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- Femtosecond spectroscopy (3)
- Mass spectrometry (3)
- DNA (2)
- 2-nitrobenzyl compounds (1)
- Cellular processes (1)
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- DNA break repair (1)
- DNA curtain (1)
- DNA duplexes and nanocircles (1)
- Explosives (1)
- FRET (1)
- Fluorescence resonance energy transfer (FRET) (1)
- Holliday junction (HJ) (1)
- Homologous recombination (HR) (1)
- I-motif (1)
- Optical tweezers (1)
- Organophosphorus compounds (1)
- Pentaerythritol Tetranitrate (1)
- Reactive laser ablation in liquid; gold-silica nanoparticle; laser synthesis (1)
- Render Safe Procedure (1)
- Sensing (1)
- Single molecule (1)
- Single nucleotide polymorphism (SNP) (1)
- Single-molecule fluorescence microscopy (1)
- Smokeless Powder (1)
- Vibrational dynamics (1)
Articles 1 - 11 of 11
Full-Text Articles in Physical Sciences and Mathematics
One-Step Femtosecond Laser Ablation Synthesis Of Sub-3 Nm Gold Nanoparticles Stabilized By Silica, Mallory G. John, Katharine M. Tibbetts
One-Step Femtosecond Laser Ablation Synthesis Of Sub-3 Nm Gold Nanoparticles Stabilized By Silica, Mallory G. John, Katharine M. Tibbetts
Chemistry Publications
No abstract provided.
Conserved Vibrational Coherence In The Ultrafast Rearrangement Of 2-Nitrotoluene Radical Cation, Derrick Ampadu Boateng, Mi'kayla D. Word, Lavrenty Gutsev, Puru Jena, Katharine M. Tibbetts
Conserved Vibrational Coherence In The Ultrafast Rearrangement Of 2-Nitrotoluene Radical Cation, Derrick Ampadu Boateng, Mi'kayla D. Word, Lavrenty Gutsev, Puru Jena, Katharine M. Tibbetts
Chemistry Publications
2-Nitrotoluene (2-NT) is a good model for both photolabile protecting groups for organic synthesis and the military explosive 2,4,6-trinitrotoluene (TNT). In addition to the direct C−NO2 bond-cleavage reaction that initiates detonation in TNT, 2-NT undergoes an H atom attack reaction common to the photolabile 2-nitrobenzyl group, which forms the aci-nitro tautomer. In this work, femtosecond pump−probe measure- ments with mass spectrometric detection and density functional theory (DFT) calculations demonstrate that the initially prepared vibrational coherence in the 2-NT radical cation (2- NT+) is preserved following H atom attack. Strong-field adiabatic ionization is used to prepare 2-NT+, which can overcome a …
Probing Coherent Vibrations Of Organic Phosphonate Radical Cations With Femtosecond Time-Resolved Mass Spectrometry, Derrick Ampadu Boateng, Mi'kayla D. Word, Katharine M. Tibbetts
Probing Coherent Vibrations Of Organic Phosphonate Radical Cations With Femtosecond Time-Resolved Mass Spectrometry, Derrick Ampadu Boateng, Mi'kayla D. Word, Katharine M. Tibbetts
Chemistry Publications
Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs (732 ± 28 cm−1) oscillations with a weak feature at 610–650 cm−1, while DIMP exhibits bimodal oscillations with a period of ∼55 fs …
Single-Step Fret-Based Detection Of Femtomoles Dna, Kumar Sapkota, Anisa Kaur, Caleb Donkoh-Moore, Soma Dhakal
Single-Step Fret-Based Detection Of Femtomoles Dna, Kumar Sapkota, Anisa Kaur, Caleb Donkoh-Moore, Soma Dhakal
Chemistry Publications
Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), …
Multifaceted Water Dynamics In Spherical Nanocages, M. Von Domaros, D. Bratko, B. Kirchner, G. Hummer, A. Luzar
Multifaceted Water Dynamics In Spherical Nanocages, M. Von Domaros, D. Bratko, B. Kirchner, G. Hummer, A. Luzar
Chemistry Publications
We present a new method to study position- dependent, anisotropic diffusion tensors inside spherically confined systems—a geometry that is common to many chemical nanoreactors. We use this method to elucidate the surprisingly rich solvent dynamics of confined water. The spatial variation of the strongly anisotropic diffusion predicted by the model agrees with the results of explicit molecular dynamics simulations. The same approach can be directly transferred to the transport of solutes to and from reaction sites located at nanoreactor interfaces. We com- plement our study by a detailed analysis of wa- ter hydrogen bond kinetics, which is intimately coupled to …
Anisotropic Structure And Dynamics Of Water Under Static Electric Fields, M. Shafiei, M. Von Domaros, D. Bratko, A. Luzar
Anisotropic Structure And Dynamics Of Water Under Static Electric Fields, M. Shafiei, M. Von Domaros, D. Bratko, A. Luzar
Chemistry Publications
We study the structure and dynamics of water subject to a range of static external electric fields, using molecular dynamics simulations. In particular, we monitor the changes in hydrogen bond kinetics, reorientation dynamics, and translational motions of water molecules. We find that water molecules translate and rotate slower in elec- tric fields, because the tendency to reinstate the aligned orientation reduces the prob- ability of finding a new hydrogen bond partner and hence increases the probability of reforming already ruptured bonds. Furthermore, dipolar alignment of water mole- cules with the field results in structural and dynamic anisotropies even though the …
