Advances in enhanced sampling along adaptive paths of collective variables

Study of complex activated molecular transitions by molecular dynamics (MD) simulation can be a daunting task, especially when little knowledge is available on the reaction coordinate describing the mechanism of the process. Here, we assess the path-metadynamics enhanced sampling approach in combination with force field and ab initio [density functional theory (DFT)] MD simulations of conformational and chemical transitions that require three or more collective variables (CVs) to describe the processes. We show that the method efficiently localizes the average transition path of each process and simultaneously obtains the free energy profile along the path. The new multiple-walker implementation greatly speeds-up the calculation, with an almost trivial scaling of the number of parallel replicas. Increasing the dimensionality by expanding the set of CVs leads to a less than linear increase in the computational cost, as shown by applying the method to a conformational change in increasingly longer polyproline peptides. Combined with DFT-MD to model acid (de-)protonation in explicit water solvent, the transition path and associated free energy profile were obtained in less than 100 ps of simulation. A final application to hydrogen fuel production catalyzed by a hydrogenase enzyme showcases the unique mechanistic insight and chemical understanding that can be obtained from the average transition path. Published by AIP Publishing

Primeros datos polínicos de la secuencia "fuentillejo-1" de la laguna del Maar de Fuentillejo (Campo de Calatrava, Ciudad Real)

XV lnternational A.P.L.E. Symposium of Palynolog

The non-equilibrium work relation. Thermodynamic analysis and microscopic foundations

We discuss the conditions for which the non-equilibrium work relation is valid by means of thermodynamic and microscopic arguments.Comment: 16 pages 1 figur

Setas urticantes en tarantulas de Uruguay: ¿defensa activa o pasiva?

Most of the New World tarantulas feature specialized setae as a defense mechanism. Two mechanisms of defense have been proposed for the urticating setae (US): active defense against potential predators, and passive defense against other arthropods by incorporating the US to the molting mat and egg sacs. Uruguayan tarantulas present three different US morphological types named: types I, III and IV. It has been proposed that type I is used in passive defense whereas type III serves its purpose in active defense. There are drastic differences of biological characteristics between adult females and males. Females live most of their entire life inside their burrows, while males wander when they reach adulthood, looking for females during the reproductive season. Considering these differences, diverse defense strategies should be expected. To assess the possible role of US in active/ passive defense strategies we have counted the number of US in the abdomen of individuals of four species while making comparisons between sexes. Significant differences were found between males and females of all sampled species, with females showing a predominance of types I (except subtype Ic) or IV setae over other types or subtypes, suggesting these type of US takes part in passive defense.La mayoría de las tarántulas del nuevo mundo presentan setas especializadas como defensa. Dos mecanismos de defensa han sido propuestos para las setas urticantes (US): defensa activa contra potenciales depredadores y defensa pasiva contra otros artrópodos mediante la incorporación de US a las telas de mudas u ootecas. Las tarántulas uruguayas presentan tres tipos morfológicos de US llamados: I, III y IV. Se ha propuesto que el tipo I se utiliza principalmente en defensa pasiva mientras que el tipo III en defensa activa. Hembras y machos adultos presentan diferencias drásticas en su biología. Las hembras permanecen la mayor parte de su vida en sus cuevas mientras que los machos, una vez que se hacen adultos, salen y buscan activamente hembras durante la época reproductiva. Considerando estas diferencias se presumen diferentes estrategias defensivas entre los sexos. Para conocer el uso de los diferentes tipos de US en defensa activa o pasiva se estudiaron las dotaciones de US en individuos de cuatro especies de tarántulas de Uruguay, comparando machos y hembras. Se encontraron diferencias sexuales en todas las especies, las hembras muestran predominancia de US de los tipos I (excepto subtipo Ic) o IV sobre otros tipos y subtipos de US, lo que sugiere su participación en defensa pasiva

