Electrophoretic behavior of cerebellar granule neurons

The electrophoresis of cerebellar granule neurons is observed, and a theoretical model proposed to simulate its electrophoretic behavior. We assume that the surface of a neuronal cell carries dissociable acidic functional groups, and the liquid phase contains a mixed (a:b) + (c:b) electrolyte, where a and c are the valences of cations and b is the valence of anions. The cations of valence c are allowed to bind to dissociated functional groups. The model proposed is readily applicable to the prediction of the surface properties of cerebellar granule neurons such as the density of dissociable functional groups and the equilibrium constant of the dissociation reaction. The applicability of the present model is justified by fitting it to the measured electrophoretic mobility data.     

First principles potential for the acetylene dimer and refinement by fitting to experiments

We report the definition and refinement of a new first principles potential for the acetylene dimer. The ab initio calculations were performed with the DFT-SAPT combination of symmetry-adapted intermolecular perturbation method and density functional theory, and fitted to a model site-site functional form. Comparison of the calculated microwave spectrum with experimental data revealed that the barriers to isomerization were too low. This potential was refined by fitting the model parameters in order to reproduce the observed transitions, an excellent agreement within ~1 MHz being achieved.     

Poisson-transformed density fitting in relativistic four-component Dirac-Kohn-Sham theory

We present recent developments in the implementation of the density fitting approach for the Coulomb interaction within the four-component formulation of relativistic density functional theory [Belpassi et al., J. Chem. Phys. 124, 124104 (2006)]. In particular, we make use of the Poisson equation to generate suitable auxiliary basis sets and simplify the electron repulsion integrals [Manby and Knowles, Phys. Rev. Lett. 87, 163001 (2001)]. We propose a particularly simple and efficient method for the generation of accurate Poisson auxiliary basis sets, based on already available standard Coulomb fitting sets. Just as is found in the nonrelativistic case, we show that the number of standard auxiliary fitting functions that need to be added to the Poisson-generated functions in order to achieve a fitting accuracy equal or, in some cases, better than that of the standard procedure is remarkably small. The efficiency of the present implementation is demonstrated in a detailed study of the spectroscopic properties and energetics of several gold containing systems, including the Au dimer and the CsAu molecule. The extraction reaction of a H(2)O molecule from a Au(H(2)O)(9) (+) cluster is also calculated as an example of mixed heavy-light-atom molecular systems. The scaling behavior of the algorithm implemented is illustrated for some closed shell gold clusters up to Au(5) (+). The increased sparsity of the Coulomb matrices involved in the Poisson fitting is identified, as are potential computational applications and the use of the Poisson fitting for the relativistic exchange-correlation problem.     

Initial steps toward automating the fitting of DFTB Erep(r)

The most time-consuming part of developing new parametrizations for the density functional based tight-binding (DFTB) method consists of producing accurate and transferable repulsive pair potentials. In the conventional approach to repulsive parametrization, every possible diatomic combination of the elements covered by the parametrization must be individually hand-constructed. We present an initial attempt to automate some of this time-consuming process. We consider a simple genetic algorithm-based approach to the fitting problem.     

Analytic derivatives for the Cholesky representation of the two-electron integrals

We propose a formalism for calculating analytic derivatives of the electronic energy with respect to nuclear coordinates using Cholesky decomposition of the two-electron integrals. The formalism is derived by exploiting the equivalence of Cholesky decomposition and density fitting when a suitable auxiliary basis set is used for expanding atomic orbital product densities in the latter. An implementation of gradients at the nonhybrid density functional theory level is presented, and sample calculations demonstrate that the errors in equilibrium geometries due to the Cholesky representation of the integrals can be controlled by adjusting the decomposition threshold.     

Efficient parametrization of complex molecule–surface force fields

We present an efficient scheme for parametrizing complex molecule–surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. © 2015 Wiley Periodicals, Inc.     

