DFT molecular dynamics and free energy analysis of a charge density wave surface system

This Accepted Manuscript will be available for reuse under a CC BY-NC-ND licence after 24 months of embargo periodThe K/Si(111):B 3×3 surface, with one K atom per 3×3 unit cell, is considered a prototypical case of a surface Mott phase at room temperature. Our Density Functional Theory (DFT) Molecular Dynamics (MD) and free energy calculations show, however, a 23×3 Charge Density Wave (CDW) ground state. Our analysis shows that at room temperature the K atoms easily diffuse along the lines of a honeycomb network on the surface and that the 3×3 phase appears as the result of the dynamical fluctuations between degenerate CDW states. DFT-MD free energy calculations also show a 23×3↔3×3 transition temperature below 90 K. The competing electron-electron and electron-phonon interactions at low temperature are also analyzed; using DFT calculations, we find that the electron-phonon negative-U * is larger than the electron-electron Hubbard U, indicating that the CDW survives at very low temperatureThis work was supported by grant nos. MAT2014-59966-R and MAT2017-88258-R from the Ministerio de Economía, Industria y Competitividad (Spain

Two-step ATP-driven opening of cohesin head.

The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the “head” structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.post-print4709 K

Significance of nuclear quantum effects in hydrogen bonded molecular chains

In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of {\pi}-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to new electronic in-gap states localized at the ends. These findings demonstrate the identification of a new class of isomeric hydrogen bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. We anticipate that this work will open new research directions towards the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling

Macrociclos funcionales multicomponente ensamblados mediante enlace de hidrógeno

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Física Teórica de la Materia Condensada. Fecha de lectura: 12-05-202

Medidas preventivas centradas en la interfaz urbano-rural protegen a las comunidades rurales productoras de alimentos del SARS-CoV-2

Introduction: Rural food-producing communities are fundamental for the development of economic activities associated with sustainability and food security. However, despite the importance of rurality in Colombia, preventive strategies continue to be implemented homogeneously, without considering the dynamics of SARS-CoV-2 in rural food-producing communities.Objective: To model real areas in Colombia involving rural and urban populations that have intrinsic SARS-CoV-2 transmission dynamics. Characterize rural-urban interactions by means of a parameter that provides different scenarios and allows us to identify interactions capable of preventing SARS-CoV-2 transmission in rural food-producing communities.Materials and methods: The dynamics of SARS-CoV-2 infection was modeled in five case studies (Boyacá, Caquetá, Cundinamarca, Santander and Sucre) considering urban and rural areas and their interaction (connectivity) in the urban-rural interface. For this purpose, an epidemiological compartmental model considering a classification of individuals according to their economic activity and their epidemiological status was assessed. Results: Preventive measures focused on the urban-rural interface impact the number of deaths in rural areas. Hence, it is possible to assume that the dynamics of the disease in rural areas depend on the constant interaction with infected individuals from urban areas, which occurs due to the food production dynamics in the urban-rural interface. Conclusions: Preventive measures should focus on places of high transmissibility and risk for rural communities, such as the urban-rural interface. This work highlights the importance of national heterogeneous preventive measures and the protection of rural communities from the social and economic impacts of SARS-CoV-2.Introducción. Las comunidades rurales productoras de alimentos son fundamentales para el desarrollo de actividades económicas asociadas a la sostenibilidad y la seguridad alimentaria. Sin embargo, a pesar de la importancia de la ruralidad en Colombia, las estrategias de prevención continúan siendo implementadas homogéneamente, sin considerar la dinámica del SARS-CoV-2 en estas comunidades.Objetivo. Modelar la dinámica del SARS-CoV-2 en poblaciones rurales colombianas. Se quiso caracterizar la interacción rural-urbana mediante un parámetro que proporciona diferentes contextos y permite identificar una interacción rural-urbana capaz de prevenir la transmisión del SARS-CoV-2 en comunidades rurales productoras de alimentos. Materiales y métodos. La dinámica de transmisión del SARS-CoV-2 se modeló en cinco estudios de caso (Boyacá, Caquetá, Cundinamarca, Santander y Sucre) considerando áreas urbanas y rurales, así como su interacción (conectividad) en la interfaz urbanorural. Para ello, se empleó un modelo epidemiológico compartimental que considera una clasificación de los individuos según su actividad económica y su estado epidemiológico. Resultados. Las medidas preventivas enfocadas en la interfaz urbano-rural impactan el número de muertes en áreas rurales. Por lo tanto, es posible asumir que la dinámica de la enfermedad en las áreas rurales depende del contacto constante con los individuos infectados de las áreas urbanas, lo que ocurre debido a la dinámica de los sistemas de producción de alimentos en la interfaz urbano-rural.Conclusiones. Las medidas de prevención deben enfocarse en lugares con gran transmisibilidad y riesgo para las comunidades rurales, como la interfaz urbano-rural. En este trabajo se destaca la importancia de las medidas preventivas heterogéneas y la protección de las comunidades rurales contra los impactos sociales y económicos del SARS-CoV-2

Mulliken-Dipole Population Analysis

Atomic charge is one of the most important concepts in Chemistry. Mulliken population analysis is historically the most important method to calculate atomic charges and is still widely used. One basic hypothesis of this method is the half-and-half partition of the overlap populations, Q(μ, v), into equal charges in orbitals μ and v. This partition preserves the monopole moment of the overlap density but, other than that, is arbitrary. In this work we derive a new population analysis (which we designate Mulliken-Dipole population analysis) based on the conservation of both the monopole moment and the dipole moment along the bond direction. Test calculations show that the Mulliken-Dipole atomic charges are in accord to the chemical intuition; also they are very different from the Mulliken ones, being quite similar to the Hirshfeld atomic charges. Mulliken-Dipole atomic charges are conceptually appealing and very easy to calculate. In a further step, we also show how this Mulliken-Dipole population analysis can be used to derive atomic charges for atomistic simulations that reproduce the total dipole moment of the molecule, yielding at the same time a good description of the local charges and dipole moments for the molecular fragments.<br /

Effect of traditional and modern culinary processing, bioaccessibility, biosafety and bioavailability of eritadenine, a hypocholesterolemic compound from edible mushrooms

Eritadenine is a hypocholesterolemic compound that is found in several mushroom species such as Lentinula edodes, Marasmius oreades, and Amanita caesarea (1.4, 0.7 and 0.6 mg per g dry weight, respectively). It was synthesized during all developmental stages, being present in higher concentrations in the skin of shiitake fruiting bodies. When subjected to traditional cooking, grilling followed by frying were more adequate methodologies than boiling or microwaving to maintain its levels. Modern culinary processes such as texturization (with agar-agar) and spherification (with alginate) also interfered with its release. Grilling and gelling using gelatin enhanced eritadenine's bioaccessibility in an in vitro digestion model. An animal model (where male and female rats were administered 21 and 10 mg per kg animal per day of eritadenine) indicated that intake of the compound was safe under these concentrations; it reached the liver and reduced the atherogenic index (TC/HDL) in rat sera. Thus, it might be used to design a functional food.This research was supported by a national R&D program from the Spanish Ministry of Science and Innovation (project AGL2014-56211-R) and a regional program from the Community of Madrid, Spain (S2013/ABI-2728).Peer reviewe

Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA

A double proton transfer reaction in a guanine-cytosine (GC) base pair has been proposed as a possible mechanism for rare tautomer (G*C*) formation and thus a source of spontaneous mutations. We analyze this system with free energy calculations based on extensive Quantum Mechanics/Molecular Mechanics simulations to properly consider the influence of the DNA biomolecular environment. We find that, although the G*C* rare tautomer is metastable in the gas phase, it is completely unstable in the conditions found in cells. Thus, our calculations show that a double proton reaction cannot be the source of spontaneous point mutations. We have also analyzed the intrabase H transfer reactions in guanine. Our results show that the DNA environment gives rise to a large free energy difference between the rare and canonical tautomers. These results show the key role of the DNA biological environment for the stability of the genetic code.pre-print19829 K