Importance of force decomposition for local stress calculations in biomembrane molecular simulations

Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving-Kirkwood-Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise contributions. However, such a decomposition is not unique in general, leading to an ambiguity in the definition of the stress tensor, particularly for multibody potentials. Furthermore, a theoretical treatment of constraints in local stress calculations has been lacking. Here, we present a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decomposition, that leads to a symmetric stress tensor by construction. We focus on biomembranes, although the methodology presented here is widely applicable. Our results show that some unphysical behavior obtained with previous implementations (e.g. nonconstant normal stress profiles along an isotropic bilayer in equilibrium) is a consequence of an improper treatment of constraints. Furthermore, other valid force decompositions produce significantly different stress profiles, particularly in the presence of dihedral potentials. Our methodology reveals the striking effect of unsaturations on the bilayer mechanics, missed by previous stress calculation implementations

Evaluation of the Tobii EyeX Eye tracking controller and Matlab toolkit for research

The Tobii Eyex Controller is a new low-cost binocular eye tracker marketed for integration in gaming and consumer applications. The manufacturers claim that the system was conceived for natural eye gaze interaction, does not require continuous recalibration, and allows moderate head movements. The Controller is provided with a SDK to foster the development of new eye tracking applications. We review the characteristics of the device for its possible use in scientific research. We develop and evaluate an open source Matlab Toolkit that can be employed to interface with the EyeX device for gaze recording in behavioral experiments. The Toolkit provides calibration procedures tailored to both binocular and monocular experiments, as well as procedures to evaluate other eye tracking devices. The observed performance of the EyeX (i.e. accuracy < 0.6°, precision < 0.25°, latency < 50 ms and sampling frequency ≈55 Hz), is sufficient for some classes of research application. The device can be successfully employed to measure fixation parameters, saccadic, smooth pursuit and vergence eye movements. However, the relatively low sampling rate and moderate precision limit the suitability of the EyeX for monitoring micro-saccadic eye movements or for real-time gaze-contingent stimulus control. For these applications, research grade, high-cost eye tracking technology may still be necessary. Therefore, despite its limitations with respect to high-end devices, the EyeX has the potential to further the dissemination of eye tracking technology to a broad audience, and could be a valuable asset in consumer and gaming applications as well as a subset of basic and clinical research settings

Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

Coiled-coils are filamentous proteins that form the basic building block of important force-bearing cellular elements, such as intermediate filaments and myosin motors. In addition to their biological importance, coiled-coil proteins are increasingly used in new biomaterials including fibers, nanotubes, or hydrogels. Coiled-coils undergo a structural transition from an a-helical coil to an unfolded state upon extension, which allows them to sustain large strains and is critical for their biological function. By performing equilibrium and out-of-equilibrium all-atom molecular dynamics (MD) simulations of coiledcoils in explicit solvent, we show that two-state models based on Kramers&rsquo; or Bell&rsquo;s theories fail to predict the rate of unfolding at high pulling rates. We further show that an atomistically informed continuum rod model accounting for phase transformations and for the hydrodynamic interactions with the solvent can reconcile two-state models with our MD results. Our results show that frictional forces, usually neglected in theories of fibrous protein unfolding, reduce the thermodynamic force acting on the interface, and thus control the dynamics of unfolding at different pulling rates. Our results may help interpret MD simulations at high pulling rates, and could be pertinent to cytoskeletal networks or protein-based artificial materials subjected to shocks or blasts