N-, (N-1)-, and (N+1)-electron systems, it is found, for a set of 14 closed shell molecules, that the difference between the eigenvalues of the highest occupied molecular orbitals of the N- and (N+1)-electron systems leads to rather accurate values, when the correct asymptotic behavior is incorporated, and that a second-order one-body perturbation approach that only requires information from the N-electron system leads to reasonable values.     

The Kohn-Sham kinetic energy density as indicator of the electron localization: atomic shell structure

In this report, it is shown that the Kohn-Sham (KS) kinetic energy density (KED) contains the average local electrostatic potential (ALEP) and the average local ionization energy (ALIE); the shell structure in atomic systems is presented as one application of the KS-KED. By writing the KS-KED from the KS equations, this quantity was divided in three contributions: orbital, Coulomb, and exchange correlation. By studying several closed and open shell atoms, the shell structure was established by the maxima presented by the Coulomb contribution and the minima in the orbital contribution of the KS-KED. The exchange-correlation contribution to the KS-KED does not show maxima or minima, but this quantity shows bumps where the division between shells is expected. The results obtained in this work were compared with other shell structure indicators such as the electron localization function, the ALEP, the ALIE, and the radial distribution function. The most important result in this work is related to the fact that even when the ALEP and the ALIE functions were built with different arguments to each other, they are contained in the KS-KED. In this way, the KS-KED shows its importance to reveal the electron localization in atomic systems.     

GridMass: a fast two‐dimensional feature detection method for LC/MS

One of the initial and critical procedures for the analysis of metabolomics data using liquid chromatography and mass spectrometry is feature detection. Feature detection is the process to detect boundaries of the mass surface from raw data. It consists of detected abundances arranged in a two‐dimensional (2D) matrix of mass/charge and elution time. MZmine 2 is one of the leading software environments that provide a full analysis pipeline for these data. However, the feature detection algorithms provided in MZmine 2 are based mainly on the analysis of one‐dimension at a time. We propose GridMass, an efficient algorithm for 2D feature detection. The algorithm is based on landing probes across the chromatographic space that are moved to find local maxima providing accurate boundary estimations. We tested GridMass on a controlled marker experiment, on plasma samples, on plant fruits, and in a proteome sample. Compared with other algorithms, GridMass is faster and may achieve comparable or better sensitivity and specificity. As a proof of concept, GridMass has been implemented in Java under the MZmine 2 environment and is available at http://bioinformatica.mty.itesm.mx/GridMass and MASSyPup. It has also been submitted to the MZmine 2 developing community. Copyright © 2015 John Wiley & Sons, Ltd.     

非平衡态/不可逆过程的热力学理论(Ⅱ)

<正> 7 解的唯一性 如果不考虑非平衡态和不可逆性,则等能密度理论中的基本命题与经典弹性理论中的在形式上完全相同。无论整个系统的动能是大还是小,图6中(sumform)_o上的面力T_i和在(sumform)_c和在的位移u_i将始终在空间坐标系x_i和时刻i下给出。与一般力学中相同,必须知道有关位移u_i及其时间导数的初始条件。它们的影响则可通过(38)和(39)向等能面转化,从而得到