Comment on “Molecular origin of aging of pure Se glass: Growth of inter-chain structural correlations, network compaction, and partial ordering” [J. Chem. Phys. 146, 224506 (2017)]

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

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`Diet GMKTN55' Offers Accelerated Benchmarking Through a Representative Subset Approach

10.26434/chemrxiv.7038428.v2 ◽

2018 ◽

Author(s):

Tim Gould

Keyword(s):

Density Functional ◽

Chem Phys ◽

Comprehensive Analysis ◽

Genetic Approach ◽

Representative Subset ◽

Phys Chem Chem Phys

The GMTKN55 benchmarking protocol introduced by [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] allows comprehensive analysis and ranking of density functional approximations with diverse chemical behaviours. But this comprehensiveness comes at a cost: GMTKN55's 1500 benchmarking values require energies for around 2500 systems to be calculated, making it a costly exercise. This manuscript introduces three subsets of GMTKN55, consisting of 30, 100 and 150 systems, as `diet' substitutes for the full database. The subsets are chosen via a stochastic genetic approach, and consequently can reproduce key results of the full GMTKN55 database, including ranking of approximations.

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Porous Aluminophosphates as Adsorbents for the Separation of CO2/CH4 and CH4/N2 Mixtures – a Monte Carlo Simulation Study

10.26434/chemrxiv.6133346.v2 ◽

2018 ◽

Author(s):

Michael Fischer

Keyword(s):

Monte Carlo ◽

Landfill Gas ◽

Experimental Studies ◽

Chem Phys ◽

Monte Carlo Simulation Study ◽

Mixture Adsorption ◽

Vacuum Swing Adsorption ◽

Separation Of Co2 ◽

Pressure Swing ◽

Gcmc Simulations

<div>Aluminophosphates with zeolite-like topologies (AlPOs) have received considerable attention as potential adsorbents for use in the separation of methane-containing gas mixtures. Such separations, especially the removal of carbon dioxide and nitrogen from methane, are of great technological relevance in the context of the “upgrade” of natural gas, landfill gas, and biogas. While more than 50 zeolite frameworks have been synthesised in aluminophosphate composition or as heteroatom substituted AlPO derivatives, only a few of them have been characterised experimentally with regard to their adsorption and separation behaviour. In order to predict the potential of a variety of AlPO frameworks for applications in CO2/CH4 and CH4/N2 separations, atomistic grand-canonical Monte Carlo (GCMC) simulations were performed for 53 different structures. Building on previous work, which studied CO2/N2 mixture adsorption in AlPOs (M. Fischer, Phys. Chem. Chem. Phys., 2017, 19, 22801–22812), force field parameters for methane adsorption in AlPOs were validated through a comparison to available experimental adsorption data. Afterwards, CO2/CH4 and CH4/N2 mixture isotherms were computed for all 53 frameworks for room temperature and total pressures up to 1000 kPa (10 bar), allowing the prediction of selectivities and working capacities for conditions that are relevant for pressure swing adsorption (PSA) and vacuum swing adsorption (VSA). For CO2/CH4 mixtures, the GIS, SIV, and ATT frameworks were found to have the highest selectivities and CO2 working capacities under VSA conditions, whereas several frameworks, among them AFY, KFI, AEI, and LTA, show higher working capacities under PSA conditions. For CH4/N2 mixtures, all frameworks are moderately selective for methane over nitrogen, with ATV exhibiting a significantly higher selectivity than all other frameworks. While some of the most promising topologies are either not available in pure-AlPO4 composition or collapse upon calcination, others can be synthesised and activated, rendering them interesting candidates for future experimental studies. In addition to predictions of mixture adsorption isotherms, further simulations were performed for four selected systems in order to investigate the microscopic origins of the macroscopic adsorption behaviour, e.g. with regard to the very high CH4/N2 selectivity of ATV and the loading-dependent evolution of the heat of CO2 adsorption and CO2/CH4 selectivity of AEI and GME.</div>

