Computer-aided drug design and ADMET predictions for identification and evaluation of novel potential farnesyltransferase inhibitors in cancer therapy

We have used various computational methodologies including molecular dynamics, density functional theory, virtual screening, ADMET predictions and molecular interaction field studies to design and analyze four novel potential inhibitors of farnesyltransferase (FTase). Evaluation of two proposals regarding their drug potential as well as lead compounds have indicated them as novel promising FTase inhibitors, with theoretically interesting pharmacotherapeutic profiles, when Compared to the very active and most cited FTase inhibitors that have activity data reported, which are launched drugs or compounds in clinical tests. One of our two proposals appears to be a more promising drug candidate and FTase inhibitor, but both derivative molecules indicate potentially very good pharmacotherapeutic profiles in comparison with Tipifarnib and Lonafarnib, two reference pharmaceuticals. Two other proposals have been selected with virtual screening approaches and investigated by LIS, which suggest novel and alternatives scaffolds to design future potential FTase inhibitors. Such compounds can be explored as promising molecules to initiate a research protocol in order to discover novel anticancer drug candidates targeting farnesyltransferase, in the fight against cancer. (C) 2009 Elsevier Inc. All rights reserved.

Half-Filled Layered Organic Superconductors and the Resonating-Valence-Bond Theory of the Hubbard-Heisenberg Model

We present a resonating-valence-bond theory of superconductivity for the Hubbard-Heisenberg model on an anisotropic triangular lattice. Our calculations are consistent with the observed phase diagram of the half-filled layered organic superconductors, such as the beta, beta('), kappa, and lambda phases of (BEDT-TTF)(2)X [bis(ethylenedithio)tetrathiafulvalene] and (BETS)(2)X [bis(ethylenedithio)tetraselenafulvalene]. We find a first order transition from a Mott insulator to a d(x)(2)-y(2) superconductor with a small superfluid stiffness and a pseudogap with d(x)(2)-y(2) symmetry.

Trace Semantics for the Owicki-Gries Theory Integrated with the Progress Logic from UNITY

The theory of Owicki and Gries has been used as a platform for safety-based verifcation and derivation of concurrent programs. It has also been integrated with the progress logic of UNITY which has allowed newer techniques of progress-based verifcation and derivation to be developed. However, a theoretical basis for the integrated theory has thus far been missing. In this paper, we provide a theoretical background for the logic of Owicki and Gries integrated with the logic of progress from UNITY. An operational semantics for the new framework is provided which is used to prove soundness of the progress logic.

Extended GCD and Hermite normal form algorithms via lattice basis reduction

Extended gcd calculation has a long history and plays an important role in computational number theory and linear algebra. Recent results have shown that finding optimal multipliers in extended gcd calculations is difficult. We present an algorithm which uses lattice basis reduction to produce small integer multipliers x(1), ..., x(m) for the equation s = gcd (s(1), ..., s(m)) = x(1)s(1) + ... + x(m)s(m), where s1, ... , s(m) are given integers. The method generalises to produce small unimodular transformation matrices for computing the Hermite normal form of an integer matrix.

Formal derivation of finite state machines for class testing

Previous work on generating state machines for the purpose of class testing has not been formally based. There has also been work on deriving state machines from formal specifications for testing non-object-oriented software. We build on this work by presenting a method for deriving a state machine for testing purposes from a formal specification of the class under test. We also show how the resulting state machine can be used as the basis for a test suite developed and executed using an existing framework for class testing. To derive the state machine, we identify the states and possible interactions of the operations of the class under test. The Test Template Framework is used to formally derive the states from the Object-Z specification of the class under test. The transitions of the finite state machine are calculated from the derived states and the class's operations. The formally derived finite state machine is transformed to a ClassBench testgraph, which is used as input to the ClassBench framework to test a C++ implementation of the class. The method is illustrated using a simple bounded queue example.

A 2D numerical model for simulating the physics of fault systems

Simulations provide a powerful means to help gain the understanding of crustal fault system physics required to progress towards the goal of earthquake forecasting. Cellular Automata are efficient enough to probe system dynamics but their simplifications render interpretations questionable. In contrast, sophisticated elasto-dynamic models yield more convincing results but are too computationally demanding to explore phase space. To help bridge this gap, we develop a simple 2D elastodynamic model of parallel fault systems. The model is discretised onto a triangular lattice and faults are specified as split nodes along horizontal rows in the lattice. A simple numerical approach is presented for calculating the forces at medium and split nodes such that general nonlinear frictional constitutive relations can be modeled along faults. Single and multi-fault simulation examples are presented using a nonlinear frictional relation that is slip and slip-rate dependent in order to illustrate the model.

