Physics Commons^™

Antimicrobial Properties Of Nano-Silver: A Cautionary Approach To Ionic Interference, Kate Sheehy, Alan Casey, Anna Murphy, Gordon Chambers

Articles

Hypothesis: Metallic nanoparticles such as nano-silver have found many applications as alternative antimicrobials in recent years. However methods for determining their proposed antimicrobial activity have received little attention to date. The disk diffusion assay is commonly used as a demonstration of antimicrobial properties and is a regular feature in synthetic nanoparticle papers. The aim of this study was to assess its effectiveness in demonstrating the ‘‘nanoparticle specific’’ antimicrobial properties in the absence of ionic contributions from unreacted reducing agents and or impurities. Experiments: The disk diffusion assay was carried out on a range of silver nanoparticles, both in-house synthesised and …

Competitive Evaluation Of Data Mining Algorithms For Use In Cassification Of Leukocyte Subtypes With Raman Microspectroscopy, Adrian Maguire, I. Vega-Carrascal, Jane Bryant, Lisa White, Orla Howe, Fiona Lyng, Aidan Meade

Articles

Raman microspectroscopy has been investigated for some time for use in label-free cell sorting devices. These approaches require coupling of the Raman spectrometer to complex data mining algorithms for identification of cellular subtypes such as the leukocyte subpopulations of lymphocytes and monocytes. In this study, three distinct multivariate classification approaches, (PCA-LDA, SVMs and Random Forests) are developed and tested on their ability to classify the cellular subtype in extracted peripheral blood mononuclear cells (T-cell lymphocytes from myeloid cells), and are evaluated in terms of their respective classification performance. A strategy for optimisation of each of the classification algorithm is presented …

Rational Design Of Small-Molecule Stabilizers Of Spermine Synthase Dimer By Virtual Screening And Free Energy-Based Approach, Zhe Zhang, Virginie Martiny, David Lagorce, Yoshihiko Ikeguchi, Emil Alexov, Maria A. Miteva

Publications

Snyder-Robinson Syndrome (SRS) is a rare mental retardation disorder which is caused by the malfunctioning of an enzyme, the spermine synthase (SMS), which functions as a homo-dimer. The malfunctioning of SMS in SRS patients is associated with several identified missense mutations that occur away from the active site. This investigation deals with a particular SRS-causing mutation, the G56S mutation, which was shown computationally and experimentally to destabilize the SMS homo-dimer and thus to abolish SMS enzymatic activity. As a proof-of-concept, we explore the possibility to restore the enzymatic activity of the malfunctioning SMS mutant G56S by stabilizing the dimer through …

Problm Web Server: Protein And Membrane Placement And Orientation Package, Taylor Kimmett, Nicholas Smith, Shawn Witham, Marharyta Petukh, Subhra Sarkar, Emil Alexov

Publications

The 3D structures of membrane proteins are typically determined without the presence of a lipid bilayer. For the purpose of studying the role of membranes on the wild type characteristics of the corresponding protein, determining the position and orientation of transmembrane proteins within a membrane environment is highly desirable. Here we report a geometry-based approach to automatically insert a membrane protein with a known 3D structure into pregenerated lipid bilayer membranes with various dimensions and lipid compositions or into a pseudomembrane. The pseudomembrane is built using the Protein Nano-Object Integrator which generates a parallelepiped of user-specified dimensions made up of …

Binding Of Solvated Peptide (Eplqlkm) With A Graphene Sheet Via Simulated Coarse-Grained Approach, Somayyeh Sheikholeslami, R. B. Pandey, Nadiya Dragneva, Wely Floriano, Oleg Rubel, Stephen A. Barr, Zhifeng Kuang, Rajiv Berry, Rajesh Naik, Barry Farmer

Faculty Publications

Binding of a solvated peptide A1 (¹E ²P ³L ⁴Q ⁵L ⁶K ⁷M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and …

Computational And Experimental Approaches To Reveal The Effects Of Single Nucleotide Polymorphisms With Respect To Disease Diagnostics, Tugba G. Kucukkal, Ye Yang, Susan C. Chapman, Weiguo Cao, Emil Alexov

Publications

DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and …

Chronic Beryllium Disease: Revealing The Role Of Beryllium Ion And Small Peptides Binding To Hla-Dp2, Marharyta Petukh, Bohua Wu, Shannon Stefl, Nick Smith, David Hyde-Volpe, Li Wang, Emil Alexov

