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Biological and Chemical Physics

2017

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Full-Text Articles in Physics

Folding Of Bovine Pancreatic Trypsin Inhibitor (Bpti) Is Faster Using Aromatic Thiols And Their Corresponding Disulfides, Ram Prasad Marahatta Nov 2017

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 ...


Mixing Times Of Organic Molecules Within Secondary Organic Aerosol Particles: A Global Planetary Boundary Layer Perspective, Adrian M. Maclean, Christopher L. Butenhoff, James W. Grayson, Kelley Barsanti, Jose L. Jimenez, Allan K. Bertram Nov 2017

Mixing Times Of Organic Molecules Within Secondary Organic Aerosol Particles: A Global Planetary Boundary Layer Perspective, Adrian M. Maclean, Christopher L. Butenhoff, James W. Grayson, Kelley Barsanti, Jose L. Jimenez, Allan K. Bertram

Physics Faculty Publications and Presentations

When simulating the formation and life cycle of secondary organic aerosol (SOA) with chemical transport models, it is often assumed that organic molecules are well mixed within SOA particles on the timescale of 1 h. While this assumption has been debated vigorously in the literature, the issue remains unresolved in part due to a lack of information on the mixing times within SOA particles as a function of both temperature and relative humidity. Using laboratory data, meteorological fields, and a chemical transport model, we estimated how often mixing times are < 1 h within SOA in the planetary boundary layer (PBL), the region of the atmosphere where SOA concentrations are on average the highest. First, a parameterization for viscosity as a function of temperature and RH was developed for α-pinene SOA using room-temperature and low-temperature viscosity data for α-pinene SOA generated in the laboratory using mass concentrations of ∼ 1000 µg m−3. Based on this parameterization, the mixing times within α-pinene SOA are < 1 h for 98.5 % and 99.9 % of the occurrences in the PBL during January and July, respectively, when concentrations are significant (total organic aerosol concentrations are > 0.5 µg m−3 at the surface). Next, as ...


Interfacial Self-Assembly Of Polyelectrolyte-Capped Gold Nanoparticles, Honghu Zhang, Srikanth Nayak, Wenjie Wang, Surya K Mallapragada, David Vaknin Oct 2017

Interfacial Self-Assembly Of Polyelectrolyte-Capped Gold Nanoparticles, Honghu Zhang, Srikanth Nayak, Wenjie Wang, Surya K Mallapragada, David Vaknin

Ames Laboratory Accepted Manuscripts

We report on pH- and salt-responsive assembly of nanoparticles capped with polyelectrolytes at vapor–liquid interfaces. Two types of alkylthiol-terminated poly(acrylic acid) (PAAs, varying in length) are synthesized and used to functionalize gold nanoparticles (AuNPs) to mimic similar assembly effects of single-stranded DNA-capped AuNPs using synthetic polyelectrolytes. Using surface-sensitive X-ray scattering techniques, including grazing incidence small-angle X-ray scattering (GISAXS) and X-ray reflectivity (XRR), we demonstrate that PAA-AuNPs spontaneously migrate to the vapor–liquid interfaces and form Gibbs monolayers by decreasing the pH of the suspension. The Gibbs monoalyers show chainlike structures of monoparticle thickness. The pH-induced self-assembly is attributed ...


Off-Axis Electron Holography Of Bacterial Cells And Magnetic Nanoparticles In Liquid, Tanya Prozorov, Trevor Alemeida, András Kovács, Rafal E. Dunin-Borkowski Oct 2017

Off-Axis Electron Holography Of Bacterial Cells And Magnetic Nanoparticles In Liquid, Tanya Prozorov, Trevor Alemeida, András Kovács, Rafal E. Dunin-Borkowski

Ames Laboratory Accepted Manuscripts

The mapping of electrostatic potentials and magnetic fields in liquids using electron holography has been considered to be unrealistic. Here, we show that hydrated cells of Magnetospirillum magneticum strain AMB-1 and assemblies of magnetic nanoparticles can be studied using off-axis electron holography in a fluid cell specimen holder within the transmission electron microscope. Considering that the holographic object and reference wave both pass through liquid, the recorded electron holograms show sufficient interference fringe contrast to permit reconstruction of the phase shift of the electron wave and mapping of the magnetic induction from bacterial magnetite nanocrystals. We assess the challenges of ...


