Batch tautomer generation with MolTPC

Besides all their conformational degrees of freedom, drug‐like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring‐chain tautomerism. Here, we describe an adjustable fully automatic tautomer enumeration approach, which is freely available and also incorporates the detection of ring‐chain variants. The algorithm is implemented in the MolTPC framework and accessible on SourceForge. © 2013 Wiley Periodicals, Inc.     

Haplotype assembly from aligned weighted SNP fragments

Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211-213)). In this paper we show that the general WMLF model is NP-hard even for the gapless case. However the algorithmic solutions for selected variants of WMFL can exist and we propose a heuristic algorithm based on a dynamic clustering technique. We also introduce a new formulation of the haplotype assembly problem that we call COMPLETE WMLF (CWMLF). This model and algorithms for its implementation take into account a simultaneous presence of multiple kinds of data errors. Extensive computational experiments indicate that the algorithmic implementations of the CWMLF model achieve higher accuracy of haplotype reconstruction than the WMLF-based algorithms, which in turn appear to be more accurate than those based on MLF.     

Algorithmic methods of reference-line construction for estimating long-term strength of plastic pipe system

Two simple and error free methods (direct and interpolation) for obtaining mathematical models for constructing reference lines were developed and successfully applied to the hydrostatic stress-rupture data of polyethylene pipes. Both methods employed an algorithmic process that analyzed the observed stress-rupture data along with its mathematical model of the 50% regression (LTHS) line. For each method, a shift value Δc was determined and was used to obtain the mathematical model for constructing reference lines that satisfied the requirement of ISO TS 26873. That is, the reference lines so constructed accommodated at least 97.5% of all stress-rupture data points on or above this line, in addition to being parallel to and vertically shifted below the 50% regression lines by an amount Δc. In the direct method, the reference line was made to pass directly over the data point that is equal to or the first data point greater than the 97.5% data position among all data points. On the other hand, the interpolation method extracted a shift value that corresponded to the 97.5% data position by interpolating between the first data points over and below 97.5%. In this case, the reference lines were made to pass through the interpolated position of 97.5% at every temperature. The advantage of the proposed algorithmic methods is that the determination of mathematical models for reference lines only involves finding the data position(s) with a vertical shift value of Δc that satisfies the ≤97.5% requirement. With these methods, uncertainties and errors associated with the current trial and error approach for constructing reference lines can be eliminated. In this paper, the details of the algorithmic process for obtaining a proper shift value and using it to develop the mathematical model are described for each method. Also, examples of constructing reference lines using these models are illustrated for polyethylene pipes.     

A closed-loop identification protocol for nonlinear dynamical systems

A previous work introduced an optimal identification (OI) technique for reliably extracting model parameters of biochemical reaction systems from tailored laboratory experiments. The notion of optimality enters through seeking an external control in the laboratory producing data that leads to minimum uncertainties in the identified parameter distributions. A number of algorithmic and operational improvements are introduced in this paper to OI, aiming to build a more practical and efficient closed-loop identification protocol/procedure (CLIP) for nonlinear dynamical systems. The improvements in CLIP include (a) inversion cost function modification to preferably search for the upper and lower boundaries of the parameter distributions consistent with the observed data, (b) dynamic search range updating of the unknown parameters to better exploit the information from the prior iterative experiments, (c) replacing the control genetic algorithm by the simplex method to enable better balance between operational cost and inversion quality, and (d) utilizing virtual sensitivity optimization techniques to further reduce the laboratory costs. The workings of CLIP utilizing these new algorithms are illustrated in indentifying a simulated tRNA proofreading model, and the results demonstrate enhanced performance of CLIP in terms of algorithmic reliability and efficiency.     

