arXiv subjects

Hossam Elgabarty

Publications and source records attributed to Hossam Elgabarty.

12 recordsLinked to original sources

arXiv2026

CP2K: An electronic structure and molecular dynamics software package - Dynamics, Transport, and Spectroscopic Response

One of the distinguishing aspects of CP2K is its seamless integration of diverse structural and transition-state optimization techniques with advanced sampling approaches including Monte Carlo, molecular dynamics, and metadynamics, enabling the efficient exploration of complex potential- and free-energy landscapes, including rare events. These capabilities are combined with a broad hierarchy of energy and force evaluation methods, ranging from classical and machine-learned interaction potentials and mixed quantum-classical multiscale and semiempirical schemes, to highly accurate quantum-mechanical electronic-structure approaches. At the heart of the latter lies the Gaussian and plane-wave framework, along with its augmented all-electron generalization, which have been described in detail in our previous code review [T. D. K\"uhne et al., J. Chem. Phys. 152, 194103 (2020)]. Building on this foundation, the present work revisits the methods within CP2K that turn electronic structure into dynamics, transport, and spectroscopic response. Particular emphasis is placed on the coupling between static response calculations and nuclear motion: spectra may be evaluated at optimized structures, averaged over thermally sampled configurations, obtained from time-correlation functions along ab-initio or path integral molecular trajectories, or followed in real time together with electronic and nuclear dynamics. The same modular structure also enables equilibrium and biased transport simulations, from Kubo-type linear response to open-boundary approaches under external potentials, highlighting CP2K's unique capability to unify quantum chemistry with quantum and statistical mechanics within a versatile, holistic simulation environment.

physics.chem-ph↗

arXiv2026

Terahertz-induced local-field dynamics and transient birefringence in aqueous electrolytes

Terahertz Kerr-effect (TKE) spectroscopy provides a time-domain optical probe of the intermolecular structural dynamics of liquids, but the measured birefringence can only be interpreted microscopically if transient molecular structure, local electric fields, and nonlinear optical response are treated on the same footing. We combine terahertz-driven non-equilibrium molecular dynamics with a hyperpolarizability-enhanced dipole-induced-dipole (DID) response model to connect the measured TKE signal of water and aqueous electrolytes to molecular-scale hydration dynamics. Starting from a multipolar expansion of the field-dependent molecular energy, the optical response is written as a differential polarizability in which first and second molecular hyperpolarizabilities are coupled to the instantaneous local field generated by the evolving liquid structure. For neat water, these local-field terms convert an insufficiently structured intramolecular response into the experimentally observed bipolar TKE line shape. For aqueous MgCl2, polarizable force-field trajectories combined with the extended optical response reproduce the concentration-dependent enhancement of the negative birefringence, whereas non-polarizable trajectories yield the wrong trend. Species-resolved analysis assigns the high-concentration response to strongly field-polarized anions and, more importantly, to water molecules bridging cations and anions. The work identifies TKE birefringence as a sensitive readout of ion-hydration local-field dynamics and shows that induced polarization in both the trajectory and the optical response is required to recover the structural dynamics encoded in electrolyte TKE measurements.

physics.chem-ph↗

arXiv2026

Accelerated "on-the-fly" coupled-cluster path-integral molecular dynamics: Impact of nuclear quantum effects on an asymmetric proton

We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is based on our quantum ring-polymer contraction (qRPC) technique, in which the inexpensive Hartree-Fock potential is evaluated on the full ring-polymer, while the expensive coupled-cluster correction is evaluated on the centroid only. This qRPC decomposition is combined with a second-generation Car-Parrinello-like dynamics of the Hartree-Fock reference and a basis-consistent extrapolation of the coupled-cluster and de-excitation amplitudes. The combination of all three acceleration layers is essential for making correlated PIMD calculations feasible. We apply the method to a proton shared by water and formaldehyde. Relative to classical nuclei, nuclear quantum effects broaden covalent X--H bond-length distributions, reduce the bias of the shared proton toward formaldehyde, and shift the mean proton-transfer coordinate from 0.206 to 0.135A. The probability of finding the proton closer to formaldehyde decreases from 81.7$\%$ to 61.1$\%$. The corresponding nuclear magnetic shielding tensors show that electron correlation and nuclear quantum effects are of comparable magnitude and can act in opposite directions. These results demonstrate that predictive simulations of asymmetric hydrogen bonds require a simultaneous treatment of correlated electronic structure and nuclear quantum fluctuations.