Publications

Chronic Beryllium (Be) Disease (CBD) is a granulomatous disorder that predominantly affects the lung. The CBD is caused by Be exposure of individuals carrying the HLA-DP2 protein of the major histocompatibility complex class II (MHCII). While the involvement of Be in the development of CBD is obvious and the binding site and the sequence of Be and peptide binding were recently experimentally revealed [1], the interplay between induced conformational changes and the changes of the peptide binding affinity in presence of Be were not investigated. Here we carry out in silico modeling and predict the Be binding to be within …

On The Modeling Of Polar Component Of Solvation Energy Using Smooth Gaussian-Based Dielectric Function, Lin Li, Chuan Li, Emil Alexov

Publications

Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine …

On The Electrostatic Properties Of Homodimeric Proteins, Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li

Publications

A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily …

A Novel P.Leu(381)Phe Mutation In Presenilin 1 Is Associated With Very Early Onset And Unusually Fast Progressing Dementia As Well As Lysosomal Inclusions Typically Seen In Kufs Disease, Natalia Dolzhanskaya, Michael A. Gonzalez, Fiorella Sperziani, Shannon Stefl, Jeffrey Messing, Guang Y. Wen, Emil Alexov, S Stephan Zuchner, Milen Velinov

Publications

Whole exome sequencing in a family with suspected dominant Kufs disease identified a novel Presenilin 1 mutation p.Leu(381)Phe in three brothers who, along with their father, developed progressive dementia and motor deficits in their early 30s. All affected relatives had unusually rapid disease progression (on average 3.6 years from disease onset to death). In silico analysis of mutation p.Leu(381)Phe predicted more detrimental effects when compared to the common Presenilin 1 mutation p.Glu(280)Ala. Electron microscopy study of peripheral fibroblast cells of the proband showed lysosomal inclusions typical for Kufs disease. However his brain autopsy demonstrated typical changes of Alzheimer disease.

Voltage Gating Interactions Of The Protein Lysenin With Metal Ions In An Artificial Lipid Bilayer, Tyler Clark, Sheenah Bryant, Steve Rossland, Eric Krueger, Charles Hanna, Daniel Fologea

College of Arts and Sciences Presentations

Non-specific ion conductance channels can be formed in lipid membranes by the poreforming toxin lysenin. These channels are voltage regulated and are responsive to changes in metal ion concentration. In our research, we studied the effects of metal ion concentration on the lysenin channel’s voltage regulated gating, using both multivalent and monovalent metals. A model was developed to explain the apparent subunit cooperativity within the lysenin channel. The model allows for the complex reaction to changing concentration of metal ions, and offers knowledge of the lysenin channel’s internal workings.

Searching For Effective Forces In Laboratory Insect Swarms, James G. Puckett, Douglas H. Kelley, Nicholas T. Ouellette

Physics and Astronomy Faculty Publications

Collective animal behaviour is often modeled by systems of agents that interact via effective social forces, including short-range repulsion and long-range attraction. We search for evidence of such effective forces by studying laboratory swarms of the flying midge Chironomus riparius. Using multi-camera stereoimaging and particle-tracking techniques, we record three-dimensional trajectories for all the individuals in the swarm. Acceleration measurements show a clear short-range repulsion, which we confirm by considering the spatial statistics of the midges, but no conclusive long-range interactions. Measurements of the mean free path of the insects also suggest that individuals are on average very weakly coupled, but …

Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi

FIU Electronic Theses and Dissertations

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions …

Wave Function For Harmonically Confined Electrons In Time-Dependent Electric And Magnetostatic Fields, Hong-Ming Zhu, Jin-Wang Chen, Xiao-Yin Pan, Viraht Sahni

Publications and Research

We derive via the interaction “representation” the many-body wave function for harmonically confined electrons in the presence of a magnetostatic field and perturbed by a spatially homogeneous time-dependent electric field—the Generalized Kohn Theorem (GKT) wave function. In the absence of the harmonic confinement – the uniform electron gas – the GKT wave function reduces to the Kohn Theorem wave function. Without the magnetostatic field, the GKTwave function is the Harmonic Potential Theorem wave function. We further prove the validity of the connection between the GKT wave function derived and the system in an accelerated frame of reference. Finally, we provide …

A Numerical Assessment Of Cosmic-Ray Energy Diffusion Through Turbulent Media, M. Fatuzzo, F. Melia

Faculty Scholarship

No abstract provided.

Effects Of Turbulence On Cosmic Ray Propagation In Protostars And Young Stars, M. Fatuzzo, F. C. Adams

Faculty Scholarship

No abstract provided.

