Search results for " SIMULATIONS"
showing 10 items of 243 documents
Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-…
2020
Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS…
Multi-scale dynamics simulations of molecular polaritons: The effect of multiple cavity modes on polariton relaxation
2021
It is included two versions of this item: the Accepted Version which is already Open Access and the Published Version which is under an embargo period till 2022-03-09.
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
2011
BackgroundAvidin is a chicken egg-white protein with high affinity to vitamin H, also known as D-biotin. Many applications in life science research are based on this strong interaction. Avidin is a homotetrameric protein, which promotes its modification to symmetrical entities. Dual-chain avidin, a genetically engineered avidin form, has two circularly permuted chicken avidin monomers that are tandem-fused into one polypeptide chain. This form of avidin enables independent modification of the two domains, including the two biotin-binding pockets; however, decreased yields in protein production, compared to wt avidin, and complicated genetic manipulation of two highly similar DNA sequences i…
The Missing Link in the Magnetism of Hybrid Cobalt Layered Hydroxides: The Odd‐Even Effect of the Organic Spacer
2021
A dramatic change in the magnetic behaviour, which solely depends on the parity of the organic linker molecules, has been found in a family of layered CoII hydroxides covalently functionalized with dicarboxylic molecules. These layered hybrid materials have been synthesized at room temperature using a one-pot procedure through the epoxide route. While hybrids connected by odd alkyl chains exhibit coercive fields (Hc) below ca. 3500 Oe and show spontaneous magnetization at temperatures (TM) below 20 K, hybrids functionalized with even alkyl chains behave as hard magnets with Hc>5500 Oe and display a TM higher than 55 K. This intriguing behaviour was studied by density functional theory with …
Distant Homology Modeling of LCAT and Its Validation through In Silico Targeting and In Vitro and In Vivo Assays
2013
LCAT (lecithin:cholesterol acyltransferase) catalyzes the transacylation of a fatty acid of lecithin to cholesterol, generating a cholesteryl ester and lysolecithin. The knowledge of LCAT atomic structure and the identification of the amino acids relevant in controlling its structure and function are expected to be very helpful to understand the enzyme catalytic mechanism, as involved in HDL cholesterol metabolism. However - after an early report in the late '90 s - no recent advance has been made about LCAT three-dimensional structure. In this paper, we propose an LCAT atomistic model, built following the most up-to-date molecular modeling approaches, and exploiting newly solved crystallog…
Experimental and theoretical studies of Stark profiles of Ar I 696.5 nm spectral line in laser-induced plasma
2019
Abstract We report the results of the Stark profile studies of the 696.543 nm Ar I spectral line in laser-induced plasma generated by a nanosecond Nd:YAG laser radiation at 532 nm in argon at reduced pressure. Plasma diagnostics was performed with the use of the laser Thomson scattering method, free from assumptions about the plasma thermodynamic equilibrium, its composition but also independently of plasma emission spectra. The profiles were investigated in wide range of electron densities and temperatures, from 2.81 · 1022 m − 3 to 5.69 · 1023 m − 3 and from 10 430 K to 73 400 K, respectively. Stark profiles were calculated using a semi-classical method as well as by N-body numerical simu…
Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection
2013
Bioprotection by sugars, and in particular trehalose peculiarity, is a relevant topic due to the implications in several fields. The underlying mechanisms are not yet clearly elucidated, and remain the focus of current investigations. Here we revisit data obtained at our lab on binary sugar/water and ternary protein/sugar/water systems, in wide ranges of water content and temperature, in the light of the current literature. The data here discussed come from complementary techniques (Infrared Spectroscopy, Molecular Dynamics simulations, Small Angle X-ray Scattering and Calorimetry), which provided a consistent description of the bioprotection by sugars from the atomistic to the macroscopic …
Design of a reactor operating in supercritical water conditions using CFD simulations. Examples of synthesized nanomaterials
2011
International audience; Direct information about fluids under supercritical water conditions is unfeasible due to the engineering restrictions at high pressure and high temperature. Numerical investigations based on computational fluid dynamics (CFD) calculations are widely used in order to get extensive information on the fluid behavior, particularly to help the design of a new reactor. This paper presents the numerical investigations performed on an original supercritical water device, especially in the level of the reactor. CFD calculations allow to design and optimize the present reactor described in this study. Currently, this process produces some nanometric oxide powders in continuou…
Time evolution of size and polydispersity of an ensemble of nanoparticles growing in the confined space of AOT reversed micelles by computer simulati…
2005
The time dependence of size and polydispersity of an ensemble of nanoparticles growing in the confined space of water-containing AOT reversed micelles has been investigated by computer simulations. It has been found that, in a wide time range, the mean nanoparticle size can be described by power laws whose exponent is critically dependent on the efficiency of the intermicellar material exchange process while the nanoparticle polydispersity increases with time. From the analysis of all the disentangled effects arising from the variation of internal and external parameters provided by simulations, useful suggestions for a better and rationale control of the nanoparticle synthetic procedure ar…
From Behavior of Water on Hydrophobic Graphene Surfaces to Ultra-Confinement of Water in Carbon Nanotubes
2021
In recent years and with the achievement of nanotechnologies, the development of experiments based on carbon nanotubes has allowed to increase the ionic permeability and/or selectivity in nanodevices. However, this new technology opens the way to many questionable observations, to which theoretical work can answer using several approximations. One of them concerns the appearance of a negative charge on the carbon surface, when the latter is apparently neutral. Using first-principles density functional theory combined with molecular dynamics, we develop here several simulations on different systems in order to understand the reactivity of the carbon surface in low or ultra-high confinement. …