Extracting multiscale Information from Time Series Characterizing Single-molecule Systems under the Influence of Time Dependent External Forces

Date:Friday, May 29, 2009
Time:10:30am - 11:30am
Location:Bldg. 50B, Room 4205

Speaker:
Christopher Calderon
Department of Computational and Applied Mathematics
Rice University

Abstract:
Single-molecule experiments and computer simulations have generated
data sets containing useful information about the dynamics of
complex biomolecules. However the many degrees of freedom present,
time dependent external forces, and multiple time-scale fluctuations
inherent at this level of detail complicate the task of summarizing
the interesting information in these dynamical systems. I
demonstrate how a collection of surrogate processes, estimated from
a relatively small number non-equilibrium time series, can assist in
characterizing these systems. Both thermodynamic (e.g. potential of
mean force) and kinetic information (e.g. effective molecular
friction) can be extracted using the collection of surrogate models.
The methods are also useful when a good set of reaction coordinates
is unknown or not experimentally accessible, e.g. a collection of
surrogate models can also be used to infer information about slowly
evolving degrees of freedom not directly monitored [1-2].
Illustrative results obtained using various MD simulations [2-3] and
AFM experiments are presented [3-4]. I also discuss new algorithms
and computational techniques that were developed to assist in
modeling the single-molecule time series data [5-6] .

    [1] Calderon, Harris, Kiang & Cox, /J. Phys. Chem. B/, 113, 138 (2009).
    [2] Calderon & Arora, /J. Chem. Theory Comp./, 5, 47 (2009).
    [3] Calderon, Janosi, & Kosztin, /J. Chem. Phys./, 130, 144908 (2009).
    [4] Calderon, Chen, Lin, Harris & Kiang, /J. Phys.: Cond. Mat/, 21,
    034114 (2009).
    [5] Calderon, Martinez, Carroll, Sorensen, /Annals of Applied
    Statistics/ (submitted).
    [6] Calderon, Martinez, Carroll, Sorensen, /J. Comput. Graph. Stat./
    (submitted).

Host of Seminar:

    Esmond Ng