Biological and Chemical Physics Commons^™

Energetyka Niskoemisyjna, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.

Physical Basis Of The Inducer-Dependent Cooperativity Of The Central Glycolytic Genes Repressor/Dna Complex, Denis Chaix, Matthew L. Ferguson, Cedric Atmanene, Alain Van Dorsselaer, Sarah Sanglier-Cianférani, Catherine A. Royer, Nathalie Declerck

Matthew L. Ferguson

The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphosphate (FBP), reduces the binding cooperativity of the CggR/DNA complex. Here, we have determined the effect of FBP on the size, shape and stoichiometry of CggR complexes with full-length and half-site operator sequence by small-angle X-ray scattering, size-exclusion chromatography, fluorescence cross-correlation spectroscopy and noncovalent mass spectrometry (MS). Our results show that CggR forms a compact …

Computational Analysis Of Missense Mutations Causing Snyder-Robinson Syndrome, Zhe Zhang, Shaolei Teng, Liangjiang Wang, Charles E. Schwartz, Emil Alexov

Publications

The Snyder-Robinson syndrome is caused by missense mutations in the spermine sythase gene that encodes a protein (SMS) of 529 amino acids. Here we investigate, in silico, the molecular effect of three missense mutations, c.267G>A (p.G56S), c.496T>G (p.V132G), and c.550T>C (p.I150T) in SMS that were clinically identified to cause the disease. Single-point energy calculations, molecular dynamics simulations, and pKa calculations revealed the effects of these mutations on SMS's stability, flexibility, and interactions. It was predicted that the catalytic residue, Asp276, should be protonated prior binding the substrates. The pKa calculations indicated the p.I150T mutation causes pKa changes …

Hydration Dynamics At Fluorinated Protein Surfaces, Oh-Hoon Kwon, Tae Hyeon Yoo, Christina M. Othon, James A. Van Deventer, David A. Tirrell, Ahmed H. Zewail

Christina M Othon

Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface.

Structural And Magnetic Properties Of Iron Clusters, Andrew Mohrland, Eunja Kim

Undergraduate Research Opportunities Program (UROP)

Electronic, magnetic, and chemical properties of Fe nanoparticles are of particular interest for materials science, engineering, and metallurgical applications, including biomedical applications (e.g., medical imaging, cancer treatment, etc.). In this study, we search for the most stable geometries of the Fe clusters, Fen, up to n=8. Binding energies, magnetic moments, bond lengths, bond angles, and charge densities of clusters are computed and compared to the available experimental data. The various cluster isomers were examined energetically. We found that, in general, higher dimensional geometries are more stable than lower dimensions (i.e., 1-dimension or 2-dimension). Calculations for the Fe dimer yield a …

Laser Microraman Study Of Reduced Synthesized Spinel Powders, Alexandra J. Leandre, Michael M. Rodriguez, Joseph Lussier, Brittany Morgan, Brian Hosterman, John W. Farley

Undergraduate Research Opportunities Program (UROP)

The Raman effect is the excitation or de-excitation of vibrational modes resulting from the inelastic scattering of light from a gas, liquid, or solid with a shift in energy from that of the usually incident radiation. Raman microscopy was performed on synthesized spinel powders of solid solution FexCr3-xO4 to determine the dependence of the vibrational modes upon the metal cations. The powders were synthesized in a combustion reaction using metal nitrates and urea. The oxide powders were reduced in a hydrogen/argon gas flow at high temperature.

Potassium Chlorate Decomposition Under High Pressure, Harrison Ruiz, Michael G. Pravica, Martin Galley

Undergraduate Research Opportunities Program (UROP)

High pressure physics involves placing various substances under high pressure and observing changes in that substance. In this experiment this high amount of pressure is induced using a diamond anvil cell. A diamond anvil cell uses a metal gasket to hold the sample between two diamonds, which will press on the sample to reach high pressures. High pressures are reached with a moderate amount of force by exerting that force over a small area. Diamonds are used for the compression because of their hardness and ability to resist compression. The pressure being exerted on the sample using a diamond anvil …

High Pressure X-Ray Diffraction Studies On Zrfe2: A Potential Hydrogen Absorption Medium, Dylan D. Wood, Ravhi S. Kumar

Undergraduate Research Opportunities Program (UROP)

The potential application of intermetallic compounds (IMC) under high hydrogen pressure in studies of hydrogen sorption properties is defined by two important properties. Intermetallics of Laves phases have a suitable binding energy for hydrogen which allows its absorption or desorption near room temperature and atmospheric pressure. High pressures allow to efficiently interact hydrogen with intermetallics, which were considered nonhydride forming [1,2]. For example, ZrFe2, ZrCo2, and ZrFe2 possess fairly high hydrogen absorption capacity at high pressures [3]. A nonactivated ZrFe2 sample starts to interact with hydrogen only at 80 MPa, while equilibrium absorption and desorption pressures of the activated alloy …

