Search results for " MOLECULAR DYNAMICS"

The self-association equilibria of doxorubicin at high concentration and ionic strength characterized by fluorescence spectroscopy and molecular dyna…

2019

Abstract The self-association equilibria of doxorubicin hydrochloride (DX), at high drug and NaCl concentrations, are studied by temperature scan fluorescence spectroscopy, with the support of molecular dynamics (MD) calculations. Even though all anthracyclines show dimerization equilibria, DX only can further associate into long polymeric chains according to DXmon ⇄ DXdim ⇄ DXpol. This is reflected not only in the mechanical properties of DXpol solutions (behaving as thixotropic gels) but also in their spectroscopic behaviour. Fluorescence, in particular, is the technique of election to study this complex set of equilibria. Upon increasing the temperature, DXpol melts into DXdim, which in …

Sodium bis(2-ethylhexyl)sulfosuccinate self-aggregation in vacuo: molecular dynamics simulation.

2010

Molecular dynamics (MD) simulations were conducted for systems in vacuo consisting of n AOT(-) anions (bis(2-ethylhexyl)sulfosuccinate ions) and n+/- 1 or n Na(+) ions up to n = 20. For n = 15, positively charged systems with Li(+), K(+), and Cs(+) cations were also considered. All systems were observed to form reverse micelle-like aggregates whose centre is occupied by cations and polar heads in a very compact solid-like way, while globally the aggregate has the form of an elongated and rather flat ellipsoid. Various types of statistical analyses were carried out on the systems to enlighten structural and dynamical properties including gyration radius, atomic pair correlation functions, at…

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

2018

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both impli…

Water adsorption on amorphous silica surfaces: A Car-Parrinello simulation study

2005

A combination of classical molecular dynamics (MD) and ab initio Car-Parrinello molecular dynamics (CPMD) simulations is used to investigate the adsorption of water on a free amorphous silica surface. From the classical MD SiO_2 configurations with a free surface are generated which are then used as starting configurations for the CPMD.We study the reaction of a water molecule with a two-membered ring at the temperature T=300K. We show that the result of this reaction is the formation of two silanol groups on the surface. The activation energy of the reaction is estimated and it is shown that the reaction is exothermic.

Non-syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A

2018

International audience; Filamin A (FLNa), expressed in endocardial endothelia during fetal valve morphogenesis, is key in cardiac development. Missense mutations in FLNa cause non-syndromic mitral valve dysplasia (FLNA-MVD). Here, we aimed to reveal the currently unknown underlying molecular mechanism behind FLNA-MVD caused by the FLNa P637Q mutation. The solved crystal structure of the FLNa3-5 P637Q revealed that this mutation causes only minor structural changes close to mutation site. These changes were observed to significantly affect FLNa's ability to transmit cellular force and to interact with its binding partner. The performed steered molecular dynamics simulations showed that signi…

A multi-scale method for complex flows of non-Newtonian fluids

2021

We introduce a new heterogeneous multi-scale method for the simulation of flows of non-Newtonian fluids in general geometries and present its application to paradigmatic two-dimensional flows of polymeric fluids. Our method combines micro-scale data from non-equilibrium molecular dynamics (NEMD) with macro-scale continuum equations to achieve a data-driven prediction of complex flows. At the continuum level, the method is model-free, since the Cauchy stress tensor is determined locally in space and time from NEMD data. The modelling effort is thus limited to the identification of suitable interaction potentials at the micro-scale. Compared to previous proposals, our approach takes into acco…

Environmental Noise and Nonlinear Relaxation in Biological Systems

2012

We analyse the effects of environmental noise in three different biological systems: (i) mating behaviour of individuals of 'Nezara viridula' (L.) (Heteroptera Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by a Verhulst model with a multiplicative Lèvy noise. Specifically, we report on experiments on the behavioural response of 'N. viridula' individuals to sub-threshold deterministic signals in the presence of noise. We analyse the insect response by directionality tests performed on a group of male individuals at different noise intensities. The percentage of insects which react to the sub-threshold signal shows a non-monotonic behavior, charac…

Ab Initio Phase Diagram of Chromium to 2.5 TPa

2022

Chromium possesses remarkable physical properties such as hardness and corrosion resistance. Chromium is also a very important geophysical material as it is assumed that lighter Cr isotopes were dissolved in the Earth’s molten core during the planet’s formation, which makes Cr one of the main constituents of the Earth’s core. Unfortunately, Cr has remained one of the least studied 3d transition metals. In a very recent combined experimental and theoretical study (Anzellini et al., Scientific Reports, 2022), the equation of state and melting curve of chromium were studied to 150 GPa, and it was determined that the ambient body-centered cubic (bcc) phase of crystalline Cr re…

The Interaction of Metal Complexes with G-quadruplex DNA

Un approccio computazionale è stato proposto per lo studio dell’interazione di complessi metallici di basi di Schiff con DNA. Nel capitolo 2, è stato investigato il meccanismo di azione di complessi di Nichel(II), Rame(II) e Zinco(II) con B e G-quadruplex DNA. Il G-quadruplex è una conformazione non canonica adottata da particolari sequenze ricche in guanina. Recentemente, è stata dimostrata la sua esistenza in cellule umane, in regioni telomeriche e non telomeriche, ed è stato proposto come un possibile target per una nuova categoria di agenti antineoplastici. I capitoli successivi sono basati su dati raccolti durante due periodi di ricerca all’estero. Nel capitolo 3, basato sugli studi es…

Simulation of the dynamics of hard ellipsoids

2008

We study a system of uniaxial hard ellipsoids by molecular dynamics simulations, changing both the aspect-ratio X-0 (X-0 = a/b, where a is the length of the revolution axis and b is the length of the two other axes) and the packing fraction phi. We calculate the translational and rotational mean squared displacements, the translational D-trans and the rotational D-rot diffusion coefficients and the associated isodiffusivity lines in the phi - X-0 plane. For the first time, we characterize the cage effect through the logarithmic time derivative of log and log . These quantities exhibit a minimum if the system is supercooled and we show that, consistently with our previous findings, for large…