Stochastic Resonance In A Proton Pumping Complex I Of Mitochondria Membranes, Davneet Kaur, Ilan Filonenko, Lev Mourokh, Cornelius Fendler, Robert H. Blick Sep 2017

Stochastic Resonance In A Proton Pumping Complex I Of Mitochondria Membranes, Davneet Kaur, Ilan Filonenko, Lev Mourokh, Cornelius Fendler, Robert H. Blick

Publications and Research

We make use of the physical mechanism of proton pumping in the so-called Complex I within mitochondria membranes. Our model is based on sequential charge transfer assisted by conformational changes which facilitate the indirect electron-proton coupling. The equations of motion for the proton operators are derived and solved numerically in combination with the phenomenological Langevin equation describing the periodic conformational changes. We show that with an appropriate set of parameters, protons can be transferred against an applied voltage. In addition, we demonstrate that only the joint action of the periodic energy modulation and thermal noise leads to efficient uphill proton ...


Differential Uptake Of Gold Nanoparticles By 2 Species Of Tadpole, The Wood Frog (Lithobates Sylvaticus) And The Bullfrog (Lithobates Catesbeianus), Lucas B. Thompson, Gerardo L.F. Carfagno, Kurt Andresen, Andrea J. Sitton, Taylor B. Bury, Laura L. Lee, Kevin T. Lerner, Peter P. Fong Aug 2017

Differential Uptake Of Gold Nanoparticles By 2 Species Of Tadpole, The Wood Frog (Lithobates Sylvaticus) And The Bullfrog (Lithobates Catesbeianus), Lucas B. Thompson, Gerardo L.F. Carfagno, Kurt Andresen, Andrea J. Sitton, Taylor B. Bury, Laura L. Lee, Kevin T. Lerner, Peter P. Fong

Biology Faculty Publications

Engineered nanoparticles are aquatic contaminants of emerging concern that exert ecotoxicological effects on a wide variety of organisms. We exposed cetyltrimethylammonium bromide–capped spherical gold nanoparticles to wood frog and bullfrog tadpoles with conspecifics and in combination with the other species continuously for 21 d, then measured uptake and localization of gold. Wood frog tadpoles alone and in combination with bullfrog tadpoles took up significantly more gold than bullfrogs. Bullfrog tadpoles in combination with wood frogs took up significantly more gold than controls. The rank order of weight-normalized gold uptake was wood frogs in combination > wood frogs alone > bullfrogs in ...


Polar Intermetallics Pr5co2ge3 And Pr7co2ge4 With Planar Hydrocarbon‐Like Metal Clusters, Qisheng Lin, Kaiser Aguirre, Scott M. Saunders, Timothy A. Hackett, Yong Liu, Valentin Taufour, Durga Paudyal, Sergey L. Bud’Ko, Paul C. Canfield, Gordon J. Miller Aug 2017

Polar Intermetallics Pr5co2ge3 And Pr7co2ge4 With Planar Hydrocarbon‐Like Metal Clusters, Qisheng Lin, Kaiser Aguirre, Scott M. Saunders, Timothy A. Hackett, Yong Liu, Valentin Taufour, Durga Paudyal, Sergey L. Bud’Ko, Paul C. Canfield, Gordon J. Miller

Chemistry Publications

Planar hydrocarbon‐like metal clusters may foster new insights linking organic molecules with conjugated π–π bonding interactions and inorganic structures in terms of their bonding characteristics. However, such clusters are uncommon in polar intermetallics. Herein, we report two polar intermetallic phases, Pr5Co2Ge3 and Pr7Co2Ge4, both of which feature such planar metal clusters, namely, ethylene‐like [Co2Ge4] clusters plus the concatenated forms and polyacene‐like [Co2Ge2]n ribbons in Pr5Co2Ge3, and 1,2,4,5‐tetramethylbenzene‐like [Co4Ge6] cluster in Pr7Co2Ge4. Just as in the related planar organic structures, these metal–metalloid species are dominated by covalent bonding interactions. Both ...


Angular Distribution Of Single-Photon Superradiance In A Dilute And Cold Atomic Ensemble, A. S. Kuraptsev, I. M. Sokolov, M. D. Havey Aug 2017

Angular Distribution Of Single-Photon Superradiance In A Dilute And Cold Atomic Ensemble, A. S. Kuraptsev, I. M. Sokolov, M. D. Havey

Physics Faculty Publications

On the basis of a quantum microscopic approach we study the dynamics of the afterglow of a dilute Gaussian atomic ensemble excited by pulsed radiation. Taking into account the vector nature of the electromagnetic field we analyze in detail the angular and polarization distribution of single-photon superradiance of such an ensemble. The dependence of the angular distribution of superradiance on the length of the pulse and its carrier frequency as well as on the size and the shape of the atomic clouds is studied. We show that there is substantial dependence of the superradiant emission on the polarization and the ...


