skip to main content

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 11:00 PM ET on Thursday, February 13 until 2:00 AM ET on Friday, February 14 due to maintenance. We apologize for the inconvenience.


Search for: All records

Creators/Authors contains: "Li, Xinyang"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Abstract Identifying prostate cancer patients that are harboring aggressive forms of prostate cancer remains a significant clinical challenge. Here we develop an approach based on multispectral deep-ultraviolet (UV) microscopy that provides novel quantitative insight into the aggressiveness and grade of this disease, thus providing a new tool to help address this important challenge. We find that UV spectral signatures from endogenous molecules give rise to a phenotypical continuum that provides unique structural insight (i.e., molecular maps or “optical stains") of thin tissue sections with subcellular (nanoscale) resolution. We show that this phenotypical continuum can also be applied as a surrogate biomarker of prostate cancer malignancy, where patients with the most aggressive tumors show a ubiquitous glandular phenotypical shift. In addition to providing several novel “optical stains” with contrast for disease, we also adapt a two-part Cycle-consistent Generative Adversarial Network to translate the label-free deep-UV images into virtual hematoxylin and eosin (H&E) stained images, thus providing multiple stains (including the gold-standard H&E) from the same unlabeled specimen. Agreement between the virtual H&E images and the H&E-stained tissue sections is evaluated by a panel of pathologists who find that the two modalities are in excellent agreement. This work has significant implications towards improving our ability to objectively quantify prostate cancer grade and aggressiveness, thus improving the management and clinical outcomes of prostate cancer patients. This same approach can also be applied broadly in other tumor types to achieve low-cost, stain-free, quantitative histopathological analysis. 
    more » « less
  2. We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity. 
    more » « less
  3. Abstract

    Recent experiments demonstrate the control of chemical reactivities by coupling molecules inside an optical microcavity. In contrast, transition state theory predicts no change of the reaction barrier height during this process. Here, we present a theoretical explanation of the cavity modification of the ground state reactivity in the vibrational strong coupling (VSC) regime in polariton chemistry. Our theoretical results suggest that the VSC kinetics modification is originated from the non-Markovian dynamics of the cavity radiation mode that couples to the molecule, leading to the dynamical caging effect of the reaction coordinate and the suppression of reaction rate constant for a specific range of photon frequency close to the barrier frequency. We use a simple analytical non-Markovian rate theory to describe a single molecular system coupled to a cavity mode. We demonstrate the accuracy of the rate theory by performing direct numerical calculations of the transmission coefficients with the same model of the molecule-cavity hybrid system. Our simulations and analytical theory provide a plausible explanation of the photon frequency dependent modification of the chemical reactivities in the VSC polariton chemistry.

     
    more » « less
  4. A two-frame phase-shifting interferometric wavefront reconstruction method based on deep learning is proposed. By learning from a large number of simulation data based on a physical model, the wrapped phase can be calculated accurately from two interferograms with an unknown phase step. The phase step can be any value excluding the integral multiples of π and the size of interferograms can be flexible. This method does not need a pre-filtering to subtract the direct-current term, but only needs a simple normalization. Comparing with other two-frame methods in both simulations and experiments, the proposed method can achieve better performance.

     
    more » « less