Excitons in carbon nanotubes: an ab initio symmetry-based approach

The optical absorption spectrum of the carbon (4,2) nanotube is computed using an ab-initio many-body approach which takes into account excitonic effects. We develop a new method involving a local basis set which is symmetric with respect to the screw symmetry of the tube. Such a method has the advantages of scaling faster than plane-wave methods and allowing for a precise determination of the symmetry character of the single particle states, two-particle excitations, and selection rules. The binding energy of the lowest, optically active states is approximately 0.8 eV. The corresponding exciton wavefunctions are delocalized along the circumference of the tube and localized in the direction of the tube axis.Comment: 4 pages, 1 LaTex file + 4 eps figure

Nuclear quantum effects in solids using a colored-noise thermostat

We present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasi-harmonic system. By properly fitting the correlation function of the noise, one can vary the fluctuations in positions and momenta as a function of the vibrational frequency, and fit them so as to reproduce the quantum-mechanical behavior, with minimal a priori knowledge of the details of the system. We discuss the application of the thermostat to diamond and to ice Ih. We find that results in agreement with path-integral molecular dynamics can be obtained using only a fraction of the computational effort.Comment: submitted for publicatio

Does Ménière's Disease in the Elderly Present Some Peculiar Features?

Object. Aim of our study was to establish some peculiar features of Ménière's Disease (MD) in a group of elderly MD patients, in which the first vertigo spell happened when over 65 years old. Material and Methods. We analyzed a group of 73 younger than 65-years-old and a group of 30 elderly MD patients. All patients underwent a neurotological evaluation, an anamnestic evaluation including a lifetime history of migraine, and blood withdrawal for autoantibody screening. Results. Some differences were found between elderly and younger MD patients. Elderly MD patients presented a higher prevalence of Tumarkin attacks and a lower prevalence of lifetime history of migraine; moreover, they presented a faster develop of hearing loss and vertigo spells than a subgroup of 32 younger patients matched for the duration of illness. Conclusions. Some clinical features of MD in elderly have been pointed out. Particularly, the lower rate of migrainous history and positivity for autoantibodies often associated with MD, in our opinion, support the hypothesis of a vascular disorder acting as a predisposing factor for MD in elderly

Colored-noise thermostats \`a la carte

Recently, we have shown how a colored-noise Langevin equation can be used in the context of molecular dynamics as a tool to obtain dynamical trajectories whose properties are tailored to display desired sampling features. In the present paper, after having reviewed some analytical results for the stochastic differential equations forming the basis of our approach, we describe in detail the implementation of the generalized Langevin equation thermostat and the fitting procedure used to obtain optimal parameters. We discuss in detail the simulation of nuclear quantum effects, and demonstrate that, by carefully choosing parameters, one can successfully model strongly anharmonic solids such as neon. For the reader's convenience, a library of thermostat parameters and some demonstrative code can be downloaded from an on-line repository

During a winter of storms in a small UK catchment, hydrology and water quality responses follow a clear rural-urban gradient

This paper presents the hydrological and water quality response from a series of extreme storm events that passed across the UK during the winter of 2013/2014, in an experimental catchment with a strong rural-urban gradient across four nested sub-catchment areas. The Ray catchment in the upper Thames basin, UK, was extensively monitored using in-situ, high-resolution (15 minute) flow and water quality instrumentation. Dissolved oxygen, ammonium, turbidity and specific conductivity are used to characterise the water quality dynamics. The impact of the Swindon sewage treatment works (SSTW) on water chemistry at the catchment outlet is considerable. Hydrological and water-quality response varies considerably during the events, with the rural catchments exhibiting a much slower hydrological response compared to urban areas. A simple hydrological model (TETIS) was developed to provide insight into water sources in nested subcatchments, highlighting the disparity of the hydrological dynamics across contrasting land-uses during events. The variation in stormwater runoff sources impacts water quality signals with urban sites contributing to dilution dynamics in ammonium, whereas the more rural site experiences a peak in ammonium during the same event. Dissolved oxygen concentrations vary on a rural-urban gradient and experience a notable sag at the Water Eaton outlet (4.4mg/l) during the events, that would have resulted in significant ecological harm had they occurred during the summer in warmer temperatures. The water-quality legacy of these storms in the wider context of the hydrological year is somewhat negligible, with markedly poorer water quality signals being observed during the summer months of 2014. Although ammonium concentrations during the events are elevated (above the ‘good’ status threshold under the WFD), higher values are observed during spring and summer months. The high flows actually appear to flush contaminants out of the Ray and its subcatchments, though the urban sites demonstrate a resupply dynamic during interim dry periods. Data suggest winter storms following dry spells in urban catchments cause some short-lived and spatially extensive deteriorations in water quality. More chronic effects, although prolonged, are only seen downstream of SSTW. These are indicative of capacity of infrastructure being reached, and from the data do not appear to be severe enough to cause ecological harm

Asymmetric base-pair opening drives helicase unwinding dynamics

The opening of a Watson-Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered “half-closed” intermediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials

Students’ Evolving Meaning About Tangent Line with the Mediation of a Dynamic Geometry Environment and an Instructional Example Space

In this paper I report a lengthy episode from a teaching experiment in which fifteen Year 12 Greek students negotiated their definitions of tangent line to a function graph. The experiment was designed for the purpose of introducing students to the notion of derivative and to the general case of tangent to a function graph. Its design was based on previous research results on students’ perspectives on tangency, especially in their transition from Geometry to Analysis. In this experiment an instructional example space of functions was used in an electronic environment utilising Dynamic Geometry software with Function Grapher tools. Following the Vygotskian approach according to which students’ knowledge develops in specific social and cultural contexts, students’ construction of the meaning of tangent line was observed in the classroom throughout the experiment. The analysis of the classroom data collected during the experiment focused on the evolution of students’ personal meanings about tangent line of function graph in relation to: the electronic environment; the pre-prepared as well as spontaneous examples; students’ engagement in classroom discussion; and, the role of researcher as a teacher. The analysis indicated that the evolution of students’ meanings towards a more sophisticated understanding of tangency was not linear. Also it was interrelated with the evolution of the meaning they had about the inscriptions in the electronic environment; the instructional example space; the classroom discussion; and, the role of the teacher

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models

The process of RNA base fraying (i.e., the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics