arXiv subjects
Publications and source records attributed to Luigi Delle Site.
The formalization of First Passage schemes is revisited and the emerging of a conceptual contradiction is underlined. We then show why, despite such a contradiction, the numerical results are not explicitly affected. Through a different formalization of the problem, we recast the current principles of the algorithm in a more solid conceptual framework, and numerical evidence gives further justification to our claims.
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of natural and artificially induced phenomena which are of major relevance to several leading fields of academic research and modern technology. In this progress report I will present an overview of problems in current materials science and chemical physics where the corresponding computational approaches require the concept of an electronic system with open boundaries. Quantum and Quantum/Classical computational techniques treat the exchange of electrons with the environment at different computational efficiency, conceptual rigorousness and numerical accuracy. The overall emerging picture shows a rich availability of interesting ideas, some with a higher weight on the pragmatic side, others with higher weight on the conceptual side; possible combinations, in perspective, may push the field much beyond its current frontiers.
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, we construct a combined, explicit reservoir by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed.
We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region.
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a subsystem of interest with atomistic details and a reservoir of coarse-grained particles leads to satisfactory results. The challenging aspect of this study, compared to previous AdResS simulations, is the presence of charged particles and the necessity of addressing the question about the minimal physical input needed to model the coarse-grained particles in the reservoir. We propose two different approaches and show that in both cases they are sufficient to capture the decisive physical characteristics that allow a valid system-reservoir coupling. The technical satisfactory result paves the way for multiscale analysis of ionic liquids and for truly open boundary molecular simulations.
A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. T he Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.
We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several field of theoretical and applied physics, and the thermodynamic approach currently favoured by practitioners is based on a phenomenological definition of an interface energy associated with the partition, due to a lack of easily computable expressions for a microscopic (i.e.~particle-based) interface energy. In this article, we outline a general approach to derive sharp and computable bounds for the interface free energy in terms of microscopic statistical quantities. We discuss potential applications in nanothermodynamics and outline possible future directions.
We discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within $10-15\%$ accuracy, is given by the Amdahl's Law adapted to the specific quantities involved in the problem. The derivation of the predictive formula is general enough that it may be applied to the general case of molecular dynamics approaches where a reduction of degrees of freedom in a multiscale fashion occurs.
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.
Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in the way the change of molecular resolution is made in a buffer/transition region. In particular a central question concerns the possibility of the existence of a global Hamiltonian which, by describing the change of resolution, is at the same time physically consistent, mathematically well defined and numerically accurate. In this paper we present an asymptotic analysis of the adaptive process complemented by numerical results and show that under certain mathematical conditions a Hamiltonian, which is physically consistent and numerically accurate, may exist. Such conditions show that molecular simulations in the current computational implementation require systems of large size and thus a Hamiltonian approach as the one proposed, at this stage, would not be practical from the numerical point of view. However, the Hamiltonian proposed provides the basis for a simplification and generalization of the numerical implementation of adaptive resolution algorithms to other molecular dynamics codes.
We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems, liquid parahydrogen at extreme thermodynamic conditions and liquid water at ambient conditions; the reproduction of structural as well as dynamical results of reference systems are highly satisfactory. The capability of performing GC-AdResS CMD simulations allows for the treatment of a system characterized by some quantum features and open boundaries. This latter characteristic not only is of computational convenience, allowing for equivalent results of much larger and computationally more expensive systems, but also suggests a tool of analysis so far not explored, that is the unambiguous identification of the essential (quantum) degrees of freedom required for a given property.
Liouville's theorem in a grand ensemble, that is for situations where a system is in equilibrium with a reservoir of energy and particles, is a subject that, to our knowledge, has not been explicitly treated in literature related to molecular simulation. Instead Liouville's theorem, a central concept for the correct employment of molecular simulation techniques, is implicitly considered only within the framework of systems where the total number of particles is fixed. However the pressing demand of applied science in treating open systems leads to the question of the existence and possible exact formulation of Liouville's theorem when the number of particles changes during the dynamical evolution of the system. The intention of this note is to stimulate a debate about this crucial issue for molecular simulation.
We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to correctly account for the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however computationally this technique is very demanding. The abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in literature. The comparison of our results with those reported in literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.
This article deals with the molecular dynamics simulation of open systems that can exchange energy and matter with a reservoir; the physics of the reservoir and its interactions with the system are described by the model introduced by Bergmann and Lebowitz.Despite its conceptual appeal, the model did not gain popularity in the field of molecular simulation and, as a consequence, did not play a role in the development of open system molecular simulation techniques, even though it can provide the conceptual legitimation of simulation techniques that mimic open systems. We shall demonstrate that the model can serve as a tool to devise both numerical procedures and conceptual definitions of physical quantities that cannot be defined in a straightforward way by systems with a fixed number of molecules. In particular, we discuss the utility of the Bergmann-Lebowitz (BL) model for the calculation of equilibrium time correlation functions within the Grand Canonical Adaptive Resolution method (GC-AdResS) and report numerical results for the case of liquid water.
We describe the adaptive resolution multiscale method AdResS. The conceptual evolution as well as the improvements of its technical efficiency are described step by step, with an explicit reference to current limitations and open problems.
In this paper I will discuss the overlap between the concept of Shannon Entropy and the concept of electronic correlation. Quantum Monte Carlo numerical results for the uniform electron gas are also presented; these latter on the one hand enhance the hypothesis of a direct link between the two concepts but on the other hand leave a series of open questions which may be employed to trace a roadmap for the future research in the field.
We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonical-like version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, $μ^{ex}$, of various liquids and mixtures. We compare our results with those obtained from full atomistic simulations using the technique of thermodynamic integration and show a satisfactory agreement. In GC-AdResS the procedure to calculate $μ^{ex}$ corresponds to the process of standard initial equilibration of the system; this implies that, independently of the specific aim of the study, $μ^{ex}$, for each molecular species, is automatically calculated every time a GC-AdResS simulation is performed.