arXiv subjects

Luigi Delle Site

Publications and source records attributed to Luigi Delle Site.

At least 55 records · Page 3Linked to original sources

arXiv2014

On Some Open Problems in Many-Electron Theory

Mel Levy and Elliott Lieb are two of the most prominent researchers who have dedicated their efforts to the investigation of fundamental questions in many-electron theory. Their results have not only revolutionized the theoretical approach of the field, but, directly or indirectly, allowed for a quantum jump in the computational treatment of realistic systems as well. For this reason, at the conclusion of our book where the subject is treated across different disciplines, we have asked Mel Levy and Elliott Lieb to provide us with some open problems, which they believe will be a worth challenge for the future also in the perspective of a synergy among the various disciplines.

quant-ph↗

arXiv2014

Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.

physics.chem-ph↗

arXiv2013

Is there a third order phase transition for supercritical fluids?

We prove that according to Molecular Dynamics (MD) simulations of liquid mixtures of Lennard-Jones (L-J) particles, there is no third order phase transition in the supercritical regime beyond Andrew's critical point. This result is in open contrast with recent theoretical studies and experiments which instead suggest not only its existence but also its universality regarding the chemical nature of the fluid. We argue that our results are solid enough to go beyond the limitations of MD and the generic character of L-J models, thus suggesting a rather smooth liquid-vapor thermodynamic behavior of fluids in supercritical regime.

physics.chem-ph↗

arXiv2013

Levy-Lieb Principle meets Quantum Monte Carlo

We review an approach where the energy functional of Density-Functional Theory (DFT) can be determined without empiricism via a Quantum Monte Carlo (QMC) procedure. The idea consists of a nested iterative loop where the configurational space of the electrons in the QMC procedure is determined by a trial oneparticle electron density; this allows then for the determination of a first guess for the energy functional, which is then in turn used for a DFT minimization process. This latter delivers a new electron density and the loop is repeated iteratively until convergence is reached and thus the electronic structure of the system determined. In essence, from the applied point of view, such an approach is a compromise between the large computational cost but high accuracy of QMC and the reasonable computational cost but lower accuracy of DFT. The proposed approach goes beyond the standard Kohn-Sham method, which is the standard in DFT, and requires neither orbitals nor the a priori specification of the exchange and correlation functional. From the conceptual point of view, the relevant aspect is that the 3N-dimensional wavefunction is derived as a function(al) of the three-dimensional electron density, which is the key principle of DFT.

cond-mat.str-el↗

arXiv2013

pH-dependent coarse-grained model of peptides

We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer its main physical features to the coarse-grained resolution according the principle of "consistency across the scales". The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use the such parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different response to pH variations, showing a highly satisfactory performance of the model.

physics.bio-ph↗

arXiv2013

pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study

In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This protein structure presents a remarkable chain stiffness andis formed by two or more long helical peptides that are interacting like the strands of a rope. Chain length and rigidity are the key aspects needed to extend previous peptide interaction potentials to this particular case; however the original model is naturally recovered when the length or the ridigity of the simulated chain are reduced. We apply the model and discuss results for two cases: (a) the folding/unfolding transition of a generic coiled coil as a function of pH; (b) behavior of a specific sequence as a function of the acidity conditions. In this latter case results are compared with experimental data from the literature in order to comment about the consistency of our approach.

physics.bio-ph↗

arXiv2013

Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique

In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive resolution simulation (AdResS) technique in sampling the Grand Canonical ensemble. We demonstrate that the correct density and radial distribution functions in the hybrid region, where molecules change resolution, are two necessary conditions for considering the atomistic and coarse-grained regions in AdResS equivalent to subsystems of a full atomistic system with an accuracy up to the second order with respect to the probability distribution of the system. Moreover, we show that the work done by the thermostat and a thermodynamic force in the transition region is formally equivalent to balance the chemical potential difference between the different resolutions. From these results follows the main conclusion that the atomistic region exchanges molecules with the coarse-grained region in a Grand Canonical fashion with an accuracy up to (at least) second order. Numerical tests, for the relevant case of liquid water at ambient conditions, are carried out to strengthen the conclusions of the theoretical analysis. Finally, in order to show the computational convenience of AdResS as a Grand Canonical set up, we compare our method to the Insertion Particle Method (IMP) in its most efficient computational implementation. This fruitful combination of theoretical principles and numerical evidence candidates the adaptive resolution technique as a natural, general and efficient protocol for Grand Canonical Molecular Dynamics for the case of large systems.

cond-mat.stat-mech↗

arXiv2012

Autocatalytic and cooperatively-stabilized dissociation of water on a stepped platinum surface

