The Beckman Institute Graduate Student Seminar Series presents the work of outstanding graduate students working in Beckman research groups. The seminars are open to the UIUC campus.
Stability and Dynamics of Viruses Described by Computer Simulations
Anton Arkhipov (TCB)
Viruses are parasitic organisms responsible for many diseases. Consisting of a genome enclosed in a protein shell (capsid), often with additional components, viruses are complex macromolecular structures capable of self-assembling, protecting their interior, and disassembling when infecting a host cell. Because of the role of viruses in causing human disease, it is important to understand the mechanisms of viral infection and replication to design better antiviral drugs. Fortunately, computational modeling has become capable of describing complete viruses at atomic level. Recently, we performed the first all-atom simulation of a complete virus, elucidating steps in its self-assembly process. We have also developed highly simplified mechanical models of several viral capsids, allowing one to reach timescales much longer than those accessible in all-atom simulations. The results of simulations with these simplified models agree with data from all-atom simulations and with experimental observations, where available. Among the studied capsids, some were found stable while others collapsed rapidly when simulated without the corresponding viral genome, implying different self-assembly routes for different viruses.
Affect in Language
Cecilia Ovesdotter Alm (AI)
As technology and human-computer interaction advances, there is an increased interest in the field of affective computing. One of the current challenges in computational speech and text processing is to address meaning components which extend beyond informative content. This work is about computational methods for exploring affect in language. I will discuss the motivations, applications, models, methods, and challenges involved, as well as present a newly developed corpus resource annotated for affect, and introduce methods used for automated linguistic affect analysis.
In Vivo Quantification of Skeletal Muscle Fiber and Microvasculature Architecture with Diffusion-Weighted MRI
The non-invasive probing of skeletal muscle histoarchitecture and perfusion is essential in quantifying muscle quality and function in health (e.g., exercise physiology) and disease (e.g. obesity and adult diabetes). Skeletal muscles are highly organized hierarchical structures characterized by an anisotropic arrangement of muscle fibers (myocytes) in bundles, with each myocyte perfused with aligned capillary networks. Due to its unique non-invasive microstructure probing capabilities, diffusion-weighted Magnetic Resonance Imaging (DW-MRI) constitutes a valuable tool in the study of such ordered biological tissues. We have implemented a DW-MRI sequence with highly sensitive directional encoding to quantify the microarchitectural properties (i.e., pennation angle, fiber fractional anisotropy) of human calf muscles at rest. The microarchitectural results offer new insights into the geometry of the myocytes in resting skeletal muscles. We have also explored the capability of dense q-space encoding to characterize the directional anisotropy of the muscle microvasculature at rest and during post ischemic reactive hyperemia.