Microfluidic Electrical Sorting Of Particles Based On Shape In A Spiral Microchannel, John Dubose, Xinyu Lu, Saurin Patel, Shizhi Qian, Sang Woo Joo

Mechanical & Aerospace Engineering Faculty Publications

Shape is an intrinsic marker of cell cycle, an important factor for identifying a bioparticle, and also a useful indicator of cell state for disease diagnostics. Therefore, shape can be a specific marker in label-free particle and cell separation for various chemical and biological applications. We demonstrate in this work a continuous-flow electrical sorting of spherical and peanut-shaped particles of similar volumes in an asymmetric double-spiral microchannel. It exploits curvature-induced dielectrophoresis to focus particles to a tight stream in the first spiral without any sheath flow and subsequently displace them to shape-dependent flow paths in the second spiral without any …

An Unexpected Particle Oscillation For Electrophoresis In Viscoelastic Fluids Through A Microchannel Constriction, Xinyu Lu, Saurin Patel, Meng Zhang, Sang Woo Joo, Shizhi Qian, Amod Ogale, Xiangchun Xuan

Mechanical & Aerospace Engineering Faculty Publications

Electrophoresis plays an important role in many applications, which, however, has so far been extensively studied in Newtonian fluids only. This work presents the first experimental investigation of particle electrophoresis in viscoelastic polyethylene oxide (PEO) solutions through a microchannel constriction under pure DC electric fields. An oscillatory particle motion is observed in the constriction region, which is distinctly different from the particle behavior in a polymer-free Newtonian fluid. This stream-wise particle oscillation continues until a sufficient number of particles form a chain to pass through the constriction completely. It is speculated that such an unexpected particle oscillating phenomenon is a …

The Utility Of Deformable Image Registration For Small Artery Visualisation In Contrast-Enhanced Whole Body Mr Angiography, Daniel Foley, Jacinta Browne, Xiahai Zhuang, Barry Sheane, Dearbhail O'Driscoll, Daniel Cannon, Niall Sheehy, James Meaney, Andrew Fagan

Articles

Purpose;

An investigation was carried out into the effect of three image registration techniques on the diagnostic image quality of contrast-enhanced magnetic resonance angiography (CE-MRA) images.

Methods Whole-body CE-MRA data from the lower legs of 27 patients recruited onto a study of asymptomatic atherosclerosis were processed using three deformable image registration algorithms. The resultant diagnostic image quality was evaluated qualitatively in a clinical evaluation by four expert observers, and quantitatively by measuring contrast-to-noise ratios and volumes of blood vessels, and assessing the techniques’ ability to correct for varying degrees of motion.

Results The first registration algorithm (‘AIR’) introduced significant stenosis-mimicking …

Breast Cancer Detection Using Interferometric Music: Experimental And Numerical Assessment, Giuseppe Ruvio, Raffaele Solimene, Antonio Cuccaro, Domenico Gaetano, Jacinta Browne, Max Ammann

Articles

Purpose: In microwave breast cancer detection it is often beneficial to arrange sensors in close proximity to the breast. The resulting coupling generally changes the antenna response. As an a priori characterization of the radio-frequency system becomes difficult, this can lead to severe degradation of the detection efficacy. The purpose of this paper is to demonstrate advantages of adopting an Interferometric Multiple Signal Classification (I-MUSIC) approach due to its limited dependence 25 from a priori information on the antenna. The performance of I-MUSIC detection was measured in terms of Signal-to-Clutter Ratio (SCR), Signal-to-Mean Ratio (SMR) and Spatial Displacement (SD) and …

A First-Principles Computational Study Of Structural And Elastic Properties Of Zno, Jeevake Attapattu, Changfeng Chen

McNair Poster Presentations

The purpose of this study is to determine structural and mechanical properties of zinc oxide (ZnO) using first-principles computational methods. ZnO is a semiconductor widely used in many electronic and optical applications. ZnO is also economically and environmentally desirable – first, both the constituent elements are abundant on Earth and therefore inexpensive for large-scale applications; second, it is non- toxic. The most significant contribution of this study is the simulations of the high-pressure phases. These high-pressure simulations are important because the rock salt phase of ZnO obtained at high pressure can be recovered at ambient pressure, and this new structural …

The Synthesis Of A Bisbenzothiophene (Bbt) Based Organic Semiconductor With Increased Function And Increased Solubility, Mary England

Senior Honors Theses

Organic semiconductors are growing in applications for use in modern technology.¹ The main interest in these molecules can be attributed to their low cost (compared to silicon) and their ability to be used on flexible substrates. There are four features that make a good organic semiconductor. First, the molecule should be conjugated, having alternating single and double bonds (lone electron pairs act similarly to double bonds). Secondly, the molecule should be planar, or flat, in shape. Thirdly, the molecule should have a narrow band gap to increase the overall conductivity. Lastly, the molecule should be soluble to ease application. …