Complex temporal patterns in molecular dynamics:a direct measure of the phase-space exploration by the trajectory at macroscopic time scales

Computer simulated trajectories of bulk water molecules form complex spatiotemporal structures at the picosecond time scale. This intrinsic complexity, which underlies the formation of molecular structures at longer time scales, has been quantified using a measure of statistical complexity. The method estimates the information contained in the molecular trajectory by detecting and quantifying temporal patterns present in the simulated data (velocity time series). Two types of temporal patterns are found. The first, defined by the short-time correlations corresponding to the velocity autocorrelation decay times (â‰0.1â€ps), remains asymptotically stable for time intervals longer than several tens of nanoseconds. The second is caused by previously unknown longer-time correlations (found at longer than the nanoseconds time scales) leading to a value of statistical complexity that slowly increases with time. A direct measure based on the notion of statistical complexity that describes how the trajectory explores the phase space and independent from the particular molecular signal used as the observed time series is introduced. © 2008 The American Physical Society.

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.

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory

We investigate the sensitivity of a Markov model with states and transition probabilities obtained from clustering a molecular dynamics trajectory. We have examined a 500 ns molecular dynamics trajectory of the peptide valine-proline-alanine-leucine in explicit water. The sensitivity is quantified by varying the boundaries of the clusters and investigating the resulting variation in transition probabilities and the average transition time between states. In this way, we represent the effect of clustering using different clustering algorithms. It is found that in terms of the investigated quantities, the peptide dynamics described by the Markov model is sensitive to the clustering; in particular, the average transition times are found to vary up to 46%. Moreover, inclusion of nonphysical sparsely populated clusters can lead to serious errors of up to 814%. In the investigation, the time step used in the transition matrix is determined by the minimum time scale on which the system behaves approximately Markovian. This time step is found to be about 100 ps. It is concluded that the description of peptide dynamics with transition matrices should be performed with care, and that using standard clustering algorithms to obtain states and transition probabilities may not always produce reliable results.

Identifying and correcting non-Markov states in peptide conformational dynamics

Conformational transitions in proteins define their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We test this assumption by analyzing the transitions obtained directly from the dynamics of a molecular dynamics simulated peptide valine-proline-alanine-leucine and states defined phenomenologically using clustering in dihedral space. We find that the transitions are Markovian at the time scale of ˜ 50 ps and longer. However, at the time scale of 30–40 ps the dynamics loses its Markov property. Our methodology reveals the mechanism that leads to non-Markov behavior. It also provides a way of regrouping the conformations into new states that now possess the required Markov property of their dynamics.

Memory for emotional faces in naturally occurring dysphoria and induced sadness

The aim was to establish if the memory bias for sad faces, reported in clinically depressed patients (Gilboa-Schechtman, Erhard Weiss, & Jeczemien, 2002; Ridout, Astell, Reid, Glen, & O'Carroll, 2003) generalises to sub-clinical depression (dysphoria) and experimentally induced sadness. Study 1: dysphoric (n = 24) and non-dysphoric (n = 20) participants were presented with facial stimuli, asked to identify the emotion portrayed and then given a recognition memory test for these faces. At encoding, dysphoric participants (DP) exhibited impaired identification of sadness and neutral affect relative to the non-dysphoric group (ND). At memory testing, DP exhibited superior memory for sad faces relative to happy and neutral. They also exhibited enhanced memory for sad faces and impaired memory for happy relative to the ND. Study 2: non-depressed participants underwent a positive (n = 24) or negative (n = 24) mood induction (MI) and were assessed on the same tests as Study 1. At encoding, negative MI participants showed superior identification of sadness, relative to neutral affect and compared to the positive MI group. At memory testing, the negative MI group exhibited enhanced memory for the sad faces relative to happy or neutral and compared to the positive MI group. Conclusion: MCM bias for sad faces generalises from clinical depression to these sub-clinical affective states.

Demand side management within a regional electricity company

The work presented in this thesis concerns itself with the application of Demand Side Management (DSM) by industrial subsector as applied to the UK electricity industry. A review of the origins of DSM in the US and the relevance of experience gained to the UK electricity industry is made. Reviews are also made of the current status of the UK electricity industry, the regulatory system, and the potential role of DSM within the prevalent industry environment. A financial appraisal of DSM in respect of the distribution business of a Regional Electricity Company (REC) is also made. This financial appraisal highlights the economic viability of DSM within the context of the current UK electricity industry. The background of the work presented above is then followed by the construction of a framework detailing the necessary requirements for expanding the commercial role of DSM to encompass benefits for the supply business of a REC. The derived framework is then applied, in part, to the UK ceramics manufacturing industry, and in full to the UK sanitaryware manufacturing industry. The application of the framework to the UK sanitaryware manufacturing industry has required the undertaking of a unique first-order energy audit of every such manufacturing site in the UK. As such the audit has revealed previously unknown data on the timings and magnitude of electricity demand and consumption attributable to end-use manufacturing technologies and processes. The audit also served to reveal the disparity in the attitudes toward energy services, and thus by implication towards DSM, of manufacturers within the same Standard Industrial Classification (SIC) code. In response to this, attempt is made to identify the underlying drivers which could cause this variation in attitude. A novel approach to the market segmentation of the companies within the UK ceramics manufacturing sector has been utilised to classify these companies in terms of their likelihood to participate in DSM programmes through the derived Energy Services approach. The market segmentation technique, although requiring further development to progress from a research based concept, highlights the necessity to look beyond the purely energy based needs of manufacturing industries when considering the utilisation of the Energy Services approach to facilitate DSM programs.

