Browsing by Subject "Topology"
Now showing items 117 of 17


AgeDependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence
(Public Library of Science, 20130628)Proteins interact in complex protein–protein interaction (PPI) networks whose topological properties—such as scalefree topology, hierarchical modularity, and dissortativity—have suggested models of network evolution. ... 
Course summary of geometry and topology
(20110105)The foundation of Luecke’s course M: 396 Geometry and Topology is that collaboration amongst mathematicians and biologists caused tremendous gains in DNA research. The field of topology has led to significant strides in ... 
Creating and utilizing symbolic representations of spatial knowledge using mobile robots
(20120904)A map is a description of an environment allowing an agenta human, or in our case a mobile robotto plan and perform effective actions. From a single location, an agent’s sensors can not observe the whole structure of ... 
Developing a qualitative geometry from the conceptions of young children
(20101202)More than half a century ago, Piaget concluded from an investigation of children’s representational thinking about the nature of space that the development of children’s representational thought is topological before it ... 
Exotic smoothings via large R⁴’s in Stein surfaces
(20151203)We study the relationship between exotic R⁴'s and Stein surfaces as it applies to smoothing theory on more general open 4–manifolds. In particular, we construct the first known examples of large exotic R⁴'s that embed in ... 
Integrating topology into the standard high school geometry curriculum
(20121127)This report conveys some of the modern investigations surrounding the use of topology in a contextual setting. Topics discussed include applications of topology relating to the modeling of biological structures and common ... 
Networkonchip architectures for scalability and service guarantees
(20120713)Rapidly increasing transistor densities have led to the emergence of richlyintegrated substrates in the form of chip multiprocessors and systemsonachip. These devices integrate a variety of discrete resources, such as ... 
On some residual and locally virtual properties of groups
(20100921)We define a strong form of subgroup separability, which we call RS separability, and we use this to combine LERF and Agol’s RFRS condition on groups into a property called LVRSS. We show that some infinite classes of groups ... 
PipeSynth : automated topological and parametric design of fluid networks
(20110216)PipeSynth is a design automation approach that combines various optimization research and artificial intelligence methods for synthesizing fluid networks. Starting with only the port locations, PipeSynth generates and ... 
Pretzel knots of length three with unknotting number one
(20120712)This thesis provides a partial classification of all 3stranded pretzel knots K=P(p,q,r) with unknotting number one. ScharlemannThompson, and independently Kobayashi, have completely classified those knots with unknotting ... 
RAxML and FastTree: Comparing Two Methods for LargeScale Maximum Likelihood Phylogeny Estimation
(Public Library of Science, 20130506)Statistical methods for phylogeny estimation, especially maximum likelihood (ML), offer high accuracy with excellent theoretical properties. However, RAxML, the current leading method for largescale ML estimation, can ... 
Smaller Gene Networks Permit Longer Persistence in FastChanging Environments
(Public Library of Science, 20130506)The environments in which organisms live and reproduce are rarely static, and as the environment changes, populations must evolve so that phenotypes match the challenges presented. The quantitative traits that map to ... 
Smaller, ScaleFree Gene Networks Increase Quantitative Trait Heritability and Result in Faster Population Recovery
(Public Library of Science, 20130506)One of the goals of biology is to bridge levels of organization. Recent technological advances are enabling us to span from genetic sequence to traits, and then from traits to ecological dynamics. The quantitative genetics ... 
State sums in two dimensional fully extended topological field theories
(20110601)A state sum is an expression approximating the partition function of a ddimensional field theory on a closed dmanifold from a triangulation of that manifold. To consider state sums in completely local 2dimensional ... 

Treelength Optimization for Phylogeny Estimation
(Public Library of Science, 20130523)The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, ...