Physics Commons^™

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Advanced Raman Spectroscopy Detection Of Oxidative Damage In Nucleic Acid Bases: Probing Chemical Changes And Intermolecular Interactions In Guanosine At Ultralow Concentration, Francesca Ripanti, Claudia Fasolato, Flavia Mazzarda, Simonetta Palleschi, Marina Ceccarini, Chunchun Li, Margherita Bignami, Enrico Bodo, Steven E.J. Bell, Filomena Mazzei, Paolo Postorino

Bioelectrics Publications

DNA/RNA synthesis precursors are especially vulnerable to damage induced by reactive oxygen species occurring following oxidative stress. Guanosine triphosphates are the prevalent oxidized nucleotides, which can be misincorporated during replication, leading to mutations and cell death. Here, we present a novel method based on micro-Raman spectroscopy, combined with ab initio calculations, for the identification, detection, and quantification of oxidized nucleotides at low concentration. We also show that the Raman signature in the terahertz spectral range (<100 >cm(-1)) contains information on the intermolecular assembly of guanine in tetrads, which allows us to further boost the oxidative damage detection limit. Eventually, we …

Enhanced Acidity Of Acetic And Pyruvic Acids On The Surface Of Water, Alexis J. Eugene, Elizabeth A. Pillar, Agustín J. Colussi, Marcelo I. Guzman

Chemistry Faculty Publications

Understanding the acid–base behavior of carboxylic acids on aqueous interfaces is a fundamental issue in nature. Surface processes involving carboxylic acids such as acetic and pyruvic acids play roles in (1) the transport of nutrients through cell membranes, (2) the cycling of metabolites relevant to the origin of life, and (3) the photooxidative processing of biogenic and anthropogenic emissions in aerosols and atmospheric waters. Here, we report that 50% of gaseous acetic acid and pyruvic acid molecules transfer a proton to the surface of water at pH 2.8 and 1.8 units lower than their respective acidity constants pK_{a …}

Folding Of Bovine Pancreatic Trypsin Inhibitor (Bpti) Is Faster Using Aromatic Thiols And Their Corresponding Disulfides, Ram Prasad Marahatta

FIU Electronic Theses and Dissertations

Improvement in the in vitro oxidative folding of disulfide-containing proteins, such as extracellular and pharmaceutically important proteins, is required. Traditional folding methods using small molecule aliphatic thiol and disulfide, such as glutathione (GSH) and glutathione disulfide (GSSG) are slow and low yielding. Small molecule aromatic thiols and disulfides show great potentiality because aromatic thiols have low pKa values, close to the thiol pKa of protein disulfide isomerase (PDI), higher nucleophilicity and good leaving group ability. Our studies showed that thiols with a positively charged group, quaternary ammonium salts (QAS), are better than thiols with negatively charged groups such as phosphonic …

Determination Of The Zinc Concentration In Human Fingernails By Laser-Induced Breakdown Spectroscopy, Steven J. Rehse, Vlora A. Riberdy, Christopher J. Frederickson

Physics Publications

The absolute concentration of zinc in human fingernail clippings tested ex vivo was determined by 1064 nm laser-induced breakdown spectroscopy and confirmed by speciated isotope dilution mass spectrometry. A nail testing protocol that sampled across the nail (perpendicular to the direction of growth) was developed and validated by scanning electron microscopy energy dispersive x-ray spectroscopy. Using this protocol, a partial least squares regression model predicted the zinc concentration in five subjects’ fingernails to within 7 ppm on average. The variation of the zinc concentration with depth into the nail as determined by laser-induced breakdown spectroscopy was studied and found to …

First-Principles Calculated Decomposition Pathways For Libh4 Nanoclusters, Zhi-Quan Huang, Wei-Chih Chen, Feng-Chuan Chuang, Eric Majzoub, Vidvuds Ozoliņš

