MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations

Bolstered by recent calculations of exact functional-driven errors (FEs) and density-driven errors (DEs) of semi-local density functionals in the water dimer binding energy [Kanungo et al., J. Phys. Chem. Lett. 2023, 15, 323], we investigate approximate FEs and DEs in neutral water clusters containing up to 20 monomers, charged water clusters, and alkali- and halide-water clusters. Our proxy for the exact density is r2SCAN50, a 50% global hybrid of exact exchange with r2SCAN, which may be less correct than r2SCAN for the compact water monomer but importantly more correct for long-range electron transfers in the non-compact water clusters. We show that SCAN makes substantially larger FEs for neutral water clusters than r2SCAN, while both make essentially the same DEs. Unlike the case for barrier heights, these FEs are small in a relative sense, and become large in an absolute sense only due to an increase in cluster size. SCAN@HF produces a cancellation of errors that makes it chemically accurate for predicting the absolute binding energies of water clusters. Likewise, adding a long-range dispersion correction to r2SCAN@HF, as in the composite method HF-r2SCAN-DC4, makes its FE more negative than in r2SCAN@HF, permitting a near-perfect cancellation of FE and DE. r2SCAN by itself (and even more so, r2SCAN evaluated on the r2SCAN50 density), is almost perfect for the energy differences between water hexamers, and thus probably also for liquid water away from the boiling point. Thus the accuracy of composite methods like SCAN@HF and HF-r2SCAN-DC4 is not due to the HF density being closer to the exact density, but …

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in …

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in …

ACS Applied Materials & Interfaces

Wetting of a solid by a liquid is relevant for a broad range of natural and technological processes. This process is complex and involves the generation of heat, which is still poorly understood especially in nanoconfined systems. In this article, scanning transitiometry was used to measure and evaluate the pressure-driven heat of intrusion of water into solid ZIF-8 powder within the temperature range of 278.15–343.15 K. The conditions examined included the presence and absence of atmospheric gases, basic pH conditions, solid sample origins, and temperature. Simultaneously with these experiments, molecular dynamics simulations were conducted to elucidate the changing behavior of water as it enters into ZIF-8. The results are rationalized within a temperature-dependent thermodynamic cycle. This cycle describes the temperature-dependent process of ZIF-8 filling, heating, emptying, and cooling with respect to …

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in …

Bulletin of the American Physical Society

A39. 00001: Unconventional Error Cancellation Explains the Success of Hartree-Fock Density Functional Theory for Barrier Heights*

Journal of Chemical Theory and Computation

The evaluation of Fock exchange is often the computationally most expensive part of hybrid functional density functional theory calculations in a systematically improvable, complete basis. In this work, we employ a Tucker tensor based approach that substantially accelerates the evaluation of the action of Fock exchange by transforming three-dimensional convolutional integrals into a tensor product of one-dimensional convolution integrals. Our numerical implementation uses a parallelization strategy that balances the memory and communication bottlenecks, alongside overlapping compute and communication operations to enhance computational efficiency and parallel scalability. The accuracy and computational efficiency are demonstrated on various systems, including Pt clusters of various sizes and a TiO2 cluster with 3684 electrons.

Physical Review C

A study of prompt Ξ c+ production in proton-lead collisions is performed with the LHCb experiment at a center-of-mass energy per nucleon pair of 8.16 TeV in 2016 in p Pb and Pb p collisions with an estimated integrated luminosity of approximately 12.5 and 17.4 nb− 1, respectively. The Ξ c+ production cross section, as well as the Ξ c+ to Λ c+ production cross-section ratio, are measured as a function of the transverse momentum and rapidity and compared to the latest theory predictions. The forward-backward asymmetry is also measured as a function of the Ξ c+ transverse momentum. The results provide strong constraints on theoretical calculation and are a unique input for hadronization studies in different collision systems.

The Journal of Physical Chemistry Letters

Heat and the work of compression/decompression are among the basic properties of thermodynamic systems. Being relevant to many industrial and natural processes, this thermomechanical energy is challenging to tune due to fundamental boundaries for simple fluids. Here via direct experimental and atomistic observations, we demonstrate, for fluids consisting of nanoporous material and a liquid, one can overcome these limitations and noticeably affect both thermal and mechanical energies of compression/decompression exploiting preferential intrusion of water from aqueous solutions into subnanometer pores. We hypothesize that this effect is due to the enthalpy of dilution manifesting itself as the aqueous solution concentrates upon the preferential intrusion of pure water into pores. We suggest this genuinely subnanoscale phenomenon can be potentially a strategy for controlling the thermomechanical energy …

Acta Materialia

Understanding solute segregation thermodynamics is the first step in investigating grain boundary (GB) properties, such as strong yttrium (Y) effects on grain growth and texture evolution in micro-scale polycrystalline magnesium (Mg) alloys. To estimate the average GB segregation behavior in low-solute-concentration Mg alloys (eg, 2 at.% Y), a state-of-the-art spectral approach is applied based on a per-site segregation energy spectrum for Y solute atoms at zero K obtained from molecular statistics (MS) simulations of∼ 1 0 4 GB sites in Mg symmetric tilt GBs (STGBs). Although selected MS simulation results are consistent with verification by density functional theory (DFT) calculations, estimates of average segregation tendency based on the zero-K energy spectrum deviate from experimental observations. To resolve this problem, thermodynamic integration (TI) methods based on molecular dynamics (MD …

