Search results for "Computer simulation"
showing 10 items of 1054 documents
Measurement of elastic forces between iron colloidal particles in a nematic liquid crystal.
2006
The forces that arise between two iron particles in a nematic liquid crystal with a strong homeotropic anchoring were studied. For the first time, the short range repulsive force resulting from the presence of a hedgehog defect between two particles was precisely determined thanks to application of a small magnetic field and observation of the equilibrium position resulting from the balance between the elastic and magnetic forces. Above a given threshold force, the particles stuck together whereas the hedgehog defect was expelled and transformed into a Saturn ring located between the particles. The attractive part of the interparticle force was determined with the same method on the entire …
Field theoretic study of bilayer membrane fusion: I. Hemifusion mechanism
2003
Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of flexible amphiphilic chains dissolved in hydrophilic solvent is employed to describe these self-assembled structures. We find that the barrier to formation of the initial stalk is much smaller than previously estimated by phenomenological theories. Therefore its creation it is not the rate limiting process. The barrier which is relevant is associated with the rather limited radial expansion of the stalk into a hemifusion diaphragm. It is strongly affected by…
Pore Formation by a Bax-Derived Peptide: Effect on the Line Tension of the Membrane Probed by AFM
2007
AbstractBax is a critical regulator of physiological cell death that increases the permeability of the outer mitochondrial membrane and facilitates the release of the so-called apoptotic factors during apoptosis. The molecular mechanism of action is unknown, but it probably involves the formation of partially lipidic pores induced by Bax. To investigate the interaction of Bax with lipid membranes and the physical changes underlying the formation of Bax pores, we used an active peptide derived from helix 5 of this protein (Bax-α5) that is able to induce Bax-like pores in lipid bilayers. We report the decrease of line tension due to peptide binding both at the domain interface in phase-separa…
Photoinduced intersystem crossing in DNA oxidative lesions and epigenetic intermediates
2020
[EN] The propensity of 5-formyluracil and 5-formylcytosine, i.e. oxidative lesions and epigenetic intermediates, in acting as intrinsic DNA photosensitizers is unraveled by using a combination of molecular modeling, simulation and spectroscopy. Exploration of potential energy surfaces and non-adiabatic dynamics confirm a higher intersystem crossing rate for 5-formyluracil, whereas the kinetic models evidence different equilibria in the excited states for both compounds.
Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase
2008
Molecular simulations based on the use of hybrid quantum mechanics/molecular mechanics methods are able to provide detailed information about the complex enzymatic reactions and the consequences of specific mutations on the activity of the enzyme. In this work, the reduction of pyruvate to lactate catalysed by wild-type and Asp168Ala mutant lactate dehydrogenase (LDH) has been studied by means of simulations using a very flexible molecular model consisting of the full tetramer of the enzyme, together with the cofactor NADH, the substrate and solvent water molecules. Our results indicate that the Asp168Ala mutation provokes a shift in the p K a value of Glu199 that becomes unprotonated at n…
Carbon nanorings: A challenge to theoretical chemistry
2006
High-level quantum-chemical methods show that the binding in the inclusion complex of hexamethylbenzene (HMB) in 6-cycloparaphenilacetylene (6-CPPA) cannot be explained only in terms of electrostatic interactions - caused by the polarization associated to curved Ï-conjugated systems - and the inclusion of dispersion forces is definitely needed. The theoretical description of van der Waals interactions is notoriously complicated and in fact some DFT methods cannot even predict the existence of the relatively small supramolecular nanoring studied here. However, ab initio MP2 calculations agree with experimental data and show that, in the considered complex, the HMB fragment is placed at the …
Effect of elliptical deformation on molecular polarizabilities of model carbon nanotubes from atomic increments.
2003
The interacting induced dipole polarization model implemented in our program POLAR is used for the calculation of the dipole-dipole polarizability alpha. The method is tested with single-wall carbon nanotube models as a function of nanotube radius and elliptical deformation. The results for polarizability follow the same trend as reference calculations performed with our version of the program PAPID. For the zigzag tubes, the polarizability is found to follow a remarkably simple law, that is, it varies as the inverse of the radius. A dramatic effect is also found with elliptical deformation. It is found that the polarizability and related properties can be modified continuously and reversib…
Random walks and random numbers from supercontinuum generation
2012
International audience; We report a numerical study showing how the random intensity and phase fluctuations across the bandwidth of a broadband optical supercontinuum can be interpreted in terms of the random processes of random walks and L´evy flights. We also describe how the intensity fluctuations can be applied to physical random number generation. We conclude that the optical supercontinuum provides a highly versatile means of studying and generating a wide class of random processes at optical wavelengths.
Multiple IgE recognition on the major allergen of the Parietaria pollen Par j 2
2015
The interaction between IgE antibodies and allergens is a key event in triggering an allergic reaction. The characterization of this region provides information of paramount importance for diagnosis and therapy. Par j 2 Lipid Transfer Protein is one of the most important allergens in southern Europe and a well-established marker of sensitization in Parietaria pollen allergy. The main aim of this study was to map the IgE binding regions of this allergen and to study the pattern of reactivity of individual Parietaria-allergic patients. By means of gene fragmentation, six overlapping peptides were expressed in Escherichia coli, and their IgE binding activity was evaluated by immunoblotting in …
Effects of confinement and external fields on structure and transport in colloidal dispersions in reduced dimensionality
2012
In this work, we focus on low-dimensional colloidal model systems, via simulation studies and also some complementary experiments, in order to elucidate the interplay between phase behavior, geometric structures and transport properties. In particular, we try to investigate the (nonlinear!) response of these very soft colloidal systems to various perturbations: uniform and uniaxial pressure, laser fields, shear due to moving boundaries and randomly quenched disorder.We study ordering phenomena on surfaces or in monolayers by Monte Carlo computer simulations of binary hard-disk mixtures, the influence of a substrate being modeled by an external potential. Weak external fields allow a control…