There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows r...

We extend the formalism of local exchange methods to calculate and investigate the electronic structure of metals. It is well-known that the Hatree-Fock method when applied to metals shows unphysical behaviour, however the accurate treatment of exchange via DFT’s exact exchange method (EXX) and using our local Fock exchange method (LFX) can be used to describe metallic band structures accurately.

This paper presents a simple but effective sentence-length informed method to select informative sentences for active learning (AL) based SMT. A length factor is introduced to penalize short sentences to balance the “exploration” and “exploitation” problem. The penalty is dynamically updated at each iteration of sentence selection by the ratio of the current candidate sentence length and the ov...

This article discusses some ideas concerning an ‘average-pair-density functional theory’, in which the ground-state energy of a many-electron system is rewritten as a functional of the spherically and system-averaged pair density. These ideas are further clarified with simple physical examples. Then it is shown that the proposed formalism can be combined with density functional theory to build ...

A polarizable water pair potential was determined by fitting a potential form to microwave, terahertz, and mid-infrared (D2O)2 spectra through a rigorous calculation of the water dimer eigenstates. It accurately reproduces most ground state vibration-rotation-tunneling spectra and yields excellent second viral coefficients. The calculated dimer structure and dipole moment are very close to thos...

We report on the construction of colloidal stars: 1 microm polystyrene beads grafted with a dense brush of 1 microm long and 10 nm wide charged semiflexible filamentous viruses. The pair interaction potentials of colloidal stars are measured using an experimental implementation of umbrella sampling, a technique originally developed in computer simulations in order to probe rare events. The infl...

A force matching technique based on previous work by Voth and co-workers is developed and employed to coarse grain intermolecular potentials for three common solvents: carbon tetrachloride, benzene, and water. The accuracy of the force-matching approach is tested by comparing radial distribution functions (RDF) obtained from simulations using the atomistic and coarse-grained potentials. Atomist...

We analyze the effect of polydispersity in the arm number on the effective interactions , structural correlations and the phase behavior of star polymers in a good solvent. The effective interaction potential between two star polymers with different arm numbers is derived using scaling theory. The resulting expression is tested against monomer-resolved molecular dynamics simulations. We find th...

Since pair programming appeared in the literature as an effective method of teaching computer programming, many systems were developed to cover the application of pair programming over distance. Today’s systems serve personal, professional and educational purposes allowing distributed teams to work together on the same programming project. The current research focuses in distributed pair progra...

Pair programming has been shown to be an effective method of improving the learning outcomes of students in introductory computer science courses. However, much of the existing literature related to pair programming does not focus how to effectively implement pair programming. Researchers studying multiple aspects of pair programming have conducted several empirical studies at our university ov...