Diffusion-controlled reactions in vinyl chloride suspension polymerization

The vinyl chloride suspension polymerization is kinetically modeled with a general approach for the independent calculation of diffusion effects on polymerization reactions. For the initiator decomposition, propagation and termination an apparent rate coefficient is determined, built up from two contributions: the intrinsic rate coefficient and a diffusional contribution. The diffusional contribution is calculated with the Smoluchowski model, the diffusion coefficients being determined from the free volume theory. When applying the free volume theory no adjustable parameters are used. The intrinsic rate coefficients are taken from the literature. Hence, a model without any adjustable parameters is obtained. Calculations show that the glass effect appears only at (very) high conversions. Due to the cage effect the initiator efficiency decreases strongly as soon as the monomer phase has disappeared. The gel effect always occurs in the polymer-rich phase and results in a decrease of the termination rate coefficient at the start of the third stage in the polymerization process. There is a good agreement with experimental results.     

Kinetics Model of Destabilization of Oil Droplets in Oily Wastewater Emulsions

In this article, a mathematical model that accounts for the kinetics of flocculation and coalescence of emulsion drops was developed to quantify the kinetics of emulsion stability. The model is similar to that developed by Borwankar et al. in 1992 with corrections in coalescence rate constant and collision efficiency factor. It includes a term to describe efficiency of collisions. Also, the coalescence rate constant was defined as a function of the total number of particles that were present in the system at the moment. The model has four adjustable parameters, and nonlinear least square optimization is used to obtain the adjustable parameters. The obtained adjustable parameters by the model served as parameters that can be used to quantitatively evaluate the effectiveness of a set of different demulsifiers by measuring total numbers of drops versus time and by determining the adjustable parameters and comparing them. The results of the presented model and the model of Borwankar et al. were compared with experimental data. The results of the new model were in good agreement with experimental data and showed the model's ability for dispalying the behavior of droplets during the destabilization processes of emulsions.     

New techniques for the analysis of fine-scaled clustering phenomena within atom probe tomography (APT) data.

Nanoscale atomic clusters in atom probe tomographic data are not universally defined but instead are characterized by the clustering algorithm used and the parameter values controlling the algorithmic process. A new core-linkage clustering algorithm is developed, combining fundamental elements of the conventional maximum separation method with density-based analyses. A key improvement to the algorithm is the independence of algorithmic parameters inherently unified in previous techniques, enabling a more accurate analysis to be applied across a wider range of material systems. Further, an objective procedure for the selection of parameters based on approximating the data with a model of complete spatial randomness is developed and applied. The use of higher nearest neighbor distributions is highlighted to give insight into the nature of the clustering phenomena present in a system and to generalize the clustering algorithms used to analyze it. Maximum separation, density-based scanning, and the core linkage algorithm, developed within this study, were separately applied to the investigation of fine solute clustering of solute atoms in an Al-1.9Zn-1.7Mg (at.%) at two distinct states of early phase decomposition and the results of these analyses were evaluated.     

空间距离在三维分子相似度计算中的应用

采用Tripos公司的MOPAC模块计算分子的空间距离,所得距离矩阵用带有约束条件的空间距离方法计算分子的相似度,同时通过4组化合物的计算,与纯空间距离方法进行比较,得到了较为满意的结果。     

Multiparametric curve fitting--V: The general program 'ABLET', a system for regression analysis in studies of solution equilibria

The general program ABLET is a system of subprograms for non-linear regression analysis of experimental data to find an appropriate model. The structure of ABLET provides a suitable organizational framework in which just two specific subroutines have to be supplied by the user. The resulting program can estimate non-linear model parameters with their standard deviations, test the agreement between experimental data and a mathematical model, test the accuracy and reliability of the parameters found, and simulate synthetic data for preselected parametric values. Heuristic, and/or algorithmic minimization strategies aid examination of the local and overall minima. The method of construction of the program for a particular system is discussed.     