arXiv preprint arXiv:2404.05200

Are quasicrystals stable or metastable? Density functional theory (DFT) is often used to evaluate thermodynamic stability, but quasicrystals are long-range aperiodic and their energies cannot be calculated using conventional ab initio methods. Here, we perform first-principles calculations on quasicrystal nanoparticles of increasing sizes, from which we can directly extrapolate their bulk and surface energies. Using this technique, we determine with high confidence that the icosahedral quasicrystals ScZn7.33 and YbCd5.7 are ground-state phases--revealing that translational symmetry is not a necessary condition for the T = 0 K stability of inorganic solids. Although we find the ScZn7.33 quasicrystal to be thermodynamically stable, we show on a mixed thermodynamic and kinetic phase diagram that its solidification from the melt is nucleation-limited, which illustrates why even stable materials may be kinetically challenging to grow. Our techniques here broadly open the door to first-principles investigations into the structure-bonding-stability relationships of aperiodic materials.

SOLAR RRL

Within one decade, lead halide perovskite solar cells have reached power conversion efficiencies (PCEs) compatible with that of silicon solar cells. While in the beginning, they suffered from short device lifetimes, those have also been strongly improved over time. However, their content of toxic lead still poses a risk of environmental pollution and human health on exposure. The double perovskite (DP) Cs2AgBiBr6 offers the potential to be a lead-free alternative lightharvesting material. Herein, the fabrication of hole transport material (HTM)-free Cs2AgBiBr6-based solar cells is presented, in which the DP surface is modified via a n-butylammonium posttreatment to create a 2D/3D mixed interface. Additionally, the commonly utilized metal electrode and HTM are substituted with a carbon black back electrode (CBE) consisting of up-cycled biowaste. Through the 2D/3D interface modification, charge recombination is suppressed, and band alignment is improved at the perovskite/CBE interface. Additionally, density functional theory calculations reveal that an increasing 2D modification thickness enhances the probability for holes in Cs2AgBiBr6 to be located close to the perovskite/CBE interface, further supporting their extraction. Overall, the PCE of the HTM-free solar cells is improved through the implementation of a low-cost and end-of-waste fabrication strategy.

Advanced Materials

Perovskite solar cells (PSCs) have attracted great attention in the past few years due to their rapid increase in efficiency and low‐cost fabrication. However, instability against thermal stress and humidity is a big issue hindering their commercialization and practical applications. Here, by combining thermally stable formamidinium–cesium‐based perovskite and a moisture‐resistant carbon electrode, successful fabrication of stable PSCs is reported, which maintain on average 77% of the initial value after being aged for 192 h under conditions of 85 °C and 85% relative humidity (the “double 85” aging condition) without encapsulation. However, the mismatch of energy levels at the interface between the perovskite and the carbon electrode limits charge collection and leads to poor device performance. To address this issue, a thin‐layer of poly(ethylene oxide) (PEO) is introduced to achieve improved interfacial energy …

Journal of High Energy Physics

The production of prompt D+ and mesons is studied in proton-lead collisions at a centre-of-mass energy of= 5. 02 TeV. The data sample corresponding to an integrated luminosity of (1. 58±0. 02) nb− 1 is collected by the LHCb experiment at the LHC. The differential production cross-sections are measured using D+ and candidates with transverse momentum in the range of 0< p T< 14 GeV/c and rapidities in the ranges of 1. 5< y∗< 4. 0 and–5. 0< y∗<–2. 5 in the nucleon-nucleon centre-of-mass system. For both particles, the nuclear modification factor and the forward-backward production ratio are determined. These results are compared with theoretical models that include initial-state nuclear effects. In addition, measurements of the cross-section ratios between D+, and D 0 mesons are presented, providing a baseline for studying the charm hadronization in lead-lead collisions at LHC energies.

arXiv preprint arXiv:2403.14073

This work introduces Extent of Violation Indices (EVIs), a novel metric for quantifying how well exchange-correlation functionals adhere to local conditions. Applying EVIs to a diverse set of molecules for GGA functionals reveals widespread violations, particularly for semi-empirical functionals. We leverage EVIs to explore potential connections between these violations and errors in chemical properties. While no correlation is observed for atomization energies, a link emerges between EVIs and total energies. Similarly, the analysis of reaction energies suggests weak positive correlations for specific conditions, but definitive conclusions about error cancellation require advancements in both functional accuracy and our understanding of cancellation mechanisms. Overall, this study highlights EVIs as a powerful tool for analyzing functional behavior and adherence to local conditions, paving the way for future research to fully elucidate the impact of violations on energy errors.

arXiv preprint arXiv:2403.19035

MiMiC is a framework for performing multiscale simulations, where individual subsystems are handled at different resolutions and/or levels of theory by loosely coupled external programs. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

arXiv preprint arXiv:2403.19035

MiMiC is a framework for performing multiscale simulations, where individual subsystems are handled at different resolutions and/or levels of theory by loosely coupled external programs. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

arXiv preprint arXiv:2403.19035

MiMiC is a framework for performing multiscale simulations, where individual subsystems are handled at different resolutions and/or levels of theory by loosely coupled external programs. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

arXiv preprint arXiv:2403.19035

MiMiC is a framework for performing multiscale simulations, where individual subsystems are handled at different resolutions and/or levels of theory by loosely coupled external programs. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

arXiv preprint arXiv:2403.19035

MiMiC is a framework for performing multiscale simulations, where individual subsystems are handled at different resolutions and/or levels of theory by loosely coupled external programs. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.