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Babbitt’s Beguiling Surfaces, Improvised Inside; Part I: Freedoms

10.30535/smtv.5.1 ◽

2019 ◽

Vol 5 (1) ◽

Cited By ~ 1

Author(s):

Joshua Banks Mailman

Keyword(s):

Partial Ordering ◽

Personal Traits ◽

Milton Babbitt ◽

Iconic Figure ◽

Inside Part

Milton Babbitt has been a controversial and iconic figure, which has indirectly led to fallacious assumptions about how his music is made, and therefore to fundamental misconceptions about how it might be heard and appreciated. This video (the first of a three-part video essay) reconsiders his music in light of both his personal traits and a more precise examination of the constraints and freedoms entailed by his unusual and often misunderstood compositional practices, which are based inherently on partial ordering (as well as pitch repetition), which enables a surprising amount of freedom to compose the surface details we hear. The opening of Babbitt’s Composition for Four Instruments (1948) and three recompositions (based on re-ordering of pitches) demonstrate the freedoms intrinsic to partial ordering.

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Purines and Pyrimidines: Metabolism, Function and Potential as therapeutic options in neurodegenerative diseases

Current Protein and Peptide Science ◽

10.2174/1389203721999201208200605 ◽

2020 ◽

Vol 21 ◽

Author(s):

Debanjan Kundu ◽

Vikash Kumar Dubey

Keyword(s):

Neurodegenerative Diseases ◽

Neurodegenerative Disorders ◽

Protein Misfolding ◽

Molecular Mechanisms ◽

Treatment Regimens ◽

Loss Of Balance ◽

Current Scenario ◽

Unexplored Area ◽

Molecular Origin ◽

Purines And Pyrimidines

Abstract:: Various neurodegenerative disorders have molecular origin but some common molecular mechanisms. In the current scenario, there are very few treatment regimens present for advanced neurodegenerative diseases. In this context, there is an urgent need for alternate options in the form of natural compounds with an ameliorating effect on patients. There have been individual scattered experiments trying to identify potential values of various intracellular metabolites. Purines and Pyrimidines, which are vital molecules governing various aspects of cellular biochemical reactions, have been long sought as crucial candidates for the same, but there are still many questions that go unanswered. Some critical functions of these molecules associated with neuromodulation activities have been identified. They are also known to play a role in foetal neurodevelopment, but there is a lacuna in understanding their mechanisms. In this review, we have tried to assemble and identify the importance of purines and pyrimidines, connecting them with the prevalence of neurodegenerative diseases. The leading cause of this class of diseases is protein misfolding and the formation of amyloids. A direct correlation between loss of balance in cellular homeostasis and amyloidosis is yet an unexplored area. This review aims at bringing the current literature available under one umbrella serving as a foundation for further extensive research in this field of drug development in neurodegenerative diseases.

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Minimal distributions in a stochastic partial ordering and bounds for Gaussian processes

Journal of Applied Probability ◽

10.1017/s0021900200023780 ◽

1983 ◽

Vol 20 (03) ◽

pp. 529-536

Author(s):

W. J. R. Eplett

Keyword(s):

Gaussian Process ◽

Gaussian Processes ◽

Partial Ordering ◽

Boundary Crossing ◽

Conditional Probabilities ◽

Life Distribution ◽

Life Distributions ◽

Bounded Below ◽

Crossing Probabilities

A natural requirement to impose upon the life distribution of a component is that after inspection at some randomly chosen time to check whether it is still functioning, its life distribution from the time of checking should be bounded below by some specified distribution which may be defined by external considerations. Furthermore, the life distribution should ideally be minimal in the partial ordering obtained from the conditional probabilities. We prove that these specifications provide an apparently new characterization of the DFRA class of life distributions with a corresponding result for IFRA distributions. These results may be transferred, using Slepian's lemma, to obtain bounds for the boundary crossing probabilities of a stationary Gaussian process.

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