Santa Fe Institute

About: Santa Fe Institute is a nonprofit organization based out in Santa Fe, New Mexico, United States. It is known for research contribution in the topics: Population & Complex network. The organization has 558 authors who have published 4558 publications receiving 396015 citations. The organization is also known as: SFI.

Modeling the interaction of the immune system with HIV

Abstract: The interactions between the human immune system and HIV are potentially complex. In this paper I review some of these interactions and sketch the beginnings of a general model that can potentially account for many of the immunological consequences of HIV infection. This model involves a large number of ordinary differential equations and many parameters. To make progress, I simplify the general model and develop a four-equation model that involves free HIV and uninfected, latently infected and actively infected CD4+ T cells. Using reasonable guesses for parameter values, I show that this model can account for some of the puzzling features of AIDS: the long latent period, the almost complete absence of free virus particles, the low frequency of infected T4 cells and the slow T cell depletion seen during the course of the disease. Further, the model suggests why the latent period may be significantly shorter in children than in adults.

Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits

Abstract: Many important evolutionary adaptations originate in the modification of gene regulatory circuits to produce new gene activity phenotypes. How do evolving populations sift through an astronomical number of circuits to find circuits with new adaptive phenotypes? The answer may often involve phenotypic plasticity. Phenotypic plasticity allows a genotype to produce different - alternative - phenotypes after non-genetic perturbations that include gene expression noise, environmental change, or epigenetic modification. We here analyze a well-studied model of gene regulatory circuits. A circuit's genotype encodes the regulatory interactions among circuit genes, and its phenotype corresponds to a stable gene activity pattern the circuit forms. For this model, we study how genotypes are arranged in genotype space, where the distance between two genotypes reflects the number of regulatory mutations that set those genotypes apart. Specifically, we address whether this arrangement favors adaptive evolution mediated by plasticity. We find that plasticity facilitates the origin of genotypes that produce a new phenotype in response to non-genetic perturbations. We also find that selection can then stabilize the new phenotype genetically, allowing it to become a circuit's dominant gene expression phenotype. These are generic properties of the circuits we study here. Taken together, our observations suggest that phenotypic plasticity frequently facilitates the evolution of novel beneficial gene activity patterns in gene regulatory circuits.

Random quantum states

Abstract: This paper examines the statistical properties of random quantum states, for four different kinds of random state:(1) a pure state chosen at random with respect to the uniform measure on the unit sphere in a finite-dimensional Hilbert space;(2) a random pure state in a real space;(3) a pure state chosen at random except that a certain expectation value is fixed;(4) a random mixed state with fixed eigenvalues. For the first two of these, we give examples of simple states of a model system, the kicked top, which have the statistical properties of random states. Interestingly, examples of both kinds of randomness can be found in the same system. In studying the last two kinds of random state, we obtain new results concerning the application of information theory to quantum systems.

Detectability Thresholds and Optimal Algorithms for Community Structure in Dynamic Networks

Abstract: Dynamic networks are common in complex systems, and coarse-graining their evolving structure is a key step to understanding them. General mathematical tools for identifying the theoretical limits of such methods are presented.