May the contact lens force be with you

FULL TEXT: Like many people one of my favourite pastimes over the holiday season is to watch the great movies that are offered on the television channels and new releases in the movie theatres or catching up on those DVDs that you have been wanting to watch all year. Recently we had the new ‘Star Wars’ movie, ‘The Force Awakens’, which is reckoned to become the highest grossing movie of all time, and the latest offering from James Bond, ‘Spectre’ (which included, for the car aficionados amongst you, the gorgeous new Aston Martin DB10). It is always amusing to see how vision correction or eye injury is dealt with by movie makers. Spy movies and science fiction movies have a freehand to design aliens with multiples eyes on stalks or retina scanning door locks or goggles that can see through walls. Eye surgery is usually shown in some kind of day case simplified laser treatment that gives instant results, apart from the great scene in the original ‘Terminator’ movie where Arnold Schwarzenegger's android character encounters an injury to one eye and then proceeds to remove the humanoid covering to this mechanical eye over a bathroom sink. I suppose it is much more difficult to try and include contact lenses in such movies. Although you may recall the film ‘Charlie's Angels’, which did have a scene where one of the Angels wore a contact lens that had a retinal image imprinted on it so she could by-pass a retinal scan door lock and an Eddy Murphy spy movie ‘I-Spy’, where he wore contact lenses that had electronic gadgetry that allowed whatever he was looking at to be beamed back to someone else, a kind of remote video camera device. Maybe we aren’t quite there in terms of devices available but these things are probably not the behest of science fiction anymore as the technology does exist to put these things together. The technology to incorporate electronics into contact lenses is being developed and I am sure we will be reporting on it in the near future. In the meantime we can continue to enjoy the unrealistic scenes of eye swapping as in the film ‘Minority Report’ (with Tom Cruise). Much more closely to home, than in a galaxy far far away, in this issue you can find articles on topics much nearer to the closer future. More and more optometrists in the UK are becoming registered for therapeutic work as independent prescribers and the number is likely to rise in the near future. These practitioners will be interested in the review paper by Michael Doughty, who is a member of the CLAE editorial panel (soon to be renamed the Jedi Council!), on prescribing drugs as part of the management of chronic meibomian gland dysfunction. Contact lenses play an active role in myopia control and orthokeratology has been used not only to help provide refractive correction but also in the retardation of myopia. In this issue there are three articles related to this topic. Firstly, an excellent paper looking at the link between higher spherical equivalent refractive errors and the association with slower axial elongation. Secondly, a paper that discusses the effectiveness and safety of overnight orthokeratology with high-permeability lens material. Finally, a paper that looks at the stabilisation of early adult-onset myopia. Whilst we are always eager for new and exciting developments in contact lenses and related instrumentation in this issue of CLAE there is a demonstration of a novel and practical use of a smartphone to assisted anterior segment imaging and suggestions of this may be used in telemedicine. It is not hard to imagine someone taking an image remotely and transmitting that back to a central diagnostic centre with the relevant expertise housed in one place where the information can be interpreted and instruction given back to the remote site. Back to ‘Star Wars’ and you will recall in the film ‘The Phantom Menace’ when Qui-Gon Jinn first meets Anakin Skywalker on Tatooine he takes a sample of his blood and sends a scan of it back to Obi-Wan Kenobi to send for analysis and they find that the boy has the highest midichlorian count ever seen. On behalf of the CLAE Editorial board (or Jedi Council) and the BCLA Council (the Senate of the Republic) we wish for you a great 2016 and ‘may the contact lens force be with you’. Or let me put that another way ‘the CLAE Editorial Board and BCLA Council, on behalf of, a great 2016, we wish for you!’

Robust spatially resolved pressure measurements using MRI with novel buoyant advection-free preparations of stable microbubbles in polysaccharide gels

MRI of fluids containing lipid coated microbubbles has been shown to be an effective toot for measuring the local fluid pressure. However, the intrinsically buoyant nature of these microbubbles precludes lengthy measurements due to their vertical migration under gravity and pressure-induced coalescence. A novel preparation is presented which is shown to minimize both these effects for at least 25 min. By using a 2% polysaccharide gel base with a small concentration of glycerol and 1,2-distearoyl-sn-glycero-3-phosphocholine coated gas microbubbles, MR measurements are made for pressures between 0.95 and 1.44 bar. The signal drifts due to migration and amalgamation are shown to be minimized for such an experiment whilst yielding very high NMR sensitivities up to 38% signal change per bar.

