Revisiting the need for formal education in visualization.

Defining visualization education is still a work in progress. Visualization education is not just a subject within computer science. Computer scientists are not always the appropriate choice to teach visualization courses on their own. Visualization is not just mastering a set of concepts but acquiring skills. Student should learn by doing, either using one tool or a variety of tools, depending on the course's focus.     

Designing amino acid sequences to fold with good hydrophobic cores

We present two methods for designing amino acid sequences ofproteins that will fold to have good hydrophobic cores. Giventhe coordinates of the desired target protein or polymer structure,the methods generate sequences of hydrophobic (H) and polar(P) monomers that are intended to fold to these structures.One method designs hydrophobic inside, polar outside; the otherminimizes an energy function in a sequence evolution process.The sequences generated by these methods agree at the levelof 60–80% of the sequence positions in 20 proteins inthe Protein Data Bank. A major challenge in protein design isto create sequences that can fold uniquely, i.e. to a singleconformation rather than to many. While an earlier lattice-basedsequence evolution method was shown not to design unique folders,our method generates unique folders in lattice model tests.These methods may also be useful in designing other types offoldable polymer not based on amino acids     

Parameter optimization for the Gaussian model of protein folding

Computational models of protein folding and ligand docking are large and complex. Few systematic methods have yet been developed to optimize the parameters in such models. We describe here an iterative parameter optimization strategy that is based on minimizing a structural error measure by descent in parameter space. At the start, we know the ‘correct’ native structure that we want the model to produce, and an initial set of parameters representing the relative strengths of interactions between the amino acids. The parameters are changed systematically until the model native structure converges as closely as possible to the correct native structure. As a test, we apply this parameter optimization method to the recently developed Gaussian model of protein folding: each amino acid is represented as a bead and all bonds, covalent and noncovalent, are represented by Hooke's law springs. We show that even though the Gaussian model has continuous degrees of freedom, parameters can be chosen to cause its ground state to be identical to that of Go-type lattice models, for which the global ground states are known. Parameters for a more realistic protein model can also be obtained to produce structures close to the real native structures in the protein database.     

Gender differences in mediated communication: Women connect more than do men

Past research in gender differences in the overall Internet use has been contradictory. Some asserted men used it more than women, while others asserted there were no gender difference. Both camps concluded that men and women differed in their motivation and utilization of time spent online. The purpose of the present research was to take a contemporary look at these gender differences. Using an online survey, we asked participants about their experiences with multiple forms of mediated communication: social networking sites, e-mail, video calls, instant messaging, texting, and phone calls. Our results indicated that women, compared to men, are generally more frequent mediated communication users. Compared to men, women prefer and more frequently use text messaging, social media, and online video calls. These results suggest that the nature of mediated social interaction is changing.     

Retention mechanisms of reversed-phase liquid chromatography: determination of solute-solvent interaction free energies

Mean-field statistical thermodynamics theory has recently been developed to account for the partitioning of solutes from aqueous mobile phases into reversed-phase liquid chromatography stationary phases. Several predictions are tested here against an extensive data base of nearly 350 sets of experiments. In agreement with theory, we find that (i) the dependence of retention on mobile phase composition can often be suitably linearized through use of a type of composition plot recently suggested by Dill, (ii) retention measurements can be used to determine the binary interaction constants of solutes with solvents, and (iii) ET-30 solvent probe experiments appear to provide a direct measure of the binary interaction constants. This work suggests that the simple random-mixing approximation for solutes with solvents is often useful even for complex chromatographic solutions.     

Efficient algorithms for approximate time separation of events

Finding bounds on time separation of events is a fundamental problem in the verification and analysis of asynchronous and concurrent systems. Unfortunately, even for systems without repeated events or choice, computing exact bounds on time separation of events is an intractable problem when both min and max type timing constraints are present. In this paper, we describe a method for approximating min and max type constraints, and develop a polynomial-time algorithm for computing approximate time separation bounds in choice-free systems without repeated events. Next, we develop a pseudo-polynomial time technique for analysing a class of asynchronous systems in which events repeat over time. Unlike earlier works, our algorithms can analyse systems with both min and max type timing constraints efficiently. Although the computed bounds are conservative in the worst-case, experimental results indicate that they are fairly accurate in practice. We present formal proofs of correctness of our algorithms, and demonstrate their efficiency and accuracy by applying them to a suite of benchmarks. A complete asynchronous chip has been modelled and analysed using the proposed technique, revealing potential timing problems (already known to designers) in the datapath design.