Physics Commons^™

Correct Spectral Conversion Between Surface‐Enhanced Raman And Plasmon Resonance Scattering From Nanoparticle Dimers For Single‐Molecule Detection, Kyuwan Lee

Kyuwan Lee

Simultaneous measurement of surface-enhanced Raman scattering (SERS) and localized surface plasmon resonance (LSPR) in nanoparticle dimers presents outstanding opportunities in molecular identification and in the elucidation of physical properties, such as the size, distance, and deformation of target species. SERS–LSPR instrumentation exists and has been used under limited conditions, but the extraction of SERS and LSPR readouts from a single measurement is still a challenge. Herein, the extraction of LSPR spectra from SERS signals is reported and a tool for measuring the interparticle distance from Raman enhancement data by the standardization of the SERS signal is proposed. The SERS nanoruler …

Toward High-Performance Nanostructured Thermoelectric Materials: The Progress Of Bottom-Up Solution Chemistry Approaches, Yixin Zhao, Jeffrey S. Dyck, Clemens Burda

Jeffrey Dyck

Significant research effort has recently gone into the synthesis of thermoelectric nanomaterials through different chemical approaches since nanomaterials chemistry became a promising strategy for improving thermoelectric performance. Different thermoelectric nanocrystals, especially PbTe, Bi2Te3 and CoSb3, with various compositions and morphologies have been successfully prepared by solvo/hydrothermal, electrochemical, and ligand-based synthesis methods. Such nanoscale materials show not only substantial reduction in thermal conductivity due to increased phonon scattering at nanoscale grain boundaries and lower densities of phonon states but possibly also an enhancement in thermopower due to electronic quantum size effects. More recently, the notoriously low power factors of thermoelectric nanomaterials …

Structure Inhomogeneities, Shallow Defects, And Charge Transport In The Series Of Thermoelectric Materials K2bi8−Xsbxse13, Jeffrey S. Dyck, T. Kyratski, E. Hatzikraniotis, K. M. Paraskevopoulos, C. D. Malliakas, C. Uher, M. G. Kanatzidis

Jeffrey Dyck

The charge transport properties of the low-dimensional thermoelectric materials K2Bi8-xSbxSe13 (02Bi8-xSbxSe13 was analyzed on the basis of the classical semiconductor theory and discussed in the context of recent band calculations. The results suggest that the K2Bi8-xSbxSe13 materials possess coexisting domains with semimetallic and semiconducting characters whose ratio is influenced by the value of x and by local defects. The extent and relative distribution of these domains control the charge transport properties. Electron diffraction experiments performed on samples of K2Bi8-xSbxSe13 with x=1.6 show evidence for such domains by indicating regions with long range ordering of K+/Bi3+ atoms and regions with increased …

Fast Absolute Quantification Of In Vivo Water And Fat Content With Magnetic Resonance Imaging, Yifan Cui

Electronic Thesis and Dissertation Repository

Quantitative water fat imaging offers a non-invasive method for monitoring and staging diseases associated with changes in either water or fat content in tissue. In this work absolute water and fat mass density measurement with in vivo Magnetic Resonance Imaging (MRI) is demonstrated. T₁ independent, T₂^* corrected chemical shift based water-fat separated images are acquired. By placing a phantom with known mass density in the field of view for signal intensity calibration, absolute water or fat mass density can be computed, assuming the B₁⁺ (transmit) and B₁^- (receive) fields can be measured. Phantom …

Confinement Effects Of Solvation On A Molecule Physisorbed On A Metal Particle, Jacob Fosso Tande

Doctoral Dissertations

We describe and present results of the implementation of the surface and volume polarization for electrostatics~(SVPE) and the iso-density surface solvation models. Unlike most other implementation of the solvation models where the solute and the solvent are described with multiple numerical representation, our implementation uses a multiresolution, adaptive multiwavelet basis to describe both solute and the solvent. This requires reformulation to use integral equations throughout as well as a conscious management of numerical properties of the basis.

