this paper presents density functional theory and non-equilibrium green’s function based first principles calculations to explore the sensing property of adenine and thymine based hetero-junction chins for ammonia and phosphine gas molecules. this modeling and simulation technique plays an important and crucial role in the fast growing semiconductor based nanotechnology field. the hetero-juncti...

Very important part of theoretical simulations is a process of structure preparation, geometry editing and detailed examination of properties. Here we present advanced molecular modeling package called Nemesis [1]. The software is mainly focused on the molecular structure preparation for calculations, taking into account typical user problems. Nemesis is open-source, multi-platform, modular, in...

The mechanisms of three protocellular functions have been studied using molecular modeling techniques. These functions are (1) the transport of ions across membranes, (2) the formation of photoactivated proton gradient that could drive chemical synthesis in the protocell, and (3) the organization of small peptides necessary for catalytic activity. In all these processes, membranes play an essen...

ethylene was homopolymerized over ziegler-natta catalyst and the homopolymerization was modeled using moment equations. mechanism was modeled according to five different reaction centers of catalyst. for each center, there are different reaction rate coefficients; therefore the final product of each center would be expected to be different. modeling results showed good conformity to the experim...

experimental determination of solubility and ternary phase diagram of chiral compound are of tedious and time consuming tasks, and in many cases, there is not enough experimental data for different enantiomeric compositions to access the experimental ternary phase diagram. using thermodynamic models with predictive capability, having less dependency on experimental data, affords a great advanta...

Neste manuscrito, o desempenho de alguns aceleradores do tipo sulfenamidas foi avaliado quanto à vulcanização elastômeros. Dados teóricos, gerados através da modelagem moléculas das espécies químicas e suas reações no processo, foram confrontados com dados experimentais referentes a cura borracha natural copolímero estireno-butadieno. A complexidade envolvidas na vulcanização, assim como elastô...

Article history: Received 1 March 2013 Accepted 30 June 2013 Available online 12 July 2013

Crystallographic studies play a major role in current efforts towards protein structure determination. However, despite recent advances in computational tools for molecular modeling and graphics, the task of constructing a model of the tertiary structure of a protein from experimental data remains complex and time-consuming, requiring extensive expert intervention. This paper describes an appro...

A hypothetical evolutionary pathway from a ribozyme to a catalytic RNA-protein complex (RNP) is proposed and examined. In this hypothesis for an early phase of molecular evolution, one RNA-RNA interaction in the starting ribozyme is replaced with an RNA-protein interaction via two intermediary stages. At each stage, the original RNA-RNA interaction and a newly introduced RNA-protein interaction...