Publications
Estimation and Inference of Diffusion Coefficients in
Complex Biomolecular Environments
C.P. Calderon, J. Chem. Theory Comput. [in press] (2011).
P-Splines Using Derivative Information C.P. Calderon, J.G. Martinez, R.J. Carroll, and D.C. Sorensen. SIAM Multiscale Model. Sim. 8 (2010).
Detection of Subtle Dynamical Changes Induced by Unresolved "Conformational Coordinates" in
Single-Molecule Trajectories via Goodness-of-Fit Tests
C.P. Calderon J. Phys. Chem. B 114 (2010).
A Data-driven Approach to Decomposing Complex Enzyme Kinetics with Surrogate Models
C.P. Calderon Phys. Rev. E, 80 (2009).
Using Stochastic Models Calibrated from Nanosecond Non-equilibrium
Simulations to Approximate Mesoscale Information
C.P. Calderon L. Janosi, and I. Kosztin, J. Chem. Phys., 130 (2009).
Analyzing
Single-Molecule Manipulation Experiments
C.P. Calderon, N.C Harris, C.-H. Kiang, and D.D. Cox, J. Mol. Recognit., 22
(2009).
Quantifying Multiscale Noise Sources in Single-
Molecule Experiments via Pathwise Statistical Inference Procedures
C.P. Calderon, N.C Harris, C.-H. Kiang, and D.D. Cox, J. Phys. Chem. B 113 (2009).
Extracting Kinetic and Stationary Distribution Information from Short MD Trajectories
via a Collection of Surrogate Diffusion Models Quantifying DNA Melting Transitions Using Single-Molecule Force Spectroscopy Approximating Nonequilibrium Processes Using a Collection of Surrogate Diffusion Models Local Diffusion Models for Stochastic Reacting Systems:Estimation Issues in Equation-free Numerics Fitting Effective Diffusion Models to Data Associated with a "Glassy Potential": Estimation, Classical Inference Procedures, and Some Heuristics On the Use of Local Diffusion Models in Path Ensemble Averaging in Potential of Mean Force Computations Coarse-Graining the Cyclic Lotka-Volterra Model: SSA and Local Maximum Likelihood Estimation Comment on "Reversing the Perturbation in Nonequilibrium Molecular Dynamics: An Easy Way to Calculate the Shear Viscosity of Fluids" Technical Reports / Submitted Manuscripts:
C.P. Calderon and K. Arora, J. Chem. Theory Comput. 5 (2009).
Supporting Material Text.
See erratum note for this paper.
C.P. Calderon, W.-H Chen, K.-J. Lin, N.C Harris, and C.-H. Kiang, J. Phys.: Condensed Matter
21 (2009).
C.P. Calderon and R. Chelli, J. Chem. Phys., 128, 145103 (2008).
C.P. Calderon, Mol. Sim., 33, 713-731 (2007).
C.P. Calderon, SIAM Multiscale Model. Sim., 6, 656 (2007).
C.P. Calderon, J. Chem. Phys., 126, 084106 (2007).
C.P. Calderon, G. A. Tsekouras, A. Provata, and I.G. Kevrekidis, (in Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena, A. Gorban, N. Kazantzis, Y. Kevrekidis, H.C. Ottinger, C. Theodoropoulos [Eds.], Springer, Berlin--Heidelberg--New York, 2006).
C.P. Calderon, Ashurst, W.T., Phys. Rev. E, 66, 013201 (2002).