High Pressure Structural Studies On Eus Nano Particles Up To 52 Gpa, Kristie Canaday, Ravhi S. Kumar

Undergraduate Research Opportunities Program (UROP)

Crystal size reduction in bulk materials changes the structural and magnetic properties considerably [1]. More importantly the transition pressure is strongly influenced by temperature, pressure, and the crystallite size effect. Rare earth europium chalcogenides crystallize in the NaCl (rock salt) type structure. The interest in Eu nanomaterials is motivated by the possibility of their use in magnetic devices [2,3]. Recent studies suggest that europium chalcogenide nanocrystals exhibit significant changes in their structural and magnetic properties, compared to bulk chalcogenides, when the nanocrystal diameter decreases. The crystal structure and phase transition behavior of EuS nanoparticles have been investigated and compared as …

High Pressure Studies Of Titanium Hydride Up To 50 Gpa With Synchrotron X-Ray Diffraction, Greg Harding, Patricia Kalita, Stanislav Sinogeikin, Andrew Cornelius

Undergraduate Research Opportunities Program (UROP)

Titanium dihydride has the potential to play an important role in the efficiency of high density hydrogen storage. The structural instability of TiH2 at high pressures makes an accurate characterization of its structure a vital part of understanding its behavior. A sample of TiH2 was placed in a diamond anvil cell and studied from ambient pressure up to 53 GPa using in situ synchrotron x-ray diffraction at the Advanced Photon Source (APS) of Argonne National Laboratory (Sector 16, HPCAT). From data of the evolution of the structure with pressure, an equation of state was obtained to model the behavior of …

High Pressure Infrared Studies Of Hmx, Jennifer Wojno, Michael G. Pravica, Martin Galley

Undergraduate Research Opportunities Program (UROP)

We are studying the effects of pressure on HMX (Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) using infrared spectroscopy. The sample is put under pressure using a diamond anvil cell at ambient temperature, data is collected at the National Synchrotron Light Source in Brookhaven National Laboratory. In analyzing this data, we hope to learn more about the molecular vibrations as the molecule bends and deforms under pressure. Such understanding could aid in determining new safety standards or more efficient ways of using HMX. In future studies, we intend to include the aspect of temperature variation in addition to pressure, with the goal of describing the molecule …

The Mechanical Stress–Strain Properties Of Single Electrospun Collagen Type I Nanofibers, Christine C. Helms, Corentin Coulais, Martin Guthold

Physics Faculty Publications

Knowledge of the mechanical properties of electrospun fibers is important for their successful application in tissue engineering, material composites, filtration and drug delivery. In particular, electrospun collagen has great potential for biomedical applications due to its biocompatibility and promotion of cell growth and adhesion. Using a combined atomic force microscopy (AFM)/optical microscopy technique, the single fiber mechanical properties of dry, electrospun collagen type I were determined. The fibers were electrospun from a 80 mg ml⁻¹ collagen solution in 1,1,1,3,3,3-hexafluro-2-propanol and collected on a striated surface suitable for lateral force manipulation by AFM. The small strain modulus, calculated from three-point …

Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn

All HMC Faculty Publications and Research

Locomotory muscles typically operate over a narrow range of contraction frequencies, characterized by the predominant fiber types and functional roles. The highest documented frequencies in the synchronous sound-producing muscles of insects (550 Hz) and toadfish (200 Hz) far exceed the contraction frequencies observed in weight-bearing locomotory muscles, which have maximum documented frequencies below 15-30 Hz. Laws of scaling, however, predict that smaller arthropods may employ stride frequencies exceeding this range. In this study we measured running speed and stride frequency in two undescribed species of teneriffiid mites from the coastal sage scrub of southern California. Relative speeds of both species …

Understanding The Role Of Electrostatics On Protein-Protein Binding, Rooplekha C Mitra

All Theses

Ionized groups carry net charge and thus play a major role in the electrostatic interactions between the ligand and receptor. So understanding the role of electrostatics on protein-protein interactions is crucial for understanding the contribution of ionizable groups to the binding. However, their ionization states depend on many factors including pH of water phase. The complexity comes from the fact that the pKa's of ionizable groups may be quite different from their standard values and even may change due to protein-protein binding. The main difficulty in modeling plausible ionization changes induced by the complex formation arises from the differences in …

Improving Thermoelectric Properties Of Chemically Synthesized Bi2te3-Based Nanocrystals By Annealing, Yixin Zhao, Jeffrey Dyck, Brett Hernandez, Clemens Burda