Crystal Structure, Homogeneity Range And Electronic Structure Of Rhombohedral Γ-Mn5al8, Srinivasa Thimmaiah, Zachary Tener, Tej N. Lamichhane, Paul C. Canfield, Gordon J. Miller Jul 2017

Crystal Structure, Homogeneity Range And Electronic Structure Of Rhombohedral Γ-Mn5al8, Srinivasa Thimmaiah, Zachary Tener, Tej N. Lamichhane, Paul C. Canfield, Gordon J. Miller

Chemistry Publications

The γ-region of the Mn–Al phase diagram between 45 and 70 at.% Al was re-investigated by a combination of powder and single crystal X-ray diffraction as well as EDS analysis to establish the distribution of Mn and Al atoms. Single crystals of γ-Mn5–x Al8+x were grown using Sn-flux at 650 °C. The crystal structure, atomic coordinates and site occupancy parameters of γ-Mn5−x Al8+x phases were refined from single crystal X-ray data. The γ-Mn5-x Al8+x phase adopts the rhombohedral Cr5Al8-type structure rather than a cubic γ-brass structure. The refined compositions from two crystals extracted ...


Determination Of The Zinc Concentration In Human Fingernails By Laser-Induced Breakdown Spectroscopy, Steven J. Rehse, Vlora A. Riberdy, Christopher J. Frederickson Apr 2017

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 ...


Scanning Ion Conductance Microscopy For Single Cell Imaging And Analysis, Namuna Panday Mar 2017

Scanning Ion Conductance Microscopy For Single Cell Imaging And Analysis, Namuna Panday

FIU Electronic Theses and Dissertations

Most biological experiments are performed on an ensemble of cells under the assumption that all cells are identical. However, recent evidence from single cells studies reveals that this assumption is incorrect. Individual cells within the same generation may differ dramatically, and these differences have important consequences for the health and function of the entire living body. I have used Scanning Ion Conductance Microscopy (SICM) for imaging and analysis of topographical change of single cell membrane, which is difficult to be revealed by optical microscopes. Morphological change in the fixed and live HeLa cell membrane during endocytosis of conjugated polymer nanoparticles ...


A Molecular Debye-Hückel Theory And Its Applications To Electrolyte Solutions: The Size Asymmetric Case, Tiejen Xiao, Xueyu Song Mar 2017

A Molecular Debye-Hückel Theory And Its Applications To Electrolyte Solutions: The Size Asymmetric Case, Tiejen Xiao, Xueyu Song

Chemistry Publications

A molecular Debye-Hückel theory for electrolyte solutions with size asymmetry is developed, where the dielectric response of an electrolyte solution is described by a linear combination of Debye-Hückel-like response modes. As the size asymmetry of an electrolyte solution leads to a charge imbalanced border zone around a solute, the dielectric response to the solute is characterized by two types of charge sources, namely, a bare solute charge and a charge distribution due to size asymmetry. These two kinds of charge sources are screened by the solvent differently, our theory presents a method to calculate the mean electric potential as well ...


Molecular Dynamics Investigations Of Structural Conversions In Transformer Proteins, Jeevan Gc Mar 2017

Molecular Dynamics Investigations Of Structural Conversions In Transformer Proteins, Jeevan Gc

FIU Electronic Theses and Dissertations

Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular ...


Higher-Order Power Harmonics Of Pulsed Electrical Stimulation Modulates Corticospinal Contribution Of Peripheral Nerve Stimulation, Chiun-Fan Chen, Marom Bikson, Li-Wei Chou, Chunlei Shan, Niranjan Khadka, Wen-Shiang Chen, Felipe Fregni Mar 2017

Higher-Order Power Harmonics Of Pulsed Electrical Stimulation Modulates Corticospinal Contribution Of Peripheral Nerve Stimulation, Chiun-Fan Chen, Marom Bikson, Li-Wei Chou, Chunlei Shan, Niranjan Khadka, Wen-Shiang Chen, Felipe Fregni

Engineering Science Faculty Publications

It is well established that electrical-stimulation frequency is crucial to determining the scale of induced neuromodulation, particularly when attempting to modulate corticospinal excitability. However, the modulatory effects of stimulation frequency are not only determined by its absolute value but also by other parameters such as power at harmonics. The stimulus pulse shape further influences parameters such as excitation threshold and fiber selectivity. The explicit role of the power in these harmonics in determining the outcome of stimulation has not previously been analyzed. In this study, we adopted an animal model of peripheral electrical stimulation that includes an amplitude-adapted pulse train ...


