UMBC Chemistry & Biochemistry Department
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Recent Submissions
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Strong coupling and induced transparency at room temperature with single quantum dots and gap plasmons
(2018 Springer Nature Limited, 2018-10-01)Coherent coupling between plasmons and transition dipole moments in emitters can lead to two distinct spectral effects: vacuum Rabi splitting at strong coupling strengths, and induced transparency (also known as Fano ... -
Surface Modification at Nanoscale; Nanoparticle-Nanowire Transition
(2018-04-15)Binary, ternary and quaternary oxides and selenides have been developed and used in multiple applications including high power lasers, detectors, dielectric energy storage and variety of optical devices. These materials ... -
Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods
(2014-06-01)Hepatitis C virus (HCV) is a global health challenge, affecting approximately 200 million people worldwide. In this study we developed SAR models with advanced machine learning classifiers Random Forest and k Nearest ... -
Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase
(Wiley, 2012-07-31)Hepatitis C virus (HCV) has infected almost 200 million people worldwide, typically causing chronic liver damage and severe complications such as liver failure. Currently, there are few approved treatments for viral ... -
Protonated heterocyclic derivatives of cyclopropane and cyclopropanone: classical species, alternate sites, and ring fragmentation
(Canadian Science, 2015-02-19)A computational study has been performed for protonated oxygen- or nitrogen-containing heterocyclic derivatives of cyclopropane and cyclopropanone. We have searched for the most stable conformations of the protonated species ... -
Three-membered ring amides — a calculational and conceptual study of the structure and energetics of 1,2-oxaziridine-3-one and aziridine-2,3-dione
(Canadian Science, 2104-07-28)Species with three-membered rings and the amide linkage are well studied. A quick perusal of the literature with SciFinder finds some 50 000 references to cyclopropanes and almost 300 000 references to amides. In the current ... -
Indenone and cyclopentadienone energetics via mass spectrometry and computations: Are these species antiaromatic or “merely” nonaromatic?
(ScienceDirect, 2014-06-14)The heat of hydrogenation of indenone was measured via two partially independent thermodynamic cycles by carrying out energetic measurements (i.e., electron affinities, proton affinities and ionization potentials) on both ... -
Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase
(2016-11-15)The RNA-dependent RNA polymerase from the Hepatitis C Virus (gene product NS5B) is a validated drug target because of its critical role in genome replication. There are at least four distinct allosteric sites on the ... -
Identifying Nonlinear Correlations in High Dimensional Data with Application to Protein Molecular Dynamics Simulations
(2013)Complex biomolecules such as proteins can respond to changes in their environment through a process called allostery, which plays an important role in regulating the function of these biomolecules. Allostery occurs when ... -
Block Cyclic Distribution of Data in pbdR and its Effects on Computational Efficiency
(2013)Programming with big data in R (pbdR), a package used to implement high-performance computing in the statistical software R, uses block cyclic distribution to organize large data across many processes. Because computations ... -
Nonlinear Measures of Correlation and Dimensionality Reduction with Application to Protein Motion
(2014)The study of allostery, a regulatory process that occurs in complex macromolecules such as proteins, is of particular interest as it has a key role in determining the function of these macromolecules. Allostery produces ... -
Computational predictions suggest that structural similarity in viral polymerases may lead to comparable allosteric binding sites.
(Elsevier, 2016-06-01)The identification of ligand-binding sites is often the first step in drug targeting and design. To date there are numerous computational tools available to predict ligand binding sites. These tools can guide or mitigate ... -
Surface Modification at Nanoscale; Nanoparticle-Nanowire Transition
(NASA, 2018-04-15)Binary, ternary and quaternary oxides and selenides have been developed and used in multiple applications including high power lasers, detectors, dielectric energy storage and variety of optical devices. These materials ... -
Design and characteristics of hydroxyapatites: effect of radiation
(Society of Photo-Optical Instrumentation Engineers (SPIE), 2018-05-14)We have prepared silicate based hard materials and have processed it with organic flux. Because of the bioactivities of hydroxyapatites with tissues, this class of materials have attracted interest for bone applications. ... -
Evaluation of passive sampling polymers and nonequilibrium adjustment methods in a multiyear surveillance of sediment porewater PCBs
(Society of Environmental Toxicology and Chemistry (SETAC), 2018-07-05)Polymeric passive sampling devices are increasingly used to measure low‐level, freely dissolved concentrations of hydrophobic organic contaminants in environmental waters. A range of polymers have been used for this purpose, ... -
Design and characteristics of hydroxyapatites: effect of radiation
(Spiedigitallibrary, 2018-05-14)We have prepared silicate based hard materials and have processed it with organic flux. Because of the bioactivities of hydroxyapatites with tissues, this class of materials have attracted interest for bone applications. ... -
Spatial alterations of De Novo purine biosynthetic enzymes by Akt-independent PDK1 signaling pathways
(PLOS ONE, 2018)A macromolecular complex of the enzymes involved in human de novo purine biosynthesis, the purinosome, has been shown to consist of a core assembly to regulate the metabolic activity of the pathway. However, it remains ... -
The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies
(PLOS ONE, 2018)The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three ... -
A Mathematical Model for Enzyme Clustering in Glucose Metabolism
(Nature, 2017)We have recently demonstrated that the rate-limiting enzymes in human glucose metabolism organize into cytoplasmic clusters to form a multienzyme complex, the glucosome, in at least three different sizes. Quantitative ...
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