Mahmoud Moradi

Works (9)

Updated: August 19th, 2023 21:16

2023 article

Addressing the Embeddability Problem in Transition Rate Estimation

Goolsby, C., Losey, J., Fakharzadeh, A., Xu, Y., Duker, M.-C., Sherman, M. G., … Moradi, M. (2023, June 28). JOURNAL OF PHYSICAL CHEMISTRY A.

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

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)
Source: Web Of Science
Added: July 19, 2023

2014 article

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

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

Source: Web Of Science
Added: August 6, 2018

2014 article

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates (vol 140, 034115, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

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

Source: Web Of Science
Added: August 6, 2018

2012 journal article

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

PLOS COMPUTATIONAL BIOLOGY, 8(4).

By: M. Moradi n, 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
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 journal article

Calculating relative transition rates with driven nonequilibrium simulations

CHEMICAL PHYSICS LETTERS, 518, 109–113.

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

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Source: Web Of Science
Added: August 6, 2018

2010 journal article

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

JOURNAL OF CHEMICAL PHYSICS, 133(12).

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
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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Source: Web Of Science
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, December). 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
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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Source: Web Of Science
Added: August 6, 2018

2009 journal article

Conformations and free energy landscapes of polyproline peptides

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(49), 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
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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Source: Web Of Science
Added: August 6, 2018

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