RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.     

Force and torque modelling of drilling simulation for orthopaedic surgery

The advent of haptic simulation systems for orthopaedic surgery procedures has provided surgeons with an excellent tool for training and preoperative planning purposes. This is especially true for procedures involving the drilling of bone, which require a great amount of adroitness and experience due to difficulties arising from vibration and drill bit breakage. One of the potential difficulties with the drilling of bone is the lack of consistent material evacuation from the drill's flutes as the material tends to clog. This clogging leads to significant increases in force and torque experienced by the surgeon. Clogging was observed for feed rates greater than 0.5 mm/s and spindle speeds less than 2500 rpm. The drilling simulation systems that have been created to date do not address the issue of drill flute clogging. This paper presents force and torque prediction models that account for this phenomenon. The two coefficients of friction required by these models were determined via a set of calibration experiments. The accuracy of both models was evaluated by an additional set of validation experiments resulting in average R² regression correlation values of 0.9546 and 0.9209 for the force and torque prediction models, respectively. The resulting models can be adopted by haptic simulation systems to provide a more realistic tactile output.     

Wind and fairness in ski jumping: A computer modelling analysis

Wind is closely associated with the discussion of fairness in ski jumping. To counter-act its influence on the jump length, the International Ski Federation (FIS) has introduced a wind compensation approach. We applied three differently accurate computer models of the flight phase with wind (M1, M2, and M3) to study the jump length effects of various wind scenarios. The previously used model M1 is accurate for wind blowing in direction of the flight path, but inaccuracies are to be expected for wind directions deviating from the tangent to the flight path. M2 considers the change of airflow direction, but it does not consider the associated change in the angle of attack of the skis which additionally modifies drag and lift area time functions. M3 predicts the length effect for all wind directions within the plane of the flight trajectory without any mathematical simplification. Prediction errors of M3 are determined only by the quality of the input data: wind velocity, drag and lift area functions, take-off velocity, and weight. For comparing the three models, drag and lift area functions of an optimized reference jump were used. Results obtained with M2, which is much easier to handle than M3, did not deviate noticeably when compared to predictions of the reference model M3. Therefore, we suggest to use M2 in future applications. A comparison of M2 predictions with the FIS wind compensation system showed substantial discrepancies, for instance: in the first flight phase, tailwind can increase jump length, and headwind can decrease it; this is opposite of what had been anticipated before and is not considered in the current wind compensation system in ski jumping.     

Monte Carlo-based assessment of the trade-off between spatial resolution,field-of-view and scattered radiation in the variable resolution X-ray CT scanner

ObjectiveThe purpose of this work is to evaluate the impact of optimization of magnification on performance parameters of the variable resolution X-ray (VRX) CT scanner.MethodsA realistic model based on an actual VRX CT scanner was implemented in the GATE Monte Carlo simulation platform. To evaluate the influence of system magnification, spatial resolution, field-of-view (FOV) and scatter-to-primary ratio of the scanner were estimated for both fixed and optimum object magnification at each detector rotation angle. Comparison and inference between these performance parameters were performed angle by angle to determine appropriate object position at each opening half angle.ResultsOptimization of magnification resulted in a trade-off between spatial resolution and FOV of the scanner at opening half angles of 90°–12°, where the spatial resolution increased up to 50% and the scatter-to-primary ratio decreased from 4.8% to 3.8% at a detector angle of about 90° for the same FOV and X-ray energy spectrum. The disadvantage of magnification optimization at these angles is the significant reduction of the FOV (up to 50%). Moreover, magnification optimization was definitely beneficial for opening half angles below 12° improving the spatial resolution from 7.5 cy/mm to 20 cy/mm. Meanwhile, the FOV increased by more than 50% at these angles.ConclusionIt can be concluded that optimization of magnification is essential for opening half angles below 12°. For opening half angles between 90° and 12°, the VRX CT scanner magnification should be set according to the desired spatial resolution and FOV.     