Jeffrey Dyck

The power factors of chemically synthesized Bi2Te3 and Bi0.5Sb1.5Te3 nanocrystals (NCs) were improved up to 2.4 and 7.8 μW cm−1 K−2, respectively, which are significantly higher than previously reported values for chemically synthesized Bi2Te3 NCs and even comparable to the recently reported highest power factor of 5 μW cm−1 K−2 for Bi2Te3 NCs consolidated by spark plasma sintering. This improvement was achieved by annealing the NCs under argon protection, and the crystal structures and morphologies of these annealed NCs were characterized via XRD, SEM, and TEM measurements. The temperature-dependent thermoelectric properties of these modified NCs were explored on cold-pressed pellets …

A Surface Femtosecond Two-Photon Photoemission Spectrometer For Excited Electron Dynamics And Time-Dependent Photochemical Kinetics, Zefeng Ren, Chuanyao Zhou, Zhibo Ma, Chun-Lei Xhao, Xinchun Mao, Dongxu Dai, Jerry L. Larue, Russell Cooper, Alec M. Wodtke, Xueming Yang

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A surface femtosecond two-photon photoemission (2PPE) spectrometer devoted to the study of ultrafast excited electron dynamics and photochemical kinetics on metal and metal oxide surfaces has been constructed. Low energy photoelectrons are measured using a hemispheri- cal electron energy analyzer with an imaging detector that allows us to detect the energy and the angular distributions of the photoelectrons simultaneously. A Mach-Zehnder interferom- eter was built for the time-resolved 2PPE (TR-2PPE) measurement to study ultrafast surface excited electron dynamics, which was demonstrated on the Cu(111) surface. A scheme for measuring time-dependent 2PPE (TD-2PPE) spectra has also been developed for studies of …

On The Ph-Optimum Of Activity And Stability Of Proteins, Kemper Tally, Emil Alexov

Publications

Biological macromolecules evolved to perform their function in specific cellular environment (subcellular compartments or tissues); therefore, they should be adapted to the biophysical characteristics of the corresponding environment, one of them being the characteristic pH. Many macromolecular properties are pH dependent, such as activity and stability. However, only activity is biologically important, while stability may not be crucial for the corresponding reaction. Here, we show that the pH-optimum of activity (the pH of maximal activity) is correlated with the pH-optimum of stability (the pH of maximal stability) on a set of 310 proteins with available experimental data. We speculate that …

Strength And Failure Of Fibrin Fiber Branch Points, Christine C. Helms, E. A. Sparks, C. Der Laughian, Martin Guthold

Physics Faculty Publications

Blood clots form rapidly in the event of vascular injury, to prevent blood loss. They may also form in undesired places, causing heart attacks, strokes, and other diseases. Blood clots can rupture, and fragments of the clotmay lodge in distal blood vessels, causing, for example, ischemic strokes or embolisms. Thus, there has been great interest in understanding the mechanical behavior and failure mechanisms of blood clots and their constituents. To develop a mechanically realistic model of a blood clot, knowledge of the mechanical properties of its constituents is required. The major structural component providing mechanical strength to the clot is …

The Mechanical Properties Of Single Fibrin Fibers, W. Liu, Christine C. Helms, E. A. Sparks, Martin Guthold

Physics Faculty Publications

Background:

Blood clots perform the mechanical task of stemming the flow of blood.

Objectives:

To advance understanding and realistic modeling of blood clot behavior we determined the mechanical properties of the major structural component of blood clots, fibrin fibers.

Methods:

We used a combined atomic force microscopy (AFM)/fluorescence microscopy technique to determine key mechanical properties of single crosslinked and uncrosslinked fibrin fibers.

Results and conclusions:

Overall, full crosslinking renders fibers less extensible, stiffer, and less elastic than their uncrosslinked counterparts. All fibers showed stress relaxation behavior (time-dependent weakening) with a fast and a slow relaxation time, 2 and 52 s. …

Understanding The Biological And Environmental Implications Of Nanomaterials, Sijie Lin

All Dissertations

The last two decades have witnessed the discovery, development, and large-scale manufacturing of novel nanomaterials. While nanomaterials bring in exciting and extraordinary properties in all areas of materials, electronics, mechanics, and medicine, they also could generate potential adverse effects in biological systems and in the environment. The currently limited application of nanomaterials in biological and ecological systems results from the insufficient and often controversial data on describing the complex behaviors of nanomaterials in living systems. The purpose of this dissertation intends to fill such a knowledge void with methodologies from the disciplines of biophysics, biology, and materials science and engineering. …