Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle.

Observing errors in a combination of error and correct models favors observational motor learning

Background Imitative learning is highly effective from infancy to old age; however, little is known about the effects of observing errors during imitative learning. This study aimed to examine how observing errors affected imitative learning performance to maximize its effect. Methods In the pre-training session, participants were instructed to pinch at a target force (8 N) with auditory feedback regarding generated force while they watched videos of someone pinching a sponge at the target force. In the pre-test, participants pinched at the target force and did not view a model or receive auditory feedback. In Experiment 1, in the main training session, participants imitated models while they watched videos of pinching at either the incorrect force (error-mixed condition) or target force (correct condition). Then, the exact force generated was measured without receiving auditory feedback or viewing a model. In Experiment 2, using the same procedures, newly recruited participants watched videos of pinching at incorrect forces (4 and 24 N) as the error condition and the correct force as the correct condition. Results In Experiment 1, the average force was closer to the target force in the error-mixed condition than in the correct condition. In Experiment 2, the average force in the correct condition was closer to the target force than in the error condition. Conclusion Our findings indicated that observing error actions combined with correct actions affected imitation motor learning positively as error actions contained information on things to avoid in the target action. It provides further information to enhance imitative learning in mixed conditions compared to that with correct action alone.

The impact of aging and reaching movements on grip stability control during manual precision tasks

Background Operating an object by generating stable hand-grip force during static or dynamic posture control of the upper extremities simultaneously is an important daily activity. Older adults require different attentional resources during grip strength control and arm movements. However, the impact of aging and reaching movements on precise grip strength and stability control among older adults is not well understood. This study investigated the impact of aging and reaching movements on grip strength and stability control in both hands of the upper extremities. Methods Fifty healthy young adults (age: 28.8 ± 14.0 years) and 54 healthy older adults (73.6 ± 6.3 years) were recruited to perform isometric grip strength test at 20% maximal voluntary contraction as the target force during three manual precision tasks simultaneously: stationary task (without arm movements), forward-reach task, and backward-reach task. The average grip force (in kg) and coefficient of variation values (expressed as a percentage) during manual precision tasks were calculated to determine the quality of participants’ grip strength. The deviation error, absolute error, and force-stability index values were calculated to determine the strength control relative to the target force. Results For both the young and older groups, the force-stability index values in both hands were significantly higher during forward- and backward-reaching movements than in the stationary condition (p < 0.05). The older group exhibited a significantly lower hand-grip strength and stability of strength control in both hands than the young group (p < 0.05). Conclusions Aging and reaching task performance reduced the grip strength of participants and increased the variations in strength control of both hands relative to the target force, indicating that older adults exhibit poor grip strength and stability control when performing arm-reaching movements. These findings may help clinical therapists in establishing objective indexes for poor grip-stability control screening and developing appropriate rehabilitation programs or health-promotion exercises that can improve grip strength and stability control in older people.

Control of a reversible electric machine included in the vehicle suspension

The relevance of the work is due to the constantly growing requirements for the ride comfort of automobiles. The purpose of the study is a rational choice and combination of principles for constructing an algorithm for controlling an electric machine, replacing a hydraulic damper in the design of a vehicle’s suspension system. The study of the behavior of suspension, depending on the applied control algorithms, was carried out by the method of mathematical modeling. In this work, the control of the suspension of one wheel was considered. The angular and longitudinal oscillations of the body were not the subject of this study. In this regard, the applied design scheme is two-mass. The positive and negative aspects of various principles for calculating the target force generated by an electric machine are considered, and an algorithm for calculating the magnetic flux and armature current of an electric machine necessary for the implementation of the target force under various conditions is developed. It is shown that the calculation of the target force should be based on a combination of several principles, since this allows significant expanding of the suspension operating conditions range.

Observing Errors in a Combination of Error and Correct Models Favors Observational Motor Learning

Background:Imitative learning is highly effective from infancy to old age, but little is known about the effects of observing errors during imitative learning. This study aims to examine how observing errors affect imitative learning performance, to maximize the effects of imitative learning. Method：In the pre-training session, participants were instructed to pinch at the target force (8 N) with auditory feedback about generated force while watching videos of someone pinching a sponge at the target force. In the pre-test, participants pinched at the target force without viewing a model or receiving auditory feedback. In Experiment 1, in the main training session, participants imitated models while watching videos of pinching at either the incorrect force (error-mixed condition) or the target force (all-correct condition). Then, the exact force they generated in pinching was measured without receiving auditory feedback or viewing a model. In Experiment 2, using the same procedure in the pre-training and pre-test sessions, newly recruited participants watched pinching at incorrect forces (4 and 24 N) as the all-error condition and the correct force as the correct condition. Results: In Experiment 1, the average force was better in the error-mixed condition than in the correct condition. In Experiment 2, the average force in the correct condition was better than that in the error condition.Conclusion: Our findings indicate that observing error actions combined with correct actions affected imitation motor learning positively, because error actions contain what-not-to-do information about the target action, unlike correct actions, which provide more information to enhance imitative learning.

