A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

We describe a novel coarse grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a viscoelastic continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obtained for proteins in general from atomistic molecular dynamics simulations

Dynamics of Micropollutant Adsorption to Polystyrene Surfaces Probed by Angle-Resolved Second Harmonic Scattering

Angle-resolved second harmonic scattering is used to probe the adsorption dynamics of aqueous cationic and anionic dye molecules onto polystyrene surfaces. The adsorptions of malachite green to negatively charged polystyrene and naphthol yellow S to positively charged polystyrene are both highly favorable, with Î"GAds values of -10.9 ± 0.2 and -10.27 ± 0.09 kcal/mol, respectively. A competitive displacement methodology was employed to obtain values for the adsorption free energies of various smaller neutral organic molecules, including the important micropollutant ascorbic acid, caffeine, and pentoxifylline. For charged adsorbers, electrostatic interactions appear to significantly contribute to adsorption behavior. However, electrostatic repulsion does not necessarily deter the adsorption of molecules with large uncharged moieties (e.g., surfactants). In these cases, the mechanism of adsorption is dominated by van der Waals interactions, with the surface charge playing a relatively minor role

Insights into the Fallback Path of Best-Effort Hardware Transactional Memory Systems

DOI 10.1007/978-3-319-43659-3Current industry proposals for Hardware Transactional Memory (HTM) focus on best-effort solutions (BE-HTM) where hardware limits are imposed on transactions. These designs may show a significant performance degradation due to high contention scenarios and different hardware and operating system limitations that abort transactions, e.g. cache overflows, hardware and software exceptions, etc. To deal with these events and to ensure forward progress, BE-HTM systems usually provide a software fallback path to execute a lock-based version of the code. In this paper, we propose a hardware implementation of an irrevocability mechanism as an alternative to the software fallback path to gain insight into the hardware improvements that could enhance the execution of such a fallback. Our mechanism anticipates the abort that causes the transaction serialization, and stalls other transactions in the system so that transactional work loss is mini- mized. In addition, we evaluate the main software fallback path approaches and propose the use of ticket locks that hold precise information of the number of transactions waiting to enter the fallback. Thus, the separation of transactional and fallback execution can be achieved in a precise manner. The evaluation is carried out using the Simics/GEMS simulator and the complete range of STAMP transactional suite benchmarks. We obtain significant performance benefits of around twice the speedup and an abort reduction of 50% over the software fallback path for a number of benchmarks.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A systematic review of commercial cognitive training devices: Implications for use in sport

 This is the final version. Available from Frontiers Media via the DOI in this record.Background: Cognitive training (CT) aims to develop a range of skills, like attention and decision-making, through targeted training of core cognitive functions. While CT can target context specific skills, like movement anticipation, much CT is domain general, focusing on core abilities (e.g., selective attention) for transfer to a range of real-world tasks, such as spotting opponents. Commercial CT (CCT) devices are highly appealing for athletes and coaches due to their ease of use and eye-catching marketing claims. The extent to which this training transfers to performance in the sporting arena is, however, unclear. Therefore, this paper sought to provide a systematic review of evidence for beneficial training effects of CCT devices and evaluate their application to sport. Methods: An extensive search of electronic databases (PubMed, PsychInfo, GoogleScholar, and SportDiscus) was conducted to identify peer-reviewed evidence of training interventions with commercially available CT devices. Forty-three studies met the inclusion criteria and were retained for quality assessment and synthesis of results. Seventeen studies assessed transfer effects beyond laboratory cognitive tests, but only 1 directly assessed transfer to a sporting task. Results: The review of evidence showed limited support for far transfer benefits from CCT devices to sporting tasks, mainly because studies did not target the sporting environment. Additionally, a number of methodological issues with the CCT literature were identified, including small sample sizes, lack of retention tests, and limited replication of findings by researchers independent of the commercial product. Therefore, evidence for sporting benefits is currently limited by the paucity of representative transfer tests and a focus on populations with health conditions. Conclusions: Currently there is little direct evidence that the use of CCT devices can transfer to benefits for sporting performance. This conclusion, however, stems more from a lack of experimental studies in the sporting field and a lack of experimental rigor, rather than convincing null effects. Subsequently, there is an opportunity for researchers to develop more reliable findings in this area through systematic assessment in athletic populations and major methodological improvements.Defence Human Capability Science and Technology Centre, U