Testing the Equality of Dependent Variances

The likelihood ratio test for testing equality of vgE;2 correlated variables is developed. In general, evaluation of the test statistic involves the iterative optimization of a likelihood function with 1 + v(v – 1)/2 parameters. The explicit form of the test statistic is derived in the bivariate case, and an iterative algorithm for determining the maximum likelihood estimates is suggested. A limited Monte Carlo study determines the behavior of the proposed procedure under the null hypothesis and variety of parameter values.     

Can altered muscle synergies control unimpaired gait?

Recent studies have postulated that the human motor control system recruits groups of muscles through low-dimensional motor commands, or muscle synergies. This scheme simplifies the neural control problem associated with the high-dimensional structure of the neuromuscular system. Several lines of evidence have suggested that neurological injuries, such as stroke or cerebral palsy, may reduce the dimensions that are available to the motor control system, and these altered dimensions or synergies are thought to contribute to impaired walking patterns. However, no study has investigated whether impaired low-dimensional control spaces necessarily lead to impaired walking patterns. In this study, using a two-dimensional model of walking, we developed a synergy-based control framework that can simulate the dynamics of walking. The simulation analysis showed that a synergy-based control scheme can produce well-coordinated movements of walking matching unimpaired gait. However, when the dimensions available to the controller were reduced, the simplified emergent pattern deviated from unimpaired gait. A system with two synergies, similar to those seen after neurological injury, could not produce an unimpaired walking pattern. These findings provide further evidence that altered muscle synergies can contribute to impaired gait patterns and may need to be directly addressed to improve gait after neurological injury.     

Molecular dynamics simulation of isothermal crystallisation of polymer chains around single polymer lamella

The isothermal crystallisation of polyethylene (PE) chains around single PE lamella in vacuum is investigated by molecular dynamic simulation. The crystallisation process is analysed in terms of the orientational order parameters, principal moments of inertia for the simulated systems. The effects of charge interactions between the polymer chains and lamella are discussed. It is found that the crystallisation process for uncharged systems can be divided into three stages: (1) adsorption, (2) orientation and (3) arrangement. The single polymer lamella changes a little during the three stages. PE chains are arranged parallel to the chain direction of the stems in the crystalline state. When considering the effect of charge interactions between the polymer chains and lamella, a different crystallisation process appears. The single polymer lamella is affected by the charged polymer chains.     

Novel Monte Carlo dose calculation algorithm for robotic radiosurgery with multi leaf collimator: Dosimetric evaluation

PurposeAt introduction in 2014, dose calculation for the first MLC on a robotic SRS/SBRT platform was limited to a correction-based Finite-Size Pencil Beam (FSPB) algorithm. We report on the dosimetric accuracy of a novel Monte Carlo (MC) dose calculation algorithm for this MLC, included in the Precision™ treatment planning system.MethodsA phantom was built of one slab (5.0 cm) of lung-equivalent material (0.09…0.29 g/cc) enclosed by 3.5 cm (above) and 5 cm (below) slabs of solid water (1.045 g/cc). This was irradiated using rectangular (15.4 × 15.4 mm² to 53.8 × 53.7 mm²) and two irregular MLC-fields. Radiochromic film (EBT3) was positioned perpendicular to the slabs and parallel to the beam. Calculated dose distributions were compared to film measurements using line scans and 2D gamma analysis.ResultsMeasured and MC calculated percent depth dose curves showed a characteristic dose drop within the low-density region, which was not correctly reproduced by FSPB. Superior average gamma pass rates (2%/1 mm) were found for MC (91.2 ± 1.5%) compared to FSPB (55.4 ± 2.7%). However, MC calculations exhibited localized anomalies at mass density transitions around 0.15 g/cc, which were traced to a simplification in electron transport. Absence of these anomalies was confirmed in a modified build of the MC engine, which increased gamma pass rates to 96.6 ± 1.2%.ConclusionsThe novel MC algorithm greatly improves dosimetric accuracy in heterogeneous tissue, potentially expanding the clinical use of robotic radiosurgery with MLC. In-depth, independent validation is paramount to identify and reduce the residual uncertainties in any software solution.