Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Modelling the carbon Snoek peak in ferrite: Coupling molecular dynamics and kinetic Monte-Carlo simulations
2008
Abstract Molecular statics, molecular dynamics and kinetic Monte-Carlo are used to model the carbon Snoek peak in ferrite. Using an interatomic EAM potential for the Fe–C system, saddle point energies for the diffusion of carbon have been evaluated under uniaxial stress by molecular statics. These energies have been reintroduced in a kinetic Monte-Carlo scheme to predict the repartition of carbon atoms in different octahedral sites. This repartition leads to an anelastic deformation calculated by molecular dynamics, which causes internal friction (the Snoek peak) for cyclic stress. This approach leads to quantitative predictions of the internal friction, which are in good agreement with exp…
Encapsulation of xenon by bridged resorcinarene cages with high 129Xe NMR chemical shift and efficient exchange dynamics
2023
Functionalized cages encapsulating xenon atoms enable highly sensitive, background-free molecular imaging through a technique known as HyperCEST 129Xe MRI. Here, we introduce a class of potential biosensor cage structures based on two resorcinarene macrocycles bridged either by aliphatic carbon chains or piperazines. First-principles-based modeling predicts a high chemical shift (about 345 ppm) outside the typical experimental observation window for 129Xe encapsulated by the aliphatically bridged cage and two 129Xe resonances for the piperazine-bridged cages corresponding to single and double loading. Based on the computational predictions as well as 129Xe chemical exchange saturation trans…
Histopathology of Skeletal Muscle in a Distal Motor Neuropathy Associated with a Mutant CCT5 Subunit: Clues for Future Developments to Improve Differ…
2023
Genetic chaperonopathies are rare but, because of misdiagnosis, there are probably more cases than those that are recorded in the literature and databases. This occurs because practitioners are generally unaware of the existence and/or the symptoms and signs of chaperonopathies. It is necessary to educate the medical community about these diseases and, with research, to unveil their mechanisms. The structure and functions of various chaperones in vitro have been studied, but information on the impact of mutant chaperones in humans, in vivo, is scarce. Here, we present a succinct review of the most salient abnormalities of skeletal muscle, based on our earlier report of a patient who carried…
Natural payload delivery of the doxorubicin anticancer drug from boron nitride oxide nanosheets
2019
International audience; We studied the behavior of doxorubicin (DOX; an anticancer drug) molecules loaded on a boron nitride oxide nanosheet (BNO-NS) using the density functional theory (DFT), time-dependent density functional theory (TDDFT), and molecular dynamic (MD) simulation methods. We found that DOX molecules in pi-pi or covalent interaction with BNO-NS preserve their optical properties in water. Moreover, the BNO-NS vector allowed stabilizing the DOX molecules on a cellular membrane contrary to isolated DOX that randomly moved in the solvent box without any interaction with the cell membrane. From these results, we conclude that hydrophilic BNO-NS represents a good candidate for DOX…
Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids
2017
Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation of fluorinated dom…
CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin
2013
Abstract: Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate…
Simulations of Glassforming Network Fluids: Classical Molecular Dynamics versus Car-Parrinello Molecular Dynamics
2010
Abstract Static and dynamic Properties of molten germanium dioxide are studied by two simulation methods, classical Molecular Dynamics (MD) using the Oeffner-Elliott (OE) potential, and “ab initio” Car-Parrinello Molecular Dynamics (CPMD). While CPMD provides a (presumably) more accurate description of the local structure and the forces, it severely suffers from finite size effects when the structure beyond the first neighbor shells is considered. For glassforming fluids, the demanding equilibrium needs are a further reason, why simply MD is still preferable, when a “good” effective potential is available.
The interplay between structure and ionic motions in glasses
2003
We present research examples that demonstrate how molecular dynamics simulations of real materials have reached a high level of sophistication. For simplicity, we focus on examples taken from our own research-although many other groups have done similarly valuable work on other systems and problems.
The inhibition of glycerol permeation through aquaglyceroporin-3 induced by mercury(II)
2016
Mercurial compounds are known to inhibit water permeation through aquaporins (AQPs). Although in the last years some hypotheses were proposed, the exact mechanism of inhibition is still an open question and even less is known about the inhibition of the glycerol permeation through aquaglyceroporins. Molecular dynamics (MD) simulations of human aquaporin-3 (AQP3) have been performed up to 200 ns in the presence of Hg2+ ions. For the first time, we have observed the unbiased passage of a glycerol molecule from the extracellular to cytosolic side. Moreover, the presence of Hg2+ ions covalently bound to Cys40 leads to a collapse of the aromatic/arginine selectivity filter (ar/R SF), blocking th…
Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy
2021
High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF)…