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.     

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.     

Computational Oral Absorption Simulation for Low‐Solubility Compounds

Bile micelles play an important role in oral absorption of low‐solubility compounds. Bile micelles can affect solubility, dissolution rate, and permeability. For the pH–solubility profile in bile micelles, the Henderson–Hasselbalch equation should be modified to take bile‐micelle partition into account. For the dissolution rate, in the Nernst–Brunner equation, the effective diffusion coefficient in bile‐micelle media should be used instead of the monomer diffusion coefficient. The diffusion coefficient of bile micelles is 8‐ to 18‐fold smaller than that of monomer molecules. For permeability, the effective diffusion coefficient in the unstirred water layer adjacent to the epithelial membrane, and the free fraction at the epithelial membrane surface should be taken into account. The importance of these aspects is demonstrated here using several in vivo and clinical oral‐absorption data of low‐solubility model compounds. Using the theoretical equations, the food effect on oral absorption is further discussed.     

Dynamic Time Warping compared to established methods for validation of musculoskeletal models

By means of Multi-Body musculoskeletal simulation, important variables such as internal joint forces and moments can be estimated which cannot be measured directly. Validation can ensued by qualitative or by quantitative methods. Especially when comparing time-dependent signals, many methods do not perform well and validation is often limited to qualitative approaches. The aim of the present study was to investigate the capabilities of the Dynamic Time Warping (DTW) algorithm for comparing time series, which can quantify phase as well as amplitude errors. We contrast the sensitivity of DTW with other established metrics: the Pearson correlation coefficient, cross-correlation, the metric according to Geers, RMSE and normalized RMSE.This study is based on two data sets, where one data set represents direct validation and the other represents indirect validation. Direct validation was performed in the context of clinical gait-analysis on trans-femoral amputees fitted with a 6 component force-moment sensor. Measured forces and moments from amputees' socket-prosthesis are compared to simulated forces and moments. Indirect validation was performed in the context of surface EMG measurements on a cohort of healthy subjects with measurements taken of seven muscles of the leg, which were compared to simulated muscle activations.Regarding direct validation, a positive linear relation between results of RMSE and nRMSE to DTW can be seen. For indirect validation, a negative linear relation exists between Pearson correlation and cross-correlation.We propose the DTW algorithm for use in both direct and indirect quantitative validation as it correlates well with methods that are most suitable for one of the tasks. However, in DV it should be used together with methods resulting in a dimensional error value, in order to be able to interpret results more comprehensible.     

Hydrological Forecasting in the Oder Estuary using a Three- Dimensional Hydrodynamic Model

A three-dimensional operational hydrodynamic model, developed at the Institute of Oceanography, University of Gdańsk was used to forecast hydrological conditions in the Oder Estuary. The model was based on the coastal ocean circulation model known as the Princeton Ocean Model (POM). Because of wind-driven water backup in the Oder mouth, a simplified operational model of river discharge, based on water budget in a stream channel, was developed. Linking these two models into a single system made it possible to forecast water levels, currents, water temperature, and salinity in the estuary. A good fit between the observed and computed data allowed to consider the model as a reliable environmental tool. Obtaining a hydrological forecast via a quick website access gives potential users an opportunity to predict the day-by-day course of processes that may affect different areas of human life and activities, e.g., navigation, port operations, flood protection of coastal areas; the predictions may also be used in studies of coastal processes in the estuary.