Outlying Charge,Stability, Efficiency,and Algorithmic Enhancements in the Quantum‐Mechanical Solvation Method,COSab‐GAMESS

In this work, we present algorithmic modifications and extensions to our quantum‐mechanical approach for the inclusion of solvent effects by means of molecule‐shaped cavities. The theory of conductor‐like screening, modified and extended for quantum‐mechanical techniques, serves as the basis for our solvation methodology. The modified method is being referred to as COSab‐GAMESS and is available within the GAMESS package. Our previous work has emphasized the implementation of this model by way of a distributed multipole approach for handling the effects of outlying charge. The method has been enabled within the framework of open‐ and closed‐shell RHF and MP2. In the present work, we present a) a second method to handle outlying charge effects, b) algorithmic extensions to open‐ and closed‐shell density‐functional theory, second‐derivative analysis, and reaction‐path following, and c) enhancements to improve performance, convergence, and predictability. The method is now surtable for large molecular systems. New features of the enhanced continuum model are highlighted by means of a set of neutral and charged species. Computations on a series of structures with roughly the same molecular shape and volume provides an evaluation of cavitation effects.     

Surface tension correlation for pure polar fluids by a new molecular model and SRK equation of state

In this work, a new model based on molecular thermodynamic was presented to correlate the surface tension of pure polar liquids. This model was developed based on the Davis theory. According to this theory, the surface tension is defined as a function of radial distribution function (RDF) and potential function (PF) as well. The proposed model includes three additive terms; hard sphere, dispersion and polar interactions. The RDF of Kolafa equation of state and Dirac delta function as a PF were used for hard sphere interaction. The RDF expression of Xu and Hu was considered for both dispersion and polar interactions. The presented model has two adjustable parameters, size and energy, which were obtained by optimization of an objective function for each pure fluid. This proposed approach was used for 19 pure polar fluids divided into 6 groups; organic acids, alcohols, ketones, ethers, aldehydes, and water. The average absolute deviation percent (AAD%) obtained for 19 fluids are 0.74. Also the surface tension of these 19 fluids was calculated by the use of SRK EOS and Sugden empirical formula in two cases. In case 1, Sugden's Parachor was calculated from Hugill and van Welsenes correlation and in case 2, it was obtained by optimization of an objective function for each component. The values of AAD% are 43.544 and 2.281 for cases 1 and 2, respectively. These results show the new model, which includes two adjustable parameters, can correlate the surface tension of the pure polar liquids with a high accuracy.     

Calculation of pVT and vapor–liquid equilibria of copolymer systems based on an equation of state

A molecular thermodynamic model for copolymers and their mixtures has been established by adopting the hard-sphere-chain fluid as a reference and a square-well (SW) term as well as an association term as a perturbation. The latter is introduced to consider various associating functions in a chain-like molecule based on the shield-sticky model of chemical association. The model adopts five molecular parameters, i.e. r_i, σ_ii ε_ii/k, δε_ii/k and ω_ii, for a polymer species i, where the last two are responsible for association. These parameters can be obtained from the pVT data of the corresponding molten homopolymer i. The model can be used to correlate pVT data for molten copolymers with an adjustable parameter describing the interaction between different polymer species. The model can also be used to calculate vapor–liquid equilibria (VLE) for copolymer solutions with three adjustable interaction parameters.     

Nonrandom factor model for the excess Gibbs free energy of weak electrolytes including phosphoric acid

The Electrolyte Nonrandom Two Liquid-Nonrandom Factor (NRTL-NRF) model of Haghtalab and Vera was modified to determine the excess Gibbs free energy of weak electrolyte systems. The model was applied to the phosphoric acid solution as a weak and complex electrolyte. Its thermodynamic behavior was investigated in a wide range of concentration by choosing an appropriate equilibrium reaction between molecular and ionic species. The model contains four adjustable parameters which were determined using osmotic experimental data. The results of dissociation and of activity coefficients are presented separately.     

On extension of UNIQUAC-NRF model to study the phase behavior of aqueous two phase polymer–salt systems

The UNIQUAC-NRF model for aqueous two-phase polymer–polymer systems is extended to correlate liquid–liquid equilibria of aqueous polymer–salt two-phase systems. The systems investigated are polyethylene glycol+ammonium sulfate+water and polyethylene glycol+potassium monohydrogen phosphate (K₂HPO₄)+water for five molecular weights of PEG. In this model, the nonrandom state is selected as a reference state. The model has six binary adjustable parameters that were determined by an optimization program. The Debye–Huckel equation based on Fowller–Guggenheim equation is used to calculate the long-range electrostatic interaction of the ions. The results obtained by this model are in good agreement with experimental data.     

