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.
author keywords: Trinucleotide hexanucleotide repeats; CAG; GAC; CTG; CUG; CCG; GGC; GGGGCC; GGCCCC; Hairpin loops; smFRET; Molecular dynamics
doi.org (publisher)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
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.
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)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
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).
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)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
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).
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)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
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.
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).
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)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
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.
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)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
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