Search results for " MOLECULAR DYNAMICS"

Spectral broadening of the Soret band in myoglobin: an interpretation by the full spectrum of low-frequency modes from a normal modes analysis.

2005

In this work the temperature dependence of the Soret band line shape in carbon-monoxy myoglobin is re-analyzed by using both the full correlator approach in the time domain and the frequency domain approach. The new analyses exploit the full density of vibrational states of carbon-monoxy myoglobin available from normal modes analysis, and avoid the artificial division of the entire set of vibrational modes coupled to the Soret transition into "high-frequency" and "low-frequency" subsets; the frequency domain analysis, however, makes use of the so-called short-times approximation, while the time domain one avoids it. Time domain and frequency domain analyses give very similar results, thus s…

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

2014

Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both confo…

Large scale motions in models of human nicotinic receptors

2014

A first estimate of $\eta/s$ in Au+Au reactions at E$_{\rm lab}=1.23$ $A$GeV

2020

The HADES experiment at GSI has recently provided data on the flow coefficients $v_1,...,v_4$ for protons in Au+Au reactions at $E_{\rm lab} = 1.23$~$A$GeV (or $\sqrt{s_\mathrm{NN}}=2.4$ GeV). This data allows to estimate the shear viscosity over entropy ratio, $\eta/s$ at low energies via a coarse graining analysis of the UrQMD transport simulations of the flow harmonics in comparison to the experimental data. By this we can provide for the first time an estimate of $\eta/s\approx0.65\pm0.15$ (or $(8\pm2)\,(4\pi)^{-1}$) at such low energies.

Micelles of the chiral biocompatible surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl)dimethylammonium bromide (DMEB): molecular dynamics …

2017

RATIONALE: The study of self-assembly processes of surfactant molecules in the gas phase is of great interest for several theoretical and technological reasons related to their possible exploitation as drug carriers, protein shields and cleaning agents in the gas phase. METHODS: The stability and fragmentation patterns of singly and multiply charged (either positively or negatively) aggregates of the surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl)dimethyl ammonium bromide (DMEB) in the gas phase have been studied by ion mobility mass spectrometry and tandem mass spectrometry. Molecular dynamics (MD) simulations of positively and negatively singly and multiply charged DMEB aggre…

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…

Ionization potential of Al6 and Al7 as a function of temperature

1999

The temperature-depence of the ionization potential of Al6 and Al7 clusters is studied by using ab initio molecular dynamics. The threshold regions of theoretical photoionization efficiency curves are obtained from the calculated ionization potential distributions by integration and the determined ionization potentials are compared with the experimental ones. Two important effects, which complicate the determination of ionization potential from photoionization efficiency curves, are observed: the thermal tail effect and the isomerization. Also a link between the adiabatic ionization potential and the threshold of the photoionization efficiency curve is discussed. In the case of Al7, this of…

Plenty of motion at the bottom: atomically thin liquid gold membrane

2015

The discovery of graphene some ten years ago was the first proof of a free-standing two-dimensional (2D) solid phase. Here, using quantum molecular dynamics simulations of nanoscale gold patches suspended in graphene pores, we predict the existence of an atomically thin, free-standing 2D liquid phase. The liquid phase, enabled by the exceptional planar stability of gold due to relativistic effects, demonstrates extreme fluxionality of metal nanostructures and opens possibilities for a variety of nanoscale phenomena.

Proposal of a Computational Approach for Simulating Thermal Bosonic Fields in Phase Space

2019

When a quantum field is in contact with a thermal bath, the vacuum state of the field may be generalized to a thermal vacuum state, which takes into account the thermal noise. In thermo field dynamics, this is realized by doubling the dimensionality of the Fock space of the system. Interestingly, the representation of thermal noise by means of an augmented space is also found in a distinctly different approach based on the Wigner transform of both the field operators and density matrix, which we pursue here. Specifically, the thermal noise is introduced by augmenting the classical-like Wigner phase space by means of Nos&eacute

Second generation Car-Parrinello molecular dynamics

2014

Computer simulation methods, such as Monte Carlo or molecular dynamics, are very powerful theoretical techniques to provide detailed and essentially exact informations on rather complex classical many-body problems. With the advent of ab initio molecular dynamics (AIMD), where finite-temperature dynamical trajectories are generated using interatomic forces which are calculated on the fly using accurate electronic structure calculations, the scope of computational research has been greatly extended. This review is intended to outline the basic principles as well as being a survey of the field. Beginning with the derivation of Born–Oppenheimer molecular dynamics, the Car–Parrinello method and…