arXiv subjects

Barak Hirshberg

Publications and source records attributed to Barak Hirshberg.

29 records · Page 2Linked to original sources

arXiv2024

Unveiling a crystal's entropy of disorder via electron diffraction. A statistical mechanics approach

Upon melting, the molecules in the crystal explore numerous configurations, reflecting an increase in disorder. The molar entropy of disorder can be defined by Bolzmann's formula dSd = Rln(Wd) where Wd is the increase in the number of microscopic states, so far inaccessible experimentally. We found that the Arrhenius frequency factor A of the electron diffraction signal decay provides Wd via an experimental equation A = AINTWd where AINT is an inelastic scattering cross-section. The method connects Clausius and Boltzmann experimentally and supplements the Clausius approach, being applicable to a femtogram quantity of thermally unstable and biomolecular crystals. The data also showed that crystal disordering and crystallization of melt are reciprocal, both governed by the entropy change, but manifesting in opposite directions.

physics.chem-ph↗

arXiv2024

The effect of ligands on the size distribution of copper nanoclusters: insights from molecular dynamics simulations

Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesis involves a complex system of solvents, ligands, and copper precursors with intertwining effects on the size of the nanoclusters. We combine molecular dynamics simulations and DFT calculations to provide insight into the nucleation mechanism in the presence of a triphenylphosphite ligand. We identify the crucial role of the strength of the metal-phosphine bond in inhibiting the cluster's growth. We demonstrate computationally several practical routes to fine-tune the bond strength by modifying the side groups of the additive. Our work provides molecular insight into the complex nucleation process of protected copper nanocrystals, which can assist in controlling their size distribution and, eventually, their morphology.

physics.chem-ph↗

arXiv2023

Fermionic physics from ab initio path integral Monte Carlo simulations of fictitious identical particles

The \emph{ab initio} path integral Monte Carlo (PIMC) method is one of the most successful methods in statistical physics, quantum chemistry and related fields, but its application to quantum degenerate Fermi systems is severely hampered by an exponential computational bottleneck: the notorious fermion sign problem. Very recently, Xiong and Xiong [J. Chem. Phys. 157, 094112 (2022)] have suggested to partially circumvent the sign problem by carrying out PIMC simulations of fictitious systems which contain an interpolating continuous variable $ξ\in[-1,1]$ in their partition function, with the physical Fermi- and Bose-statistics corresponding to the endpoint limits $ξ=-1$ and $ξ=1$. It has been proposed that thermodynamic information about the fermionic limit might be obtained by path integral calculations within the bosonic sector $ξ>0$ combined with a quadratic $ξ$ extrapolation throughout the fermionic sector $ξ<0$, essentially bypassing the sign problem. In this work, we show how the inclusion of the artificial parameter $ξ$ can be interpreted as an effective penalty on the formation of permutation cycles in the PIMC simulation. We empirically demonstrate that the proposed extrapolation method breaks down for moderate to high quantum degeneracy. Instead, the method constitutes a valuable tool for the description of large Fermi-systems of weak quantum degeneracy. This is demonstrated for electrons in a 2D harmonic trap and for the archetypal uniform electron gas (UEG), where we find excellent agreement ($\sim0.5\%$) with exact configuration PIMC results in the high-density regime while attaining a speed-up exceeding eleven orders of magnitude. Finally, we extend the idea beyond the energy and analyze the radial density distribution (2D trap), as well as the static structure factor and imaginary-time density-density correlation function (UEG).

physics.comp-ph↗

arXiv2023

Resetting Metadynamics

Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective variables are usually not known a priori, and finding them can be very challenging. We recently presented a collective variables-free approach to enhanced sampling using stochastic resetting. Here, we combine the two methods for the first time, showing that it can lead to greater acceleration than either of them separately. We also demonstrate that resetting Metadynamics simulations performed with suboptimal collective variables can lead to speedups comparable with those obtained with optimal collective variables. Therefore, the application of stochastic resetting can be an alternative to the challenging task of improving suboptimal collective variables, at almost no additional computational cost. Finally, we propose a method to extract unbiased mean first-passage times from Metadynamics simulations with resetting, resulting in an improved tradeoff between speedup and accuracy. This work opens the way for combining stochastic resetting with other enhanced sampling methods to accelerate a broad range of molecular simulations.

physics.chem-ph↗

arXiv2022

Collective Variables for Conformational Polymorphism in Molecular Crystals

Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, μs$). We present an efficient procedure for identifying collective variables that promote transitions between conformational polymorphs in molecular dynamics simulations. It involves applying a simple dimensionality reduction algorithm to data from short ($\sim ps$) simulations of the isolated conformers that correspond to each polymorph. We demonstrate the utility of our method in the challenging case of the important energetic material, CL-20, which has three anhydrous conformational polymorphs at ambient pressure. Using these collective variables in Metadynamics simulations, we observe transitions between all solid polymorphs in the biased trajectories. We reconstruct the free energy surface and identify previously unknown defect and intermediate forms in the transition from one known polymorph to another. Our method provides insights into complex conformational polymorphic transitions of flexible molecular crystals.

