Neuron models.

The nervous system is made up of several kinds of cells which should ideally be examined separately in biochemical studies. Since we are not yet able to isolate the different kinds of cells, use is made of cell lines derived from a single cell which are isolated from tumors of the nervous system and which can be reproduced at will in the same way as bacteria. They include cell lines isolated from a mouse neuroblastoma which exhibit some of the properties of nerve cells. Hybrid cells obtained by fusion of mouse neuroblastoma cells with rat glioma cells display even more characteristics of nerve cells. This article considers properties which justify our regarding the hybrid cells as neuron models. Application of the cells to problems of the nervous system is then demonstrated: (1) processing of information arriving in the form of mutually opposing hormonal signals; (2) mode of action of morphine.     

One-dimensional models of polymer dynamics. I. Dashpot-spring models applied to a single rotor

The proposion of Clark and Zimm that a dashpot and a spring can be used in place of a set of rotational barriers in polymer dynamics is studied. The simplest possible case is examined here, that of a single rotor. Reasons for altering the Clark–Zimm diffusion equation are presented and an alternative diffusion equation is proposed. The results of both diffusion equations for the correlation function 〈exp[?iθ(0)] exp[iθ(t)]〉 (θ is the angular position of the rotor) are compared with the correlation function for a rotor in an n-fold cosine potential. Although the two diffusion equations differ, both agree well with the n-fold cosine model for barriers above a few k_BT. This agreement is obtained in the absence of adjustable parameters, and motivates the application of these two diffusion equations to polymeric systems.     

Evolving interpretable structure-activity relationship models. 2. Using multiobjective optimization to derive multiple models

A multiobjective evolutionary algorithm (MOEA) is described for evolving multiple structure-activity relationships (SARs). The SARs are encoded in easy-to-interpret reduced graph queries which describe features that are preferentially present in active compounds compared to inactives. The MOEA addresses a limitation associated with many machine learning methods; that is, the inherent tradeoff that exists in recall and precision which is usually handled by combining the two objectives into a single measure with a consequent loss of control. By simultaneously optimizing recall and precision, the MOEA generates a family of SARs that lie on the precision-recall (PR) curve. The user is then able to select a query with an appropriate balance in the two objectives: for example, a low recall-high precision query may be preferred when establishing the SAR, whereas a high recall-low precision query may be more appropriate in a virtual screening context. Each query on the PR curve aims at capturing the structure-activity information into a single representation, and each can be considered as an alternative (equally valid) solution. We then investigate combining individual queries into teams with the aim of capturing multiple SARs that may exist in a data set, for example, as is commonly seen in high-throughput screening data sets. Team formation is carried out iteratively as a postprocessing step following the evolution of the individual queries. The inclusion of uniqueness as a third objective within the MOEA provides an effective way of ensuring the queries are complementary in the active compounds they describe. Substantial improvements in both recall and precision are seen for some data sets. Furthermore, the resulting queries provide more detailed structure-activity information than is present in a single query.     

Intracule functional models. II. Analytically integrable kernels

We present, within the framework of intracule functional theory (IFT), a class of kernels whose correlation integrals can be found in closed form. This approach affords three major advantages over other kernels that we have considered previously; ease of implementation, computational efficiency, and numerical stability. We show that even the simplest member of the class yields reasonable estimates of the correlation energies of 18 atomic and 56 molecular systems and we conclude that this kernel class will prove useful in the development of future IFT models.     

Finite jellium models. I. Restricted Hartree-Fock calculations

Restricted Hartree-Fock calculations have been performed on the Fermi configurations of n electrons confined within a cube. The self-consistent-field orbitals have been expanded in a basis of N particle-in-a-box wave functions. The difficult one- and two-electron integrals have been reduced to a small set of canonical integrals that are calculated accurately using quadrature. The total energy and exchange energy per particle converge smoothly toward their limiting values as n increases; the highest occupied molecular orbital-lowest unoccupied molecular orbital gap and Dirac coefficient converge erratically. However, the convergence in all cases is slow.     

A problem-oriented analysis of database models.

Which is the most convenient database model considering specific applications? The goal of this paper is to try to answer this question by the use of a chemical example. Examples of requests describe the problems of insertion, deletion, and updating; these requests are analyzed for the hierarchical model and are expressed in a relational language defined by the authors and in Socrate for the network model.     

Reduction with polymer -bound nadh models.

We have performed numerous reductions with a NADH model grafted on a Merrifield resin. The yields are generally excellent and in all cases always superior to those obtained with “free” models.     

Polystyrene models. II. Ab initio study of isobutylbenzene

The structure and stability of the various conformations of isobutylbenzene are studied using ab initio molecular orbital theory. The calculations show that coupling between the structural units is important. The results indicate that complete geometry optimization of the stable and transition structures of isobutylbenzene produce significant changes in geometrical parameters and charge distributions of this molecule when compared with the corresponding results obtained using the rigid-rotor approximation. These changes are particularly noticeable in one of the gauche conformations and in transition structures of isobutylbenzene generated by the phenyl group rotation. For polystyrene, these results present evidence that there is a strong coupling between the chain-backbone folding and the rotation of the phenyl group. Multidimensional potential energy surfaces are displayed using a topological representation. © 1992 John Wiley & Sons, Inc.     