Physics Faculty Works

We analyze thermodynamic stability and decomposition pathways of LiBH4 nanoclusters using grand-canonical free-energy minimization based on total energies and vibrational frequencies obtained from density-functional theory (DFT) calculations. We consider (LiBH4)n nanoclusters with n = 2 to 12 as reactants, while the possible products include (Li)n, (B)n, (LiB)n, (LiH)n, and Li2BnHn; off-stoichiometric LinBnHm (m ≤ 4n) clusters were considered for n = 2, 3, and 6. Cluster ground-state configurations have been predicted using prototype electrostatic ground-state (PEGS) and genetic algorithm (GA) based structural optimizations. Free-energy calculations show hydrogen release pathways markedly differ from those in bulk LiBH4. While experiments have found …

Multimode Analysis Of Nanoscale Biomolecular Interactions, Purushottam Babu Tiwari

FIU Electronic Theses and Dissertations

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical …

Does A Plastron Improve Heat Transfer?, Madani A. Khan, Jeffrey Alston, Andrew Guenthner

STAR Program Research Presentations

Superamphiphobic surfaces strongly repel both water and oils. In this work, aluminum coupons are processed by sanding with various grit of sand paper to impart microscale roughness. Subsequent submersion of the aluminum substrate in boiling water grows nanoscale grass-like structures. The oxide layer of Al is slightly soluble in water. During a fast diffusion/equilibrium, Al₂O₃ nanograss grows on the surface. A low energy coating is then deposited on the surface. The micro and nanoscale features create re-entrant structures that trap air enabling contact liquid to be in a Cassie-Baxter state. Superamphiphobicity of the samples were confirmed by …

Evaluation Report, Alan Peterfreund

STEM Digital

This evaluation report synthesizes the results of evaluation activities conducted by SageFox Consulting Group of the STEM DIGITAL project led by the UMass STEM Ed Institute for its no-cost extension year, covering the period September 2013 to August 2014. The goals of the program are to facilitate the participants’ abilities to stimulate student interest in STEM careers while engaging them in ways to think critically about their environment. Participating teachers incorporated digital cameras and Analyzing Digital Images (ADI) software into lab activities focusing on environmental science. STEM DIGITAL materials focused on three strands related to (1) ozone and air quality, …

K-Shell X-Ray Spectroscopy Of Atomic Nitrogen, M. M. Sant'anna, Gunnar Ohrwall, Wayne C. Stolte, Alfred S. Schlachter, Dennis W. Lindle, B. M. Mclaughlin

Chemistry and Biochemistry Faculty Research

Absolute K-shell photoionization cross sections for atomic nitrogen have been obtained from both experiment and state-of-the-art theoretical techniques. Because of the difficulty of creating a target of neutral atomic nitrogen, no high-resolution K-edge spectroscopy measurements have been reported for this important atom. Interplay between theory and experiment enabled identification and characterization of the strong 1s → np resonance features throughout the threshold region. An experimental value of 409.64 ± 0.02 eV was determined for the K-shell binding energy.

Institute Overview, Morton Sternheim

STEM Digital

Digital cameras and computers are widely available for students and teachers. However, they are mainly used for documentation: creating PPT presentations, handouts, posters, etc. STEM DIGITAL shows how digital image analysis can be applied to environmental (and other) research in STEM courses. Application to studies of air quality, water quality, arsenic contamination, climate change, diffusion, etc.

Digital Camera Basics, Stephen Schneider

STEM Digital

No abstract provided.

Measuring Lengths And Areas With Adi. Student Guide, Morton Sternheim

STEM Digital

No abstract provided.

Measuring G With Movie Tracker, Stephen Schneider

STEM Digital

No abstract provided.

Detecting And Mixing Colors, Rob Snyder

STEM Digital

How can Analyzing Digital Images software reveal the differences between primary colors of light and primary colors of paints or pigments?

Measuring The Acceleration Of Falling Objects, John Pickle

STEM Digital

Earth's gravity pulls all objects toward its center, and near the Earth's surface. Objects in free fall accelerate at 9.8 m/s² vertically downward, provided air resistance is negligible. This value of acceleration is often referred to as "g". There are many ways to measure this rate of acceleration, and most require a timing device. Typically, stopwatches are the least expensive technology, so these are commonly available in high school science classrooms. With the recent addition of movie cameras on cell phones and digital cameras, another timing tool is available at moderate cost (free if the school policy …

Leaf Leaching Experiment, David Reckhow

STEM Digital

Water treatment engineers and public health officials need to pay careful attention to the presence of dissolved organic matter in water supplies selected for human consumption (i.e., raw drinking waters).