Formal methods within a totally functional approach to programming

Taking functional programming to its extremities in search of simplicity still requires integration with other development (e.g. formal) methods. Induction is the key to deriving and verifying functional programs, but can be simplified through packaging proofs with functions, particularly folds, on data (structures). Totally Functional Programming avoids the complexities of interpretation by directly representing data (structures) as platonic combinators - the functions characteristic to the data. The link between the two simplifications is that platonic combinators are a kind of partially-applied fold, which means that platonic combinators inherit fold-theoretic properties, but with some apparent simplifications due to the platonic combinator representation. However, despite observable behaviour within functional programming that suggests that TFP is widely-applicable, significant work remains before TFP as such could be widely adopted.

Signature of mott-insulator transition with ultracold fermions in a one-dimensional optical lattice

Using the exact Bethe ansatz solution of the Hubbard model and Luttinger liquid theory, we investigate the density profiles and collective modes of one-dimensional ultracold fermions confined in an optical lattice with a harmonic trapping potential. We determine a generic phase diagram in terms of a characteristic filling factor and a dimensionless coupling constant. The collective oscillations of the atomic mass density, a technique that is commonly used in experiments, provide a signature of the quantum phase transition from the metallic phase to the Mott-insulator phase. A detailed experimental implementation is proposed.

Ferromagnetism, paramagnetism, and a Curie-Weiss metal in an electron-doped Hubbard model on a triangular lattice

Motivated by the unconventional properties and rich phase diagram of NaxCoO2 we consider the electronic and magnetic properties of a two-dimensional Hubbard model on an isotropic triangular lattice doped with electrons away from half-filling. Dynamical mean-field theory (DMFT) calculations predict that for negative intersite hopping amplitudes (t < 0) and an on-site Coulomb repulsion, U, comparable to the bandwidth, the system displays properties typical of a weakly correlated metal. In contrast, for t > 0 a large enhancement of the effective mass, itinerant ferromagnetism, and a metallic phase with a Curie-Weiss magnetic susceptibility are found in a broad electron doping range. The different behavior encountered is a consequence of the larger noninteracting density of states (DOS) at the Fermi level for t > 0 than for t < 0, which effectively enhances the mass and the scattering amplitude of the quasiparticles. The shape of the DOS is crucial for the occurrence of ferromagnetism as for t > 0 the energy cost of polarizing the system is much smaller than for t < 0. Our observation of Nagaoka ferromagnetism is consistent with the A-type antiferromagnetism (i.e., ferromagnetic layers stacked antiferromagnetically) observed in neutron scattering experiments on NaxCoO2. The transport and magnetic properties measured in NaxCoO2 are consistent with DMFT predictions of a metal close to the Mott insulator and we discuss the role of Na ordering in driving the system towards the Mott transition. We propose that the Curie-Weiss metal phase observed in NaxCoO2 is a consequence of the crossover from a bad metal with incoherent quasiparticles at temperatures T > T-* and Fermi liquid behavior with enhanced parameters below T-*, where T-* is a low energy coherence scale induced by strong local Coulomb electron correlations. Our analysis also shows that the one band Hubbard model on a triangular lattice is not enough to describe the unusual properties of NaxCoO2 and is used to identify the simplest relevant model that captures the essential physics in NaxCoO2. We propose a model which allows for the Na ordering phenomena observed in the system which, we propose, drives the system close to the Mott insulating phase even at large dopings.

Developing logic programs from specifications using stepwise refinement

In this paper we demonstrate a refinement calculus for logic programs, which is a framework for developing logic programs from specifications. The paper is written in a tutorial-style, using a running example to illustrate how the refinement calculus is used to develop logic programs. The paper also presents an overview of some of the advanced features of the calculus, including the introduction of higher-order procedures and the refinement of abstract data types.