physics.chem-ph↗

arXiv2022

Stochastic Resetting for Enhanced Sampling

We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations. This is often caused by broad transition time distributions in which extremely slow events have a non-negligible probability. Stochastic resetting, i.e., restarting simulations at random times, was recently shown to significantly expedite processes that follow such distributions. Here, we employ resetting for enhanced sampling of molecular simulations for the first time. We show that it accelerates long-timescale processes by up to an order of magnitude in examples ranging from simple models to molecular systems. Most importantly, we recover the mean transition time without resetting - typically too long to be sampled directly - from accelerated simulations at a single restart rate. Stochastic resetting can be used as a standalone method or combined with other sampling algorithms to further accelerate simulations.

physics.chem-ph↗

arXiv2021

Prediction of a supersolid phase in high-pressure deuterium

Supersolid is a mysterious and puzzling state of matter whose possible existence has stirred a vigorous debate among physicists for over 60 years. Its elusive nature stems from the coexistence of two seemingly contradicting properties, long-range order and superfluidity. We report computational evidence of a supersolid phase of deuterium under high pressure ($p >800$ GPa) and low temperature (T $<$ 1.0 K). In our simulations, that are based on bosonic path integral molecular dynamics, we observe a highly concerted exchange of atoms while the system preserves its crystalline order. The exchange processes are favoured by the soft core interactions between deuterium atoms that form a densely packed metallic solid. At the zero temperature limit, Bose-Einstein condensation is observed as the permutation probability of $N$ deuterium atoms approaches $1/N$ with a finite superfluid fraction. Our study provides concrete evidence for the existence of a supersolid phase in high-pressure deuterium and could provide insights on the future investigation of supersolid phases in real materials.

cond-mat.mtrl-sci↗

arXiv2020

Attenuating the fermion sign problem in path integral Monte Carlo simulations using the Bogoliubov inequality and thermodynamic integration

Accurate thermodynamic simulations of correlated fermions using path integral Monte Carlo (PIMC) methods are of paramount importance for many applications such as the description of ultracold atoms, electrons in quantum dots, and warm-dense matter. The main obstacle is the fermion sign problem (FSP), which leads to an exponential increase in computation time both with increasing the system-size and with decreasing temperature. Very recently, Hirshberg et al. [J. Chem. Phys. 152, 171102 (2020)] have proposed to alleviate the FSP based on the Bogoliubov inequality. In the present work, we extend this approach by adding a parameter that controls the perturbation, allowing for an extrapolation to the exact result. In this way, we can also use thermodynamic integration to obtain an improved estimate of the fermionic energy. As a test system, we choose electrons in 2D and 3D quantum dots and find in some cases a speed-up exceeding 10^6 , as compared to standard PIMC, while retaining a relative accuracy of $\sim0.1\%$. Our approach is quite general and can readily be adapted to other simulation methods.

physics.comp-ph↗

arXiv2020

Metadynamics of paths

We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time correlation functions are conveniently computed via reweighted averages along a single trajectory and kinetic rates are accessed at no additional cost. These abilities are illustrated analyzing a model potential and the umbrella inversion of NH$_3$ in water. The algorithm allows a parallel implementation and promises to be a powerful tool for the study of rare events.

physics.comp-ph↗

arXiv2020

Path Integral Molecular Dynamics for Fermions: Alleviating the Sign Problem with the Bogoliubov Inequality

We present a method for performing path integral molecular dynamics (PIMD) simulations for fermions and address its sign problem. PIMD simulations are widely used for studying many-body quantum systems at thermal equilibrium. However, they assume that the particles are distinguishable and neglect bosonic and fermionic exchange effects. Interacting fermions play a key role in many chemical and physical systems, such as electrons in quantum dots and ultracold trapped atoms. A direct sampling of the fermionic partition function is impossible using PIMD since its integrand is not positive definite. We show that PIMD simulations for fermions are feasible by employing our recently developed method for bosonic PIMD and reweighting the results to obtain fermionic expectation values. The approach is tested against path integral Monte Carlo (PIMC) simulations for up to 7 electrons in a two-dimensional quantum dot for a range of interaction strengths. However, like PIMC, the method suffers from the sign problem at low temperatures. We propose a simple approach for alleviating it by simulating an auxiliary system with a larger average sign and obtaining an upper bound to the energy of the original system using the Bogoliubov inequality. This allows fermions to be studied at temperatures lower than would otherwise have been feasible using PIMD, as demonstrated in the case of a three-electron quantum dot. Our results extend the boundaries of PIMD simulations of fermions and will hopefully stimulate the development of new approaches for tackling the sign problem.

physics.chem-ph↗

arXiv2019

Path Integral Molecular Dynamics for Bosons

Trapped Bosons exhibit fundamental physical phenomena and are potentially useful for quantum technologies. We present a method for simulating Bosons using path integral molecular dynamics. A main challenge for simulations is including all permutations due to exchange symmetry. We show that evaluation of the potential can be done recursively, avoiding explicit enumeration of permutations, and scales cubically with system size. The method is applied to Bosons in a 2D trap and agrees with essentially exact results. An analysis of the role of exchange with decreasing temperature is also presented.

cond-mat.quant-gas↗