Controlling protein molecular dynamics:how to accelerate folding while preserving the native state

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1 micros. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

The impact of visual-verbal relationships on native-nonnative english speakers' reading processes and comprehension

The aim of this study was to comparatively investigate the impact of visual-verbal relationships that exist in expository texts on the reading process and comprehension of readers from different language background: native speakers of English (LI) and speakers of English as a foreign language (EFL). The study focussed, in this respect, on the visual elements (VEs) mainly graphs and tables that accompanied the selected texts. Two major experiments were undertaken. The first, was for the reading process using the post-reading questionnaire technique. Participants were 163 adult readers representing three groups: 77 (LI), 56 (EFL postgraduates); and 30 (EFL undergraduates). The second experiment was for the reading comprehension using cloze procedure. Participants were 123 representing the same above gorups: 50, 33 and 40 respectively. It was hypothesised that the LI readers would make use of VEs in the reading process in ways different from both EFL groups and that use would enhance each group's comprehension in different aspects and to different levels. In the analysis of the data of both experiments two statistical measurements were used. The chi-square was used to measure the differences between frequencies and the t-test was used to measure the differences between means. The results indicated a significant relationship between readers' language background and the impact of visual-verbal relationships on their reading processes and comprehension of such type of texts. The results also revealed considerable similarities between the two EFL groups in the reading process of texts accompanied by VEs. In the reading comprehension, however, the EFL undergraduates seemed to benefit from the visual-verbal relationships in their comprehension more than the postgraduates, suggesting a weak relationship of this impact for older EFL readers. Furthermore, the results showed considerable similarities between the reading process of texts accompanied by VEs and of whole prose texts. Finally an evaluation of this study was undertaken as well as practical implications for EFL readers and suggestions for future research.

Coherence and understanding in informal conversations between native and non-native speakers of English

This study investigates informal conversations between native English speakers and international students living and studying in the UK. 10 NNS participants recorded themselves during conversations with native speakers. The audio-recordings were transcribed and a fine-grained, qualitative analysis was employed to examine how the participants jointly achieved both coherence and understanding in the conversations, and more specifically how the NNSs contributed to this achievement. The key areas of investigation focused on features of topic management, such as topic initiations, changes and transitions, and on the impact which any communicative difficulties may have on the topical continuity of the conversations. The data suggested that these conversations flowed freely and coherently, and were marked by a relative scarcity of the communicative difficulties often associated with NS-NNS interactions. Moreover, language difficulties were found to have minimal impact on the topic development of the conversations. Unlike most previous research in the field, the data further indicated that the NNSs were able to make active contributions to the initiation and change of topics, and to employ a range of strategies to manage these effectively and coherently. The study considers the implications which the findings may have for teaching and learning, for second language acquisition research, and for non-native speakers everywhere.