A network graph can be defined for any chemical space by connecting similar molecules (nodes of t... more A network graph can be defined for any chemical space by connecting similar molecules (nodes of the network) by edges. Through analysis of large molecular databases (such as PubChem and ZINC) in terms of atom type environment similarity and similarity of electronic property distributions, network topology and degree distribution are constructed for chemical spaces. This network topology is being employed to address questions such as: * Do different chemical subspaces possess different topology? * Can these characteristics be used to refine compound libraries for specific applications? * When can QSAR models constructed within a given chemical subspace be expected to be robust to random deletion of a significant fraction of training molecules? * How sensitive is the dependence of network characteristics on the similarity measures employed for construction of the network? The answers to these questions have obvious implications for the design of high throughput screening libraries.
Applications of Metaheuristics in Process Engineering, 2014
ABSTRACT Genetic algorithms (GA) have been widely used in quantitative structure–activity/propert... more ABSTRACT Genetic algorithms (GA) have been widely used in quantitative structure–activity/property relationship (QSAR/QSPR) modeling in recent years and have been shown to generate accurate and robust predictions. In a GA, a population of “chromosomes” is evolved through the processes of random mutation and crossover and evaluated using a fitness function. Here, we will review the basic principles underlying GA and provide a survey of recent applications in QSAR/QSPR, bioinformatics, and in silico drug design, with particular emphasis on the use of GAs in feature selection and dimensionality reduction, model optimization, conformational search, docking, and diversity analysis.
Cellular Automata (CA) are discrete dynamical systems constructed from a large number of simple i... more Cellular Automata (CA) are discrete dynamical systems constructed from a large number of simple identical components with local interactions, which are together capable of complex self‐organizing behaviour. The complexity is generated by the cooperative effect of the many components. The use of CA in molecular and solid state dynamical calculations is relatively new and untested. Such methods, however, reduce the quantum molecular problem from one of solving differential equations to the computation of simple algebraic rules synchronously on a lattice of sites. We have demonstrated that the second quantized formalism of field operators in coordinate representation is readily implementable in terms of CA collision rules on a lattice. The Su‐Schrieffer‐Heeger (SSH) Hamiltonian for quasi‐one‐dimensional polymer chains has been examined in terms of CA rules. The CA consists of a 1‐D lattice of sites, each with a finite set of possible values, representing elements of electronic charge and phonon number, evolv...
Electron density is one of the fundamental concepts underpinning modern chemistry, and this book ... more Electron density is one of the fundamental concepts underpinning modern chemistry, and this book presents a conceptual treatment of the subject with equal emphasis on computational and philosophical questions. Beginning with the use of probabilities in statistical physics and the origins of quantum mechanics, the conceptual and statistical framework developed is employed to treat quantum entanglement, Bader’s theory of atoms in molecules, open systems, and the theory of insulators. Employing a coherent and logical structure, the book is accessible to students and faculty working in chemistry and computational materials science.
A network graph can be defined for any chemical space by connecting similar molecules (nodes of t... more A network graph can be defined for any chemical space by connecting similar molecules (nodes of the network) by edges. Through analysis of large molecular databases (such as PubChem and ZINC) in terms of atom type environment similarity and similarity of electronic property distributions, network topology and degree distribution are constructed for chemical spaces. This network topology is being employed to address questions such as: * Do different chemical subspaces possess different topology? * Can these characteristics be used to refine compound libraries for specific applications? * When can QSAR models constructed within a given chemical subspace be expected to be robust to random deletion of a significant fraction of training molecules? * How sensitive is the dependence of network characteristics on the similarity measures employed for construction of the network? The answers to these questions have obvious implications for the design of high throughput screening libraries.
Applications of Metaheuristics in Process Engineering, 2014
ABSTRACT Genetic algorithms (GA) have been widely used in quantitative structure–activity/propert... more ABSTRACT Genetic algorithms (GA) have been widely used in quantitative structure–activity/property relationship (QSAR/QSPR) modeling in recent years and have been shown to generate accurate and robust predictions. In a GA, a population of “chromosomes” is evolved through the processes of random mutation and crossover and evaluated using a fitness function. Here, we will review the basic principles underlying GA and provide a survey of recent applications in QSAR/QSPR, bioinformatics, and in silico drug design, with particular emphasis on the use of GAs in feature selection and dimensionality reduction, model optimization, conformational search, docking, and diversity analysis.
Cellular Automata (CA) are discrete dynamical systems constructed from a large number of simple i... more Cellular Automata (CA) are discrete dynamical systems constructed from a large number of simple identical components with local interactions, which are together capable of complex self‐organizing behaviour. The complexity is generated by the cooperative effect of the many components. The use of CA in molecular and solid state dynamical calculations is relatively new and untested. Such methods, however, reduce the quantum molecular problem from one of solving differential equations to the computation of simple algebraic rules synchronously on a lattice of sites. We have demonstrated that the second quantized formalism of field operators in coordinate representation is readily implementable in terms of CA collision rules on a lattice. The Su‐Schrieffer‐Heeger (SSH) Hamiltonian for quasi‐one‐dimensional polymer chains has been examined in terms of CA rules. The CA consists of a 1‐D lattice of sites, each with a finite set of possible values, representing elements of electronic charge and phonon number, evolv...
Electron density is one of the fundamental concepts underpinning modern chemistry, and this book ... more Electron density is one of the fundamental concepts underpinning modern chemistry, and this book presents a conceptual treatment of the subject with equal emphasis on computational and philosophical questions. Beginning with the use of probabilities in statistical physics and the origins of quantum mechanics, the conceptual and statistical framework developed is employed to treat quantum entanglement, Bader’s theory of atoms in molecules, open systems, and the theory of insulators. Employing a coherent and logical structure, the book is accessible to students and faculty working in chemistry and computational materials science.
Uploads
Papers by Dr.N Sukumar