No Arabic abstract
A Lagrangian flow network is constructed for the atmospheric blocking of eastern Europe and western Russia in summer 2010. We compute the most probable paths followed by fluid particles which reveal the {it Omega}-block skeleton of the event. A hierarchy of sets of highly probable paths is introduced to describe transport pathways when the most probable path alone is not representative enough. These sets of paths have the shape of narrow coherent tubes flowing close to the most probable one. Thus, even when the most probable path is not very significant in terms of its probability, it still identifies the geometry of the transport pathways.
In the past decades, boreal summers have been characterized by an increasing number of extreme weather events in the Northern Hemisphere extratropics, including persistent heat waves, droughts and heavy rainfall events with significant social, economic and environmental impacts. Many of these events have been associated with the presence of anomalous large-scale atmospheric circulation patterns, in particular persistent blocking situations, i.e., nearly stationary spatial patterns of air pressure. To contribute to a better understanding of the emergence and dynamical properties of such situations, we construct complex networks representing the atmospheric circulation based on Lagrangian trajectory data of passive tracers advected within the atmospheric flow. For these Lagrangian flow networks, we study the spatial patterns of selected node properties prior to, during and after different atmospheric blocking events in Northern Hemisphere summer. We highlight the specific network characteristics associated with the sequence of strong blocking episodes over Europe during summer 2010 as an illustrative example. Our results demonstrate the ability of the node degree, entropy and harmonic closeness centrality based on outgoing links to trace important spatio-temporal characteristics of atmospheric blocking events. In particular, all three measures capture the effective separation of the stationary pressure cell forming the blocking high from the normal westerly flow and the deviation of the main atmospheric currents around it. Our results suggest the utility of further exploiting the Lagrangian flow network approach to atmospheric circulation in future targeted diagnostic and prognostic studies.
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are removed and simulating the entire reaction in atomistic details using existing computers becomes feasible. In addition, this formalism provides a natural framework to investigate the relationships between thermodynamical and kinetic aspects of the folding. For example, it is possible to show that, in order to have a large probability to remain unchanged under Langevin diffusion, the native state has to be characterized by a small conformational entropy. We discuss how to determine the most probable folding pathway, to identify configurations representative of the transition state and to compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine di-peptide, within an all-atom model based on the empiric GROMOS96 force field.
Modeling is a very important tool for scientific processes, requiring long-term dedication, desire, and continuous reflection. In this work, we discuss several aspects of modeling, and the reasons for doing it. We discuss two major modeling systems that have been built by us over the last 10 years. It is a long and arduous process but the reward of understanding can be enormous, as demonstrated in the examples shown in this work. We found that long-range transport of emerging Asian pollutants can be interpreted using a Lagrangian framework for wind analysis. More detailed processes still need to be modeled but an accurate representation of the wind structure is the most important thing above all others. Our long-term chemistry integrations reveal the capability of the IMS model in simulating tropospheric chemistry on a climate scale. These long-term integrations also show ways for further model development. Modeling is a quantitative process, and the understanding can be sustained only when theories are vigorously tested in the models and compared with high quality measurements. We should also not over look the importance of data visualization techniques. Humans feel more confident when they see things. Hence, modeling is an incredible journey, combining data collection, theoretical formulation, detailed computer coding and harnessing computer power. The best is yet to come.
Perhaps because of the popularity that trajectory-based methodologies have always had in Chemistry and the important role they have played, Bohmian mechanics has been increasingly accepted within this community, particularly in those areas of the theoretical chemistry based on quantum mechanics, e.g., quantum chemistry, chemical physics, or physical chemistry. From a historical perspective, this evolution is remarkably interesting, particularly when the scarce applications of Madelungs former hydrodynamical formulation, dating back to the late 1960s and the 1970s, are compared with the many different applications available at present. As also happens with classical methodologies, Bohmian trajectories are essentially used to described and analyze the evolution of chemical systems, to design and implement new computational propagation techniques, or a combination of both. In the first case, Bohmian trajectories have the advantage that they avoid invoking typical quantum-classical correspondence to interpret the corresponding phenomenon or process, while in the second case quantum-mechanical effects appear by themselves, without the necessity to include artificially quantization conditions. Rather than providing an exhaustive revision and analysis of all these applications (excellent monographs on the issue are available in the literature for the interested reader, which can be consulted in the bibliography here supplied), this Chapter has been prepared in a way that it may serve the reader to acquire a general view (or impression) on how Bohmian mechanics has permeated the different traditional levels or pathways to approach molecular systems in Chemistry: electronic structure, molecular dynamics and statistical mechanics. This is done with the aid of some illustrative examples -- theoretical developments in some cases and numerical simulations in other cases.
The connectivity pattern of networks, which are based on a correlation between ground level temperature time series, shows a dominant dense stripe of links in the southern ocean. We show that statistical categorization of these links yields a clear association with the pattern of an atmospheric Rossby wave, one of the major mechanisms associated with the weather system and with planetary scale energy transport. It is shown that alternating densities of negative and positive links (correlations) are arranged in half Rossby wave distances around 3,500 km, 7,000 km and 10,000 km and are aligned with the expected direction of energy flow, distribution of time delays and the seasonality of these waves. It is also shown that long distance links (i.e., of distances larger than 2,000 km) that are associated with Rossby waves are the most dominant in the climate network. Climate networks may thus be used as an efficient new way to detect and analyze Rossby waves, based on reliable and available ground level measurements, in addition to the frequently used 300 hPa reanalysis meridional wind data.