Search results
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Title
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A new obligate CXCL4-CXCL12 heterodimer for studying chemokine heterodimer activities and mechanisms
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Author
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Nesmelova, Irina, Ngyuen, Khanh T.P., Dreau, Didier, Volkman, Brian
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Date Created
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2022
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Subjects--Topical
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Chemokines, Proteins
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Description
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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...
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Title
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A virtual pebble game to ensemble average graph rigidity
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Author
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Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
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Date Created
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2015
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Subjects--Topical
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Probabilities, Proteins
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Description
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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...
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Title
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Ball lens-assisted cellphone imaging with submicron resolution
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Author
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Jin, Boya, Jean, Amstrong R., Maslov, Alexey V., Astratov, Vasily N.
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Date Created
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2023
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Subjects--Topical
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Microscopes, Optical instruments
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Description
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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...
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Title
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Best probability density function for random sampled data
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Author
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Jacobs, Donald J.
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Date Created
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2009
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Subjects--Topical
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Statistics, Probabilities
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Description
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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 ...
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Title
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CFD and experimental investigation of AM surfaces with different build orientations
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Author
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Mandloi, Kuldeep, Allen, Angela, Miller, Jimmie, Duttrer, Brian
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Date Created
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2023
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Subjects--Topical
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Differential topology, Additive manufacturing
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Description
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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...
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Title
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Calculating ensemble averaged descriptions of protein rigidity without sampling
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Author
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Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
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Date Created
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2012
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Subjects--Topical
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Biology, Proteins
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Description
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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...
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Title
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Changes in Lysozyme flexibility upon mutation are frequent, large and long-ranged
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Author
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Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
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Date Created
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2012
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Subjects--Topical
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Bioinformatics, Statistics
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Description
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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 ...
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Title
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Conformational entropy of an ideal cross-linking polymer chain
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Author
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Jacobs, Donald J., Vorov, Oleg, Livesay, Dennis R.
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Date Created
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2008
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Subjects--Topical
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Proteins, Entropy
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Description
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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...
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Title
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Controlled coherence plasmonic light sources
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Author
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Gbur, Greg, Smith, Matt
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Date Created
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2021
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Subjects--Topical
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Physics, Optics
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Description
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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...
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Title
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Cycle of phase, coherence and polarization singularities in Young's three-pinhole experiment
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Author
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Gbur, Greg, Pang, Xiaoyan, Visser, Taco D.
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Date Created
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2015
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Subjects--Topical
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Physics, Optics
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Description
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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...
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Title
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Dynamic aerosol and dynamic air-water interface curvature effects on a 2-Gbit/s free-space optical link using orbital-angular-momentum multiplexing
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Author
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Gbur, Greg, Song, Haoqian, Zhang, Runzhou, Hu, Nanzhe
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Date Created
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2022
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Subjects--Topical
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Physics, Optics
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Description
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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, ...
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Title
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Fractional vortex Hilbert's Hotel
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Author
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Gbur, Greg
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Date Created
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2016
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Subjects--Topical
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Physics, Optics
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Description
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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 ...
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Title
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Functional dynamics of substrate recognition in tem beta-lactamase
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Author
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Jacobs, Donald J., Avery, Chris, Baker, Lonnie
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Date Created
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2022
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Subjects--Topical
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Machine learning, Molecular dynamics
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Description
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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...
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Title
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High order plasmonic vortex generation based on spiral nanoslits
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Author
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Gbur, Greg, Yu, Jiayi, Fang, Jing, Cai, Yangjian
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Date Created
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2021
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Subjects--Topical
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Physics, Optics
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Description
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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...
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Title
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High throughput nonparametric probability density estimation
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Author
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Jacobs, Donald J., Farmer, Jenny
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Date Created
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2018
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Subjects--Topical
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Statistics, Probabilities
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Description
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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...
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Title
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JED: a Java essential dynamics program for comparative analysis of protein trajectories
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Author
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Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
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Date Created
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2017
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Subjects--Topical
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Biology, Proteins
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Description
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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...