Phase Coexistence in Hamiltonian Hybrid Particle-Field Theory Using a Multi-Gaussian Approach.

This study introduces an implementation of multiple Gaussian filters within the Hamiltonian hybrid particle-field (HhPF) theory, aimed at capturing phase coexistence phenomena in mesoscopic molecular simulations. By employing a linear combination of two Gaussians, we demonstrate that HhPF can generate potentials with attractive and steric components analogous to Lennard-Jones (LJ) potentials, which are crucial for modeling phase coexistence. We compare the performance of this method with the multi-Gaussian core model (MGCM) in simulating liquid-gas coexistence for a single-component system across various densities and temperatures.

Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics.

We develop ∂-HylleraasMD (∂-HyMD), a fully end-to-end differentiable molecular dynamics software based on the Hamiltonian hybrid particle-field formalism, and use it to establish a protocol for automated optimization of force field parameters. ∂-HyMD is templated on the recently released HylleraaasMD software, while using the JAX autodiff framework as the main engine for the differentiable dynamics. ∂-HyMD exploits an embarrassingly parallel optimization algorithm by spawning independent simulations, whose trajectories are simultaneously processed by reverse mode automatic differentiation to calculate the gradient of the loss function, which is in turn used for iterative optimization of the force-field parameters.

Quantum Definition of Molecular Structure.

Molecular structure, a key concept of chemistry, has remained elusive from the perspective of all-particle quantum mechanics, despite many efforts. Viewing molecular structure as a manifestation of strong statistical correlation between nuclear positions, we propose a practical method based on Markov chain Monte Carlo sampling and unsupervised machine learning. Application to the D molecule unambiguously shows that it possesses an equilateral triangular structure.

SANS Spectra with PLUMED: Implementation and Application to Metainference.

Using small-angle scattering with either X-ray or neutron sources has become common in the investigation of soft-matter systems. These experiments provide information about the coarse shape of the scattered objects, but obtaining more-detailed information can usually only be achieved with the aid of molecular simulations. In this Application Note, we report the implementation of an extension in PLUMED to compute the small-angle neutron scattering (SANS), which can be used for data processing as well for enhanced sampling, in particular with the metainference method to bias simulations and sample structures with a resulting spectrum in agreement with an experimental reference.

Accelerating Lipid Flip-Flop at Low Concentrations: A General Mechanism for Membrane Binding Peptides.

We report a physicochemical investigation of the lipid transport properties of model lipid membranes in the presence of the antimicrobial peptide indolicidin through comparisons of experimental SANS/SAXS scattering techniques to fully atomistic molecular dynamics simulations. In agreement with the experiment, we show that upon peripheral binding of the peptides, even at low concentrations, lipid flip-flop dynamics is greatly accelerated. Computer modeling elucidates the interplay between structural changes and lipid dynamics induced by peptides and proposes a mechanism for the mode of action of antimicrobial peptides, assessing the major role of entropy for the catalysis of the flipping events.

Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand.

Understanding the interactions and the solvent effects on the distribution of several species in equilibrium and how it can influence the H-NMR properties, spectroscopy (UV-vis absorption), and the acid-base equilibria can be especially challenging. This is the case of a bis-bidentate bridging ligand bis(2-pyridyl)-benzo-bis(imidazole), where the two pyridyl and four imidazolyl nitrogen atoms can be protonated in different ways, depending on the solvent, generating many isomeric/tautomeric species. Herein, we report a combined theoretical-experimental approach based on a sequential quantum mechanics/molecular mechanics procedure that was successfully applied to describe in detail the acid-base characterization and its effects on the electronic properties of such a molecule in solution.

A QM/MM study of the conformation stability and electronic structure of the photochromic switches derivatives of DHA/VHF in acetonitrile solution.

We present a detailed theoretical study of the electronic absorption spectra and thermochemistry of molecular photoswitches composed of one and two photochromic units of dihydroazulene (DHA)/vinylheptafulvene (VHF) molecules. Six different isomers are considered depending on the ring opening/closure forms of the DHA units. The solvent effect of acetonitrile is investigated using a sequential Molecular Mechanics/Quantum Mechanics approach.

DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method.

Solute-solvent systems are an important topic of study, as the effects of the solvent on the solute can drastically change its properties. Theoretical studies of these systems are done with methods, molecular simulations, or a combination of both. The simulations of molecular systems are usually performed with either molecular dynamics (MD) or Monte Carlo (MC) methods.

Thermodynamic properties of 55-atom Pt-based nanoalloys: Phase changes and structural effects on the electronic properties.

Atomistic understanding of thermodynamic processes such as phase transitions in nanoalloys is crucial to improve real-life applications of Pt-based nanocatalysts. In this work, we investigate the thermodynamic properties of 55-atom PtCo and PtNi nanoalloys and compare them to reference unary systems, Pt, Co, and Ni. Our results are based on the combination of the parallel tempering Monte Carlo and the revised basin-hopping Monte Carlo algorithms with many-body Gupta potentials, and furthermore, density functional theory calculations were employed to validate the adopted Gupta parameters and to analyze electronic effects induced by structural changes derived from temperature effects.

Parallel tempering Monte Carlo combined with clustering Euclidean metric analysis to study the thermodynamic stability of Lennard-Jones nanoclusters.

A basic requirement for an atom-level understanding of nanoclusters is the knowledge of their atomic structure. This understanding is incomplete if it does not take into account temperature effects, which play a crucial role in phase transitions and changes in the overall stability of the particles. Finite size particles present intricate potential energy surfaces, and rigorous descriptions of temperature effects are best achieved by exploiting extended ensemble algorithms, such as the Parallel Tempering Monte Carlo (PTMC).

A basin-hopping Monte Carlo investigation of the structural and energetic properties of 55- and 561-atom bimetallic nanoclusters: the examples of the ZrCu, ZrAl, and CuAl systems.

We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species.