The Impact Of Base Stacking On The Conformations And Electrostatics Of Single-Stranded Dna, Alex Plumridge, Steve P. Meisburger, Kurt Andresen, Lois Pollack Feb 2017

The Impact Of Base Stacking On The Conformations And Electrostatics Of Single-Stranded Dna, Alex Plumridge, Steve P. Meisburger, Kurt Andresen, Lois Pollack

Physics and Astronomy Faculty Publications

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy ...


Student Resources For: From Photon To Neuron, Light, Imaging, Vision, Philip C. Nelson Feb 2017

Student Resources For: From Photon To Neuron, Light, Imaging, Vision, Philip C. Nelson

Department of Physics Papers

This zip archive contains datasets and additional media associated to the book "From Photon to Neuron (Princeton University Press, 2017).


Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans Jan 2017

Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans

Physics and Astronomy Publications

We perform a tracer counterpermeation (TCP) analysis for a stochastic model of diffusive transport through a narrow linear pore where passing of species within the pore is inhibited or even excluded (single-file diffusion). TCP involves differently labeled but otherwise identical particles from two decoupled infinite reservoirs adsorbing into opposite ends of the pore, and desorbing from either end. In addition to transient behavior, we assess steady-state concentration profiles, spatial correlations, particle number fluctuations, and diffusion fluxes through the pore. From the profiles and fluxes, we determine a generalized tracer diffusion coefficient Dtr(x), at various positions x within the pore ...


Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian Jan 2017

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build ...


Including Wrist Flexion In The Human Arm Model Changes Everything!, William B. Laing Iii, Austin Johnson, Albert D. Gonzalez, Chris S. Hansen Jan 2017

Including Wrist Flexion In The Human Arm Model Changes Everything!, William B. Laing Iii, Austin Johnson, Albert D. Gonzalez, Chris S. Hansen

Faculty Works

Does your introductory physics laboratory experiment that analyzes the human arm as a lever assume an inflexible wrist? If so, the analysis of the biceps force required to perform a biceps curl will lead to results that contradict experience: one does not expect the required biceps force to decrease as the mass is raised. We will show that allowing for wrist flexion leads to agreement with empirical data: that the required force does increase as the mass is raised if the wrist angle is allowed to be optimal.


Tailoring Nanoscale Morphology Of Polymer: Fullerene Blends Using Electrostatic Field, Moneim Elshobaki, Ryan S. Gebhardt, John Carr, William Lindemann, Wenjie Wang, Eric Grieser, Swaminathan Venkatesan, Evan Ngo, Ujjal Bhattacharjee, Joseph Strzalka, Zhang Jiang, Qiquan Qiao, Jacob W. Petrich, David Vaknin, Sumit Chaudhary Jan 2017

Tailoring Nanoscale Morphology Of Polymer: Fullerene Blends Using Electrostatic Field, Moneim Elshobaki, Ryan S. Gebhardt, John Carr, William Lindemann, Wenjie Wang, Eric Grieser, Swaminathan Venkatesan, Evan Ngo, Ujjal Bhattacharjee, Joseph Strzalka, Zhang Jiang, Qiquan Qiao, Jacob W. Petrich, David Vaknin, Sumit Chaudhary

Chemistry Publications

To tailor the nanomorphology in polymer/fullerene blends, we study the effect of electrostatic field (E-field) on the solidification of poly(3-hexylthiophene-2, 5-diyl) (P3HT):[6,6]-phenyl-C61-butyric acid methyl ester (PC60BM) bulk heterojunction (BHJ). In addition to control; wet P3HT:PC60BM thin films were exposed to E-field of Van de Graaff (VDG) generator at three different directions—horizontal (H), tilted (T), and vertical (V)—relative to the plane of the substrate. Surface and bulk characterizations of the field-treated BHJs affirmed that fullerene molecules can easily penetrate the spaghetti-like P3HT and move up and down following the E-field. Using E-field treatment ...