Application of water-activated carbon isotherm models to water adsorption isotherms of single-walled carbon nanotubes

The objective of this study is to understand the interactions of water with novel nanocarbons by implementing semiempirical models that were developed to interpret adsorption isotherms of water in common carbonaceous adsorbents. Water adsorption isotherms were gravimetrically determined on several single-walled carbon nanotube (SWNT) and activated carbon samples. Each isotherm was fitted to the Dubinin-Serpinsky (DS) equation, the Dubinin-Astakov equation, the cooperative multimolecular sorption theory, and the Do and Do equations. The applicability of these models was evaluated by high correlation coefficients and the significance of fitting parameters, especially those that delineate the concentration of hydrophilic functional groups, micropore volume, and the size of water clusters. Samples were also characterized by spectroscopic and adsorption techniques, and properties complementary to those quantified by the fitting parameters were extracted from the data collected. The comparison of fitting parameters with sample characterization results was used as the methodology for selecting the most informative and the best-fitting model. We conclude that the Do equation, as modified by Marban et al., is the most suitable semiempirical equation for predicting from experimental isotherms alone the size of molecular clusters that facilitate adsorption in SWNTs, deconvoluting the experimental isotherms into two subisotherms: adsorption onto hydrophilic groups and filling of micropores, and quantifying the concentration of hydrophilic functional groups, as well as determining the micropore volume explored by water. With the exception of the DS equation, the application of other water isotherm models to SWNTs is not computationally tractable. The findings from this research should aid studies of water adsorption in SWNTs by molecular simulation, which remains the most popular tool for understanding the microscopic behavior of water in nanocarbons.     

Approximate electric potentials

It is shown that the electrostatic energy functional is the only one available for fitting a given potential using approximate electric potentials arising from point charges. The significance of this fitting is examined in terms of splines. To illustrate the method the electron densities of atoms are modelled using point charges at the vertices of tetrahedra and of cubes.     

Hierarchical modeling of ammonia adsorption in functionalized metal-organic frameworks

The adsorption of ammonia in four metal-organic frameworks modified with different functional groups (-OH, -C=O, -Cl, -COOH) was investigated using a hierarchical molecular modeling approach. To describe the hydrogen bonding and other strong interactions between NH(3) and the surface functional groups, a set of Morse potential parameters were obtained by fitting to energies from quantum chemical calculations at the MP2 level of theory. We describe a systematic force field parameterization process, in which the Morse parameters were fitted using simulated annealing to match a large number of single-point MP2 energies at various distances and angles. The fitted potentials were then used in grand canonical Monte Carlo simulations to predict ammonia adsorption isotherms and heats of adsorption in functionalized MIL-47, IRMOF-1, IRMOF-10, and IRMOF-16. The results show that ammonia adsorption can be significantly enhanced by using materials with appropriate pore size, strongly interacting functional groups, and high density of functional groups.     

Six-dimensional potential energy surface of the dissociative chemisorption of HCl on Au(111) using neural networks

We constructed a six-dimensional potential energy surface(PES)for the dissociative chemisorption of HCl on Au(111)using the neural networks method based on roughly 70000 energies obtained from extensive density functional theory(DFT)calculations.The resulting PES is accurate and smooth,based on the small fitting errors and good agreement between the fitted PES and the direct DFT calculations.Time-dependent wave packet calculations show that the potential energy surface is very well converged with respect to the number of DFT data points,as well as to the fitting process.The dissociation probabilities of HCl initially in the ground rovibrational state from six-dimensional quantum dynamical calculations are quite diferent from the four-dimensional fixed-site calculations,indicating it is essential to perform full-dimensional quantum dynamical studies for the title molecule-surface interaction system.     

Inferring biomolecular interaction networks based on convex optimization

We present an optimization-based inference scheme to unravel the functional interaction structure of biomolecular components within a cell. The regulatory network of a cell is inferred from the data obtained by perturbation of adjustable parameters or initial concentrations of specific components. It turns out that the identification procedure leads to a convex optimization problem with regularization as we have to achieve the sparsity of a network and also reflect any a priori information on the network structure. Since the convex optimization has been well studied for a long time, a variety of efficient algorithms were developed and many numerical solvers are freely available. In order to estimate time derivatives from discrete-time samples, a cubic spline fitting is incorporated into the proposed optimization procedure. Throughout simulation studies on several examples, it is shown that the proposed convex optimization scheme can effectively uncover the functional interaction structure of a biomolecular regulatory network with reasonable accuracy.     

B2-PPW91: a promising double-hybrid density functional for the electric response properties

A new double-hybrid density functional, termed B2-PPW91, is presented which includes the Becke88 (B88) exchange in conjunction with Perdew-Wang91 (PW91) gradient-corrected correlation functional. The fitting parameters are obtained by minimization of mean absolute error of the static dipole polarizability of 4d transition metal monohalides against the CCSD(T)∕aug-cc-pVTZ∕SDD results. The performance of proposed functional has been assessed for estimation of other response properties, such as dipole moment and excitation energy, for the same species. We then proceed to explore the validity of B2-PPW91 method for calculation of the dipole polarizability of some 5d transition metal monofluorides. In all cases, the improvement compared to common density functional methods and even previously reported double-hybrid functionals such as B2-PLYP and mPW2-PLYP has been observed. This indicates that the utility of double-hybrid density functional methods can be further extended to study linear and non-linear optical properties of transition metal containing molecules.     

