Publications

Single-molecule DNA studies have improved our understanding of the DNAs' structure and their interactions with other molecules. A variety of DNA labeling dyes are available for single-molecule studies, among which the bis-intercalating dye YOYO-1 and mono-intercalating dye YO-PRO-1 are widely used. They have an extraordinarily strong affinity toward DNA and are bright with a high quantum yield (>0.5) when bound to DNAs. However, it is still not clear how these dyes behave in DNA molecules under higher ionic strength and strong buffer flow. Here, we have studied the effect of ionic strength and flow rate of buffer on their binding in single DNA molecules. The larger the flow rate and the higher the ionic strength, the faster the intercalated dyes are washed away from the DNAs. In the buffer with 1 M ionic strength, YOYO-1 and YO-PRO-1 are mostly washed away from DNA within 2 min of moderate buffer flow.

This report uses Monte Carlo simulations to connect stochastic single-molecule and ensemble surface adsorption of molecules from dilute solutions. Monte Carlo simulations often use a fundamental time resolution to simulate each discrete step for each molecule. The adsorption rate obtained from such a simulation surprisingly contains an error compared to the results obtained from the traditional method. Simulating adsorption kinetics is interesting in many processes, such as mass transportation within cells, the kinetics of drug-receptor interactions, membrane filtration, and other general reaction kinetics in diluted solutions. Thus, it is important to understand the origin of the disagreement and find a way to correct the results. This report reviews the traditional model, explains the single-molecule simulations, and introduces a method to correct the results of adsorption rate. For example, one can bin finer time steps into time steps of interest to simulate the fractal diffusion or simply introduce a correction factor for the simulations. Then two model systems, self-assembled monolayer (SAM) and biosensing on the patterned surface, are simulated to check the accuracy of the equations. It is found that the adsorption rate of SAM is highly dependent on the conditions and the uncertainty is large. However, the biosensing system is relatively accurate. This is because the concentration gradient near the interface varies significantly with reaction conditions for SAMs while relatively stable for the biosensing system.

Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer quantitative kinetic information from smFRET data is, however, complicated by experimental limitations. Diverse analysis tools have been developed to overcome these hurdles but a systematic comparison is lacking. Here, we report the results of a blind benchmark study assessing eleven analysis tools used to infer kinetic rate constants from smFRET trajectories. We test them against simulated and experimental data containing the most prominent difficulties encountered in analyzing smFRET experiments: different noise levels, varied model complexity, non-equilibrium dynamics, and kinetic heterogeneity. Our results highlight the current strengths and limitations in inferring kinetic information from smFRET trajectories. In addition, we formulate concrete recommendations and identify key targets for future developments, aimed to advance our understanding of biomolecular dynamics through quantitative experiment-derived models.

Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing, and drug delivery. Collision theory was originally developed to explain the reaction kinetics of gas reactions with no dilution. For a reaction in a diluted inert gas solution or a diluted liquid solution, diffusion often dominates the collision process. Thus, it is necessary to include diffusion in such a calculation. Traditionally, the classical Smoluchowski rate is used as a starting point to predict the collision frequency of two molecules in a diluted solution. In this report, a different collision model is derived from the adsorption of molecules on a flat surface. A surprising result is obtained, showing that the reaction order for bimolecular reactions should be 2 and 1/3 instead of 2, following a fractal reaction kinetics.

A physical chemistry lab for undergraduate students described in this report is about applying kinetic models to analyze the spread of COVID-19 in the United States and obtain the reproduction numbers. The susceptible-infectious-recovery (SIR) model and the SIR-vaccinated (SIRV) model are explained to the students and are used to analyze the COVID-19 spread data from U.S. Centers for Disease Control and Prevention (CDC). The basic reproduction number R 0 and the real-time reproduction number R t of COVID-19 are extracted by fitting the data with the models, which explains the spreading kinetics and provides a prediction of the spreading trend in a given state. The procedure outlined here shows the differences between the SIR model and the SIRV model. The SIRV model considers the effect of vaccination which helps explain the later stages of the ongoing pandemic. The predictive power of the models is also shown giving the students some certainty in the predictions they made for the following months.

