Electron-Transfer Mediated Photo-Switching in Nanoparticles

Previous publications from our lab demonstrated viable approaches to design a photo-switching nanoparticle with arguably superior brightness and photostability resulting in an improved resolution in localization-based microscopy, as compared to other photo-switching dyes or particles. As a follow-up, this dissertation is focused on two major tasks: first, developing nanoparticles with better photo-switching properties for super-resolution imaging; second, trying to achieve a better physical picture of the mechanisms involved in photo-switching, including polaron dynamics, charge transfer, and energy transfer. A new class of photo-switchable nanoparticles was developed by blending conjugated polymer semiconductor with fullerene-based electron acceptors, and further blending with polystyrene maleic anhydride could improve the bulk fluorescence quantum yield of the nanoparticle and increase the on/off contrast in single-molecule experiments, which is critical for better localization accuracy. To understand how the dynamics of polaron in nanoparticle affects apparent photo-switching properties, single-molecule fluorescence spectra were collected from nanoparticles with different blending ratios and under various excitation laser intensities. Further modulation of the excitation laser intensity led to a transient fluorescent response consistent with previously published behavior of nanoparticles in bulk suspensions. The results of those experiments further help the development of a better physical model connecting polaron generation/recombination dynamics and photo-switching properties

Polarizable force field development for lipids and their efficient applications in membrane proteins

Polarizable force fields have been developed due to the intrinsic problem of additive force fields in modeling electrostatic interactions. Because of the capability to accurately describe the behavior of systems with significant changes in their electrostatic environments, polarizable force fields might be a decent tool to study membrane-related systems, such as lipid bilayers, though not so much progresses have been made. In this overview article we described the developments of a variety of polarizable force fields, including the corresponding theories, benchmark examples, and more specifically we were focused on the applications on lipid membranes. (C) 2017 John Wiley & Sons, Lt

Hidden Conformation Events in DNA Base Extrusions: A Generalized-Ensemble Path Optimization and Equilibrium Simulation Study

DNA base extrusion is a crucial component of many biomolecular processes. Elucidating how bases are selectively extruded from the interiors of double-strand DNAs is pivotal to accurately understanding and efficiently sampling this general type of conformational transitions. In this work, the on-the-path random walk (OTPRW) method, which is the first generalized-ensemble sampling scheme designed for finite-temperature-string path optimizations, was improved and applied to obtain the minimum free-energy path (MFEP) and the free-energy profile of a classical B-DNA major-groove base-extrusion pathway. Along the MFEP, an intermediate state and the corresponding transition state were located and characterized. The MFEP result suggests that a base-plane-elongation event rather than the commonly focused base-flipping event is dominant in the transition-state (TS) formation portion of the pathway; and the energetic penalty at the transition state is mainly introduced by the stretching of the Watson–Crick base pair. Moreover, to facilitate the essential base-plane-elongation dynamics, the surrounding environment of the flipped base must be intimately involved. Further taking advantage of the extended-dynamics nature of the OTPRW Hamiltonian, an equilibrium generalized ensemble simulation was performed along the optimized path; based on the collected samples, several base-flipping (opening) angle collective variables were evaluated. In correspondence with the MFEP result, the collective variable analysis result reveals that none of these commonly employed flipping (opening) angles alone can adequately represent the base-extrusion pathway, especially in the pre-TS portion. As further revealed by the collective variable analysis, the base-pairing partner of the extrusion target undergoes a series of in-plane rotations to facilitate the base-plane-elongation dynamics. A base-plane rotation angle is identified to be a possible reaction coordinate to represent these in-plane rotations. Notably, these in-plane rotation motions may play a pivotal role in determining the base-extrusion selectivity

The Potential of Latent Class Analysis: the Czech Television Audience Case Study

The thesis "The Potential of Latent Class Analysis: the Czech Television Audience Case Study" deals with latent class analysis and it's potential as a segmentation method. Three different approaches are examined - latent class analysis for joint data from six research waves, simultaneous latent class analysis for each wave separately and latent class analysis for joint data transferred into dichotomous form. The results of all three methods are compared through secondary analysis of data from case study focused on audience's perception of the Czech Television; their strong and weak points are described and the most suitable solution is chosen. Based on these findings, four identified segments of the audience are then interpreted from the point of their characteristic features and sociodemographic parameters. This paper is supported by works of classic authors in the area of latent class analysis; the thesis refers to their findings that also served as basis for composition of the research hypotheses

Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections

Classical molecular dynamic (MD) simulation of membrane proteins faces significant challenges in accurately reproducing and predicting experimental observables such as ion conductance and permeability due to its incapability of precisely describing the electronic interactions in heterogeneous systems. In this work, the free energy profiles of K+ and Na+ permeating through the gramicidin A channel are Characterized by using the AMOEBA polarizable force field with a total sampling time of 1 mu s. Our results indicated that by explicitly introducing the multipole terms and polarization into the electrostatic potentials, the permeation free energy barrier of K+ through the gA channel is considerably reduced compared to the overestimated results obtained from the fixed-charge model. Moreover; the estimated maximum conductance, without any corrections, for both K+ and Na+ passing through the gA channel are much closet to the experimental results than any classical MD simulations, demonstrating the power of AMOEBA in investigating the membrane proteins

Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions

Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization

Understanding enzyme reactions using enhanced sampling techniques

Enhanced sampling is an essential and powerful tool to study complex biochemical processes, notably macromolecular conformational change and chemical reactions. Here we review basic components of some milestones of sampling techniques, focusing especially on the use in understanding enzyme reactions, including reaction path finding, free energy surface construction

The relationship between incorrect translation proportion and amino acid supply.

<p>In Fig 3a, 3b and 3c, the vertical axis shows the total length fraction of the three kinds of released peptide chains which are the premature chains, mature chains with error, and the incorrect chains. In Fig 3a and 3b, the horizontal axis shows the amino acids supply coefficient. So in Fig 3a, all amino acid numbers were multiplied by the same coefficient, and in Fig 3b, only the number of Arg was multiplied by the coefficient while the number of other amino acids were kept unchanged. In Fig 3c, 10 simulations were run under Condition 3 independently and the horizontal axis shows the simulation index. The result shows that stress of unbalanced amino acid supply can lead to incorrect translation.</p

The effect of mismatch on the rate of correct translation.

<p>The vertical axis shows the average correct translation rate of one ribosome in a second. In Fig 6a and 6b, the horizontal axis shows the amino acids supply coefficient. The number of amino acid is equal to the normal condition number multiplied by the coefficient. So in Fig 6a, all amino acid numbers are multiplied by the same coefficient, and in Fig 6b, only the number of arg is multiplied by the coefficient, other amino acids keep unchanged. In Fig 6c, all the 10 simulations are under the Condition 3 that all amino acid supplies are randomly modified with the coefficient less than 1, and different amino acid has different coefficient.</p

An initial miscoding event results in an overall drop in yield of full-length peptides.

<p>(adapted from nature. 2009, 457(8):161, with permission from NATURE) Proposed model for the events after a miscoding event with the steps contributing to the quality control described here highlighted by green arrows. PT, peptidyl transfer.</p