Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Inhibited Al diffusion and growth roughening on Ga-coated Al (100)

Ab initio calculations indicate that the ground state for Ga adsorption on Al (100) is on-surface with local unit coverage. On Ga-coated Al (100), the bridge diffusion barrier for Al is large, but the Al$\rightarrow$Ga {\it exchange barrier is zero}: the ensuing incorporation of randomly deposited Al's into the Ga overlayer realizes a percolation network, efficiently recoated by Ga atoms. Based on calculated energetics, we predict rough surface growth at all temperatures; modeling the growth by a random deposition model with partial relaxation, we find a power-law divergent roughness $w\sim t^{\,0.07\pm0.02}$.Comment: 4 pages RevTeX-twocolumn, no figures. to appear in Phys. Rev. Lett., July 199

Physical and Mental Fatigue Reduce Psychomotor Vigilance in Professional Football Players

Purpose: Professional football players experience both physical and mental fatigue (MF). The main aims of this randomized crossover study were to investigate the effect of MF on repeated-sprint ability (RSA) and the effects of both physical fatigue and MF on psychomotor vigilance. Methods: Seventeen male professional football players performed 10 maximal 20-m shuttle sprints interspaced by incomplete recovery (RSA test). Running speed, heart rate, brain oxygenation, and rating of perceived exertion were monitored during each sprint. The RSA test was preceded by either a 30-minute Stroop task to induce MF or by watching a documentary for 30 minutes (control [CON]) in a randomized counterbalanced order. Participants performed a psychomotor vigilance test at baseline, after the cognitive task (MF or CON), and after the RSA test. Results: Heart rate and rating of perceived exertion significantly increased, while running speed and brain oxygenation significantly decreased over the repeated sprints (P .001) with no significant differences between conditions. Response speed during the psychomotor vigilance test significantly declined after the Stroop task but not after CON (P = .001). Response speed during the psychomotor vigilance test declined after the RSA test in both conditions (P .001) and remained lower in the MF condition compared to CON (P = .012). Conclusions: MF does not reduce RSA. However, the results of this study suggest that physical fatigue and MF have negative and cumulative effects on psychomotor vigilance. Therefore, strategies to reduce both physical fatigue and MF should be implemented in professional football players

Global and regional IUCN red list assessments: 6

In this contribution, the conservation status assessment of four vascular plants according to IUCN categories and criteria are presented. It includes the assessment of Epipactis maricae (Croce, Bongiorni, De Vivo & Fori) Presser & S.Hertel at global level, and the regional assessment of Cerinthe retorta Sm. (Italy), Platanthera kuenkelei H.Baumann subsp. kuenkelei (Europe) and Typha elephantina Roxb. (Egypt)

Prevalence and risk factors for chronic obstructive lung disease in HIV-infected patients in the HAART era

Our results suggest a role for HIV infection itself and for current cigarette smoking in the development of respiratory symptoms and COPD in HIV-infected patients. HAART did not seem to reduce the risk of respiratory symptoms and COPD, in our cases. Thus, our results suggest that HIV-infected patients should be screened for chronic respiratory disease in order to early identify those at risk or those who need specific treatment

New intravenous calcimimetic agents: New options, new problems. an example on how clinical, economical and ethical considerations affect choice of treatment

Background. Dialysis treatment is improving, but several long-term problems remain unsolved, including metabolic bone disease linked to chronic kidney disease (CKD-MBD). The availability of new, efficacious but expensive drugs (intravenous calcimimetic agents) poses ethical problems, especially in the setting of budget limitations. Methods. Reasons of choice, side effects, biochemical trends were discussed in a cohort of 15 patients (13% of the dialysis population) who stared treatment with intravenous calcimimetics in a single center. All patients had previously been treated with oral calcimimetic agents; dialysis efficacy was at target in 14/15; hemodiafiltration was employed in 10/15. Median Charlson Comorbidity Index was 8. The indications were discussed according to the principlist ethics (beneficience, non maleficience, justice and autonomy). Biochemical results were analyzed to support the clinical-ethical choices. Results. In the context of a strict clinical and biochemical surveillance, the lack of side effects ensured “non-maleficence”; efficacy was at least similar to oral calcimimetic agents, but tolerance was better. Autonomy was respected through a shared decision-making model; all patients appreciated the reduction of the drug burden, and most acknowledged better control of their biochemical data. The ethical conflict resides in the balance between the clinical “beneficience, non-maleficience” advantage and “justice” (economic impact of treatment, potentially in attrition with other resources, since the drug is expensive and included in the dialysis bundle). The dilemma is more relevant when a patient’s life expectancy is short (economic impact without clear clinical advantages), or when non-compliance is an issue (unclear advantage if the whole treatment is not correctly taken). Conclusions. In a context of person-centered medicine, autonomy, beneficence and non-maleficence should weight more than economic justice. While ethical discussions are not aimed at finding “the right answer” but asking “the right questions”, this example can raise awareness of the importance of including an ethical analysis in the choice of “economically relevant” drugs

Metodologia de monitoramento de cobertura vegetal: estudo de caso no município de Goiânia, GO.

Este trabalho apresenta uma proposta para a análise da variação da cobertura vegetal, utilizando dados de acesso público. Os procedimentos de análise multitemporal propostos foram aplicados no município de Goiânia, GO, como estudo de caso. Aplicou-se o índice de vegetação por diferença normalizada (NDVI), obtido a partir de imagens Landsat-5, em três anos de referência: 1997, 2004, 2011. Consideraram-se três classes de cobertura: ?corpos d?água?, ?vegetação? e ?outros usos?. Foram utilizadas técnicas de processamento digital de imagens, visando à correção de erros gerados pela influência da atmosfera e à obtenção de uma melhor qualidade espectral dos alvos. Para esse fim, o modelo adotado foi o dark object subtraction (DOS). O resultado mostrou-se satisfatório, considerando-se a disponibilidade dos dados e suas limitações.bitstream/item/84894/1/0000010346-BPD-Cobert-vegetal.pd

Infraestrutura Nacional de Dados Espaciais: Aspectos Computacionais.

O objetivo deste documento é apresentar os principais conceitos relacionados aos pilares ?tecnologia? e ?padrões?, com enfoque em seus aspectos computacionais. A intenção é sumarizar os fundamentos teóricos envolvidos na especificação da INDE e reunir as principais referências de softwares open source atualmente disponíveis e amplamente adotados pela comunidade para a implantação da INDE.bitstream/item/84963/1/COMUN-TECNICO-1-GESTAO-TERRITORIAL-Infraestrut-Nac-Dados-Espac-ed01-2013.pd

Global and Regional IUCN Red List Assessments: 6

In this contribution, the conservation status assessment of four vascular plants according to IUCN categories and criteria are presented. It includes the assessment of Epipactis maricae (Croce, Bongiorni, De Vivo & Fori) Presser & S.Hertel at global level, and the regional assessment of Cerinthe retorta Sm. (Italy), Platanthera kuenkelei H.Baumann subsp. kuenkelei (Europe) and Typha elephantina Roxb. (Egypt)