Mahmoud Moradi

Works (10)

Updated: June 5th, 2025 07:21

2025 article

Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats

Fakharzadeh, A., Moradi, M., Sagui, C., & Roland, C. (2025, May 16). Journal of Chemical Information and Modeling, Vol. 5.

By: A. Fakharzadeh n, M. Moradi*, C. Sagui n  & C. Roland n 

topics (OpenAlex): DNA and Nucleic Acid Chemistry; RNA and protein synthesis mechanisms; RNA Interference and Gene Delivery
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 27, 2025

2023 article

Addressing the Embeddability Problem in Transition Rate Estimation

Goolsby, C., Losey, J., Fakharzadeh, A., Xu, Y., Düker, M.-C., Sherman, M. G., … Moradi, M. (2023, June 28). The Journal of Physical Chemistry A.

By: C. Goolsby*, J. Losey *, A. Fakharzadeh n, Y. Xu *, M. Düker *, M. Sherman*, D. Matteson *, M. Moradi*

topics (OpenAlex): Protein Structure and Dynamics; Spectroscopy and Quantum Chemical Studies; Advanced Chemical Physics Studies
TL;DR: Six different methods to overcome the embeddability problem of MSM are described and a one-dimensional toy model is used to show the workings of these methods and discuss the robustness of each method in terms of its dependence in lag time and trajectory length. (via Semantic Scholar)
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Source: Web Of Science
Added: July 19, 2023

2014 article

Publisher's Note: “Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities” [J. Chem. Phys. 140, 034114 (2014)]

Moradi, M., Sagui, C., & Roland, C. (2014, February 10). The Journal of Chemical Physics, Vol. 140.

By: M. Moradi n, C. Sagui n  & C. Roland n 

topics (OpenAlex): Advanced Thermodynamics and Statistical Mechanics; Spectroscopy and Quantum Chemical Studies; Quantum Mechanics and Applications
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2014 article

Publisher's Note: “Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates” [J. Chem. Phys. 140, 034115 (2014)]

Moradi, M., Sagui, C., & Roland, C. (2014, February 12). The Journal of Chemical Physics, Vol. 140.

By: M. Moradi n, C. Sagui n  & C. Roland n 

topics (OpenAlex): Advanced Thermodynamics and Statistical Mechanics; Quantum Electrodynamics and Casimir Effect; Quantum Mechanics and Applications
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2012 article

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2012, April 26). PLoS Computational Biology.

By: M. Moradi*, V. Babin n, C. Roland  n & C. Sagui  n

MeSH headings : Amino Acid Sequence; Animals; Computer Simulation; Humans; Models, Chemical; Models, Molecular; Molecular Sequence Data; Neurodegenerative Diseases / metabolism; Peptides / chemistry; Peptides / metabolism; Protein Conformation; Statistics as Topic
topics (OpenAlex): Genetic Neurodegenerative Diseases; RNA Research and Splicing; Fungal and yeast genetics research
TL;DR: It is argued that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2011 article

Calculating relative transition rates with driven nonequilibrium simulations

Moradi, M., Sagui, C., & Roland, C. (2011, November 3). Chemical Physics Letters, Vol. 518, pp. 109–113.

By: M. Moradi n, C. Sagui n  & C. Roland n 

topics (OpenAlex): Advanced Thermodynamics and Statistical Mechanics; Quantum Mechanics and Applications; Spectroscopy and Quantum Chemical Studies
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2010 article

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

Moradi, M., Babin, V., Roland, C., & Sagui, C. (2010, September 24). The Journal of Chemical Physics, Vol. 133.

By: M. Moradi n, V. Babin n, C. Roland n  & C. Sagui n 

MeSH headings : Molecular Dynamics Simulation; Peptides / chemistry; Phase Transition; Protein Conformation; Thermodynamics
topics (OpenAlex): Protein Structure and Dynamics; Spectroscopy and Quantum Chemical Studies; Advanced Physical and Chemical Molecular Interactions
TL;DR: This work characterized the conformations and the free energy landscapes of Ace-(Pro)(n)-Nme, n=2,3, ... ,9, and 13 peptides both in vacuo and in an implicit solvent environment and quantitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2010 journal article

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

International Journal of Quantum Chemistry, 110(15), 2865–2879.

By: M. Moradi, J. Lee, V. Babin, C. Roland  & C. Sagui 

Source: NC State University Libraries
Added: August 6, 2018

2009 article

Adaptively biased molecular dynamics: An umbrella sampling method with a time‐dependent potential

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009, August 27). International Journal of Quantum Chemistry, Vol. 109, pp. 3666–3678.

By: V. Babin n, V. Karpusenka n, M. Moradi n, C. Roland n  & C. Sagui n 

author keywords: free energy; nonequilibrium; simulation
topics (OpenAlex): Protein Structure and Dynamics; Spectroscopy and Quantum Chemical Studies; Advanced Chemical Physics Studies
TL;DR: The workings of the ABMD method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short -turn peptide. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 article

Conformations and free energy landscapes of polyproline peptides

Moradi, M., Babin, V., Roland, C., Darden, T. A., & Sagui, C. (2009, November 18). Proceedings of the National Academy of Sciences, Vol. 106, pp. 20746–20751.

By: M. Moradi n, V. Babin n, C. Roland n , T. Darden & C. Sagui n 

author keywords: cis-trans isomerization; left-handed helix; molecular dynamics; PPI; PPII
MeSH headings : Peptides / chemistry; Protein Conformation; Thermodynamics
topics (OpenAlex): Chemical Synthesis and Analysis; Protein Structure and Dynamics; Supramolecular Self-Assembly in Materials
TL;DR: Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the exist of stable heterogeneous subpopulations in PPII polyproline. (via Semantic Scholar)
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7. Affordable and Clean Energy (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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