One-dimensional models of polymer dynamics. II. A dashpot-spring model

The assumption of Clark and Zimm that coupled dashpots and springs can be used to model the dynamics of polymer molecules is here applied to a model different from that of Clark and Zimm. The precise differences are given in the preceding paper. The dielectric relaxation spectrum of the model is computed in time and frequency domains. The relaxation spectrum can be fitted reasonably well by the empirical Williams–Watts and Havriliak–Negami functions. The best-fit Williams–Watts and Havriliak–Negami parameters are given as functions of the parameters of the model. The model is compared with several related models found in the literature and possible interpretations are given.     

Studies on the synthesis of furanosteroids. I. Viridin models

Alkyne oxazoles of general structure I are transformed directly to furo[2,3-b]phenol derivatives II by a sequence involving intramolecular Diels-Alder/retro-Diels-Alder reaction followed by tautomerization. Suitably functionalized phenols II undergo an intramolecular phenol-dienone-aldol condensation, generating the A,B,E-ring skeleton III characteristic of the viridin (1) class of furanosteroids.     

Parametric analysis of kinetic models. I. The simplest autocatalytic oscillator

A series of mechanisms allowing oscillations and differring in the form of their buffer steps (step 3)

Ab initio dynamic polarizabilities of polymers. I. Hydrogen chain models

Ab initio dynamic polarizabilities per unit cell of infinite stereoregular molecular hydrogen chains are calculated at the coupled Hartree-Fock level of approximation by using the random-phase approximation and the STO -3G and double-zeta atomic basis sets. Comparison with molecular calculations on increasingly large oligomeric chains emphasizes the nice extrapolation property of the polymeric technique that provides asymptotic values very close to the largest oligomeric values. The poles of the polarization propagator associated with the electric dipole polarizability correspond to the singlet excitation energies. Comparisons are performed with other techniques that provide the band gap. © 1996 John Wiley & Sons, Inc.     

Theoretical models for diffusion in glassy polymers. II

The author refines and generalizes a model for diffusion in glassy polymers which he previously introduced. The model unifies many diverse observations by explicity formulating the common property of a glassy polymer in all its various modes, namely the finite relaxation time due to its slow response to changing conditions. An integral approximation method is used to study the motion of the penetrant front and the glass-gel interface and a useful polynomial approximation method is introduced for use in special simple situations.     

Intracule functional models: I. Angle-corrected correlation kernels

We explore the merits of applying a simple angle-dependent correction to the correlation kernel within the framework of Hartree-Fock-Wigner theory. Based on numerical results for the first eighteen atoms, we conclude that such a correction offers a significant improvement over the action kernel that we and others have explored previously.     

Foldamer dynamics expressed via Markov state models. II. State space decomposition

The structural landscape of poly-phenylacetylene (pPA), otherwise known as m-phenylene ethynylene oligomers, has been shown to consist of a very diverse set of conformations, including helices, turns, and knots. Defining a state space decomposition to classify these conformations into easily identifiable states is an important step in understanding the dynamics in relation to Markov state models. We define the state decomposition of pPA oligomers in terms of the sequence of discretized dihedral angles between adjacent phenyl rings along the oligomer backbone. Furthermore, we derive in mathematical detail an approach to further reduce the number of states by grouping symmetrically equivalent states into a single parent state. A more challenging problem requires a formal definition for knotted states in the structural landscape. Assuming that the oligomer chain can only cross the ideal helix path once, we propose a technique to define a knotted state derived from a helical state determined by the position along the helical nucleus where the chain crosses the ideal helix path. Several examples of helical states and knotted states from the pPA 12-mer illustrate the principles outlined in this article.     

Harmonic analysis of large systems. II. Comparison of different protein models

A series of normal mode analyses of bovine pancreatic trypsin inhibitor (BPTI) has been performed. The results of modifying the long-range truncation of electrostatics, reducing the conformational space of the system (reduced basis normal mode analysis), and using different parameter sets and models for the potential function are reported. Both explicit (904 atoms) and polar hydrogen (580 atoms) representations of BPTI were examined and produced nearly identical normal mode vectors but slightly modified vibrational frequencies. The truncation methods—no cutoff, shift, and switch—were examined, and the use of a short switching function was found to alter harmonic motion greatly. A table relating the different cutoff methods to several previously published frequencies for BPTI indicates that the diversity of published lowest frequencies is due to the use of different electrostatic models rather than to inherent differences in the models or energy parameters. Examining reduced basis results demonstrates that a dihedral basis yields similar normal mode vectors, though the vibrational frequencies are shifted to higher values. The analysis of BPTI harmonic dynamics using a spherical harmonic reduced basis set yields significantly altered dynamics, indicating that BPTI is not well represented as a homogeneous object at low temperatures. © 1995 John Wiley & Sons, Inc.

1 This article is a U.S. Government work and, as such, is in the public domain in the United States of America.