Search results for "Statistical physics"
showing 10 items of 1402 documents
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…
Electronic transport in molecular junctions : The generalized Kadanoff–Baym ansatz with initial contact and correlations
2021
The generalized Kadanoff-Baym ansatz (GKBA) offers a computationally inexpensive approach to simulate out-of-equilibrium quantum systems within the framework of nonequilibrium Green's functions. For finite systems the limitation of neglecting initial correlations in the conventional GKBA approach has recently been overcome [Phys. Rev. B 98, 115148 (2018)]. However, in the context of quantum transport the contacted nature of the initial state, i.e., a junction connected to bulk leads, requires a further extension of the GKBA approach. In this work, we lay down a GKBA scheme which includes initial correlations in a partition-free setting. In practice, this means that the equilibration of the …
Iron’s Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex
2020
Recently synthetized iron complexes have achieved long-lived excited states and stabilities which are comparable, or even superior, to their ruthenium analogues, thus representing an eco-friendly and cheaper alternative to those materials based on rare metals. Most of computational tools which could help unravel the origin of this large efficiency rely on ab-initio methods which are not able, however, to capture the nanosecond time scale underlying these photophysical processes and the influence of their realistic environment. Therefore, it exists an urgent need of developing new low-cost, but still accurate enough, computational methodologies capable to deal with the steady-state and trans…
Collective behaviours: from biochemical kinetics to electronic circuits
2013
In this work we aim to highlight a close analogy between cooperative behaviors in chemical kinetics and cybernetics; this is realized by using a common language for their description, that is mean-field statistical mechanics. First, we perform a one-to-one mapping between paradigmatic behaviors in chemical kinetics (i.e., non-cooperative, cooperative, ultra-sensitive, anti-cooperative) and in mean-field statistical mechanics (i.e., paramagnetic, high and low temperature ferromagnetic, anti-ferromagnetic). Interestingly, the statistical mechanics approach allows a unified, broad theory for all scenarios and, in particular, Michaelis-Menten, Hill and Adair equations are consistently recovered…
Modified Gaussian models applied to the description and deconvolution of peaks in chiral liquid chromatography.
2020
Abstract The description of the profiles of chromatographic peaks has been studied extensively, with a large number of proposed mathematical functions. Among them, the accuracy achieved with modified Gaussian models that describe the deviation of an ideal Gaussian peak as a change in the peak variance or standard deviation over time, has been highlighted. These models are, in fact, a family of functions of different complexity with great flexibility to adjust chromatographic peaks over a wide range of asymmetries and shapes. However, an uncontrolled behaviour of the signal may occur outside the region being fitted, forcing the use of different strategies to overcome this problem. In this wo…
A probabilistic approach to radiant field modeling in dense particulate systems
2016
Radiant field distribution is an important modeling issue in many systems of practical interest, such as photo-bioreactors for algae growth and heterogeneous photo-catalytic reactors for water detoxification.In this work, a simple radiant field model suitable for dispersed systems showing particle size distributions, is proposed for both dilute and dense two-phase systems. Its main features are: (i) only physical, independently assessable parameters are involved and (ii) its simplicity allows a closed form solution, which makes it suitable for inclusion in a complete photo-reactor model, where also kinetic and fluid dynamic sub-models play a role. A similar model can be derived by making us…
Grand-canonical approach to density functional theory of electrocatalytic systems: Thermodynamics of solid-liquid interfaces at constant ion and elec…
2018
Properties of solid-liquid interfaces are of immense importance for electrocatalytic and electrochemical systems, but modeling such interfaces at the atomic level presents a serious challenge and approaches beyond standard methodologies are needed. An atomistic computational scheme needs to treat at least part of the system quantum mechanically to describe adsorption and reactions, while the entire system is in thermal equilibrium. The experimentally relevant macroscopic control variables are temperature, electrode potential, and the choice of the solvent and ions, and these need to be explicitly included in the computational model as well; this calls for a thermodynamic ensemble with fixed…
Phase separation of an asymmetric binary fluid mixture confined in a nanoscopic slit pore: Molecular-dynamics simulations
2008
As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types…
Kramers potential study of the Rouse-like dynamics of short alkane chains.
1999
In this work we present a Kramers potential study of the orientational dynamics and shear viscosity of short chain alkanes. In this approach the determination of the orientational relaxation time is reduced to the calculation of static moments of single chain conformations. We study a chemically realistic alkane model that asymptotically produces Gaussian chain conformations by means of a Monte Carlo simulation. Our results are applicable to single chain descriptions of polymer melt dynamics and to the intrinsic viscosity of molecules in a Theta solvent. When we map the unknown time unit of our relaxation time result for one particular chain length and temperature to the value obtained for …
Monte Carlo Simulation of a Homopolymer−Copolymer Mixture Interacting with a Surface: Bulk versus Surface Micelles and Brush Formation
2008
Using Monte Carlo simulations of the bond fluctuation model, we study the formation of micelles in a confined mixture of asymmetric AB-diblock copolymers and homopolymers. The composition of the sphere-forming AB-diblock copolymers is fA = 1/8. The mixture is confined into a thin film. The film surfaces attract the minority component of the diblock with strength, eW. To efficiently sample the micelle size distribution and establish equilibrium between the surface and the bulk, we work in the semigrandcanonical ensemble, i.e. at fixed density and fixed chemical potential difference between the two types of chains, choosing a large incompatibility χN ≃ 100 (strong segregation regime). The com…