Search results for "molecular dynamics"
showing 10 items of 1075 documents
Static and Dynamic Properties of a n-C100H202 Melt from Molecular Dynamics Simulations
1997
We present in this work results from atomistic molecular dynamics simulations of a n-C100H202 melt. This work represents a first effort to simulate a fully equilibrated ensemble of chains of suffic...
Aminoquinolines: Fluorescent sensors to DNA – A minor groove probe. Experimental and in silico studies
2023
An aminoquinoline (AQ4) was developed and proven to be a new and efficient DNA minor groove fluorescent probe. The specificity for DNA minor groove was attested by comparing it with well-established DNA probes such as Hoechst stain, acridine orange, and ethidium bromide. AQ4 was similar to the Hoechst stain, a classic minor groove probe, and opposite to acridine orange and ethidium bromide, the typical intercalating probes. An advantage of AQ4 to the Hoechst stain was the higher fluorescent signal-to-noise ratio (+DNA/-DNA). The interaction with DNA leads to an exclusive fluorescent band centered at 590 nm. The red-shifted fluorescent band is associated with a new absorption band (490 nm), …
Micelles of the chiral biocompatible surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl)dimethylammonium bromide (DMEB): molecular dynamics …
2017
Rationale The study of self-assembly process of surfactant molecules in gas phase is of actually interest for several theoretical and technological reasons related to their possible exploitation as drug carriers, protein shields and cleaning agents in gas phase. Methods Stability and fragmentation patterns of singly and multiply charged (either positively or negatively) aggregates of the surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl) dimethyl ammonium bromide (DMEB) in gas phase have been studied by ion mobility mass spectrometry and tandem mass spectrometry. Molecular dynamics (MD) simulations of positively and negatively singly and multiply charged DMEB aggregates have been …
Polysorbate 80 controls Morphology, structure and stability of human insulin Amyloid-Like spherulites
2022
AbstractAmyloid protein aggregates are not only associated with neurodegenerative diseases and may also occur as unwanted by-products in protein-based therapeutics. Surfactants are often employed to stabilize protein formulations and reduce the risk of aggregation. However, surfactants alter protein-protein interactions and may thus modulate the physicochemical characteristics of any aggregates formed. Human insulin aggregation was induced at low pH in the presence of varying concentrations of the surfactant polysorbate 80. Various spectroscopic and imaging methods were used to study the aggregation kinetics, as well as structure and morphology of the formed aggregates. Molecular dynamics s…
Liquid structure of a water-in-salt electrolyte with a remarkably asymmetric anion
2021
Water-in-salt systems, i.e., super-concentrated aqueous electrolytes, such as lithium bis(trifluoromethanesulfonyl)imide (21 mol/kgwater), have been recently discovered to exhibit unexpectedly large electrochemical windows and high lithium transference numbers, thus paving the way to safe and sustainable charge storage devices. The peculiar transport features in these electrolytes are influenced by their intrinsically nanoseparated morphology, stemming from the anion hydrophobic nature and manifesting as nanosegregation between anions and water domains. The underlying mechanism behind this structure-dynamics correlation is, however, still a matter of strong debate. Here, we enhance the apol…
Borate-driven gatelike scaffolding using mesoporous materials functionalised with saccharides.
2009
We report the development of an MCM-41 mesoporous support that is functionalised with saccharides at the pore outlets and contains the dye [Ru(bipy)(3)](2+) in the pores (solid S1; bipy = 2,2'-bipyridyl). For this hybrid system, the inhibition of mass transport of the dye from the pore voids to the bulk solution in the presence of borate is demonstrated in water at neutral pH. The formation of the corresponding boroester derivative is related to the selective reaction of borate with the appended saccharides. This control is selective and only anion borate, among several anions and cations, can act as a molecular tap and inhibit the delivery of the entrapped guest. Additionally, the S1-borat…
Fragmentation of anthracene C14H10, acridine C13H9N and phenazine C12H8N2 ions in collisions with atoms
2014
International audience; We report experimental total, absolute, fragmentation cross sections for anthracene C14H10, acridine C13H9N, and phenazine C12H8N2 ions colliding with He at center-of-mass energies close to 100 eV. In addition, we report results for the same ions colliding with Ne, Ar, and Xe at higher energies. The total fragmentation cross sections for these three ions are the same within error bars for a given target. The measured fragment mass distributions reveal significant contributions from both delayed (≫10−12 s) statistical fragmentation processes as well as non-statistical, prompt (∼10−15 s), single atom knockout processes. The latter dominate and are often followed by sec…
Characterization of the interaction of the antifungal and cytotoxic cyclic glycolipopeptide hassallidin with sterol-containing lipid membranes.
2019
Hassallidins are cyclic glycolipopeptides produced by cyanobacteria and other prokaryotes. The hassallidin structure consists of a peptide ring of eight amino acids where a fatty acid chain, additional amino acids, and sugar moieties are attached. Hassallidins show antifungal activity against several opportunistic human pathogenic fungi, but does not harbor antibacterial effects. However, they have not been studied on mammalian cells, and the mechanism of action is unknown. We purified hassallidin D from cultured cyanobacterium Anabaena sp. UHCC 0258 and characterized its effect on mammalian and fungal cells. Ultrastructural analysis showed that hassallidin D disrupts cell membranes, causin…
Recent advances in computational design of potent aromatase inhibitors: open-eye on endocrine-resistant breast cancers.
2019
Introduction: The vast majority of breast cancers (BC) are estrogen receptor positive (ER+). The most effective treatments to fight this BC type rely on estrogen deprivation therapy, by inhibiting the aromatase enzyme, which performs estrogen biosynthesis, or on blocking the estrogens signaling path via modulating/degrading the estrogen's specific nuclear receptor (estrogen receptor-?, ER?). While being effective at early disease stage, patients treated with aromatase inhibitors (AIs) may acquire resistance and often relapse after prolonged therapies. Areas covered: In this compendium, after an overview of the historical development of the AIs currently in clinical use, and of the computati…
Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture
1995
Abstract We have performed a molecular dynamics computer simulation study to investigate the dynamical behavior of a supercooled simple liquid for comparison with the predictions of mode-coupling theory (MCT). By scaling the intermediate scattering function by the α-relaxation time r we find that the correlators fall onto a master curve extending over several decades in time. Thus we find that the time temperature superposition principle holds. In the late β-relaxation regime this master curve can be fitted very well by a master curve predicted by the idealized version MCT. However, there is no evidence for the presence of the critical decay predicted by the theory for the early part of the…