Session Information (Location: Room 2408)

Mathematical Biology

Session Organizers: Selenne Bañuelos (CSU Channel Islands), Carrie Diaz Eaton (Unity College), and Alicia Prieto Langarica (Youngstown State University).
Session Speakers: Sara Del Valle (Los Alamos National Laboratory), German Enciso Ruiz (UC Irvine), Emilia Huerta-Sanchez (UC Merced), Christian Laing (Navigate BioPharma), and Joseph Teran (UCLA).

LOCATION: Room 2408

2:00 - 2:25 Joseph Teran (UCLA)
2:30 - 2:55 Emilia Huerta-Sanchez (UC Merced)
3:00 - 3:30 Coffee Break
3:30 - 3:55 German Enciso Ruiz (UC Irvine)
4:00 - 4:25 Sara Del Valle (Los Alamos National Laboratory)
4:30 - 4:55 Christian Laing (Navigate BioPharma)

Sara Del Valle (Los Alamos National Laboratory)
Title: Real-time Social Internet Data to Guide Disease Forecasting Models
Abstract: Globalization has created complex problems that can no longer be adequately forecasted and mitigated using traditional data analysis techniques and data sources. Disease spread is major health concern around the world and it is compounded by the increasing globalization of our society. As such, epidemiological modeling approaches need to account for rapid changes in human behavior and community perceptions. Social media has recently played a crucial role in informing and changing people’s response to the spread of infectious diseases. Recent events such as the 2014-2015 Ebola epidemic and the 2015-2016 Zika virus epidemic have highlighted the importance of reliable disease forecasting for decision support. In this talk, I will discuss a framework that combines clinical surveillance data with social Internet data and mathematical models to provide probabilistic forecasts of disease incidence. In addition, I will demonstrate the value of Internet data and the real-time utility of our approach.

German Enciso (UC Irvine)
Title: Cell Fate Decision in Chlamydia Trachomatis
Abstract: Chlamydia trachomatis is the most common cause of bacterial sexually transmitted infection. It can also infect the eyes and is a major cause of blindness in many developing countries. During the infection of a mammalian host, Chlamydia must decide when to proliferate and when to convert into a differentiated form, since the differentiated form is the only form to survive outside the host but cannot reproduce. We study the question of Chlamydia cell fate regulation using experimental data as well as stochastic mathematical modeling.

Emilia Huerta-Sanchez (UC Merced)
Title: The landscape of archaic variants in present-day humans
Abstract: From fossil data, we know that Neanderthals lived in Eurasia before modern humans migrated there from Africa. Neanderthals and modern humans inhabited the same continent for several thousands of years. Recent studies, using DNA sequence data from Neanderthals and modern humans, have shown that present-day humans carry traces of Neanderthal DNA providing evidence that Neanderthals interbred with modern humans. While the surviving Neanderthal DNA within a single individual is small, their DNA is harbored in genes involved in metabolism, skin pigmentation, the immune system and hypoxia potentially having a big impact. In this talk, I will discuss how we can use computational approaches to study the distribution of these variants in present-day humans to provide new insights into their biology and evolutionary history.

Christian Laing (Navigate Biopharma)
Title: Analysis of RNA tertiary structure and tertiary motifs: Insights into RNA prediction
Abstract: In recent years, many exciting discoveries have exposed the versatility of RNA. Clearly more findings are yet to come given the many novel non-protein-coding transcripts recently identified, and the structure-function relationship that exists within RNA molecules emphasizes the necessity to build more efficient computer programs to predict their structure. In this talk, I present a study on solved 3D RNA molecules, which aims to determine structural patterns and design rules that can help predict their 3D shape.

Specifically, an exhaustive analysis on the structural arrangements of RNAs revealed the existence of higher-order motifs built by a combination of smaller sub-motifs. Also it was noticed that motifs occur rarely isolated, and would rather cooperate with each other to stabilize RNAs architecture. These findings have helped recognize new levels of organization in RNA structure.

In addition, to better understand how local interactions influence global conformations of RNA 3D structure, the structure of all known RNA junctions was analyzed according to their base pair configurations, and 3D motif formation. All four-way junctions were classified into nine families according to their topology. Interestingly, it was found that junctions are composed of recurrent helical configurations, and their helical elements tend to arrange in roughly parallel and perpendicular patterns.

Furthermore, a data mining technique known as random forest was used to predict the coaxial helical stacking and junction families by using length and sequence information from known 3D junctions. The results give a reasonable prediction accuracy (~80%). These prediction scores constitute a dramatic improvement over previous attempts, and comprise an important step towards RNA 3D structure prediction.

Joseph Teran (UCLA)
Title: Elastoplasticity Simulation with the Material Point Method
Abstract: Hyperelastic constitutive models describe a wide range of materials. Examples include biomechanical soft tissues like muscle, tendon, skin etc. Elastoplastic materials consisting of a hyperelastic constitutive model combined with a notion of stress constraint (or feasible stress region) describe an even wider range of materials. In these models, the elastic potential energy only increases with the elastic part of the deformation decomposition. The evolution of the plastic part is designed to satisfy the stress constraint. A very interesting class of these models arise from frictional contact considerations. I will discuss some of the mathematical aspects of these models and present some recent results and examples in computer graphics and virtual surgery applications. I will also talk about practical simulation of these materials with recent novel Material Point Methods (MPM).

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