Analysis of the validity of perturbation density functional theory: based on extensive simulation for simple fluid at supercritical and subcritical temperature under various external potentials

Because of the scarcity of available simulation data for confined hard-core attractive Yukawa model fluid, extensive Monte Carlo (MC) simulation research for this fluid under the influence of various external potentials were carried out. The present MC simulation results were employed to test a performance of the third-order perturbation density functional theory (DFT) based on a high order direct correlation function (DCF) [S. Zhou and E. Ruckenstein, Phys. Rev. E. 61, 2704 (2000)]. It was found that the present perturbation DFT formalism is soundly structured only if the imported second-order DCF is reliable. In this case, the accuracy of the results can be satisfactory or even very high for various types of external potentials. Further, the associated adjustable parameter can be universal, i.e., independent of the particular external field responsible for the generation of a nonuniform density profile. Dependence of both the maintenance of the reliability of the formalism and holding of the universality of the adjustable parameter on the accuracy of the imported bulk second-order DCF can be strengthened by the large difference between the external field investigated and that caused by a single hard wall used for specification of the adjustable parameter. In case the gaseous density in the subcritical region is below the coexistence density, an excellent performance of the present formalism is observed even for the mean spherical approximation's second-order DCF as an input. This advantageous property, combined with the fact that the present formalism needs only the second-order DCF of fluid at the coexistence state as an input, enables the present formalism to be a very good theoretical tool for the investigations of wetting and prewetting transitions.     

On the viscosity of composite suspensions of aluminum and ammonium perchlorate particles dispersed in hydroxyl terminated polybutadiene--New empirical model

The rheological properties of fuel suspensions with various solid loadings up to close their maximum packing fraction and suspending media having different viscosities are investigated using the rotational viscometer at relatively low shear rates in which suspensions behave as Newtonian fluids. Aluminum (Al) and ammonium perchlorate (AP) particles are major solid components of any solid fuel system which should be distributed uniformly inside a polymeric binder based on hydroxyl terminated polybutadiene (HTPB). The experimental data generated in this investigation indicates that the relative viscosity of the suspensions is independent of viscosity of polymer binder, but in addition to solid content, geometrical aspects of the solid particles affect strongly the relative viscosity of suspensions. Maximum packing fraction of filler is found to be suitable quantitative measure of filler characteristics such as size, size distribution, shape and structure. Consequently, it is revealed that the relative viscosity of fuel suspension is a unique function of reduced volume fraction (Phi). Based on analogy of viscosity enhancement of reactive resin with cure conversion and suspension with filler content, an empirical model with two adjustable parameters originated from resin gelation model is suggested. According to this model and experimental results obtained in this investigation, a generalized model is proposed to describe the relative viscosity as a function of solid content in which the adjustable parameters are found to be general constants. The generalized model which is expressed as mu(r) = (1-Phi)(0.3 Phi-2) is found to be quite accurate to predict the experimental data. Furthermore, the applicability and accuracy of the generalized model are evaluated using the viscosity data of some suspension systems reported in the literature.     

ELDAR, a knowledge base system on microcomputer for electrolyte solutions. The factual knowledge of ELDAR

The knowledge base system ELDAR (ELectrolyte DAta Regensburg), consisting of data base, method base, rule base, and communication manager, classifies the knowledge of electrolyte solutions into factual, algorithmic, and rule knowledge. In this paper information is given on the factual knowledge of ELDAR and the mapping of facts in Codd's relational data model with an extension of its "1st Normal Form" to repeating attributes. ELDAR offers equal user interfaces for all factual knowledge services, such as literature, data, thesaurus, module, parameter, basic data, and rule retrieval.