Freshwater Crustaceans Decadpos: An Important Resource of Guatemala

Guatemala is a mega diversity country because it has several ecosystems and the physiography has a high diversity. However, the local population uses this biodiversity as a natural resource of food mainly. The country had three main drainage slopes for their rivers and aquatic reservoirs with several basins (the Gulf of Mexico, the Caribbean Sea, and the Pacific Sea). In these slopes, crayfish, freshwater prawns, and crabs compose the aquatic biological resources. Several fieldtrips were performed around these slopes in order to identify the species which were used as natural aquatic resources and verify if the diversity supports the food needs of the local population. Our findings were that the country has at least four crayfish species of genus Procambarus spp., those living in the high and middle altitude areas. Five freshwater prawn species with abbreviated larval development of genus Macrobrachium, that is, Macrobrachium cemai were also found. The bigger species of Macrobrachium was also identified on the three slopes as Macrobrachium americanum, Macrobrachium tenellum, Macrobrachium occidentale, and Macrobrachium digueti on the Pacific slope, while on the Gulf of Mexico and the Caribbean Sea, Macrobrachium carcinus, Macrobrachium acanthurus, Macrobrachium heterochirus, Macrobrachium olfersii, and Macrobrachium hobbsi were recorded, and therefore, the nonnative species Macrobrachium rosenbergii; with respect to other shrimps, Palaemon pandaliformis, Palaemonetes octaviae, and atyids as Atya scabra and Potimirim glabra were found. According to the freshwater crabs, the Pseudothelphusidae family is the best to represent in comparison with Trichodactylidae where only one population was recorded. Also, we register the uses of these species around the main markets in the country and we found two main ways: the first one is for the bigger species of freshwater prawns and crabs that are offered very expensive in kilogram and are almost offered in restaurants as exclusive dishes. The second one is more for the local consumption, and many families of fishery species that include crayfishes, freshwater prawns with abbreviated larval development, and smaller crabs, and so on, are sometimes found in the markets, with the prices being cheaper and can be bought only by the local people. Our findings show that Guatemala has an enormous potential in the crustaceans decapods for use as natural aquatic resources as protein sources at low cost, especially for the families with low economical level

SOFTCAR, SOFTWARE EDUCATIVO PARA EL CÁLCULO RELACIONAL COMO APOYO A LA ASIGNATURA DE BASE DE DATOS

The current paper proposes the study and learning of structured queries language for the relational algebra in data bases. Such research is based on the existing problem in the Information Engineering major at the University of Granma concerning the lack of an educational software to facilitate the students the understanding of such a matter for the Database Systems subject. It is for this reason that the objective of this work is to develop a tool that implements the necessary functions to guarantee the students the knowledge reception and assimilation in an easier and friendlier way. According to a previous study a decision was made to develop such a tool with free software, using Eclipse SDK as IDE and Java as the programming language. For modelling, the Rational Rose case tool is used, and the whole development process is based on the RUP methodology. The above stated resulted in a desktop application that responds to the current problem.El presente trabajo propone el estudio y aprendizaje del lenguaje de consultas estructuradas del cálculo relacional de bases de datos. Dicha investigación se basa en el problema existente en la carrera de Ingeniería Informática de la Universidad de Granma en cuanto a la inexistencia de un software educativo que facilite a los estudiantes comprender dicho tema de la asignatura Sistemas de Bases de Datos. Es por tal motivo que el objetivo de este trabajo es desarrollar una herramienta que implemente las funcionalidades necesarias para garantizar la recepción y asimilación del conocimiento de manera más fácil para el estudiante. Por previo estudio se tomó la decisión de desarrollar la herramienta con software libre, utilizando para ello Eclipse SDK como IDE y Java como lenguaje de programación. Para el modelado se utiliza la herramienta case Rational Rose, y todo el proceso de desarrollo está basado en la metodología RUP. Lo anteriormente planteado dio como resultado una aplicación de escritorio que responde a la problemática actual