Parameterization of a reactive force field using a Monte Carlo algorithm

Abstract Parameterization of a Molecular Dynamics force field is essential in realistically modelling the physico-chemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single parameter parabolic-search algorithm. In this study, we use a robust Metropolis Monte-Carlo algorithm with Simulated Annealing (MMC-SA) to search for the optimum parameters for the ReaxFF force field in a high-dimensional parameter space. The optimization is done against a set of quantum chemical data for M gSO 4 hydrates. The optimized force field reproduced the chemical structures, the Equations of State and the water binding curves of M gSO 4 hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable

A DFT based equilibrium study on the hydrolysis and the dehydration reactions of MgCl 2

Magnesium chloride hydrates are characterized as promising energy storage materials in the builtenvironment. During the dehydration of these materials, there are chances for the release of harmful HCl gas, which can potentially damage the material as well as the equipment. Hydrolysis reactions in magnesium chloride hydrates are subject of study for industrial applications. However, the information about the possibility of hydrolysis reaction, and its preference over dehydration in energy storage systems is still ambiguous at the operating conditions in a seasonal heat storage system. A density functional theory level study is performed to determine molecular structures, charges, and harmonic frequencies in order to identify the formation of HCl at the operating temperatures in an energy storage system. The preference of hydrolysis over dehydration is quantified by applying thermodynamic equilibrium principles by calculating Gibbs free energies of the hydrated magnesium chloride molecules. The molecular structures of the hydrates (n = 0, 1, 2, 4, and 6) of MgCl2 are investigated to understand the stability and symmetry of these molecules. The structures are found to be noncomplex with almost no meta-stable isomers, which may be related to the faster kinetics observed in the hydration of chlorides compared to sulfates. Also, the frequency spectra of these molecules are calculated, which in turn are used to calculate the changes in Gibbs free energy of dehydration and hydrolysis reactions. From these calculations, it is found that the probability for hydrolysis to occur is larger for lower hydrates. Hydrolysis occurring from the hexa-, tetra-, and dihydrate is only possible when the temperature is increased too fast to a very high value. In the case of the mono-hydrate, hydrolysis may become favorable at high water vapor pressure and at low HCl pressure

LiMeS-Lab:An Integrated Laboratory for the Development of Liquid–Metal Shield Technologies for Fusion Reactors

The liquid metal shield laboratory (LiMeS-Lab) will provide the infrastructure to develop, test, and compare liquid metal divertor designs for future fusion reactors. The main research topics of LiMeS-lab will be liquid metal interactions with the substrate material of the divertor, the continuous circulation and capillary refilling of the liquid metal during intense plasma heat loading and the retention of plasma particles in the liquid metal. To facilitate the research, four new devices are in development at the Dutch Institute for Fundamental Energy Research and the Eindhoven University of Technology: LiMeS-AM: a custom metal 3D printer based on powder bed fusion; LiMeS-Wetting, a plasma device to study the wetting of liquid metals on various substrates with different surface treatments; LiMeS-PSI, a linear plasma generator specifically adapted to operate continuous liquid metal loops. Special diagnostic protection will also be implemented to perform measurements in long duration shots without being affected by the liquid metal vapor; LiMeS-TDS, a thermal desorption spectroscopy system to characterize deuterium retention in a metal vapor environment. Each of these devices has specific challenges due to the presence and deposition of metal vapors that need to be addressed in order to function. In this paper, an overview of LiMeS-Lab will be given and the conceptual designs of the last three devices will be presented.</p

Phosphatase and tensin homologue: a therapeutic target for SMA

Spinal muscular atrophy (SMA) is one of the most common juvenile neurodegenerative diseases, which can be associated with child mortality. SMA is caused by a mutation of ubiquitously expressed gene, Survival Motor Neuron1 (SMN1), leading to reduced SMN protein and the motor neuron death. The disease is incurable and the only therapeutic strategy to follow is to improve the expression of SMN protein levels in motor neurons. Significant numbers of motor neurons in SMA mice and SMA cultures are caspase positive with condensed nuclei, suggesting that these cells are prone to a process of cell death called apoptosis. Searching for other potential molecules or signaling pathways that are neuroprotective for central nervous system (CNS) insults is essential for widening the scope of developmental medicine. PTEN, a Phosphatase and Tensin homologue, is a tumor suppressor, which is widely expressed in CNS. PTEN depletion activates anti-apoptotic factors and it is evident that the pathway plays an important protective role in many neurodegenerative disorders. It functions as a negative regulator of PIP3/AKT pathway and thereby modulates its downstream cellular functions through lipid phosphatase activity. Moreover, previous reports from our group demonstrated that, PTEN depletion using viral vector delivery system in SMN delta7 mice reduces disease pathology, with significant rescue on survival rate and the body weight of the SMA mice. Thus knockdown/depletion/mutation of PTEN and manipulation of PTEN medicated Akt/PKB signaling pathway may represent an important therapeutic strategy to promote motor neuron survival in SMA

Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCF^Slmb degron

Spinal muscular atrophy (SMA) is caused by homozygous mutations in human SMN1. Expression of a duplicate gene (SMN2) primarily results in skipping of exon 7 and production of an unstable protein isoform, SMNΔ7. Although SMN2 exon skipping is the principal contributor to SMA severity, mechanisms governing stability of survival motor neuron (SMN) isoforms are poorly understood. We used a Drosophila model system and label-free proteomics to identify the SCFSlmb ubiquitin E3 ligase complex as a novel SMN binding partner. SCFSlmb interacts with a phosphor degron embedded within the human and fruitfly SMN YG-box oligomerization domains. Substitution of a conserved serine (S270A) interferes with SCFSlmb binding and stabilizes SMNΔ7. SMA-causing missense mutations that block multimerization of full-length SMN are also stabilized in the degron mutant background. Overexpression of SMNΔ7S270A, but not wild-type (WT) SMNΔ7, provides a protective effect in SMA model mice and human motor neuron cell culture systems. Our findings support a model wherein the degron is exposed when SMN is monomeric and sequestered when SMN forms higher-order multimers

Modeling thermochemical reactions in thermal energy storage systems

The focus of this chapter is mainly on molecular modeling techniques for the hydration and dehydration (sorption and desorption) processes occurring in salt hydrates at the nano-scale. Modeling techniques such as density function theory, molecular dynamics and monte carlo are briefly introduced. Some attention is also given to micro- and macro-scale modeling techniques used at larger length scales, such as Mampel's model and the continuum approach. Before introducing all the length (and time) scales involved when modeling a heat storage system, a qualitative description is given of the hydration and dehydration processes on the nano/micro-scale

Advanced Numerical Modelling Techniques to Tune the Properties of Heat Storage Materials for Optimal Reactor Performance

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First-principles study of chemical mixtures of CaCl2 and MgCl2 hydrates for optimized seasonal heat storage

Chloride-based salt hydrates form a promising class of thermochemical materials (TCMs), having high storage capacity and fast kinetics. In the charging cycles of these hydrates however hydrolysis might appear along with dehydration. The HCl produced during the hydrolysis degrades and corrodes the storage system. Our GGA-DFT results show that the enthalpy charge during proton formation (an important step in hydrolysis) is much higher for CaCl2·2H2O (33.75 kcal/mol) than for MgCl2·2H2O (19.55 kcal/mol). This is a strong indicator that hydrolysis can be minimized by appropriate chemical mixing of CaCl2 and Mg Cl2 hydrates, which is also confirmed by recent experimental studies. GGA-DFT calculations were performed to obtain and analyze the optimized structures, charge distributions, bonding indicators and harmonic frequencies of various chemical mixtures hydrates and compared them to their elementary salts hydrates. We have further assessed the equilibrium products concentration of dehydration/hydrolysis of the chemical mixtures under a wide range of operating conditions. We observed that chemical mixing leads to an increase of the onset hydrolysis temperature with a maximum value of 79 K, thus increasing the resistance against hydrolysis with respect to the elementary salt hydrates. We also found that the chemical mixing of CaCl2 and MgCl2 hydrates widens the operating dehydration temperature range by a maximum value of 182 K (CaMg2Cl6·2H2O) and lowers the binding enthalpy with respect to the physical mixture by ≈65 kcal/mol for TCM based heat storage systems

First-Principles Study of Chemical Mixtures of CaCl₂ and MgCl₂ Hydrates for Optimized Seasonal Heat Storage

Chloride-based salt hydrates form a promising class of thermochemical materials (TCMs), having high storage capacity and fast kinetics. In the charging cycles of these hydrates however hydrolysis might appear along with dehydration. The HCl produced during the hydrolysis degrades and corrodes the storage system. Our GGA-DFT results show that the enthalpy charge during proton formation (an important step in hydrolysis) is much higher for CaCl₂·2H₂O (33.75 kcal/mol) than for MgCl₂·2H₂O (19.55 kcal/mol). This is a strong indicator that hydrolysis can be minimized by appropriate chemical mixing of CaCl₂ and Mg Cl₂ hydrates, which is also confirmed by recent experimental studies. GGA-DFT calculations were performed to obtain and analyze the optimized structures, charge distributions, bonding indicators and harmonic frequencies of various chemical mixtures hydrates and compared them to their elementary salts hydrates. We have further assessed the equilibrium products concentration of dehydration/hydrolysis of the chemical mixtures under a wide range of operating conditions. We observed that chemical mixing leads to an increase of the onset hydrolysis temperature with a maximum value of 79 K, thus increasing the resistance against hydrolysis with respect to the elementary salt hydrates. We also found that the chemical mixing of CaCl₂ and MgCl₂ hydrates widens the operating dehydration temperature range by a maximum value of 182 K (CaMg₂Cl₆·2H₂O) and lowers the binding enthalpy with respect to the physical mixture by ≈65 kcal/mol for TCM based heat storage systems