Likewise, we investigate the effects of solvation on the static properties of a molecule physisorbed on a spherical particle, modeled as a polarizable …

Protein Nano-Object Integrator (Pronoi) For Generating Atomic Style Objects For Molecular Modeling, Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov

Publications

Background

With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results

Here we report the Protein Nano-Object Integrator (ProNOI) which allows for …

Nanoroughened Surfaces For Efficient Capture Of Circulating Tumor Cells Without Using Capture Antibodies, Weiqiang Chen, Shinuo Weng, Feng Zhang, Steven Allen, Xiang Li, Liwei Bao, Raymond H. W. Lam, Jill A. Macoska, Sofia D. Merajver, Jianping Fu

Weiqiang Chen

Circulating tumor cells (CTCs) detached from both primary and metastatic lesions represent a potential alternative to invasive biopsies as a source of tumor tissue for the detection, characterization and monitoring of cancers. Here we report a simple yet effective strategy for capturing CTCs without using capture antibodies. Our method uniquely utilized the differential adhesion preference of cancer cells to nanorough surfaces when compared to normal blood cells and thus did not depend on their physical size or surface protein expression, a significant advantage as compared to other existing CTC capture techniques.

A Modular Fibrinogen Model That Captures The Stress-Strain Behavior Of Fibrin Fibers, Rodney D. Averett, Bryant Menn, Eric H. Lee, Christine C. Helms, Thomas Barker, Martin Guthold

Physics Faculty Publications

We tested what to our knowledge is a new computational model for fibrin fiber mechanical behavior. The model is composed of three distinct elements: the folded fibrinogen core as seen in the crystal structure, the unstructured α-C connector, and the partially folded α-C domain. Previous studies have highlighted the importance of all three regions and how they may contribute to fibrin fiber stress-strain behavior. Yet no molecular model has been computationally tested that takes into account the individual contributions of all these regions. Constant velocity, steered molecular dynamics studies at 0.025 Å/ps were conducted on the folded fibrinogen …

3d Imaging And Mechanical Modeling Of Helical Buckling In Medicago Truncatula Plant Roots, Jesse L. Silverberg, Roslyn D. Noar, Michael S. Packer, Maria J. Harrison, Christopher L. Henley, Itai Cohen, Sharon J. Gerbode

All HMC Faculty Publications and Research

We study the primary root growth of wild-type Medicago truncatula plants in heterogeneous environments using 3D time-lapse imaging. The growth medium is a transparent hydrogel consisting of a stiff lower layer and a compliant upper layer. We find that the roots deform into a helical shape just above the gel layer interface before penetrating into the lower layer. This geometry is interpreted as a combination of growth-induced mechanical buckling modulated by the growth medium and a simultaneous twisting near the root tip. We study the helical morphology as the modulus of the upper gel layer is varied and demonstrate that …

Characterisation Of The Colour Doppler "Twinkle" Artefact, Deirdre Cassidy, Andrew Fagan, Jacinta Browne

Articles

This investigation involved the development of a range of Colour Doppler Twinkle Artefact phantoms to characterise and quantify the “Twinkle” artefact which is often present when an irregular structure is encountered in the imaged field of view. The artefact occurs in both colour and power Doppler ultrasound imaging and manifests as a false depiction of colour velocity information in stationary soft tissue and therefore can cause significant misdiagnosis of areas of flow within the patient. It has been hypothesised that it is generated due to a strongly reflecting medium composed of individual reflectors and therefore becomes a clinical concern when …

Highly Efficient And Exact Method For Parallelization Of Grid-Based Algorithms And Its Implementation In Delphi, Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Publications

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In …

Molecular Dynamics Studies Of Water Flow In Carbon Nanotubes, Alexander D. Marshall

Electronic Thesis and Dissertation Repository

We present classical molecular dynamics (MD) simulations providing insight into the behaviour of water. We focus on confined water, the properties of which are often significantly different from the properties of bulk water.

First, we performed several simulations investigating the handling of long-range interactions in GROMACS [1], a MD simulation package. Selection of simulation protocols such as handling of long-range interactions is often overlooked, sometimes to the significant detriment of the final result [2, 3, 4]. Ensuring that the chosen simulation protocols are appropriate is a critical step in computer simulation.

Second, we performed MD simulations where water flowed between …

The Ultraviolet Spectrum Of Ocs From First Principles: Electronic Transitions, Vibrational Structure And Temperature Dependence, Johan A. Schmidt, M. S. Johnson, George C. Mcbane, Reinhard Schinke

Peer Reviewed Articles

Global three dimensional potential energy surfaces and transition dipole moment functions are calculated for the lowest singlet and triplet states of carbonyl sulfide at the multireference configuration interaction level of theory. The first ultraviolet absorption band is then studied by means of quantum mechanical wave packet propagation. excitation of the repulsive 2¹A' state gives the main contribution to the cross section. Excitation of the repulsive 1¹A" state is about a factor of 20 weaker at the absorption peak (E_ph ≈ 45 000 cm^-1) but becomes comparable to the 2¹A' state …

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 …