Numerical simulation of acoustic signal propagation in underwater acoustic duct

Object and purpose of research. The progress in numerical simulation methods significantly widens the capabilities of theoretical analysis in the tasks requiring extensive calculations and input data sets, like sound propagation at sea. This paper discusses the feasibility of a numerical model describing the physics of acoustic signal propagation in a deep-water channel. Materials and methods. Acoustic signal calculation is performed as per the ray-path theory with a numerical model taking into account depth-wise variations of sound velocity and seabed parameters. Main results. It was shown that depending on the vertical distribution of sound speed, the source depth and distance, the acoustic wave propagation direction can change over significant range of angles the in vertical plane. In this regard it is advisable to calculate the real target force of an object of complex geometry not only from heading angle in horizontal plane but also in terms of the possible range of angles in the vertical plane. Conclusion. Model-analyzed angles range of long-range wave propagation may be used for change estimation of object target force characteristics. Practical significance of the study lies in improving the methods of calculation of the real target force of complex shape objects in terms of state-of the art capabilities of simulating the propagation of acoustic signals conditions in the ocean.

An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

The alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.

Exploring the relationship between effort perception and poststroke fatigue

ObjectiveTo test the hypothesis that poststroke fatigue, a chronic, pathologic fatigue condition, is driven by altered effort perception.MethodsFifty-eight nondepressed, mildly impaired stroke survivors with varying severity of fatigue completed the study. Self-reported fatigue (trait and state), perceived effort (PE; explicit and implicit), and motor performance were measured in a handgrip task. Trait fatigue was measured with the Fatigue Severity Scale-7 and Neurologic Fatigue Index. State fatigue was measured with a visual analog scale (VAS). Length of hold at target force, overshoot above target force, and force variability in handgrip task were measures of motor performance. PE was measured with a VAS (explicit PE) and line length estimation, a novel implicit measure of PE.ResultsRegression analysis showed that 11.6% of variance in trait fatigue was explained by implicit PE (R = 0.34; p = 0.012). Greater fatigue was related to longer length of hold at target force (R = 0.421, p < 0.001). A backward regression showed that length of hold explained explicit PE in the 20% force condition (R = 0.306, p = 0.021) and length of hold and overshoot above target force explained explicit PE in the 40% (R = 0.399, p = 0.014 and 0.004) force condition. In the 60% force condition, greater explicit PE was explained by higher force variability (R = 0.315, p = 0.017). None of the correlations were significant for state fatigue.ConclusionTrait fatigue, but not state fatigue, correlating with measures of PE and motor performance, may suggest that altered perception may lead to high fatigue mediated by changes in motor performance. This finding furthers our mechanistic understanding of poststroke fatigue.

Clustering Golfers through Force Plate Analysis

Golf is a sport which requires players to use ground interaction to generate clubhead speed in order to propel the ball towards the target. Force platforms are a technology which can be used to measure these ground reaction forces. Golfers generate force through a combination of jumping, sliding or twisting actions during the swing. Understanding how golfers generate these forces and if there are any groups which golfers could be clustered into could be used to enhance golf instruction as well as clubhead design or fitting practices for golf equipment. A total of 105 right-handed experienced golfers (handicap mean = 8.32 ± 8.31) consented to participate in the study of different swing speeds (31 below 95 mph, 41 over 105 mph and 33 between 95 and 105 mph). A calibrated single force plate was used for the test which sampled at 1000 Hz and recorded force and moment data in three axes. After a self-guided warm up, the players were instructed to hit five 7-iron shots and five drives to the best of their ability in an indoor hitting bay which used a launch monitor to record the club delivery and ball flight information. It was found that handicap or swing speed did not dictate the primary force production mechanism (sliding, jumping or twisting/spinning). This knowledge could aid engineers to design equipment better suited to the individual and help coaches build individualized programs to create power and clubhead speed in all players.