CCharPPI web server: computational characterization of protein–protein interactions from structure

The atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework Programme (FP7/2007- 2013) under REA grant agreement PIEF-GA-2012-327899 and grant BIO2013-48213-R from Spanish Ministry of Economy and Competitiveness.Peer ReviewedPostprint (published version

Plasmon scattering from holes: from single hole scattering to Young's experiment

In this article, the scattering of surface plasmon polaritons (SPPs) into photons at holes is investigated. A local, electrically excited source of SPPs using a scanning tunnelling microscope (STM) produces an outgoing circular plasmon wave on a thick (200 nm) gold film on glass containing holes of 250, 500 and 1000 nm diameter. Fourier plane images of the photons from hole-scattered plasmons show that the larger the hole diameter, the more directional the scattered radiation. These results are confirmed by a model where the hole is considered as a distribution of horizontal dipoles whose relative amplitudes, directions, and phases depend linearly on the local SPP electric field. An SPP-Young's experiment is also performed, where the STM-excited SPP-wave is incident on a pair of 1 $\mu$m diameter holes in the thick gold film. The visibility of the resulting fringes in the Fourier plane is analyzed to show that the polarization of the electric field is maintained when SPPs scatter into photons. From this SPP-Young's experiment, an upper bound of $\approx$ 200 nm for the radius of this STM-excited source of surface plasmon polaritons is determined

Dopamine-sensitive alternation and collateral behaviour in a Y-maze: effects of d-amphetamine and haloperidol

Introduction: The frequency of spontaneous alternation in a Y-maze (visiting each arm in turn at p>50%) depends on the influence of the attention given to intra- and extra-maze cues. We examined the observing responses shown by rats (collateral rearing and head-turning behaviour), the habituation to the novelty and alternation responses over 15 minutes/day, four days in a row - in a Y-maze under enhanced and reduced dopamine (DA) activity (amphetamine- and haloperidol treatment). Methods: Prior to placement in a Y-maze for 15 minutes observation on 4 successive days animals were treated with either amphetamine (0.5 or 2.5 mg/kg) or pre-treated with a low dose of haloperidol (0.08 mg/kg, ip). Results: 1/ Amphetamine treated animals chose the arms at random on day 1, but after the higher dose on day 2-4 they perseverated their choice. The controls maintained their alternation over this period. 2/ The amphetamine-induced effects on alternation were prevented by prior treatment with the neuroleptic haloperidol. 3/ Amphetamine treatment increased the frequency of rearing in the middle at the choice point of the Y-maze. Haloperidol pre-treatment blocked this increase at the midpoint on day 1, and blocked the rearing behavior at the end of an arm on day 2. 4/ Amphetamine also increased the frequency of head turning and "looking", - an effect that was also prevented by haloperidol. (day 2 onwards). 5/ Haloperidol increased the duration of" looking" and of rearing at the end of an arm later in testing.. Conclusions: Two effects are postulated to have occurred. a) a conflict on day 1 between the novelty-controlled sensory or attentional effects, that leads to an alternation of arm-choice, and amphetamine-induced DA activity that facilitates an alternation of behavioural responses: -- the result was random choice and increased rearing at the choice point. b) On days 2-4 the drug-induced effects on switching motor responses came to control behaviou

Optimisation of material properties for the modelling of large deformation manufacturing processes using a finite element model of the Gleeble compression test

The finite element modelling of manufacturing processes often requires a large amount of large plastic strain flow stress data in order to represent the material of interest over a wide range of temperatures and strain rates. Compression data generated using a Gleeble thermo-mechanical simulator is difficult to interpret due to the complex temperature and strain fields, which exist within the specimen during the test. In this study, a non-linear optimisation process is presented, which includes a finite element model of the compression process to accurately determine the constants of a five-parameter Norton–Hoff material model. The optimisation process is first verified using a reduced three-parameter model and then the full five-parameter model using a known set of constants to produce the target data, from which the errors are assessed. Following this, the optimisation is performed using experimental target data starting from a set of constants derived from the test data using an initial least-squares fit and also an arbitrary starting point within the parameter space. The results of these tests yield coefficients differing by a maximum of less than 10% and significantly improve the representation of the flow stress of the material