Classifying general nonlinear force laws in cell-based models via the continuum limit

though discrete cell-based frameworks are now commonly used to simulate a whole range of biological phenomena, it is typically not obvious how the numerous different types of model are related to one another, nor which one is most appropriate in a given context. Here we demonstrate how individual cell movement on the discrete scale modeled using nonlinear force laws can be described by nonlinear diffusion coefficients on the continuum scale. A general relationship between nonlinear force laws and their respective diffusion coefficients is derived in one spatial dimension and, subsequently, a range of particular examples is considered. For each case excellent agreement is observed between numerical solutions of the discrete and corresponding continuum models. Three case studies are considered in which we demonstrate how the derived nonlinear diffusion coefficients can be used to (a) relate different discrete models of cell behavior; (b) derive discrete, intercell force laws from previously posed diffusion coefficients, and (c) describe aggregative behavior in discrete simulations.

Performance of palm- based fat blends with a low saturated fat content in puff pastry

Four fat blends based on palm fractions in combination with high oleic sunflower oil (HOSF) with a relatively low saturated fatty acid content (29.2±0.85%, i.e. less than 50% of that of butter) were prepared. The saturated fat was located in different triacylglycerols (TAG) structures in each blend. Principal saturated TAG were derived from palm stearin (POs, containing tripalmitoyl glycerol - PPP), palm mid fraction (PMF, containing 1,3-dipalmitoyl-2-oleoyl glycerol - POP) and interesterified PMF (inPMF, containing PPP, POP and rac-1,2-dipalmitoyl-3-oleoyl glycerol - PPO). Thus, in blend 1, composed of POs and HOSF, the saturates resided principally in PPP. In blend 2, composed of POs, PMF and HOSF, the principal saturate-containing TAG were PPP and POP. Blend 3, composed of inPMF and HOSF, was similar to blend 2 except that the disaturated TAG comprised a 2:1 mixture of PPO:POP. Finally, blend 4, a mixture of PMF and HOSF, had saturates present mainly as POP. The physical properties and the functionality of blends, as shortenings for puff pastry laminated in a warm bakery environment (20-30°C), were compared with each other, and with butter. Puff pastry prepared with blend 1 (POs:HOSF 29:71) and blend 4 (PMF:HOSF 41:59), was very hard; blend 2 (POs:PMF:HOSF 13:19:68) was most similar to butter in the compressibility of the baked product and it performed well in an independent baking trial; blend 3 (inPMF:HOSF 40:60) gave a product that required a higher force for compression than butter.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Extracting and validating force fields for disordered polymeric materials from neutron scattering data

We present a new approach that allows the determination and refinement of force field parameters for the description of disordered macromolecular systems from experimental neutron diffraction data obtained over a large Q range. The procedure is based on tight coupling between experimentally derived structure factors and computer modelling. By separating the potential into terms representing respectively bond stretching, angle bending and torsional rotation and by treating each of them separately, the various potential parameters are extracted directly from experiment. The procedure is illustrated on molten polytetrafluoroethylene.

Extracting force fields for disordered polymeric materials from neutron scattering data

We present a new approach that allows the determination of force-field parameters for the description of disordered macromolecular systems from experimental neutron diffraction data obtained over a large Q range. The procedure is based on a tight coupling between experimentally derived structure factors and computer modelling. We separate the molecular potential into non-interacting terms representing respectively bond stretching, angle bending and torsional rotation. The parameters for each of the potentials are extracted directly from experimental data through comparison of the experimental structure factor and those derived from atomistic level molecular models. The viability of these force fields is assessed by comparison of predicted large-scale features such as the characteristic ratio. The procedure is illustrated on molten poly(ethylene) and poly(tetrafluoroethylene).

Joint servoing for robust manipulator force control

An experimental and theoretical comparison is made of force control performance with different types of innerloop joint servoing techniques. The problem of disturbance rejection and sensitivity to plant dynamics variations (robustness) is addressed. Position, velocity, strain gauge derived joint torque, and current servos are designed and implemented on a specially instrumented industrial robot, and the end-effector force feedback performances achieved are compared. Joint strain derived torque servoing is found to provide the best overall robust force control performance. Experimental results of the robust hard-on-hard contact achieved with the novel force controller implementation based on joint torque sensing are provided. Conclusions are drawn on the force control performance achievable on a geared robot given the joint servoing technique.