Lab Home | Phone | Search
Center for Nonlinear Studies  Center for Nonlinear Studies
 Home 
 People 
 Current 
 Affiliates 
 Alumni 
 Visitors 
 Students 
 Research 
 ICAM-LANL 
 Quantum 
 Publications 
 Publications 
 2007 
 2006 
 2005 
 2004 
 2003 
 2002 
 2001 
 2000 
 <1999 
 Conferences 
 Workshops 
 Sponsorship 
 Talks 
 Colloquia 
 Colloquia Archive 
 Seminars 
 Postdoc Seminars Archive 
 Quantum Lunch 
 CMS Colloquia 
 Q-Mat Seminars 
 Q-Mat Seminars Archive 
 Archive 
 Kac Lectures 
 Dist. Quant. Lecture 
 Ulam Scholar 
 Colloquia 
 
 Jobs 
 Students 
 Summer Research 
 Student Application 
 Visitors 
 Description 
 Past Visitors 
 Services 
 General 
 PD Travel Request 
 
 History of CNLS 
 
 Maps, Directions 
 CNLS Office 
 T-Division 
 LANL 
 
Thursday, October 04, 2012
2:00 PM - 2:45 PM
CNLS Conference Room (TA-3, Bldg 1690)

Postdoc Seminar

Polymer Models for Validating Dimensionality Estimates of Disordered Protein Dynamics

Joshua Phillips
T-6 and CNLS

Intrinsically disordered proteins push the emerging view that proteins are best described as structural ensembles to the extreme, begging the question of how the free-energy landscape of these proteins differs from natively folded proteins. In particular, the dimensionality of the motion exhibited by natively folded proteins is predicted to decrease as the protein folds to its native structure, while dimensionality should stay relatively high for intrinsically disordered proteins due to their persistent flexibility. Dimensionality estimation techniques applied to molecular dynamics simulations have the potential to elucidate dynamical differences between various disordered proteins, allowing for their classification and categorization analogous to the structure-based methods currently used for classifying natively folded proteins. However, it is not clear that current dimensionality estimation techniques can actually recover the intrinsic dimensionality from simulations due to sampling limitations and the presence of thermal noise/fluctuations. In order to test their efficacy, we have developed a validation framework which utilizes a series of novel polymer models that exhibit dynamics characteristic of protein simulations, but are of known dimensionality by construction. Dimensionality estimation results from the polymer models indicate that (1) under/over estimation due to sampling/noise can be surprisingly predictable for some dynamical transitions, (2) while the estimators often fail to recover the true intrinsic dimensionality, ranking of relative estimates is still accurate, and (3) the two previous results can be leveraged to guide interpretation of results obtained from simulations of disordered and folding proteins.

Host: Kipton Barros, T-4 and CNLS