Global fitting without a global model: regularization based on the continuity of the evolution of parameter distributions

We introduce a new approach to global data fitting based on a regularization condition that invokes continuity in the global data coordinate. Stabilization of the data fitting procedure comes from probabilistic constraint of the global solution to physically reasonable behavior rather than to specific models of the system behavior. This method is applicable to the fitting of many types of spectroscopic data including dynamic light scattering, time-correlated single-photon counting (TCSPC), and circular dichroism. We compare our method to traditional approaches to fitting an inverse Laplace transform by examining the evolution of multiple lifetime components in synthetic TCSPC data. The global regularizer recovers features in the data that are not apparent from traditional fitting. We show how our approach allows one to start from an essentially model-free fit and progress to a specific model by moving from probabilistic to deterministic constraints in both Laplace transformed and nontransformed coordinates.     

Interatomic Potentials for NiZr Alloys from Experimental and Ab initio Calculations

Interatomic Potentials for NiZr Alloys from Experimental and Ab initio Calculations~~Supported by the National Natural Science Foundation of China(No.2 9892 16 6 ,2 980 30 0 6 ,2 99830 0 1)     

Analytical carbon-oxygen reactive potential

We present a reactive empirical potential with environment-dependent bond strengths for the carbon-oxygen (CO) system. The distinct feature of the potential is the use of three adjustable parameters characterizing the bond: the strength, length, and force constant, rather than a single bond order parameter, as often employed in these types of potentials. The values of the parameters are calculated by fitting results obtained from density functional theory. The potential is tested in a simulation of oxidative unzipping of graphene sheets and carbon nanotubes. Previous higher-level theoretical predictions of graphene unzipping by adsorbed oxygen atoms are confirmed. Moreover, nanotubes with externally placed oxygen atoms are found to unzip much faster than flat graphene sheets.     

Optimal charge and charge response determination through conformational space: global fitting scheme for representative charge and charge response kernel

We propose a global fitting scheme derived in the least-squares sense to estimate the optimal partial charge and charge response kernel (CRK), partial differential(Q(a))/partial differential(V(b)), with the data collected from conformational space sampling. We applied the global fitting method to the 1-butanol system and show the performance and accuracy of our global fitting procedure. In addition, we chose 1-pentanol as the test system for electronic structure change through conformational change and applied the global fitting method to it. From our study, it is indicated that intramolecular polarization can be influenced by intramolecular hydrogen bonding, and it is shown that our global fitting method can correspond to such a situation. Also, the global fitting procedure was tested on a large molecular system, 1-dodecanol. We show the results of the application of our fitting method for the system needed to sample large sets of data over a large conformational space. It is indicated that the nonlocality in intramolecular polarization in the alkyl chain sequence can be observed and that the large fluctuation of CRKs through nonbonded interactions such as intramolecular hydrogen bonding, as seen in the 1-pentanol case, can appear in common. The global fitting scheme we propose can be used for building molecular models considering polarization effects explicitly, even in the case of target systems that include many conformers.     

A new parameter-free correlation functional based on an average atomic reduced density gradient analysis

A new parameter-free correlation functional based on the local Ragot-Cortona approach [J. Chem. Phys. 121, 7671 (2004)] is presented. This functional rests on a single ansatz for the gradient correction enhancement factor: it is assumed to be given by a simple analytic expression satisfying some exact conditions and containing two coefficients. These coefficients are determined without implementing the functional and without using a fitting procedure to experimental data. Their values are determined by requiring that the functional gives a correct average reduced density gradient for atoms, which, to some extent, can be considered an intrinsic atomic property. The correlation functional is then coupled with the Perdew-Burke-Erzernhof (PBE) exchange and compared with the original PBE approach as well as with some other pure density or hybrid approaches. Standard tests for atomic and molecular systems show that our new functional significantly improves on PBE, showing very interesting properties.     

Ab initio parametrized polarizable force field for rutile-type SnO<Subscript>2</Subscript>

We report a new, polarizable classical force field for the rutile-type phase of SnO₂, casserite. This force field has been parametrized using results from ab initio (density functional theory) calculations as a basis for fitting. The force field was found to provide structural, dynamical and thermodynamic properties of tin oxide that compare well with both ab initio and experimental results at ambient and high pressures.