Browsing by Author "Zhou, Zhennan"

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Open Access
Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping
(2017-11-30) Lu, Jianfeng; Zhou, Zhennan
To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limiting, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer. A multiscale integrator for the infinite swapping limit is also proposed to enable practical sampling based on the limiting dynamics, avoiding the enumeration of all possible surface index configurations, which grows exponentially with respect to the number of beads in the ring polymer. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path integral molecular dynamics with surface hopping.
Open Access
An Exploratory Radiomics Approach to Quantifying Pulmonary Function in CT Images
(Scientific Reports, 2019-12) Lafata, Kyle J; Zhou, Zhennan; Liu, Jian-Guo; Hong, Julian; Kelsey, Chris R; Yin, Fang-Fang
Open Access
Association of pre-treatment radiomic features with lung cancer recurrence following stereotactic body radiation therapy.
(Physics in medicine and biology, 2019-01-08) Lafata, Kyle J; Hong, Julian C; Geng, Ruiqi; Ackerson, Bradley G; Liu, Jian-Guo; Zhou, Zhennan; Torok, Jordan; Kelsey, Chris R; Yin, Fang-Fang
The purpose of this work was to investigate the potential relationship between radiomic features extracted from pre-treatment x-ray CT images and clinical outcomes following stereotactic body radiation therapy (SBRT) for non-small-cell lung cancer (NSCLC). Seventy patients who received SBRT for stage-1 NSCLC were retrospectively identified. The tumor was contoured on pre-treatment free-breathing CT images, from which 43 quantitative radiomic features were extracted to collectively capture tumor morphology, intensity, fine-texture, and coarse-texture. Treatment failure was defined based on cancer recurrence, local cancer recurrence, and non-local cancer recurrence following SBRT. The univariate association between each radiomic feature and each clinical endpoint was analyzed using Welch's t-test, and p-values were corrected for multiple hypothesis testing. Multivariate associations were based on regularized logistic regression with a singular value decomposition to reduce the dimensionality of the radiomics data. Two features demonstrated a statistically significant association with local failure: Homogeneity2 (p = 0.022) and Long-Run-High-Gray-Level-Emphasis (p = 0.048). These results indicate that relatively dense tumors with a homogenous coarse texture might be linked to higher rates of local recurrence. Multivariable logistic regression models produced maximum [Formula: see text] values of [Formula: see text], and [Formula: see text], for the recurrence, local recurrence, and non-local recurrence endpoints, respectively. The CT-based radiomic features used in this study may be more associated with local failure than non-local failure following SBRT for stage I NSCLC. This finding is supported by both univariate and multivariate analyses.
Open Access
Bloch dynamics with second order Berry phase correction
(2017-04-23) Lu, Jianfeng; Zhang, Zihang; Zhou, Zhennan
We derive the semiclassical Bloch dynamics with the second order Berry phase correction, based on a two-scale WKB asymptotic analysis. For uniform external electric field, the bi-characteristics system after a positional shift introduced by Berry connections agrees with the recent result in the physics literature.
Open Access
Improved sampling and validation of frozen Gaussian approximation with surface hopping algorithm for nonadiabatic dynamics.
(J Chem Phys, 2016-09-28) Lu, Jianfeng; Zhou, Zhennan
In the spirit of the fewest switches surface hopping, the frozen Gaussian approximation with surface hopping (FGA-SH) method samples a path integral representation of the non-adiabatic dynamics in the semiclassical regime. An improved sampling scheme is developed in this work for FGA-SH based on birth and death branching processes. The algorithm is validated for the standard test examples of non-adiabatic dynamics.
Open Access
Path integral molecular dynamics with surface hopping for thermal equilibrium sampling of nonadiabatic systems
(2017-04-23) Lu, Jianfeng; Zhou, Zhennan
In this work, a novel ring polymer representation for multi-level quantum system is proposed for thermal average calculations. The proposed presentation keeps the discreteness of the electronic states: besides position and momentum, each bead in the ring polymer is also characterized by a surface index indicating the electronic energy surface. A path integral molecular dynamics with surface hopping (PIMD-SH) dynamics is also developed to sample the equilibrium distribution of ring polymer configurational space. The PIMD-SH sampling method is validated theoretically and by numerical examples.