Water-metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with flat Pt, at steps water molecules dissociate forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by hydrogen bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated attitude of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings candidate these systems as viable proton wires.

cond-mat.mtrl-sci↗

arXiv2012

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.

physics.comp-ph↗

arXiv2012

Electronic Energy Functionals: Levy-Lieb principle within the Ground State Path Integral Quantum Monte Carlo

We propose a theoretical/computational protocol based on the use of the Ground State (GS) Path Integral (PI) Quantum Monte Carlo (QMC) for the calculation of the kinetic and Coulomb energy density for a system of $N$ interacting electrons in an external potential. The idea is based on the derivation of the energy densities via the $N-1$-conditional probability density within the framework of the Levy-Lieb constrained search principle. The consequences for the development of energy functionals within the context of Density Functional Theory (DFT) are discussed. We propose also the possibility of going beyond the energy densities and extend this idea to a computational procedure where the $N-1$-conditional probability is an implicit functional of the electron density, independently from the external potential. In principle, such a procedure paves the way for an {\it on-the-fly} determination of the energy functional for any system.

cond-mat.stat-mech↗

arXiv2011

The momentum distribution of the homogeneous electron gas

We calculate the off-diagonal density matrix of the homogeneous electron gas at zero temperature using unbiased Reptation Monte Carlo for various densities and extrapolate the momentum distribution, and the kinetic and potential energies to the thermodynamic limit. Our results on the renormalization factor allows us to validate approximate G_0W_0 calculations concerning quasiparticle properties over a broad density region (1 <= r_s <= 10) and show that near the Fermi surface, vertex corrections and self-consistency aspects almost cancel each other out.

cond-mat.str-el↗

arXiv2009

Coupling different levels of resolution in molecular simulations

Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures thermodynamic equilibrium among the molecules of different representation. The robustness of the algorithm is tested for two examples, namely an adaptive resolution simulation, atomistic/coarse-grained, for a liquid of tetrahedral molecules and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.

cond-mat.stat-mech↗

arXiv2007

The design of Kinetic Functionals for Many-Body Electron Systems : Combining analytical theory with Monte Carlo sampling of electronic configurations

In a previous work [L.Delle Site, J.Phys.A 40, 2787 (2007)] the derivation of an analytic expression for the kinetic functional of a many-body electron system has been proposed. Though analytical, the formula is still non local (multidimensional) and thus not ideal for numerical applications. In this work, by treating the test case of a uniform gas of interacting spinless electrons, we propose a computational protocol which combines the previous analytic results with the Monte Carlo (MC) sampling of electronic configurations in space. This, we show, leads to an internally consistent scheme to design well founded local kinetic functionals.

quant-ph↗

arXiv2007

Modeling Diffusive Dynamics in Adaptive Resolution Simulation of Liquid Water

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice-versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of essential thermodynamic, structural and dynamical properties of liquid water at ambient conditions.

cond-mat.soft↗

arXiv2007

Solvation of positive ions in water: The dominant role of water-water interaction

Local polarization effects, induced by mono and divalent positive ions in water, influence (and in turn are influenced by) the large scale structural properties of the solvent. Experiments can only distinguish this process of interplay in a generic qualitative way. Instead, first principles quantum calculations can address the question at both electronic and atomistic scale, accounting for electronic polarization as well as geometrical conformations. For this reason we study the extension of the scales' interconnection by means of first principle Car-Parrinello molecular dynamics applied to systems of different size. In this way we identify the general aspects dominating the physics of the first solvation shell and their connection to the effects related to the formation of the outer shells and eventually the bulk. We show that while the influence of the ions is extended to the first shell only, the water-water interaction is instead playing a dominant role even within the first shell independently from the size or the charge of the ion.

cond-mat.soft↗

arXiv2007

Water on Pt(111): the importance of proton disorder

The structure of a water adlayer on Pt(111) surface is investigated by extensive first principle calculations. Only allowing for proton disorder the ground state energy can be found. This results from an interplay between water/metal chemical bonding and the hydrogen bonding of the water network. The resulting short O-Pt distance accounts for experimental evidences. The novelty of these results shed a new light on relevant aspects of water-metal interaction.

cond-mat.mtrl-sci↗

arXiv2007

A Macromolecule in a Solvent: Adaptive Resolution Molecular Dynamics Simulation

We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on-the-fly. We show that our approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.

cond-mat.soft↗

arXiv2006

Adaptive Resolution Simulation of Liquid Water

We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct description of all essential thermodynamic and structural properties of liquid water.

cond-mat.soft↗