Coherent Vibrational And Dissociation Dynamics Of Polyatomic Radical Cations, Katharine M. Tibbetts
Coherent Vibrational And Dissociation Dynamics Of Polyatomic Radical Cations, Katharine M. Tibbetts
Chemistry Publications
The ultrafast dynamics of polyatomic radical cat- ions contribute to important processes including energy transfer in photovoltaics, electron transfer in photocataly- sis, radiation-induced DNA damage, and chemical reac- tions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of polyatomic radical cations following elec- tron removal, which arises from excess electronic excita- tion of the molecule during the ionization process. This Concept article introduces the reader to how the pump- probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can overcome this challenge to capture coherent vibrational dynamics on the …
Single-Molecule Analysis Of I-Motif Within Self-Assembled Dna Duplexes And Nanocircles, Anoja Megalathan, Bobby D. Cox, Peter D. Wilkerson, Anisa Kaur, Kumar Sapkota, Joseph E. Reiner, Soma Dhakal
Single-Molecule Analysis Of I-Motif Within Self-Assembled Dna Duplexes And Nanocircles, Anoja Megalathan, Bobby D. Cox, Peter D. Wilkerson, Anisa Kaur, Kumar Sapkota, Joseph E. Reiner, Soma Dhakal
Chemistry Publications
The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif–forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif–forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the …
Homologous Recombination Under The Single-Molecule Fluorescence Microscope, Dalton R. Gibbs, Soma Dhakal
Homologous Recombination Under The Single-Molecule Fluorescence Microscope, Dalton R. Gibbs, Soma Dhakal
Chemistry Publications
Homologous recombination (HR) is a complex biological process and is central to meiosis and for repair of DNA double-strand breaks. Although the HR process has been the subject of intensive study for more than three decades, the complex protein–protein and protein–DNA interactions during HR present a significant challenge for determining the molecular mechanism(s) of the process. This knowledge gap is largely because of the dynamic interactions between HR proteins and DNA which is difficult to capture by routine biochemical or structural biology methods. In recent years, single-molecule fluorescence microscopy has been a popular method in the field of HR to …
Molecular Polarizability In Open Ensemble Simulations Of Aqueous Nanoconfinements Under Electric Field, F. Moucka, S. Zamfir, D. Bratko, A. Luzar
Molecular Polarizability In Open Ensemble Simulations Of Aqueous Nanoconfinements Under Electric Field, F. Moucka, S. Zamfir, D. Bratko, A. Luzar
Chemistry Publications
Molecular polarization at aqueous interfaces involves fast degrees of freedom that are often averaged-out in atomistic-modeling approaches. The resulting effective interactions depend on a specific environment, making explicit account of molecular polarizability particularly important in solutions with pronounced anisotropic perturbations, including solid/liquid interfaces and external fields. Our work concerns polarizability effects in nanoscale confinements under electric field, open to an unperturbed bulk environment. We model aqueous molecules and ions in hydrophobic pores using the Gaussian-charge-on-spring BK3-AH representation. This involves nontrivial methodology devel- opments in expanded ensemble Monte Carlo simulations for open systems with long-ranged multibody interactions and necessitates further improvements …
Explosive Residue Transfer From Various Explosive Ordinance Disposal (Eod) Render Safe Procedures (Rsp), Joseph A. Stein
Explosive Residue Transfer From Various Explosive Ordinance Disposal (Eod) Render Safe Procedures (Rsp), Joseph A. Stein
Master of Science in Forensic Science Directed Research Projects
Before an IED is sent to a laboratory for analysis, it needs to be rendered safe if it did not already initiate. Render safe procedures (RSPs) include utilizing a percussion-actuated non-electric (PAN) disrupter or a mineral water bottle disrupter. Each disrupter utilizes explosives to render the device safe by breaking open the container or disrupting the fuzing system. However, the same explosives used in the RSP are also used by criminals in IED construction. As such, the explosives used in the RSP can cause problems with the interpretation of the results from forensic analysis of the IED fragments. Compounds of …