Machine Learning for Screening Large Organic Molecules

Organic semiconductors are promising materials for cheap, scalable and sustainable electronics, light-emitting diodes and photovoltaics. For organic photovoltaic cells, it is a challenge to find compounds with suitable properties in the vast chemical compound space. For example, the ionization energy should fit to the optical spectrum of sun light, and the energy levels must allow efficient charge transport. Here, a machine-learning model is developed for rapidly and accurately estimating the HOMO and LUMO energies of a given molecular structure. It is build upon the SchNet model (Sch\"utt et al. (2018)) and augmented with a `Set2Set' readout module (Vinyals et al. (2016)). The Set2Set module has more expressive power than sum and average aggregation and is more suitable for the complex quantities under consideration. Most previous models have been trained and evaluated on rather small molecules. Therefore, the second contribution is extending the scope of machine-learning methods by adding also larger molecules from other sources and establishing a consistent train/validation/test split. As a third contribution, we make a multitask ansatz to resolve the problem of different sources coming at different levels of theory. All three contributions in conjunction bring the accuracy of the model close to chemical accuracy.Comment: Presented at E-MRS Fall Meeting 2022, Symposium

Molecular Dynamics Simulations of Lead and Lithium in Liquid Phase

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. Extracting dynamic and structural properties of liquid LiPb mixtures via molecular dynamics simulations, represent a crucial step for multiscale modeling efforts in order to understand the suitability of this compound for future Nuclear Fusion technologies. At present a Li-Pb cross potential is not available in the literature. Here we present our first results on the validation of two semi-empirical potentials for Li and Pb in liquid phase. Our results represent the establishment of a solid base as a previous but crucial step to implement a LiPb cross potential. Structural and thermodynamical analyses confirm that the implemented potentials for Li and Pb are realistic to simulate both elements in the liquid phase

Adding a New Dimension to DNA Melting Curves.

to be published in Europhysics LettersInternational audienceStandard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting curves of short DNA sequences by allowing us to record the degree of opening in several positions along the molecule all at once. This adds the spatial dimension to the melting curves and allows a precise investigation of the role of the base-pair sequence on the fluctuations and denaturation of the DNA double helix. We illustrate the power of the method by investigating the influence of an AT rich region on the fluctuations of neighboring domains

New simulations to qualify eutectic lithium-lead as breeder material

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues is the problem of liquid metals breeder blanket behavior. The knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT =f(PT ), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Atomistic simulations of liquids can provide much information; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to a deeper understandin

Quantum molecular dynamics and ab initio studies of the crystal structure of hydrogen and deuterium

Hydrogen isotopes play a critical role both in inertial and magnetic confinemen Nuclear Fusion. Since the preferent fuel needed for this technology is a mixture of deuterium and tritium. The study of these isotopes particularly at very low temperatures carries a technological interest in other applications. The present line promotes a deep study on the structural configuration that hydrogen and deuterium adopt at cryogenic temperatures and at high pressures. Typical conditions occurring in present Inertial Fusion target designs. Our approach is aims to determine the crystal structure characteristics, phase transitions and other parameters strongly correlated to variations of temperature and pressure

Nanocrystals in the manufacture of target for inertial confinement fusion

Systems inertial confinement fusion (ICF) need of a manufacturing process targets very accurate and efficient (Fig. A). Due to the frequency needed for energy production techniques are necessary to achieve high repetition rates, however it is also necessary to increase or maintain the quality and efficiency of these targets. In order to observe more resolution possible problems in the target manufacture (B), we propose the following theoretical methodology, by means of which analyze different phenomena present in the conditions which are fabrication and handled deuterium tritium target spheres (DT ice). Recent experiments show that addition of instabilities caused by the geometry of the solid layer of DT ice (C), and the cover (ablator), one can relate the loss of power delivery in the implosion due to different conformations of the solid layers with regarding handling conditions

Influence of termal fluctuations in radiation damage cascade production and defect dynamics in tungsten

The detailed study of the deterioration suffered by the materials of the components of a nuclear facility, in particular those forming part of the reactor core, is a topic of great interest which importance derives in large technological and economic implications. Since changes in the atomic-structural properties of relevant components pose a risk to the smooth operation with clear consequences for security and life of the plant, controlling these factors is essential in any development of engineering design and implementation. In recent times, tungsten has been proposed as a structural material based on its good resistance to radiation, but still needs to be done an extensive study on the influence of temperature on the behavior of this material under radiation damage. This work aims to contribute in this regard. Molecular Dynamics (MD) simulations were carried out to determine the influence of temperature fluctuations on radiation damage production and evolution in Tungsten. We have particularly focused our study in the dynamics of defect creation, recombination, and diffusion properties. PKA energies were sampled in a range from 5 to 50 KeV. Three different temperature scenarios were analyzed, from very low temperatures (0-200K), up to high temperature conditions (300-500 K). We studied the creation of defects, vacancies and interstitials, recombination rates, diffusion properties, cluster formation, their size and evolution. Simulations were performed using Lammps and the Zhou EAM potential for

Can one predict DNA Transcription Start Sites by studying bubbles?

It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated.Comment: 4 pages, 3 figures, accepted for publication in physical review letter

Molecular dynamics simulations of lead and lithium in liquid phase

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. Extracting dynamic and structural properties of liquid LiPb mixtures via molecular dynamics simulations, represent a crucial step for multiscale modeling efforts in order to understand the suitability of this compound for future Nuclear Fusion technologies. At present a Li-Pb cross potential is not available in the literature. Here we present our first results on the validation of two semi-empirical potentials for Li and Pb in liquid phase. Our results represent the establishment of a solid base as a previous but crucial step to implement a LiPb cross potential. Structural and thermodynamical analyses confirm that the implemented potentials for Li and Pb are realistic to simulate both elements in the liquid phase

Liquid lead and Lithium. A Comprehensive molecular dynamics study

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues in these programs is the problem of liquid metals breeder blanket behavior. Structural material of the blanket should meet high requirements because of extreme operating conditions. Therefore the knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT=f(PT), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Simulations of liquids can provide much information to the community; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to lead to the deeper understanding and better predictive behavior