The performance of the ab inito gene prediction approaches mostly depends on the effectiveness of detecting the splice sites. This paper addresses the problem of splice site detection using higher-order Markov models. The tenet of our approach is to brace the higher-order dependencies of a Markov model by a neural network that receives the inputs from low-order Markov chains. The method is able...

The fluoride ion affinities (FIAs) of 33 phosphenium ions with a range of substituents were calculated using ab inito and DFT methods. The use of these FIA data as a measure of the Lewis acidities of phosphenium ions is described and the FIAs of the species studied here are compared to FIA data for more commonly encountered Lewis acids. Phosphenium ions are often stronger Lewis acids than neutr...

We derive ab inito exchange parameters for general noncollinear magnetic configurations, in terms of a multiple scattering formalism. We show that the general exchange formula has an anisotropiclike term even in the absence of spin-orbit coupling, and that this term is large, for instance, for collinear configuration in bcc Fe, whereas for fcc Ni it is quite small. We demonstrate that keeping t...

Invoking a number of theoretical levels ranging from HF/STO-3G to CCSD(T)/aug-cc-pVQZ, we have made a detailed survey of six potential energy surfaces (NH4+, NH4*, [CH3CONHCH3]H+, [CH3CONHCH3]H*, [HCONHCH2CONH2]H+, [HCONHCH2CONH2]H*). In conjunction with this, ab inito direct dynamics calculations have been conducted, tracing out several hundred reaction trajectories to reveal details of the el...

Piezoelectricity is a unique property of materials that permits the conversion of mechanical stimuli into electrical and vice versa. On the basis of crystal symmetry considerations, pristine carbon nitride (C3N4) in its various forms is non-piezoelectric. Here we find clear evidence via piezoresponse force microscopy and quantum mechanical calculations that both atomically thin and layered grap...

the interaction of magnesium hydrate at the phosphate oxygen atom of the pyrimidine nucleotides (cmp,ump,dtmp) were studied at the hartree-fock level theory. we used lanl2dz basis set for mg and 6-31g* basis set for atoms.the basis set superposition error (bsse) begins to converge for used method/basis set. the gauge-invariant atomic orbital (giao) method and the continuous-set-of-gauge-transfo...

The Potential Energy Surface PES of (H2)2 dimer has been investigated, using five simple rigid rotor models. These models are called: head to head, symmetric side to side, L , steplike and T model. All calculations were done at two levels of ab initio  methods: MP2(Full) and QCISD (T,Full) using cc-pVTZ basis set at singlet state of spin multiplicity. The results of scanning PES were then fitte...