Multivalent ions (Mg2+) in RNA tertiary structure folding can be strongly correlated and thus cannot be treated by mean-field theories such as the Poisson-Boltzmann equation. We recently developed a statistical mechanical model (TBI) to account for ion correlation by considering ensemble of discrete ion distributions. Experimental tests show tha...
Creator:
Chen, Shi-Jie (University of Missouri)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
This talk (and a related poster) describes Lie-group-theoretic techniques that can be applied in the analysis and modeling of protein conformations. Three topics are covered: (1) Conformational transitions between two known end states; (2) proper normalization of helix-helix crossing angle data in the PDB; (3) models of the conformational entrop...
Creator:
Chirikjian, Gregory S. (Johns Hopkins University)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Can genomics provide a new level of strategic intelligence about rapidly evolving pathogens? We have developed a new approach to measure the rates of all possible evolutionary pathways in a genome, using conditional Ka/Ks to estimate their "evolutionary velocity", and have applied this to several datasets, including clinical sequencing of 50,000...
Creator:
Lee, Christopher J. (University of California, Los Angeles)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
While equilibrium free energy differences can be obtained from simulations of non-equilibrium systems,such estimates are often hampered by convergence difficulties similar to those that plague traditionalperturbation methods. In the nonequilibrium context, dissipation is the culprit behind poor convergence.I will discuss a general strategy for a...
Creator:
Jarzynski, Christopher (University of Maryland)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Efficient exploration of the configuration space of a protein is essential for its structure prediction. In this talk we will consider two recent Monte Carlo developments for such a task: (i) equi-energy (EE) sampler and (ii) fragment regrowth via energy-guided sequential sampling (FRESS). The EE sampler provides accurate estimation of the densi...
Creator:
Kou, Samuel (Harvard University)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Biological networks that arise in signal transduction, metabolism, gene control or other cellular functions frequently involve many steps and many levels of control, but are remarkably reliable in producing the desired output in response to inputs. In this talk we will discuss general characteristics such as sensitivity and adaptation of network...
Creator:
Othmer, Hans G. (University of Minnesota, Twin Cities)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
RNA tertiary motifs play an important role in RNA folding. To understand the complex organization of RNA tertiary interactions, we compiled a dataset containing 54 high-resolution RNA crystal structures. Seven RNA tertiary motifs (coaxial helix, A-minor, ribose zipper, pseudoknot, kissing hairpin, tRNA D-loop:T-loop and tetraloop-tetraloop recep...
Creator:
Laing, Christian E. (New York University)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.