Search results for "Ensembl"
showing 10 items of 165 documents
Phase behaviour of heteronuclear dimers in three-dimensional systems—a Monte Carlo study
2008
Monte Carlo simulation in the grand canonical ensemble, the histogram reweighting technique and finite size scaling are used to study the phase behaviour of dimers in three-dimensional systems. A single molecule is composed of two segments A and B, and the bond between them cannot be broken. The phase diagrams have been estimated for a set of model systems. Different structures formed by heteronuclear dimers have been found. The results show a great variety of vapour–liquid coexistence behaviour depending on the strength of the interactions between segments.
TBSSvis: Visual Analytics for Temporal Blind Source Separation
2020
Temporal Blind Source Separation (TBSS) is used to obtain the true underlying processes from noisy temporal multivariate data, such as electrocardiograms. TBSS has similarities to Principal Component Analysis (PCA) as it separates the input data into univariate components and is applicable to suitable datasets from various domains, such as medicine, finance, or civil engineering. Despite TBSS’s broad applicability, the involved tasks are not well supported in current tools, which offer only text-based interactions and single static images. Analysts are limited in analyzing and comparing obtained results, which consist of diverse data such as matrices and sets of time series. Additionally, p…
Monte Carlo Methods for the Sampling of Free Energy Landscapes
2019
In this chapter, we return to classical statistical mechanics, wherein the canonical ensemble averages of an observable \(A(\overrightarrow{x})\), where \(\overrightarrow{x} \) stands symbolically for the “microstate” coordinate in the configurational part of the phase space of the system, are given by (cf. Sect. 2.1.1)
From determination of the fugacity coefficients to estimation of hydrogen storage capacity: A convenient theoretical method
2015
Abstract The equation of state (EOS) from virial expansion (VE) is used in this work to pave the way for determining the fugacity coefficients of the hydrogen fluid at arbitrary temperature and pressure. The fugacity coefficients from our VE method have more physical meanings than the empirical values. In this way, the hydrogen storage capacity of a novel material model can be estimated by using few density functional theory (DFT) calculations with the aid of a continuum model. The efficient continuum model can provide a more accurate estimation of the hydrogen storage capacity than the pure DFT calculations. Furthermore, the expensive grand canonical ensemble (μNT) simulations combining wi…
Advanced techniques for solving groundwater and surface water problems in the context of inverse methods and climate change.
2021
[ES] El tema de la investigación se centra en técnicas avanzadas para manejar problemas de aguas subterráneas y superficiales relacionados con métodos inversos y cambio climático. Los filtros de Kalman, con especial atención en Ensemble Smoother with Multiple Data Assimilation (ES-MDA), se analizan y mejoran para la solución de diferentes tipos de problemas inversos. En particular, la principal novedad es la aplicación de estos métodos para la identificación de series temporales. La primera parte de la tesis, luego de la descripción del método, presenta el desarrollo de un software escrito en Python para la aplicación de la metodología propuesta. El software cuenta con un flujo de trabajo f…
A comparison of ensemble algorithms for item-weighted Label Ranking
2023
Label Ranking (LR) is a non-standard supervised classification method with the aim of ranking a finite collection of labels according to a set of predictor variables. Traditional LR models assume indifference among alternatives. However, misassigning the ranking position of a highly relevant label is frequently regarded as more severe than failing to predict a trivial label. Moreover, switching two similar alternatives should be considered less severe than switching two different ones. Therefore, efficient LR classifiers should be able to take into account the similarities and individual weights of the items to be ranked. The contribution of this paper is to formulate and compare flexible i…
Optimal Control of Dissipative Quantum Systems
2008
We study the control of finite dimensional quantum systems by external laser fields. After examining the concrete example of the diatomic molecular alignment in dissipative media, we are interested in the problem of optimal control, where the objective is to bring the system from an initial state into a given final state while minimizing a cost functional. The Pontryagin maximum principle (PMP) provides necessary conditions for optimality, by establishing that any optimal trajectory is the extremal solution of an extended problem of Hamiltonian structure. In this context, we perform the analysis of two particular systems. The first one is a dissipative 2-level system, for which we determine…
Hippocampo-cerebellar theta band phase synchrony in rabbits.
2009
Hippocampal functioning, in the form of theta band oscillation, has been shown to modulate and predict cerebellar learning of which rabbit eyeblink conditioning is perhaps the most well-known example. The contribution of hippocampal neural activity to cerebellar learning is only possible if there is a functional connection between the two structures. Here, in the context of trace eyeblink conditioning, we show (1) that, in addition to the hippocampus, prominent theta oscillation also occurs in the cerebellum, and (2) that cerebellar theta oscillation is synchronized with that in the hippocampus. Further, the degree of phase synchrony (PS) increased both as a response to the conditioning sti…
Modeling the Interaction of Carbon Monoxide with Flexible Graphene: From Coupled Cluster Calculations to Molecular-Dynamics Simulations
2018
The interaction of CO with graphene was studied at different theoretical levels. Quantum-mechanical calculations on finite graphene models with the use of coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there was no preferential site for adsorption and that the most important factor was the orientation of CO relative to graphene. The parallel orientation was preferred, with binding energies around 9 kJ mol-1 at the CCSD(T) and B97D levels, which was in good agreement with experimental findings. From a large number of CO-circumcoronene and CO-CO interactions, computed at different distances and randomly generated orientations, parameters were fi…
Wetting of a short chain liquid on a brush: First-order and critical wetting transitions
2001
We investigate the wetting behaviour of short chains on a surface covered with a brush of end-grafted chains of the same architecture by a combination of self-consistent field calculations and liquid-state theory. The surface interacts with the monomers via (non-retarded) van der Waals interactions of strength A. At low grafting densities, we find first-order wetting transitions. The value of the effective Hamaker constant Awet > 0, at which the transition occurs, decreases and the strength of the first-order transition becomes weaker as we increase the grafting density. In an intermediate range of grafting densities, we encounter second-order wetting transitions at a vanishing Hamaker cons…