Search results for "molecules"

Coarse-grained models of double-stranded DNA based on experimentally determined knotting probabilities

2018

Abstract To accurately model double-stranded DNA in a manner that is computationally efficient, coarse-grained models of DNA are introduced, where model parameters are selected by fitting the spectrum of observable DNA knots: We develop a general method to fit free parameters of coarse-grained chain models by comparing experimentally obtained knotting probabilities of short DNA chains to knotting probabilities that are computed in Monte Carlo simulations, resulting in coarse-grained DNA models which are tailored to reflect DNA topology in the best possible way. The method is exemplified by fitting ideal chain models as well as a bead-spring model with excluded volume interactions, to model …

Correction: Mechanical properties of provisional dental materials: A systematic review and meta-analysis.

2018

Provisional restorations represent an important phase during the rehabilitation process, knowledge of the mechanical properties of the available materials allows us to predict their clinical performance. At present, there is no systematic review, which supports the clinicians’ criteria, in the selection of a specific material over another for a particular clinical situation. The purpose of this systematic review and meta-analysis was to assess and compare the mechanical properties of dimethacrylates and monomethacrylates used in fabricating direct provisional restorations, in terms of flexural strength, fracture toughness and hardness. This review followed the PRISMA guidelines. The searche…

Carbon monoxide: mechanisms of action and potential clinical implications.

2013

International audience; Small amounts of carbon monoxide (CO) are continuously produced in mammals. The intracellular levels of CO can increase under stressful conditions following the induction of HO-1 (heme oxygnase-1), a ubiquitous enzyme responsible for the catabolism of heme. Unlike nitric oxide, which is a free radical, CO does not contain free electrons but may be involved in oxidative stress. The carbonate radical has been proposed to be a key mediator of oxidative damage resulting from peroxynitrite production, likewise, the precursor of the carbonate radical anion being bicarbonate and carbon dioxide. We report herein some of the transcription factors and protein kinases involved …

Polymer brushes in solvents of variable quality: Molecular dynamics simulations using explicit solvent

2007

The structure and thermodynamic properties of a system of end-grafted flexible polymer chains grafted to a flat substrate and exposed to a solvent of variable quality are studied by molecular dynamics methods. The macromolecules are described by a coarse-grained bead-spring model, and the solvent molecules by pointlike particles, assuming Lennard-Jones-type interactions between pairs of monomers (epsilon(pp)), solvent molecules (epsilon(ss)), and solvent monomer (epsilon(ps)), respectively. Varying the grafting density sigma(g) and some of these energy parameters, we obtain density profiles of solvent particles and monomers, study structural properties of the chain (gyration radius componen…

Solar heterogeneous photocatalysis for high added value molecules production

Mutual inductance of thick coils for arbitrary relative orientation and position

2017

An exact solution method has been developed recently which gives the mutual inductance of two thin cylindrical coils in terms of line integrals of a new kind of vector potential, induced by the primary coil, around the two circular edges of the secondary coil. This paper describes the extension of this method to thick coils, by wrapping two radial integrations around these line integrals. Results are presented for two pairs of conventional coils and a combination of a superconducting coil and a Bitter coil. Excellent agreement with existing results for non coaxial coils was obtained. The trade-off between accuracy and computing time is also examined.

Structure of a bidisperse polymer brush: Monte Carlo simulation and self-consistent field results

1992

Using the bond-fluctuation model, Monte Carlo simulations are performed for polymer brushes composed of chains of two different chain lengths under good solvent condition. Profiles of monomer density and free end density, chain linear dimensions, and average monomer position along a chain are studied. Quantities measured in the simulations are derived from the analytic self-consistent field (SCF) theory and compared with the simulation data. The structural properties can be quite accurately described by the theory only when both the long and short chains are stretched

Ferrochirality: a simple theoretical model of interacting, dynamically invertible, helical polymers, 2. Molecular field approach: supports and the de…

1995

Using a molecular field approach, the effect of interaction between reversibly invertible, helical polymers is investigated theoretically. The helices are modelled by nearest-neighbour statistical thermodynamics. If the interaction energy between two helices of common handedness is lower than that of oppositely handed ones, a critical temperature Tc exists, below which the system spontaneously must leave the racemic state, though there is no contact to any chiral centre or force. This is analogous to the second-order phase transition of ferromagnets. The critical point increases with molecular weight and optical persistence of the helices. At the critical point the system is highly sensitiv…

Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures

2016

We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…

Nonintrusive monitoring and quantitative analysis of strong laser-field-induced impulsive alignment

2004

We report the observation of impulsive alignment of $\mathrm{C}{\mathrm{O}}_{2}$ molecules produced through their interaction with a nonresonant, strong laser pulse. The periodic alignment is monitored using a polarization technique generally employed in optical Kerr effect experiments; the birefringence produced by alignment of the molecular sample is measured with a weak pulse, time-delayed with respect to the alignment pulse. The technique provides a signal proportional to $⟨{\mathrm{cos}}^{2}\phantom{\rule{0.2em}{0ex}}\ensuremath{\theta}⟩\ensuremath{-}\frac{1}{3}$, where $\ensuremath{\theta}$ is the polar angle between the molecular axis and the strong-field polarization axis. Experimen…