An Introduction to Rule-based Modeling of Immune Receptor Signaling

Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory response) depending on the type and number of receptor molecules on the cell surface and the specific intracellular signaling pathways activated by those receptors. Explicitly modeling and simulating kinetic interactions between molecules allows us to pose questions about the dynamics of a signaling network under various conditions. However, the application of chemical kinetics to biochemical signaling systems has been limited by the complexity of the systems under consideration. Rule-based modeling (BioNetGen, Kappa, Simmune, PySB) is an approach to address this complexity. In this chapter, by application to the Fc$\varepsilon$RI receptor system, we will explore the origins of complexity in macromolecular interactions, show how rule-based modeling can be used to address complexity, and demonstrate how to build a model in the BioNetGen framework. Open source BioNetGen software and documentation are available at http://bionetgen.org.Comment: 5 figure

Germanium quantum dots: Optical properties and synthesis

Three different size distributions of Ge quantum dots (>~200, 110, and 60 Å) have been synthesized via the ultrasonic mediated reduction of mixtures of chlorogermanes and organochlorogermanes (or organochlorosilanes) by a colloidal sodium/potassium alloy in heptane, followed by annealing in a sealed pressure vessel at 270 °C. The quantum dots are characterized by transmission electron microscopy, x-ray powder diffraction, x-ray photoemission, infrared spectroscopy, and Raman spectroscopy. Colloidal suspensions of these quantum dots were prepared and their extinction spectra are measured with ultraviolet/visible (UV/Vis) and near infrared (IR) spectroscopy, in the regime from 0.6 to 5 eV. The optical spectra are correlated with a Mie theory extinction calculation utilizing bulk optical constants. This leads to an assignment of three optical features to the E(1), E(0'), and E(2) direct band gap transitions. The E(0') transitions exhibit a strong size dependence. The near IR spectra of the largest dots is dominated by E(0) direct gap absorptions. For the smallest dots the near IR spectrum is dominated by the Gamma25-->L indirect transitions

Partial breakdown of quantum thermalization in a Hubbard-like model

We study the possible breakdown of quantum thermalization in a model of itinerant electrons on a one-dimensional chain without disorder, with both spin and charge degrees of freedom. The eigenstates of this model exhibit peculiar properties in the entanglement entropy, the apparent scaling of which is modified from a "volume law" to an "area law" after performing a partial, site-wise measurement on the system. These properties and others suggest that this model realizes a new, non-thermal phase of matter, known as a quantum disentangled liquid (QDL). The putative existence of this phase has striking implications for the foundations of quantum statistical mechanics.Comment: As accepted to PR

Roughening and inclination of competition interfaces

The competition interface between two growing ``Young clusters'' (diagrams), in a two-dimensional random cone, is mapped to the path of a second-class particle in the one-dimensional totally asymmetric simple exclusion process. Using the asymptotics of the second class particle and hydrodynamic limits for the exclusion process (Burgers equation), we show that the behavior of the competition interface depends on the angle of the cone: for angles in [180^o, 270^o) the competition interface has a deterministic inclination, while for angles in [90^o,180^o) the inclination is random. We relate the competition model to a model of random directed polymers, and obtain some partial results for the fluctuations of the competition interface.Comment: 4 pages, 3 figure

The dynamics and control of large flexible space structures, 3. Part A: Shape and orientation control of a platform in orbit using point actuators

The dynamics, attitude, and shape control of a large thin flexible square platform in orbit are studied. Attitude and shape control are assumed to result from actuators placed perpendicular to the main surface and one edge and their effect on the rigid body and elastic modes is modelled to first order. The equations of motion are linearized about three different nominal orientations: (1) the platform following the local vertical with its major surface perpendicular to the orbital plane; (2) the platform following the local horizontal with its major surface normal to the local vertical; and (3) the platform following the local vertical with its major surface perpendicular to the orbit normal. The stability of the uncontrolled system is investigated analytically. Once controllability is established for a set of actuator locations, control law development is based on decoupling, pole placement, and linear optimal control theory. Frequencies and elastic modal shape functions are obtained using a finite element computer algorithm, two different approximate analytical methods, and the results of the three methods compared