Search results | J. Murrey Atkins Library

Title: A new obligate CXCL4-CXCL12 heterodimer for studying chemokine heterodimer activities and mechanisms
Author: Nesmelova, Irina, Ngyuen, Khanh T.P., Dreau, Didier, Volkman, Brian
Date Created: 2022
Subjects--Topical: Chemokines, Proteins
Description: Chemokines form a family of proteins with critical roles in many biological processes in health and disease conditions, including cardiovascular, autoimmune diseases, infections, and cancer. Many chemokines engage in heterophilic interactions to f...

Title: A virtual pebble game to ensemble average graph rigidity
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Probabilities, Proteins
Description: Background: The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies...

Title: Ball lens-assisted cellphone imaging with submicron resolution
Author: Jin, Boya, Jean, Amstrong R., Maslov, Alexey V., Astratov, Vasily N.
Date Created: 2023
Subjects--Topical: Microscopes, Optical instruments
Description: One of the most significant developments in life sciences—the discovery of bacteria and protists—was accomplished by Antoni van Leeuwenhoek in the 17th century using a single ball lens microscope. It is shown that the full potential of single lens...

Title: Best probability density function for random sampled data
Author: Jacobs, Donald J.
Date Created: 2009
Subjects--Topical: Statistics, Probabilities
Description: The maximum entropy method is a theoretically sound approach to construct an analytical form for the probability density function (pdf) given a sample of random events. In practice, numerical methods employed to determine the appropriate Lagrange ...

Title: CFD and experimental investigation of AM surfaces with different build orientations
Author: Mandloi, Kuldeep, Allen, Angela, Miller, Jimmie, Duttrer, Brian
Date Created: 2023
Subjects--Topical: Differential topology, Additive manufacturing
Description: Additive manufacturing (AM) surfaces offer the possibility of novel cooling channel geometries for high temperature applications. AM processes can optimize the internal geometry of cooling channels, which is generally constrained by limitations of...

Title: Calculating ensemble averaged descriptions of protein rigidity without sampling
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Biology, Proteins
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: Changes in Lysozyme flexibility upon mutation are frequent, large and long-ranged
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Bioinformatics, Statistics
Description: We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility ...

Title: Conformational entropy of an ideal cross-linking polymer chain
Author: Jacobs, Donald J., Vorov, Oleg, Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Proteins, Entropy
Description: We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cros...

Title: Controlled coherence plasmonic light sources
Author: Gbur, Greg, Smith, Matt
Date Created: 2021
Subjects--Topical: Physics, Optics
Description: Through a computational model, we study the coherence converting capabilities of an array of holes in a surface plasmon-supporting metal plate, with an eye towards the creation of controlled coherence plasmonic light sources. We evaluate how the a...

Title: Cycle of phase, coherence and polarization singularities in Young's three-pinhole experiment
Author: Gbur, Greg, Pang, Xiaoyan, Visser, Taco D.
Date Created: 2015
Subjects--Topical: Physics, Optics
Description: It is now well-established that a variety of singularities can be characterized and observed in optical wavefields. It is also known that these phase singularities, polarization singularities and coherence singularities are physically related, but...

Title: Decomposing dynamical couplings in mutated scFv antibody fragments into stabilizing and destabilizing effects
Author: Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, Uddin, Shahid, Casas-Finet, Jose
Subjects--Topical: Amino acid sequence, Immunoglobulins
Description: Conformational fluctuations within scFv antibodies are characterized by a novel perturbation-response decomposition of molecular dynamics trajectories. Both perturbation and response profiles are stratified into stabilizing and destabilizing condi...

Title: Dielectric breakdown and sub–wavelength patterning of monolayer hexagonal boron nitride using femtosecond pulses
Author: Ahmad, Sabeeh Ifran, Dave, Arpit, Sarpong, Emmanuel, Solomon, Joel M.
Date Created: 2023
Subjects--Topical: Nanostructured materials, Nanocomposites (Materials)
Description: Hexagonal boron nitride (hBN) has emerged as a promising two-dimensional (2D) material for many applications in electronics and photonics. Although its linear and nonlinear optical properties have been extensively studied, the interaction of hBN w...

Title: Dynamic aerosol and dynamic air-water interface curvature effects on a 2-Gbit/s free-space optical link using orbital-angular-momentum multiplexing
Author: Gbur, Greg, Song, Haoqian, Zhang, Runzhou, Hu, Nanzhe
Date Created: 2022
Subjects--Topical: Physics, Optics
Description: When an orbital-angular-momentum (OAM) beam propagates through the dynamic air-water interface, the aerosol above the water and the water surface curvature could induce various degradations (e.g., wavefront distortion, beam wandering, scattering, ...

Title: Extraordinary optical transmission through multi-layered systems of corrugated metallic thin films
Author: Gbur, Greg, Gan, Choon How
Date Created: 2009
Subjects--Topical: Physics, Optics
Description: Optical transmission through multi-layered systems of corrugated metallic thin films is investigated by rigorous electromagnetic simulations based on an exact Green tensor method. Compared to a single metal slab of equivalent thickness and volume,...

Title: Fractional vortex Hilbert's Hotel
Author: Gbur, Greg
Date Created: 2016
Subjects--Topical: Physics, Optics
Description: We demonstrate how the unusual mathematics of transfinite numbers, in particular, a nearly perfect realization of Hilbert's famous hotel paradox, manifests in the propagation of light through fractional vortex plates. It is shown how a fractional ...

Title: Functional dynamics of substrate recognition in tem beta-lactamase
Author: Jacobs, Donald J., Avery, Chris, Baker, Lonnie
Date Created: 2022
Subjects--Topical: Machine learning, Molecular dynamics
Description: The beta-lactamase enzyme provides effective resistance to beta-lactam antibiotics due to substrate recognition controlled by point mutations. Recently, extended-spectrum and inhibitor-resistant mutants have become a global health problem. Here, t...

Title: High order plasmonic vortex generation based on spiral nanoslits
Author: Gbur, Greg, Yu, Jiayi, Fang, Jing, Cai, Yangjian
Date Created: 2021
Subjects--Topical: Physics, Optics
Description: Highly localized plasmonic vortices carrying orbital angular momentum are of importance for many applications. Yet, it is a challenge to generating plasmonic vortex with a high topological charge because of no available technique. Here, a novel pl...

Title: High throughput nonparametric probability density estimation
Author: Jacobs, Donald J., Farmer, Jenny
Date Created: 2018
Subjects--Topical: Statistics, Probabilities
Description: In high throughput applications, such as those found in bioinformatics and finance, it is important to determine accurate probability distribution functions despite only minimal information about data characteristics, and without using human subje...

Title: Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
Author: Jacobs, Donald J., Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Bacteria, Proteins
Description: Background: Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two do...

Title: JED: a Java essential dynamics program for comparative analysis of protein trajectories
Author: Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
Date Created: 2017
Subjects--Topical: Biology, Proteins
Description: Background: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to dete...