The COVID-19 pandemic has affected many in-person laboratory courses across the world. The viral spreading model is complicated but parameters, such as its reproduction number, R t, can be estimated with the susceptible, infectious, or recovered model. COVID-19 data for many states and countries are widely available online. This provides an opportunity for the students to analyze its spreading kinetics remotely. Here, we reported a laboratory set up online during the third week of the spring semester of 2021 to minimize social contacts. Due to the wide interest in developing online physical chemistry and analytical laboratories during the pandemic, we would like to share this laboratory design. The method, technique, procedure, and grading are described in this report. The student participants were able to apply the kinetic techniques learned in physical chemistry to successfully analyze an ongoing real-world problem through a remote learning environment and prepare this report.

Mixed-halide lead perovskites (MHLPs) are semiconductor materials with bandgaps that are tunable across the visible spectrum and have seen promising applications in photovoltaics and optoelectronics. However, their segregation into phases with enriched halide components, under resonant light illumination and/or electric field, have hindered their practical applications. Herein, we demonstrate the stabilization of the MHLP photoluminescence (PL) peak as a function of their excitation intensities. This effect is associated with the phase segregation of MHLPs and their subsequent remixing by photothermal heating. We conclude that the balance between these opposing processes dictates the equilibrium PL peak of the MHLPs. The findings in this work could serve as a potential approach to obtain MHLP with stable emission peaks under operating conditions.

For a nanostructure sitting on top of an AlGaN:Er3+ thin film, a new thermal imaging technique is presented where dual cameras collect bandpass filtered videos from the H and S bands of Er3+ emission. We combine this thermal imaging technique with our newly developed time-resolved temperature measurement technique which relies on luminescence thermometry using Er3+ emission. This technique collects time-resolved traces from the H and S bands of Er3+ emission. The H and S signal traces are then used to reconstruct the time-resolved temperature transient when a nanostructure is illuminated with a pulsed 532 nm light. Two different types of samples are interrogated with these techniques (drop-casted gold nanosphere cluster and lithographically prepared gold nanodot) on the AlGaN:Er3+ film. Steady-state and time-resolved temperature data are collected when the samples are immersed in air and water. The results of time-resolved temperature-jump measurements from a cluster of gold nanospheres show extremely slow heat transfer when the cluster is immersed in water and nearly 200-fold increase when immersed in air. The low thermal diffusivity for the cluster in water suggests poor thermal contact between the cluster and the thermal bath. The lithographically prepared nanodot has much better adhesion to the AlGaN film, resulting in much higher thermal diffusivity in both air and water. This proof-of-concept demonstration opens a new way to measure the dynamics of the local heat generation and dissipation at the nanoparticle-media interface.

Mixed-halide lead perovskites (MHPs) are promising materials for photovoltaics and optoelectronics due to their highly tunable band gaps. However, they phase segregate under continuous illumination or an electric field, the mechanism of which is still under debate. Herein we systematically measure the phase segregation behavior of polymer-encapsulated CH3NH3Pb(BrxI1-x)3 MHPs as a function of excitation intensity and the nominal halide ratio by in situ photoluminescence microspectroscopy and observe surprising phase dynamics at the beginning of the illumination. The initial phase segregation to I-rich and Br-rich phases is observed followed by the formation of a new mixed-halide phase within several seconds that has not been reported before. We propose that the photothermal effect is amplified at the small-size I-rich domains, which significantly changes the local phase segregation in the otherwise uniform film within milliseconds after illumination.

The ability to manipulate single protein molecules on a surface is useful for interfacing biology with many types of devices in optics, catalysis, bioengineering, and biosensing. Control of distance, orientation, and activity at the single molecule level will allow for the production of on-chip devices with increased biological activity. Cost effective methodologies for single molecule protein patterning with tunable pattern density and scalable coverage area remain a challenge. Herein, Hole Mask Colloidal Lithography is presented as a bench-top colloidal lithography technique that enables a glass coverslip to be patterned with functional streptavidin protein onto patches from 15-200 nm in diameter with variable pitch. Atomic force microscopy (AFM) was used to characterize the size of the patterned features on the glass surface. Additionally, single-molecule fluorescence microscopy was used to demonstrate the tunable pattern density, measure binding controls, and confirm patterned single molecules of functional streptavidin.