An external focus of attention promotes flow experience during simulated driving

This is the author accepted manuscript. The final version is available from Taylor & Francis via the DOI in this record.Achieving a state of flow is associated with positive experiences and improved sporting performance (Jackson & Csikszentmihalyi, 1999). Focused attention is a fundamental component of the flow experience, but to date there has been little investigation of whether attention plays a causal role in creating flow, or is a product of it. Consequently, this study aimed to test the effect of an attentional focus manipulation on flow and performance in a simulated driving task. It was predicted that an external focus would lead to improved visuomotor control, greater flow experience and improved performance. Thirty-three participants from a student population completed the driving task under both internal and external focus instructions. Eye movements and steering wheel movements were recorded during each race. Participants reported greater flow experience (p 0.28). These findings suggest that adopting an external focus of attention may contribute to positive performance states such as flow

To err again is human: exploring a bidirectional relationship between pressure and performance failure feedback

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordBackground and Objectives:While the potentially negative effects of pressure on skilled performance have been well studied in laboratory- based research, theoretically driven questions based on real-world performance data are lacking. Design:We aimed to test the predictions of the newly developed Attentional Control Theory: Sport (ACTS), using archived play-by-play data from the past seven seasons of the National Football League (American Football). Methods:An additive scoring system was developed to characterize the degree of pressure on 212,356 individual offensive plays and a Bayesian regression model was used to test the relationship between performance, pressure and preceding negative outcomes, as outlined in ACTS. Results:There was found to be a clear increase in the incidence of failures on high pressure plays (odds ratio = 1.20), and on plays immediately following a previous play failure (odds ratio = 1.09). Additionally, a combined interactive effect of previous failureandpressure indicated that the feedback effect of negative outcomes was greater when pressure was already high (odds ratio = 1.10), in line with the predictions of ACTS. Conclusions:Thesefindings reveal the importance of exploring momentary changes in pressure in real-world sport settings, and the role of failure feedback in influencing the pressure-performance relationship

Virtually the same? How impaired sensory information in virtual reality may disrupt vision for action

This is the final version. Available on open access from Springer via the DOI in this recordVirtual reality (VR) is a promising tool for expanding the possibilities of psychological experimentation and implementing immersive training applications. Despite a recent surge in interest, there remains an inadequate understanding of how VR impacts basic cognitive processes. Due to the artificial presentation of egocentric distance cues in virtual environments, a number of cues to depth in the optic array are impaired or placed in conflict with each other. Moreover, realistic haptic information is all but absent from current VR systems. The resulting conflicts could impact not only the execution of motor skills in VR but also raise deeper concerns about basic visual processing, and the extent to which virtual objects elicit neural and behavioural responses representative of real objects. In this brief review, we outline how the novel perceptual environment of VR may affect vision for action, by shifting users away from a dorsal mode of control. Fewer binocular cues to depth, conflicting depth information and limited haptic feedback may all impair the specialised, efficient, online control of action characteristic of the dorsal stream. A shift from dorsal to ventral control of action may create a fundamental disparity between virtual and real-world skills that has important consequences for how we understand perception and action in the virtual world.Royal Academy of Engineering (RAE

Plate-impact loading of cellular structures formed by selective laser melting

Studies of the shock loading of porous material have the potential to improve our understanding of factors such as density, crush strength and pore size on energy absorbing capability. Porous components were manufactured using Selective Laser Melting (SLM) in which layers of metal powder are fused together to create a structure specified by an electronic file. Samples have been manufactured in which a lattice is formed by an array of intersecting rods angled at 45 degrees to the surface of a 6 mm thick x ~100 mm diameter disc. The cell size is 1 mm3 and the density is 44.6% of solid. A 100 mm gas gun has been used to impact the porous samples onto solid stainless steel plates. Het-V laser interferometry was used to measure the velocity vs. time profile of the transmitted shock. The experimental results were compared with three dimensional computer predictions. It was found that the simulations reproduced the main features of the experimental record but tended to underestimate the measured velocities, suggesting that the codes were not calculating the energy absorbed by the lattice correctly. Additional calculations were performed with the aim of building a picture of the processes of energy absorption in cellular materials whose structure is varied systematically. These supporting studies suggest a possible explanation for the observed computational/experimental discrepancies. © 2012 British Crown

Correction: Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning.

Correction for 'Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning' by Hewa G. S. Wijesinghe et al., Analyst, 2021, DOI: 10.1039/d1an00546d