Search results for "Molecular simulation"

Computing absolute free energies of disordered structures by molecular simulation

2009

We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect, we discuss several properties of the …

New QM/MM implementation of the DFTB3 method in the gromacs package.

2015

The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…

Frontiers in molecular simulation of solvated ions, molecules and interfaces.

2020

This themed collection is a collection of articles on frontiers in molecular simulation of solvated ions, molecules and interfaces.

Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids

2017

Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation of fluorinated dom…

Erratum: “Computing absolute free energies of disordered structures by molecular simulation” [J. Chem. Phys. 131, 231102 (2009)]

2011

Molecular simulation of mixed gas hydrates in astrophysical conditions

2020

In this PhD work, numerical simulation methods have been used in order to model clathrate hydrates at the molecular scale, in thermodynamic conditions typical of astrophysical contexts. The aim was to characterize the trapping abilities of those peculiar structures of water, by means of the tools used in adsorption studies. The results presented in the present thesis are focused on a couple of chemical species which are found to be abundant in our astrophysical vicinity and are quite similar: carbon monoxide, CO, and nitrogen, N2. Thus, the single-component clathrates of CO and N2, and the mixed hydrate CO-N2 have been studied, mainly using grand canonical Monte Carlo simulations. First, th…

Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics.

2011

A methodology for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and validated for acetone-methanol and acetone-tetrachloromethane liquid mixtures. Fick diffusivities are obtained from Maxwell-Stefan (MS) diffusivities and the so-called thermodynamic factor. MS diffusivities describe the friction between different components, while the thermodynamic factor is the concentration derivative of the activity describing the deviation from ideal mixing behavior. It is important to note that all mutual diffusion experiments measure Fick diffusion coefficients, while molecular simulation provides MS diffusivities. The required thermodynamic fa…

Molecular Simulation of Polymer Melts and Blends: Methods, Phase Behavior, Interfaces, and Surfaces

2016

Kirkwood-Buff integrals from molecular simulation

2019

The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of RDFs over volume but can also be obtained from density fluctuations in the grand-canonical ensemble. Various methods have been proposed to estimate KB integrals from molecular simulation. In this work, we review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention is paid to finite-size effects. We also review various applications of KB integrals comput…

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

2021

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering…