Biological and Chemical Physics Commons^™

Comparative Review Of Imaging Methods Used For Diagnosing Renal Artery Stenosis (Ras), Deirdre King, Carmel Moran, Jacinta Browne

Articles

This comparative review examines the efficacy of different imaging methods to detect and quantify renal artery stenosis (RAS). Detection of RAS is important because it can lead to renovascular hypertension which is the most common form of secondary hypertension. Furthermore, it is important that a RAS is detected as early as possible as it is a potentially correctable cause of hypertension.¹ If detected at an early stage RAS can potentially be treated using a minimally invasive drug treatment regimen rather than the more invasive percutaneous transluminal renal angioplasty without or with stent placement or surgery. Currently there are a …

How The Cucumber Tendril Coils And Overwinds, Sharon J. Gerbode, Joshua R. Puzey, Andrew G. Mccormick, L. Mahadevan

All HMC Faculty Publications and Research

The helical coiling of plant tendrils has fascinated scientists for centuries, yet the underlying mechanism remains elusive. Moreover, despite Darwin’s widely accepted interpretation of coiled tendrils as soft springs, their mechanical behavior remains unknown. Our experiments on cucumber tendrils demonstrate that tendril coiling occurs via asymmetric contraction of an internal fiber ribbon of specialized cells. Under tension, both extracted fiber ribbons and old tendrils exhibit twistless overwinding rather than unwinding, with an initially soft response followed by strong strain-stiffening at large extensions. We explain this behavior using physical models of prestrained rubber strips, geometric arguments, and mathematical models of elastic …

Double Layer In Ionic Liquids: Overscreening Versus Crowding, Martin Z. Bazant, Brian D. Storey, Alexei A. Kornyshev

Brian Storey

We develop a simple Landau-Ginzburg-type continuum theory of solvent-free ionic liquids and use it to predict the structure of the electrical double layer. The model captures overscreening from short-range correlations, dominant at small voltages, and steric constraints of finite ion sizes, which prevail at large voltages. Increasing the voltage gradually suppresses overscreening in favor of the crowding of counterions in a condensed inner layer near the electrode. This prediction, the ion profiles, and the capacitance-voltage dependence are consistent with recent computer simulations and experiments on room-temperature ionic liquids, using a correlation length of order the ion size.

Angular And Dynamical Properties In Resonant Inelastic X-Ray Scattering: Case Study Of Chlorine-Containing Molecules, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Stephane Carniato, Maria Novella Piancastelli, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

Polarization-dependent resonant inelastic x-ray scattering (RIXS) has been shown to be a probe of molecular-field effects on the electronic structure of isolated molecules. In this experimental analysis we explain the linear dichroism observed in Cl 2p polarized RIXS following Cl 1s excitation of a series of chlorofluoromethanes (CF3Cl, CF2Cl2, CFCl3, and CCl4) as due to molecular-field effects, including singlet-triplet exchange. We present an approach to extract directly the 2p inner-shell electronic state populations from the experimental measurements. Using the angular properties of the measured KV emission we also are able to determine the value of the polarization anisotropy parameter βp …

Self-Assembly Of Helical Ribbons, Yevgeniya V. Zastavker, Neer Asherie, Aleksey Lomakin, Jayanti Pande, Joanne M. Donovan, Joel M. Schnur, George B. Benedek

Yevgeniya V. Zastavker

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54 ± 2°, and low pitch, with a pitch angle of 11 ± 2°. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range …

Tension-Induced Straightening Transition Of Self-Assembled Helical Ribbons, Yevgeniya V. Zastavker, Brice Smith, George B. Benedek

Yevgeniya V. Zastavker

Helical ribbons with pitch angles of either 11° or 54° self-assemble in a wide variety of quaternary surfactant-phospholipid/fatty acid-sterol-water systems. By elastically deforming these helices, we examined their response to uniaxial forces. Under sufficient tension, a low pitch helix reversibly separates into a straight domain with a pitch angle of 90° and a helical domain with a pitch angle of 16.5°. Using a newly developed continuum elastic free energy model, we have shown that this phenomenon can be understood as a first order mechanical phase transition.

Predicting Nonspecific Ion Binding Using Delphi, Marharyta Petukh, Maxim Zhenirovskyy, Chuan Li, Lin Li, Lin Wang, Emil Alexov

Publications

Ions are an important component of the cell and affect the corresponding biological macromolecules either via direct binding or as a screening ion cloud. Although some ion binding is highly specific and frequently associated with the function of the macromolecule, other ions bind to the protein surface nonspecifically, presumably because the electrostatic attraction is strong enough to immobilize them. Here, we test such a scenario and demonstrate that experimentally identified surface-bound ions are located at a potential that facilitates binding, which indicates that the major driving force is the electrostatics. Without taking into consideration geometrical factors and structural fluctuations, we …

Use Of Second Harmonic Generation (Shg) Imaging For 3-Dimensional Ultrastructural Visualization Of Muscle Repair Mechanisms, Matthew Dufner

Honors Scholar Theses

In this study, we have combined SHG imaging with various fluorescent dyes which are designed to stain nuclei and used a skeletal muscle injury and regeneration model to establish the ability of this approach to reliably and reproducibly evaluate the above nuclear parameters. By using the cobra cardiotoxin (CTX-1), which creates acute well defined injuries within the muscle, on the tibialis anterior (TA) and gastrocnemius hind limb muscles of mice, predictable and reproducible regenerative patterns (in response to acute injury) can be observed by harvesting muscle samples at specific time points during recovery. Through SHG imaging, we endeavor to document …

Delphi: A Comprehensive Suite For Delphi Software And Associated Resources, Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov

Publications

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding …

Non-Linear Dynamic Intertwining Of Rods With Self-Contact, Christopher Lee, Sachin Goyal, Noel Perkins

Christopher Lee

Twisted marine cables on the sea floor can form highly contorted three-dimensional loops that resemble tangles. Such tangles or ‘hockles’ are topologically equivalent to the plectomenes that form in supercoiled DNA molecules. The dynamic evolution of these intertwined loops is studied herein using a computationalrod model that explicitly accounts for dynamicself-contact. Numerical solutions are presented for an illustrative example of a long rod subjected to increasing twist at one end. The solutions reveal the dynamicevolution of the rod from an initially straight state, through a buckled state in the approximate form of a helix, through the dynamic collapse of this …

Nanotopography Influences Adhesion, Spreading, And Self-Renewal Of Human Embryonic Stem Cells, Weiqiang Chen, Luis G. Villa-Diaz, Yubing Sun, Shinuo Weng, Jin Koo Kim, Raymond H. W. Lam, Lin Han, Rong Fan, Paul H. Krebsbach, Jianping Fu

Weiqiang Chen

Human embryonic stem cells (hESCs) have great potentials for future cell-based therapeutics. However, their mechanosensitivity to biophysical signals from the cellular microenvironment is not well characterized. Here we introduced an effective microfabrication strategy for accurate control and patterning of nanoroughness on glass surfaces. Our results demonstrated that nanotopography could provide a potent regulatory signal over different hESC behaviors, including cell morphology, adhesion, proliferation, clonal expansion, and self-renewal. Our results indicated that topological sensing of hESCs might include feedback regulation involving mechanosensory integrin-mediated cell matrix adhesion, myosin II, and E-cadherin. Our results also demonstrated that cellular responses to nanotopography were cell-type …

Multi-State Analysis Of The Ocs Ultraviolet Absorption Including Vibrational Structure, Johan A. Schmidt, M. S. Johnson, George C. Mcbane, Reinhard Schinke

Peer Reviewed Articles

The first absorption band of OCS (carbonyl sulfide) is analyzed using potential energy surfaces and transition dipole moment functions of the lowest four singlet and the lowest four triplet states. Excitation of the 2¹A' state is predominant except at very low photon energies. It is shown that the vibrational structures in the center of the band are due to excitation of the 2³A" triplet state, whereas the structures at the very low energies are caused by bending excitation in the potential wells of states 2¹A' and 1¹A".

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.

Analyzing Effects Of Naturally Occurring Missense Mutations, Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov

Publications

Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will produce an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This paper focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein and how to assess their effects on protein wild-type characteristics. The existing methods and approaches for predicting the effects of mutation on protein stability, structure, and dynamics are outlined and discussed with respect to their underlying …

Product Angular Distributions In The Ultraviolet Photodissociation Of N2O, George C. Mcbane, Reinhard Schinke

Peer Reviewed Articles

The angular distribution of products from the ultraviolet photodissociation of nitrous oxide yielding O(¹D) and N₂(X¹Σ⁺_g) was investigated using classical trajectory calculations. The calculations modeled absorption only to the 2¹A'electronic state but used surface-hopping techniques to model nonadiabatic transitions to the ground electronic state late in the dissociation. Observed values of the anisotrophy parameter β, which decrease as the product N₂ rotational quantum number jincreases, could be well reproduced. The relatively low observed βvalues arise principally from nonaxial recoil due to the very …

Α−Α Cross-Links Increase Fibrin Fiber Elasticity And Stiffness, Christine C. Helms, Robert A.S. Ariens, S. Uitte De Willige, Kristina F. Standeven, Martin Guthold

Physics Faculty Publications

Fibrin fibers, which are ∼100 nm in diameter, are the major structural component of a blood clot. The mechanical properties of single fibrin fibers determine the behavior of a blood clot and, thus, have a critical influence on heart attacks, strokes, and embolisms. Cross-linking is thought to fortify blood clots; though, the role of α–α cross-links in fibrin fiber assembly and their effect on the mechanical properties of single fibrin fibers are poorly understood. To address this knowledge gap, we used a combined fluorescence and atomic force microscope technique to determine the stiffness (modulus), extensibility, and elasticity of …

Reconciling Molecular Regulatory Mechanisms With Noise Patterns Of Bacterial Metabolic Promoters In Induced And Repressed States, Matthew L. Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Ovidiu Radulescu, Nathalie Declerck, Catherine A. Royer

Matthew L. Ferguson

Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two Bacillus subtilis promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for …

Experimental Studies Of The Nacs 53Π0 And A3Σ+ States, Seth T. Ashman, B. Mcgeehan, C. M. Wolfe, C. Faust, K. Richter

Engineering & Physics Faculty Publications

We report high resolution measurements of 372 NaCs 53Π0(v, J) ro-vibrational level energies in the range 0 ≤ v ≤ 22. The data have been used to construct NaCs 53Π0 potential energy curves using the Rydberg–Klein-Rees and inverted perturbation approximation methods. Bound-free 53Π0(v, J) → 1(a)3Σ+ emission has also been measured, and is used to determine the repulsive wall of the 1(a)3Σ+ state and the 53Π0 → 1(a)3Σ+ relative transition dipole moment function. Hyperfine structure in the 53Π0 state has not been observed in this experiment. This null result is explained using a simple vector coupling model.

Assessing The Feasibility Of Cosmic-Ray Acceleration By Magnetic Turbulence At The Magnetic Center, M. Fatuzzo, F. Melia

Faculty Scholarship

No abstract provided.

Quantitative Study Of Spin-Flip Co-Tunneling Transport In A Quantum Dot, S. Herbert, T-M. Liu, A. N. Ngo

Faculty Scholarship

No abstract provided.