Viet Hoang Man

Works (7)

Updated: July 5th, 2023 15:40

2021 review

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

[Review of ]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 2819–2832.

By: F. Pan*, Y. Zhang *, P. Xu n, V. Man n, C. Roland n, K. Weninger n , C. Sagui n

author keywords: Trinucleotide hexanucleotide repeats; CAG; GAC; CTG; CUG; CCG; GGC; GGGGCC; GGCCCC; Hairpin loops; smFRET; Molecular dynamics
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Sources: Web Of Science, NC State University Libraries
Added: August 30, 2021

2017 journal article

Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats

BIOPHYSICAL JOURNAL, 113(1), 19–36.

By: F. Pan n, V. Man n, C. Roland n & C. Sagui n

MeSH headings : Cations / chemistry; DNA / chemistry; Hydrogen-Ion Concentration; Molecular Dynamics Simulation; Nucleic Acid Conformation; Principal Component Analysis; RNA / chemistry; Sodium / chemistry; Trinucleotide Repeats
TL;DR: Free energy and molecular dynamics studies are carried out to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats and the consequent changes in the overall structure of the RNA and DNA duplexes, finding that the global free energy minimum corresponds to A- A pairs stacked inside the core of the helix with anti-anti conformations in RNA and (high-anti)-( high-anti) (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2016 journal article

Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

JOURNAL OF CHEMICAL PHYSICS, 144(14).

By: V. Man n, F. Pan n, C. Sagui n & C. Roland n

MeSH headings : DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Lasers; Molecular Dynamics Simulation; Thermodynamics
TL;DR: It is proposed that fast melting by an infrared laser pulse could be used as a technique for a fast comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2016 journal article

Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils

JOURNAL OF CHEMICAL PHYSICS, 145(17).

By: M. Viet  n, P. Derreumaux * & P. Nguyen *

MeSH headings : Amyloid / chemistry; Gases / chemistry; Molecular Dynamics Simulation; Protein Structure, Secondary
TL;DR: An all-atom nonequilibrium molecular-dynamics simulation method is developed to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects, and may open a new, efficient way to dissociate amyloid fibrils using the Bubble cavitation technique. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2016 journal article

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(17), 11951–11958.

By: V. Man n, N. Van-Oanh *, P. Derreumaux *, M. Li *, C. Roland n, C. Sagui n, P. Nguyen *

MeSH headings : Biocompatible Materials / chemistry; Humans; Infrared Rays; Lasers; Molecular Dynamics Simulation; Poliomyelitis / virology; Poliovirus / chemistry; Poliovirus / radiation effects; Virion / chemistry; Virion / radiation effects
TL;DR: All-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, is carried out to dissociate viruses, showing a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Communication: Multiple atomistic force fields in a single enhanced sampling simulation

JOURNAL OF CHEMICAL PHYSICS, 143(2).

By: M. Viet  n, P. Derreumaux * & P. Nguyen *

MeSH headings : Molecular Dynamics Simulation; Oligopeptides / chemistry; Pattern Recognition, Automated; Protein Conformation; Solvents / chemistry; Water / chemistry
TL;DR: An automatic method that includes different force fields into a single advanced sampling simulation that is able to perform random walk in both temperature and force field spaces is proposed. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2015 journal article

Structural Determinants of Polyglutamine Protofibrils and Crystallites

ACS CHEMICAL NEUROSCIENCE, 6(4), 632–645.

By: V. Man n, C. Roland n & C. Sagui n

author keywords: Aggregation; amyloid fibrils; parallel sheets; antiparallel sheets; polyglutamine diseases; steric zippers
MeSH headings : Amyloid / chemistry; Amyloid / genetics; Hydrogen Bonding; Models, Chemical; Molecular Dynamics Simulation; Peptides / chemistry; Protein Conformation; Protein Stability; Time Factors
TL;DR: This work uses fully atomistic molecular dynamics simulations to probe the structural stability and conformational dynamics of both previously proposed and new polyglutamine aggregate models, and explains and reconcile previously reported experimental and model discrepancies about polyglUTamine aggregate structures. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

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