Localization Properties of Electronic States in Polaron Model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling are completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.Comment: 6 pages, 6 figure

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein/water interface allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On the top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line.Comment: 9 pages, 8 figure

Mathematical literacy in Plant Physiology undergraduates: results of interventions aimed at improving students' performance

The importance of mathematical literacy in any scientific career is widely recognized. However, various studies report lack of numeracy and mathematical literacy in students from various countries. In the present work we present a detailed study of the mathematical literacy of Spanish undergraduate students of Biology enrolled in a Plant Physiology course. We have performed individual analyses of results obtained during the period 2000-2011, for questions in the examinations requiring and not requiring mathematical skills. Additionally, we present the outcome of two interventions introduced with the aim of helping students improve their prospects for success in the course. Our results confirm previous research showing students' deficiencies in mathematical skills. However, the scores obtained for mathematical questions in the examinations are good predictors of the final grades attained in Plant Physiology, as there are strong correlations at the individual level between results for questions requiring and not requiring mathematical skills. The introduction of a laboratory session devoted to strengthening the application of students' previously acquired mathematical knowledge did not change significantly the results obtained for mathematical questions. Since mathematical abilities of students entering university have declined in recent years, this intervention may have helped to maintain students' performance to a level comparable to that of previous years. The outcome of self-assessment online tests indicates that though Mathematics anxiety is lower than during examinations, the poor results obtained for questions requiring mathematical skills are, at least in part, due to a lack of self-efficacy

Experimental evidence of the ferroelectric phase transition near the λ−\lambda-point in liquid water

We studied dielectric properties of nano-sized liquid water samples confined in polymerized silicates MCM-41 characterized by the porous sizes \sim 3-10nm. We report the direct measurements of the dielectric constant by the dielectric spectroscopy method at frequencies 25Hz-1MHz and demonstrate clear signatures of the second-order phase transition of ferroelectric nature at temperatures next to the \lambda- point in the bulk supercooled water. The presented results support the previously developed polar liquid phenomenology and hence establish its applicability to model actual phenomena in liquid water.Comment: 4 pages, single figur

General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity

Although general anesthetics are known to modulate the activity of ligand-gated ion channels in the Cys-loop superfamily, there is at present neither consensus on the underlying mechanisms, nor predictive models of this modulation. Viable models need to offer quantitative assessment of the relative importance of several identified anesthetic binding sites. However, to date, precise affinity data for individual sites has been challenging to obtain by biophysical means. Here, the likely role of pore block inhibition by the general anesthetics isoflurane and propofol of the prokaryotic pentameric channel GLIC is investigated by molecular simulations. Microscopic affinities are calculated for both single and double occupancy binding of isoflurane and propofol to the GLIC pore. Computations are carried out for an open-pore conformation in which the pore is restrained to crystallographic radius, and a closed-pore conformation that results from unrestrained molecular dynamics equilibration of the structure. The GLIC pore is predicted to be blocked at the micromolar concentrations for which inhibition by isofluorane and propofol is observed experimentally. Calculated affinities suggest that pore block by propofol occurs at signifcantly lower concentrations than those for which inhibition is observed: we argue that this discrepancy may result from binding of propofol to an allosteric site recently identified by X-ray crystallography, which may cause a competing gain-of-function effect. Affinities of isoflurane and propofol to the allosteric site are also calculated, and shown to be 3 mM for isoflurane and for propofol; both anesthetics have a lower affinity for the allosteric site than for the unoccupied pore

Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.

We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory

Aiming for excellence in STEM learning and teaching proceedings

While maths can be viewed as enabling learning in science and medicine, in reality we see students are bringing their maths anxiety with them to their studies. Our work focuses on dissecting the maths problem as it relates to teaching and learning in these so-called hard disciplines. We have been challenging the inertia of what we see as a stand off with students taking the view that they are unable to do maths and educators frustrated at their disengagement. We have found that the maths problem resonates with several pedagogical frameworks (e.g. Meyer and Land’s Threshold Concepts Framework, Perkins and Simmons’ four frames of understanding) and we have found these useful for unpicking where our students become disengaged. We have applied a number of interventions to assist student learning and are now using our findings to inform the design of an online diagnostic to more explicitly address dysfunctional stances that students adopt when asked to manipulate their quantitative data. Given the extent of the maths problem and the move to increase diversity in the Higher Education sector, we discuss how to enable students to shift to a more positive learning disposition