Membrane mediated aggregation of curvature inducing nematogens and membrane tubulation

The shapes of cell membranes are largely regulated by membrane associated, curvature active, proteins. We use a numerical model of the membrane with elongated membrane inclusions, recently developed by us, which posses spontaneous directional curvatures that could be different along and perpendicular to its long axis. We show that, due to membrane mediated interactions these curvature inducing membrane nematogens can oligomerize spontaneously, even at low concentrations, and change the local shape of the membrane. We demonstrate that for a large group of such inclusions, where the two spontaneous curvatures have equal sign, the tubular conformation and sometime the sheet conformation of the membrane are the common equilibrium shapes. We elucidate the factors necessary for the formation of these {\it protein lattices}. Furthermore, the elastic properties of the tubes, like their compressional stiffness and persistence length are calculated. Finally, we discuss the possible role of nematic disclination in capping and branching of the tubular membranes.Comment: 15pages, 8 figure

Semi-Empirical Model for Nano-Scale Device Simulations

We present a new semi-empirical model for calculating electron transport in atomic-scale devices. The model is an extension of the Extended H\"uckel method with a self-consistent Hartree potential. This potential models the effect of an external bias and corresponding charge re-arrangements in the device. It is also possible to include the effect of external gate potentials and continuum dielectric regions in the device. The model is used to study the electron transport through an organic molecule between gold surfaces, and it is demonstrated that the results are in closer agreement with experiments than ab initio approaches provide. In another example, we study the transition from tunneling to thermionic emission in a transistor structure based on graphene nanoribbons.Comment: 8 pages, 8 figures. Submitted to PR

Investigation of the XCAT phantom as a validation tool in cardiac MRI tracking algorithms.

PURPOSE: To describe our magnetic resonance imaging (MRI) simulated implementation of the 4D digital extended cardio torso (XCAT) phantom to validate our previously developed cardiac tracking techniques. Real-time tracking will play an important role in the non-invasive treatment of atrial fibrillation with MRI-guided radiosurgery. In addition, to show how quantifiable measures of tracking accuracy and patient-specific physiology could influence MRI tracking algorithm design. METHODS: Twenty virtual patients were subjected to simulated MRI scans that closely model the proposed real-world scenario to allow verification of the tracking technique's algorithm. The generated phantoms provide ground-truth motions which were compared to the target motions output from our tracking algorithm. The patient-specific tracking error, ep, was the 3D difference (vector length) between the ground-truth and algorithm trajectories. The tracking errors of two combinations of new tracking algorithm functions that were anticipated to improve tracking accuracy were studied. Additionally, the correlation of key physiological parameters with tracking accuracy was investigated. RESULTS: Our original cardiac tracking algorithm resulted in a mean tracking error of 3.7 ± 0.6 mm over all virtual patients. The two combinations of tracking functions demonstrated comparable mean tracking errors however indicating that the optimal tracking algorithm may be patient-specific. CONCLUSIONS: Current and future MRI tracking strategies are likely to benefit from this virtual validation method since no time-resolved 4D ground-truth signal can currently be derived from purely image-based studies

Self-organized stable pacemakers near the onset of birhythmicity

General amplitude equations for reaction-diffusion systems near to the soft onset of birhythmicity described by a supercritical pitchfork-Hopf bifurcation are derived. Using these equations and applying singular perturbation theory, we show that stable autonomous pacemakers represent a generic kind of spatiotemporal patterns in such systems. This is verified by numerical simulations, which also show the existence of breathing and swinging pacemaker solutions. The drift of self-organized pacemakers in media with spatial parameter gradients is analytically and numerically investigated.Comment: 4 pages, 4 figure

Monte Carlo simulations of fluid vesicles with in plane orientational ordering

We present a method for simulating fluid vesicles with in-plane orientational ordering. The method involves computation of local curvature tensor and parallel transport of the orientational field on a randomly triangulated surface. It is shown that the model reproduces the known equilibrium conformation of fluid membranes and work well for a large range of bending rigidities. Introduction of nematic ordering leads to stiffening of the membrane. Nematic ordering can also result in anisotropic rigidity on the surface leading to formation of membrane tubes.Comment: 11 Pages, 12 Figures, To appear in Phys. Rev.

Role of disclinations in determining the morphology of deformable fluid interfaces

We study the equilibrium shapes of vesicles, with an in-plane nematic order, using a Monte-Carlo scheme and show that highly curved shapes, like tubes and discs, with a striking similarity to the structures engendered by certain curvature sensing peripheral membrane proteins, can be spontaneously generated by anisotropic directional curvature with nematic disclinations playing and important role. We show that the coupling between nematic order and local curvature could lead to like defects moving towards each other and unlike defects moving away, in turn leading to tube formation. Thermally induced defect pair production lead to branched tubular structures. It is also shown that helical arrangement of the membrane tubes, with nematic field spiraling around it, is a dominant soft mode of the system.Comment: 6 Figures; Soft Matter, Advance Article 201

Global Hopf bifurcation in the ZIP regulatory system

Regulation of zinc uptake in roots of Arabidopsis thaliana has recently been modeled by a system of ordinary differential equations based on the uptake of zinc, expression of a transporter protein and the interaction between an activator and inhibitor. For certain parameter choices the steady state of this model becomes unstable upon variation in the external zinc concentration. Numerical results show periodic orbits emerging between two critical values of the external zinc concentration. Here we show the existence of a global Hopf bifurcation with a continuous family of stable periodic orbits between two Hopf bifurcation points. The stability of the orbits in a neighborhood of the bifurcation points is analyzed by deriving the normal form, while the stability of the orbits in the global continuation is shown by calculation of the Floquet multipliers. From a biological point of view, stable periodic orbits lead to potentially toxic zinc peaks in plant cells. Buffering is believed to be an efficient way to deal with strong transient variations in zinc supply. We extend the model by a buffer reaction and analyze the stability of the steady state in dependence of the properties of this reaction. We find that a large enough equilibrium constant of the buffering reaction stabilizes the steady state and prevents the development of oscillations. Hence, our results suggest that buffering has a key role in the dynamics of zinc homeostasis in plant cells.Comment: 22 pages, 5 figures, uses svjour3.cl

Expansion algorithm for the density matrix

A purification algorithm for expanding the single-particle density matrix in terms of the Hamiltonian operator is proposed. The scheme works with a predefined occupation and requires less than half the number of matrix-matrix multiplications compared to existing methods at low (90%) occupancy. The expansion can be used with a fixed chemical potential in which case it is an asymmetric generalization of and a substantial improvement over grand canonical McWeeny purification. It is shown that the computational complexity, measured as number of matrix multiplications, essentially is independent of system size even for metallic materials with a vanishing band gap.Comment: 5 pages, 4 figures, to appear in Phys. Rev.