physics.chem-ph↗

arXiv2025

The CP2K Program Package Made Simple

CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric crystalline solids, disordered amorphous glasses, and weakly interacting soft-matter systems in the liquid state and in solution. This review highlights CP2K's capabilities for computing both static and dynamical properties using quantum-mechanical and classical simulation methods. In contrast to the accompanying theory and code paper [J. Chem. Phys. 152, 194103 (2020)], the focus here is on the practical usage and applications of CP2K, with underlying theoretical concepts introduced only as needed.

physics.comp-ph↗

arXiv2025

Benchmarking semi-empirical quantum chemical methods on liquid water

Stimulated by the renewed interest and recent developments in semi-empirical quantum chemical (SQC) methods for noncovalent interactions, we examine the properties of liquid water at ambient conditions by means of molecular dynamics (MD) simulations, both with the conventional NDDO-type (neglect of diatomic differential overlap) methods, e.g. AM1 and PM6, and with DFTB-type (density-functional tight-binding) methods, e.g. DFTB2 and GFN-xTB. Besides the original parameter sets, some specifically reparametrized SQC methods (denoted as AM1-W, PM6-fm, and DFTB2-iBi) targeting various smaller water systems ranging from molecular clusters to bulk are considered as well. The quality of these different SQC methods for describing liquid water properties at ambient conditions are assessed by comparison to well-established experimental data and also to BLYP-D3 density functional theory-based ab initio MD simulations. Our analyses reveal that static and dynamics properties of bulk water are poorly described by all considered SQC methods with the original parameters, regardless of the underlying theoretical models, with most of the methods suffering from too weak hydrogen bonds and hence predicting a far too fluid water with highly distorted hydrogen bond kinetics. On the other hand, the reparametrized force-matchcd PM6-fm method is shown to be able to quantitatively reproduce the static and dynamic features of liquid water, and thus can be used as a computationally efficient alternative to electronic structure-based MD simulations for liquid water that requires extended length and time scales. DFTB2-iBi predicts a slightly overstructured water with reduced fluidity, whereas AM1-W gives an amorphous ice-like structure for water at ambient conditions.

physics.comp-ph↗

arXiv2023

Ultrafast two-colour X-ray emission spectroscopy reveals excited state landscape in a base metal dyad

Effective photoinduced charge transfer makes molecular bimetallic assemblies attractive for applications as active light induced proton reduction systems. For a more sustainable future, development of competitive base metal dyads is mandatory. However, the electron transfer mechanisms from the photosensitizer to the proton reduction catalyst in base metal dyads remain so far unexplored. We study a Fe-Co dyad that exhibits photocatalytic H2 production activity using femtosecond X-ray emission spectroscopy, complemented by ultrafast optical spectroscopy and theoretical time-dependent DFT calculations, to understand the electronic and structural dynamics after photoexcitation and during the subsequent charge transfer process from the FeII photosensitizer to the cobaloxime catalyst. Using this novel approach, the simultaneous measurement of the transient Kalpha X-ray emission at the iron and cobalt K-edges in a two-colour experiment is enabled making it possible to correlate the excited state dynamics to the electron transfer processes. The methodology, therefore, provides a clear and direct spectroscopic evidence of the Fe->Co electron transfer responsible for the proton reduction activity.

physics.chem-ph↗

arXiv2022

Breaking the Exascale Barrier for the Electronic Structure Problem in Ab-Initio Molecular Dynamics

