Search results
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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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Statistical measures to quantify similarity between molecular dynamics simulation trajectories
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Author
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Jacobs, Donald J., Farmer, Jenny, Kanwal, Fareeha, Nikulsin, Nikita
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Date Created
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2017
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Subjects--Topical
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Molecular dynamics, Statistics
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Description
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Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD) trajectories, functional differences are often inferred from differences in ...
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Title
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Universal sample size invariant measures for uncertainty quantification in density estimation
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Author
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Jacobs, Donald J., Farmer, Jenny, Merino, Zach, Merino, Zach
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Date Created
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2019
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Subjects--Topical
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Statistics, Entropy
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Description
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Previously, we developed a high throughput non-parametric maximum entropy method (PLOS ONE, 13(5): e0196937, 2018) that employs a log-likelihood scoring function to characterize uncertainty in trial probability density estimates through a scaled q...
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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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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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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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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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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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JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
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Author
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Jacobs, Donald J., Avery, Chris
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Date Created
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2021
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Subjects--Topical
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Biology, Proteins
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Description
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Background Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized soft...
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Title
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MATLAB tool for probability density assessment and nonparametric 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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2022
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Subjects--Topical
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Statistics, Entropy
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Description
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A MATLAB function is presented for nonparametric probability density estimation, based on an iterative method that employs the principle of maximum entropy and characteristic properties of single order statistics. Featuring a robust and adaptive d...
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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...
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Title
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Victory tax: a holistic income tax system
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Author
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Jacobs, Donald J.
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Date Created
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2021
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Subjects--Topical
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Income tax, Tax deductions
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Description
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How can an income tax system be designed to exploit human nature and a free market to create a poverty free society, while balancing budgets without disproportional tax burdens? Such a tax system, with universal character, is deduced from the foll...
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Title
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Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Chatelier's principle
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Author
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Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
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Date Created
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2014
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Subjects--Topical
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Immunoglobulins, Biology
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Description
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Le Chatelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Chatelier's principle states t...
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Title
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Molecular function recognition by supervised projection pursuit machine learning
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Author
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Jacobs, Donald J., Grear, Tyler, Avery, Chris, Patterson, John
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Date Created
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2021
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Subjects--Topical
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Molecular biology, Pharmaceutical chemistry
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Description
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Identifying mechanisms that control molecular function is a significant challenge in pharmaceutical science and molecular engineering. Here, we present a novel projection pursuit recurrent neural network to identify functional mechanisms in the co...