Measuring Albedo With Adi - An Intensity Application, Morton Sternheim

STEM Digital

Why are Polar Regions more affected by global warming than other parts of the globe? One reason (there are others) is that as sea ice melts and more open water appears, more energy is absorbed, and warming accelerates. This is a form of positive feedback and it makes the polar climate change faster than the climate in temperate areas. Increasing vegetation on land also has a similar positive feedback effect. This effect is a change in the albedo – the fraction of the incident sunlight that is reflected back to space.

Stem Digital And Adi In The Classroom, Jennifer Welborn

STEM Digital

Applications of ADI by students at Amherst Regional Middle School

Co2 Diffusion Through Gelatin Experiment, Jennifer Welborn

STEM Digital

An example of measuring lengths.

Natural Organic Matter In Water, David Reckhow

STEM Digital

Formation in Watersheds and Removal in Water Treatment

Using Adi To Quantify A Color Change In Crayfish, Jennifer Welborn

STEM Digital

Do Crayfish Change Color If Their Environment Changes? A Guided Inquiry Lab for 7th grade Life Science

Background: There is anecdotal evidence from bass fisherman that crayfish are able to change color depending on their surroundings. A (cursory) literature review of this phenomenon showed that no formal research has been done in this area. Students had an additional informal lesson about research funding (or lack thereof) because of this finding.

Students designed and conducted a controlled experiment to see the effect of changing environment color on crayfish color.

ADI was used to quantify a color change.

Human Variation In Skin Color And Race As A Social Construct, Jennifer Welborn

STEM Digital

This lesson is part of evolution unit which follows heredity and genetics

The lesson is interdisciplinary in nature in that I discuss the concept of race as a social construct and the idea that there are “black, white, red, yellow” skinned people is something that people developed. It is not based on biology. Race groupings are human-made groups.

Students first learn about mixing light and how to determine black and white from an ADI analysis. They learn that red and green = yellow, etc.

They then photograph each other’s forearms and analyze the images using ADI.

We then discuss skin …

Air Quality: Carbon Dioxide, Deborah Carlisle, Stephen Schneider

STEM Digital

Measuring CO2 with BTB and ADI.

Measuring Angles With Adi, Stephen Schneider

STEM Digital

No abstract provided.

Analyzing Digital Images (Adi) Resources, Rob Snyder

STEM Digital

Basic introduction to installing and using ADI

Arsenic Project Topics, Julian Tyson

STEM Digital

How do analytical chemists make light work in tracking potentially harmful chemicals?

Water Treatment Experiments, David Reckhow

STEM Digital

•The water industry spends a lot of money and effort on removal of natural organic matter (NOM) from drinking waters •Problems with NOM (the more NOM the bigger problem) –NOM interferes with the ability of water treatment systems to remove substances that cause disease •Pathogenic organisms •Toxic chemicals –NOM reacts with chlorine‐based disinfectants forming carcinogenic organic byproducts

Experimental Design For Ozone Projects, Deborah Carlisle, Stephen Schneider

STEM Digital

No abstract provided.

Jahn-Teller Coupling And Fragmentation After Core-Shell Excitation Ini Cf4 Investigated By Partial-Ion-Yield Spectroscopy, Renaud Guillemin, Wayne C. Stolte, Maria Novella Piancastelli, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We investigate fragmentation processes induced by core-level photoexcitation in CF4 at both the carbon and fluorine K edges by means of partial-ion-yield spectroscopy. The molecule CF₄ is a textbook example of systems in which Jahn-Teller coupling strongly manifests itself in the photoabsorption spectrum. Spectral features related to Jahn-Teller and quasi-Jahn-Teller splitting are observed, and important differences in the fragmentation pathways are revealed depending on the symmetries of the core-excited states. We interpret these experimental observations on the grounds of symmetry lowering from the Td to the C3v point group as well as preferential orientation with respect …