The non-orthogonal local submatrix method applied to electronic-structure based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32 mixed floating-point arithmetic when using 4,400 NVIDIA A100 GPUs of the Perlmutter system. This is enabled by a modification of the original method that pushes the sustained fraction of the peak performance to about 80%. Example calculations are performed for SARS-CoV-2 spike proteins with up to 83 million atoms.

physics.comp-ph↗

arXiv2022

Towards Electronic Structure-Based Ab-Initio Molecular Dynamics Simulations with Hundreds of Millions of Atoms

We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine learning potentials. We achieve this breakthrough by combining innovations in linear-scaling AIMD, efficient and approximate sparse linear algebra, low and mixed-precision floating-point computation on GPUs, and a compensation scheme for the errors introduced by numerical approximations. The core of our work is the non-orthogonalized local submatrix method (NOLSM), which scales very favorably to massively parallel computing systems and translates large sparse matrix operations into highly parallel, dense matrix operations that are ideally suited to hardware accelerators. We demonstrate that the NOLSM method, which is at the center point of each AIMD step, is able to achieve a sustained performance of 324 PFLOP/s in mixed FP16/FP32 precision corresponding to an efficiency of 67.7% when running on 1536 NVIDIA A100 GPUs.

physics.comp-ph↗

arXiv2021

Mixed-valence compounds as polarizing agents for Overhauser dynamic nuclear polarization in solids

In this paper we investigate a novel set of polarizing agents -- mixed-valence compounds -- by theoretical and experimental methods and demonstrate their performance in high-field Dynamic Nuclear Polarization (DNP) experiments in the solid state. Mixed-valence compounds constitute a group of molecules, in which molecular mobility persists even in solids. Consequently, such polarizing agents can be used to perform Overhauser-DNP experiments in solid-state, with favorable conditions for dynamic nuclear polarization formation at ultra-high magnetic fields.

cond-mat.other↗

arXiv2020

Energy Transfer within the Hydrogen Bonding Network of Water Following Resonant Terahertz Excitation

Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. Here, we investigate the dynamic energy flow in the hydrogen-bond network of liquid water by a pump-probe experiment. We resonantly excite intermolecular degrees of freedom with ultrashort single-cycle terahertz pulses and monitor its Raman response. By using ultrathin sample-cell windows, a background-free bipolar signal whose tail relaxes mono-exponentially is obtained. The relaxation is attributed to the molecular translational motions, using complementary experiments, force-field and ab initio molecular dynamics simulations. They reveal an initial coupling of the terahertz electric field to the molecular rotational degrees of freedom whose energy is rapidly transferred, within the excitation pulse duration, to the restricted-translational motion of neighboring molecules. This rapid energy transfer may be rationalized by the strong anharmonicity of the intermolecular interactions.

cond-mat.soft↗

arXiv2020

Tumbling with a Limp: Local Asymmetry in Water's Hydrogen Bond Network and its Consequences

Ab initio molecular dynamics simulations of liquid water under equilibrium ambient conditions, together with a novel energy decomposition analysis, have recently shown that a substantial fraction of water molecules exhibit a significant asymmetry between the strengths of the two donor and/or the two acceptor interactions. We refer to this recently unraveled aspect as the "local asymmetry in the hydrogen bond network". We discuss how this novel aspect was first revealed, and provide metrics that can be consistently employed on simulated water trajectories to quantify this local heterogeneity in the hydrogen bond network and its dynamics. We then discuss the static aspects of the asymmetry, pertaining to the frozen geometry of liquid water at any given instant of time and the distribution of hydrogen bond strengths therein, and also its dynamic characteristics pertaining to how fast this asymmetry decays and the kinds of molecular motions responsible for this decay. Following this we discuss the spectroscopic manifestations of this asymmetry, from ultrafast X-ray absorption spectra to infrared spectroscopy and down to the much slower terahertz regime. Finally, we discuss the implications of these findings in a broad context and its relation to the current notions about the structure and dynamics of liquid water.

cond-mat.dis-nn↗

arXiv2015

Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

physics.chem-ph↗