Arvind Ramanathan

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In contrast to most other sensory modalities, the basic perceptual dimensions of olfaction remain unclear. Here, we use non-negative matrix factorization (NMF)--a dimensionality reduction technique--to uncover structure in a panel of odor profiles, with each odor defined as a point in multi-dimensional descriptor space. The properties of NMF are favorable(More)
—Compartmental models in epidemiology are widely used as a means to model disease spread mechanisms and understand how one can best control the disease in case an outbreak of a widespread epidemic occurs. However, a significant challenge within the community is in the development of approaches that can be used to rigorously verify and validate these models.(More)
Protein-protein interactions are governed by the change in free energy upon binding, ΔG = ΔH - TΔS. These interactions are often marginally stable, so one must examine the balance between the change in enthalpy, ΔH, and the change in entropy, ΔS, when investigating known complexes, characterizing the effects of mutations, or designing optimized variants. To(More)
Collective behavior involving distally separate regions in a protein is known to widely affect its function. In this article, we present an online approach to study and characterize collective behavior in proteins as molecular dynamics (MD) simulations progress. Our representation of MD simulations as a stream of continuously evolving data allows us to(More)
We recently introduced a new method for discovering, characterizing, and monitoring spatiotemporal patterns in the conformational fluctuations in molecular dynamics simulation data ( J. Comput. Biol. 2010 , 17 ( 3 ), 309 - 324 ). Significantly, our method, called Dynamic Tensor Analysis (DTA), can be performed as the simulation is progressing. It is(More)
Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve(More)
BACKGROUND Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally(More)
Molecular dynamics simulations provide vast amount of information about a protein's dynamics. To interpret a protein's dynamics and how it may relate to its function, traditionally, two-way analysis techniques such as principal component analysis have been used. However, two-way analysis techniques are usually limited by the fact that they have to be done(More)
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in(More)
Biomolecular simulations at millisecond and longer time-scales can provide vital insights into functional mechanisms. Because post-simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function(More)