Memory bias for emotional facial expressions in major depression

Sixteen clinically depressed patients and sixteen healthy controls were presented with a set of emotional facial expressions and were asked to identify the emotion portrayed by each face. They, were subsequently given a recognition memory test for these faces. There was no difference between the groups in terms of their ability to identify emotion between from faces. All participants identified emotional expressions more accurately than neutral expressions, with happy expressions being identified most accurately. During the recognition memory phase the depressed patients demonstrated superior memory for sad expressions, and inferior memory for happy expressions, relative to neutral expressions. Conversely, the controls demonstrated superior memory for happy expressions, and inferior memory for sad expressions, relative to neutral expressions. These results are discussed in terms of the cognitive model of depression proposed by Williams, Watts, MacLeod, and Mathews (1997).

Editorial

Readers may have noted that a short but very important announcement was made in the last issue of CLAE, at the top of the contents page. CLAE has been accepted by Thomson Reuters for abstracting and indexing in its SciSearch, Journal Citation Reports, and Current Contents services. This will ensure a greater visibility to the international research community. In addition, in June 2012 CLAE will receive its very first official Impact Factor – a measure of journal influence of importance to authors and readers alike. The impact factor value has not yet been decided but internal estimates by Elsevier estimate it will be around 1, and it will be applied to all CLAE issue back to January 2009 (volume 32). I would guess readers at this stage would have one of two responses – either ‘that's good news’ or perhaps ‘what's an impact factor?’ If you are in the latter camp then allow me to try and explain. Basically the impact factor or citation index of a journal is based on how many times in the previous year papers published in that journal in the previous two years were cited by authors publishing in other journals. So the 2012 impact factor for CLAE is calculated on how many times in 2011 papers that were published in CLAE in 2010 and 2009 were cited in other journals in 2011, divided by the number of papers published in CLAE 2010 and 2009. Essentially authors will try and get their work published in journals with a higher impact factor as it is thought that the paper will be cited more by other authors or the paper will have higher visibility in the arena. For universities having its published output in higher journals is one of the markers used to judge esteem. For individual authors publishing in journals with a higher impact factor or the number of times one of their papers is published is something that they are likely to add to their CVs or demonstrate the importance of their work. Journals with higher impact factors tend to be more review journals or journals with a wider spectrum so for a relatively small journal with a specialised field like CLAE it is great to be listed with a citation index. The awarding of a citation index crowns many changes that CLAE has undergone since the current Editor took the reins in 2005. CLAE has increased from four issues (in 2004) to six issues per year with at least one review article per issue and one article with continuing education per issue. The rejection rate has gone up significantly meaning that only best papers are published (currently it stands at 37%). CLAE has been Medline/Pubmed indexed for a few years now which is also a very important factor in improving visibility of the journal. The submission and reviewing process for CLAE in now entirely online and finally the editorial board has changed from being merely a list of keynote people to being an active group of keynote people who are enthusiastically involved with the journal. From the editorial board one person is appointed as a Reviews Editor plus we have two additional editors who work as Regional Editors. As ever, on behalf of CLAE I would like to thank the BCLA Council for their continued support (especially Vivien Freeman) and Elsevier for their continuing guidance (in particular Andrew Miller and Rosie Davey) and the excellent Editorial Board (Christopher Snyder, Pauline Cho, Eric Papas, Jan Bergmanson, Roger Buckley, Patrick Caroline, Dwight Cavanagh, Robin Chalmers, Michael Doughty, Nathan Efron, Michel Guillon, Nizar Hirji, Meng Lin, Florence Malet, Philip Morgan, Deborah Sweeney, Brian Tighe, Eef van Der Worp, Barry Weissman, Mark Willcox, James Wolffsohn and Craig Woods). And finally, a big thanks to the authors and reviewers who work tirelessly putting manuscripts together for publication in CLAE. Copyright © 2012 Published by Elsevier Ltd.

Water network dynamics at the critical moment of a peptide's ß-turn formation:a molecular dynamics study

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of ß-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable ß-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the ß-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the ß-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of ß-turns.

Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems

The simulated classical dynamics of a small molecule exhibiting self-organizing behavior via a fast transition between two states is analyzed by calculation of the statistical complexity of the system. It is shown that the complexity of molecular descriptors such as atom coordinates and dihedral angles have different values before and after the transition. This provides a new tool to identify metastable states during molecular self-organization. The highly concerted collective motion of the molecule is revealed. Low-dimensional subspaces dynamics is found sensitive to the processes in the whole, high-dimensional phase space of the system. © 2004 Wiley Periodicals, Inc.