Search results for " MOLECULAR DYNAMICS"
showing 10 items of 126 documents
Many-body quantum dynamics by adiabatic path-integral molecular dynamics: Disordered Frenkel Kontorova models
2005
The spectral density of quantum mechanical Frenkel Kontorova chains moving in disordered, external potentials is investigated by means of path-integral molecular dynamics. If the second moment of the embedding potential is well defined (roughness exponent ), there is one regime in which the chain is pinned (large masses of chain particles) and one in which it is unpinned (small ). If the embedding potential can be classified as a random walk on large length scales ( ), then the chain is always pinned irrespective of the value of . For , two phonon-like branches appear in the spectra.
Fractional-order theory of heat transport in rigid bodies
2014
Abstract The non-local model of heat transfer, used to describe the deviations of the temperature field from the well-known prediction of Fourier/Cattaneo models experienced in complex media, is framed in the context of fractional-order calculus. It has been assumed (Borino et al., 2011 [53] , Mongiovi and Zingales, 2013 [54] ) that thermal energy transport is due to two phenomena: ( i ) A short-range heat flux ruled by a local transport equation; ( ii ) A long-range thermal energy transfer proportional to a distance-decaying function, to the relative temperature and to the product of the interacting masses. The distance-decaying function is assumed in the functional class of the power-law …
Transfer coefficients for evaporation of a system with a Lennard-Jones long-range spline potential
2007
International audience; Surface transfer coefficients are determined by nonequilibrium molecular dynamics simulations for a Lennard-Jones fluid with a long-range spline potential. In earlier work A. Røsjorde et al., J. Colloid Interface Sci. 240, 355 2001; J. Xu et al., ibid. 299, 452 2006, using a short-range Lennard-Jones spline potential, it was found that the resistivity coefficients to heat and mass transfer agreed rather well with the values predicted by kinetic theory. For the long-range Lennard-Jones spline potential considered in this paper we find significant discrepancies from the values predicted by kinetic theory. In particular the coupling coefficient, and as a consequence the…
Liquid-liquid phase coexistence in gold clusters. 2D or not 2D?
2006
The thermodynamics of gold cluster anions (${\mathrm{Au}}_{N}^{\ensuremath{-}}$, $N=11,\dots{},14$) is investigated using quantum molecular dynamics. Our simulations suggest that ${\mathrm{Au}}_{N}^{\ensuremath{-}}$ may exhibit a novel, freestanding planar liquid phase which dynamically coexists with a normal three-dimensional liquid. Upon cooling with experimentally realizable cooling rates, the entropy-favored three-dimensional liquid clusters often supercool and solidify into the ``wrong'' dimensionality. This indicates that experimental validation of theoretically predicted ${\mathrm{Au}}_{N}^{\ensuremath{-}}$ ground states might be more complicated than hitherto expected.
Molecular dynamics studies on Mdm2 complexes: An analysis of the inhibitor influence
2012
p53 is a powerful anti-tumoral molecule frequently inactivated by mutations or deletions in cancer. However, half of all human tumors expresses wild-type p53, and its activation, by antagonizing its negative regulator Mdm2, might offer a new strategy for therapeutic protocol. In this work, we present a molecular dynamics study on Mdm2 structure bound to two different known inhibitors with the aim to investigate the structural transitions between apo-Mdm2 and Mdm2-inhibitor complexes. We tried to gain information about conformational changes binding a benzodiazepine derivative inhibitor with respect the known nutlin and the apo form. The conformational changes alter the size of the cleft and…
Thioflavin T templates amyloid β(1–40) conformation and aggregation pathway
2015
Aβ(1-40) peptide supramolecular assembly and fibril formation processes are widely recognized to have direct implications in the progression of Alzheimer's disease. The molecular basis of this biological process is still unknown and there is a strong need of developing effective strategies to control the occurring events. To this purpose the exploitation of small molecules interacting with Aβ aggregation represents one of the possible routes. Moreover, the use specific labeling has represented so far one of the most common and effective methods to investigate such a process. This possibility in turn rests on the reliability of the probe/labels involved. Here we present evidences of the effe…
Molecular modelling and QSAR in the discovery of HIV-1 integrase inhibitors
2007
The treatment regimens for the HIV-1 have mainly included reverse transcriptase or protease inhibitors but their long-term clinical utility is limited by severe side effects and viral drug resistance. A new attractive target for chemotherapeutic intervention can be the Integrase enzyme, that mediates the integration of HIV-1 DNA into a host chromosome, for which there is no known counterparts in the host cell. A number of derivatives have been found to inhibit IN in in vitro assays, but no successful drug based on them has emerged so far, although many compounds have been proposed. Moreover most of the inhibitors do not belong to a very precise structural class: this fact makes these compou…
Investigating the inhibition of FTSJ1 a tryptophan tRNA-specific 2’-O-methyltransferase by NV TRIDs, as a mechanism of readthrough in nonsense mutate…
2023
Abstract: Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations, which generate a Premature Termination Codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ri-bosome’s capacity to skip a PTC, thus generating a full-length protein. “TRIDs” are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We in-vestigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their r…
The Interaction of Small Molecules with Biomolecules
2014
The binding of small molecules with biological targets is associated to interesting chemical and biological properties of the resulting supramolecular systems. We have recently reported on the synthesis and characterization of cationic first row transition metal complexes and the study of their DNA binding properties, in aqueous solutions at neutral pH, essentially investigated by viscosimetry and spectroscopic techniques such as circular dichroism, absorption and fluorescence in the UV-visible wavelength range. Of course, such procedure cannot furnish atomic level details of the molecule-DNA interaction. Computational Chemistry may provide support for the interpretation of experimental dat…
Bimodal Acidity at the Amorphous Silica/Water Interface
2015
International audience; Understanding the microscopic origin of the acid base behavior of mineral surfaces in contact with water is still a challenging task, for both the experimental and the theoretical communities. Even for a relatively simple material, such as silica, the origin of the bimodal acidity behavior is still a debated topic. In this contribution we calculate the acidity of single sites on the humid silica surface represented by a model for the hydroxylated amorphous surface. Using a thermodynamic integration approach based on ab initio molecular dynamics, we identify two different acidity values. In particular, some convex geminals and some type of vicinals are very acidic (pK…