Search results for "molecular dynamics"
showing 10 items of 1075 documents
Single-digit nanomolar inhibitors lock the aromatase active site via a dualsteric targeting strategy
2022
The most frequently diagnosed breast cancer (BC) type in women expresses estrogen receptor (ER) , depends on estrogens for its growth, being classified as ER positive (ER+). The gold standard therapy for the treatment of this tumor relies on the inhibition of the aromatase enzyme, which catalyzes estrogen biosynthesis. Despite the clinical success of current aromatase inhibitors (AIs), after prolonged therapeutic regimens, BC ER + patients experience acquired resistance and disease relapse. This points up the urgent need for a newer generation of AIs able to overcome resistance issues, while mitigating toxicity and side effects of current therapies. Here we performed the synthesis, biologic…
Smectic C and Nematic Phases in Strongly Adsorbed Layers of Semiflexible Polymers
2017
Molecular dynamics simulations of semiflexible polymers in a good solvent reveal a dense adsorbed layer when the solution is exposed to an attractive planar wall. This layer exhibits both a nematic and a smectic phase (smA for short and smC for longer chains) with bond vectors aligned strictly parallel to the wall. The tilt angle of the smC phase increases strongly with the contour length of the polymers. The isotropic-nematic transition is a Kosterlitz-Thouless transition and also the nematic-smectic transition is continuous. Our finding demonstrates thus a two-dimensional realization of different liquid crystalline phases, ubiquitous in three dimensions, that occurs in a single monomolecu…
Phase Behavior and Microscopic Transport Processes in Binary Metallic Alloys: Computer Simulation Studies
2009
In a binary liquid mixture, different kinds of phase transitions can occur that are associated with various mass transport phenomena in the liquid. First, there is the possibility that the liquid undergoes a liquid-liquid demixing transition [1]. Near the critical point of this transition, a slowing down of dynamic properties is observed which is characterized, e.g., by a vanishing interdiffusion coefficient at the critical point [2, 3]. Another possible phase transition is a first-order transition of the liquid into a crystalline structure. In this case, crystal nucleation and growth are limited by the diffusive transport in the liquid [1, 4]. In a binary liquid, crystal nucleation process…
Molecular dynamics study of high-pressure alumina polymorphs with a tight-binding variable-charge model
2016
Abstract A tight-binding variable-charge model aimed at performing large-scale realistic simulations of bulk, surfaces and interfaces of aluminum oxides have been developed. This model is based on the charge equilibration (QEq) method and explicitly takes into account the mixed iono–covalent character of the metal–oxygen bond by means of a tight-binding analytical approach in the second-moment approximation of the electronic structure. The parameters of the model were optimized to reproduce structural and energetic properties of the α-Al2O3 corundum structure at room temperature and pressure. The model exhibits a good transferability between five alumina polymorphs: corundum, Rh2O3(II)-type…
The smectic phase in semiflexible polymer materials: A large scale Molecular Dynamics study
2019
Abstract Semiflexible polymers in concentrated lyotropic solution are studied within a bead-spring model by molecular dynamics simulations, focusing on the emergence of a smectic A phase and its properties. We systematically vary the density of the monomeric units for several contour lengths that are taken smaller than the chain persistence length. The difficulties concerning the equilibration of such systems and the choice of appropriate ensemble (constant volume versus constant pressure, where all three linear dimensions of the simulation box can fluctuate independently) are carefully discussed. Using HOOMD-blue on graphics processing units, systems containing more than a million monomeri…
Dynamic self-assembly of non-Brownian spheres studied by molecular dynamics simulations.
2015
Granular self-assembly of confined non-Brownian spheres under gravity is studied by molecular dynamics simulations. Starting from a disordered phase, dry or cohesive spheres organize, by vibrational annealing, into body-centered-tetragonal or face-centered-cubic structures, respectively. During the self-assembling process, isothermal and isodense points are observed. The existence of such points indicates that both granular temperature and packing fraction undergo an inversion process that may be in the core of crystal nucleation. Around the isothermal point, a sudden growth of granular clusters having the maximum coordination number takes place, indicating the outcome of a first-order phas…
Semiflexible Polymers Interacting with Planar Surfaces: Weak versus Strong Adsorption
2020
Semiflexible polymers bound to planar substrates by a short-range surface potential are studied by Molecular Dynamics simulations to clarify the extent to which these chain molecules can be considered as strictly two-dimensional. Applying a coarse-grained bead-spring model, the chain length N and stiffness &kappa
Water-Hydrophobic Zeolite Systems
2012
Water intrusion-extrusion in hydrophobic microporous AFI, IFR, MTW and TON pure silica zeolites (zeosils) has been investigated through molecular dynamics (MD) simulations. It was found that intruded water volumes correlate with the free volume of the zeosil unit cells. Calculated adsorption isotherms allowed us to estimate the amounts of water intruded, and deviations from experiments (lower experimental with respect to calculated intrusion pressures) have been;explained in terms of connectivity defects in the synthesized materials. Water phase transitions in defectless zeosils occur in a narrow range at high pressure. On the basis of a simple model, we derived a thermodynamic equation tha…
Role of image charges in ionic liquid confined between metallic interfaces.
2020
The peculiar properties of ionic liquids in confinement have not only become essential for energy storage, catalysis and tribology, but still pose fundamental questions. Recently, an anomalous liquid-solid phase transition has been observed in atomic force microscopy experiments for 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), the transition being more pronounced for metallic surfaces. Image charges have been suggested as the key element driving the anomalous freezing. Using atomistic molecular dynamics simulations, we investigate the impact of image charges on structure, dynamics and thermodynamics of [BMIM][BF4] confined between gold electrodes. Our results not only unveil…
Concurrent molecular dynamics simulation of spinodal phase transition on transputer arrays
1990
Abstract We describe a concurrent implementation on cost-effective transputer arrays of a molecular dynamics program to efficiently simulate physical systems consisting of thousands of mobile particles with an interaction range much shorter than the system dimensions. This program, which uses a geometric decomposition strategy and includes a distributed dynamic load balancer, has been extensively tested by simulating the two-dimensional spinodal phase separation of a large Lennard-Jones system.