Differential inclusions and robust control theory

Uncontrolled systems (x) over dot is an element of Ax, where A is a non-empty compact set of matrices, and controlled systems (x) over dot is an element of Ax + Bu are considered. Higher-order systems 0 is an element of Px - Du, where and are sets of differential polynomials, are also studied. It is shown that, under natural conditions commonly occurring in robust control theory, with some mild additional restrictions, asymptotic stability of differential inclusions is guaranteed. The main results are variants of small-gain theorems and the principal technique used is the Krasnosel'skii-Pokrovskii principle of absence of bounded solutions.

Should optional properties be used in conceptual modelling? A theory and three empirical tests

An important feature of some conceptual modelling grammars is the features they provide to allow database designers to show real-world things may or may not possess a particular attribute or relationship. In the entity-relationship model, for example, the fact that a thing may not possess an attribute can be represented by using a special symbol to indicate that the attribute is optional. Similarly, the fact that a thing may or may not be involved in a relationship can be represented by showing the minimum cardinality of the relationship as zero. Whether these practices should be followed, however, is a contentious issue. An alternative approach is to eliminate optional attributes and relationships from conceptual schema diagrams by using subtypes that have only mandatory attributes and relationships. In this paper, we first present a theory that led us to predict that optional attributes and relationships should be used in conceptual schema diagrams only when users of the diagrams require a surface-level understanding of the domain being represented by the diagrams. When users require a deep-level understanding, however, optional attributes and relationships should not be used because they undermine users' abilities to grasp important domain semantics. We describe three experiments which we then undertook to test our predictions. The results of the experiments support our predictions.

Lattice-dome design using a knowledge-based system approach

In the design of lattice domes, design engineers need expertise in areas such as configuration processing, nonlinear analysis, and optimization. These are extensive numerical, iterative, and lime-consuming processes that are prone to error without an integrated design tool. This article presents the application of a knowledge-based system in solving lattice-dome design problems. An operational prototype knowledge-based system, LADOME, has been developed by employing the combined knowledge representation approach, which uses rules, procedural methods, and an object-oriented blackboard concept. The system's objective is to assist engineers in lattice-dome design by integrating all design tasks into a single computer-aided environment with implementation of the knowledge-based system approach. For system verification, results from design examples are presented.

Theory and applications of fuzzy Volterra integral equations

Formulations of fuzzy integral equations in terms of the Aumann integral do not reflect the behavior of corresponding crisp models. Consequently, they are ill-adapted to describe physical phenomena, even when vagueness and uncertainty are present. A similar situation for fuzzy ODEs has been obviated by interpretation in terms of families of differential inclusions. The paper extends this formalism to fuzzy integral equations and shows that the resulting solution sets and attainability sets are fuzzy and far better descriptions of uncertain models involving integral equations. The investigation is restricted to Volterra type equations with mildly restrictive conditions, but the methods are capable of extensive generalization to other types and more general assumptions. The results are illustrated by integral equations relating to control models with fuzzy uncertainties.

Quasimode theory of quantum optical processes in photonic band gap materials

This paper deals with atomic systems coupled to a structured reservoir of quantum EM field modes, with particular relevance to atoms interacting with the field in photonic band gap materials. The case of high Q cavities has been treated elsewhere using Fano diagonalization based on a quasimode approach, showing that the cavity quasimodes are responsible for pseudomodes introduced to treat non-Markovian behaviour. The paper considers a simple model of a photonic band gap case, where the spatially dependent permittivity consists of a constant term plus a small spatially periodic term that leads to a narrow band gap in the spectrum of mode frequencies. Most treatments of photonic band gap materials are based on the true modes, obtained numerically by solving the Helmholtz equation for the actual spatially periodic permittivity. Here the field modes are first treated in terms of a simpler quasimode approach, in which the quasimodes are plane waves associated with the constant permittivity term. Couplings between the quasimodes occur owing to the small periodic term in the permittivity, with selection rules for the coupled modes being related to the reciprocal lattice vectors. This produces a field Hamiltonian in quasimode form. A matrix diagonalization method may be applied to relate true mode annihilation operators to those for quasimodes. The atomic transitions are coupled to all the quasimodes, and the true mode atom-EM field coupling constants (one-photon Rabi frequencies) are related to those for the quasimodes and also expressions are obtained for the true mode density. The results for the one-photon Rabi frequencies differ from those assumed in other work. Expressions for atomic decay rates are obtained using the Fermi Golden rule, although these are valid only well away from the band gaps.