Thermodynamics of a subensemble of a canonical ensemble

Two approaches to describe the thermodynamics of a subsystem that interacts with a thermal bath are considered. Within the first approach, the mean system energy $E_{S}$ is identified with the expectation value of the system Hamiltonian, which is evaluated with respect to the overall (system+bath) equilibrium distribution. Within the second approach, the system partition function $Z_{S}$ is considered as the fundamental quantity, which is postulated to be the ratio of the overall (system+bath) and the bath partition functions, and the standard thermodynamic relation $E_{S}=-d(\ln Z_{S})/d\beta$ is used to obtain the mean system energy. % ($\beta\equiv 1/(k_{B}T)$, $k_{B}$ is the Boltzmann constant, %and $T$ is the temperature). Employing both classical and quantum mechanical treatments, the advantages and shortcomings of the two approaches are analyzed in detail for various different systems. It is shown that already within classical mechanics both approaches predict significantly different results for thermodynamic quantities provided the system-bath interaction is not bilinear or the system of interest consists of more than a single particle. Based on the results, it is concluded that the first approach is superior

Application of metabolomics and molecular networking in investigating the chemical profile and antitrypanosomal activity of British bluebells (Hyacinthoides non-scripta)

Bulb, leaf, scape and flower samples of British bluebells (Hyacinthoides non-scripta) were collected regularly for one growth period. Methanolic extracts of freeze-dried and ground samples showed antitrypanosomal activity, giving more than 50% inhibition, for 20 out of 41 samples. High-resolution mass spectrometry was used in the dereplication of the methanolic extracts of the different plant parts. The results revealed differences in the chemical profile with bulb samples being distinctly different from all aerial parts. High molecular weight metabolites were more abundant in the flowers, shoots and leaves compared to smaller molecular weight ones in the bulbs. The anti-trypanosomal activity of the extracts was linked to the accumulation of high molecular weight compounds, which were matched with saponin glycosides, while triterpenoids and steroids occurred in the inactive extracts. Dereplication studies were employed to identify the significant metabolites via chemotaxonomic filtration and considering their previously reported bioactivities. Molecular networking was implemented to look for similarities in fragmentation patterns between the isolated saponin glycoside at m/z 1445.64 [M + formic-H]− equivalent to C64H104O33 and the putatively found active metabolite at m/z 1283.58 [M + formic-H]− corresponding to scillanoside L-1. A combination of metabolomics and bioactivity-guided approaches resulted in the isolation of a norlanostane-type saponin glycoside with antitrypanosomal activity of 98.9% inhibition at 20 µM

Human cryptochrome exhibits light-dependent magnetosensitivity

Humans are not believed to have a magnetic sense, even though many animals use the Earth's magnetic field for orientation and navigation. One model of magnetosensing in animals proposes that geomagnetic fields are perceived by light-sensitive chemical reactions involving the flavoprotein cryptochrome (CRY). Here we show using a transgenic approach that human CRY2, which is heavily expressed in the retina, can function as a magnetosensor in the magnetoreception system of Drosophila and that it does so in a light-dependent manner. The results show that human CRY2 has the molecular capability to function as a light-sensitive magnetosensor and reopen an area of sensory biology that is ready for further exploration in humans

Binding energy referencing for XPS in Alkali metal-based battery materials research (II): Application to complex composite electrodes

X-ray photoelectron spectroscopy (XPS) is a key method for studying (electro-)chemical changes in metal-ion battery electrode materials. In a recent publication, we pointed out a conflict in binding energy (BE) scale referencing at alkali metal samples, which is manifested in systematic deviations of the BEs up to several eV due to a specific interaction between the highly reactive alkali metal in contact with non-conducting surrounding species. The consequences of this phenomenon for XPS data interpretation are discussed in the present manuscript. Investigations of phenomena at surface-electrolyte interphase regions for a wide range of materials for both lithium and sodium-based applications are explained, ranging from oxide-based cathode materials via alloys and carbon-based anodes including appropriate reference chemicals. Depending on material class and alkaline content, specific solutions are proposed for choosing the correct reference BE to accurately define the BE scale. In conclusion, the different approaches for the use of reference elements, such as aliphatic carbon, implanted noble gas or surface metals, partially lack practicability and can lead to misinterpretation for application in battery materials. Thus, this manuscript provides exemplary alternative solutions

Theory of Vibrationally Inelastic Electron Transport through Molecular Bridges

Vibrationally inelastic electron transport through a molecular bridge that is connected to two leads is investigated. The study is based on a generic model of vibrational excitation in resonant transmission of electrons through a molecular junction. Employing methods from electron-molecule scattering theory, the transmittance through the molecular bridge can be evaluated numerically exactly. The current through the junction is obtained approximately using a Landauer-type formula. Considering different parameter regimes, which include both the case of a molecular bridge that is weakly coupled to the leads, resulting in narrow resonance structures, and the opposite case of a broad resonance caused by strong interaction with the leads, we investigate the characteristic effects of coherent and dissipative vibrational motion on the electron transport. Furthermore, the validity of widely used approximations such as the wide-band approximation and the restriction to elastic transport mechanisms is investigated in some detail.Comment: Submited to PRB, revised version according to comments of referees (minor text changes and new citations

The Physical Basis for Long-lived Electronic Coherence in Photosynthetic Light Harvesting Systems

The physical basis for observed long-lived electronic coherence in photosynthetic light-harvesting systems is identified using an analytically soluble model. Three physical features are found to be responsible for their long coherence lifetimes: i) the small energy gap between excitonic states, ii) the small ratio of the energy gap to the coupling between excitonic states, and iii) the fact that the molecular characteristics place the system in an effective low temperature regime, even at ambient conditions. Using this approach, we obtain decoherence times for a dimer model with FMO parameters of $\approx$ 160 fs at 77 K and $\approx$ 80 fs at 277 K. As such, significant oscillations are found to persist for 600 fs and 300 fs, respectively, in accord with the experiment and with previous computations. Similar good agreement is found for PC645 at room temperature, with oscillations persisting for 400 fs. The analytic expressions obtained provide direct insight into the parameter dependence of the decoherence time scales.Comment: 5 figures; J. Phys. Chem. Lett. (2011

Semiclassical theory of spin-orbit interaction in the extended phase space

We consider the semiclassical theory in a joint phase space of spin and orbital degrees of freedom. The method is developed from the path integrals using the spin-coherent-state representation, and yields the trace formula for the density of states. We discuss special cases, such as weak and strong spin-orbit coupling, and relate the present theory to the earlier approaches.Comment: 36 pages, 8 figures. Version 2: revised Sec. 4.4 and Appendix B; minor corrections elsewher

Semiclassical Approximations in Phase Space with Coherent States

We present a complete derivation of the semiclassical limit of the coherent state propagator in one dimension, starting from path integrals in phase space. We show that the arbitrariness in the path integral representation, which follows from the overcompleteness of the coherent states, results in many different semiclassical limits. We explicitly derive two possible semiclassical formulae for the propagator, we suggest a third one, and we discuss their relationships. We also derive an initial value representation for the semiclassical propagator, based on an initial gaussian wavepacket. It turns out to be related to, but different from, Heller's thawed gaussian approximation. It is very different from the Herman--Kluk formula, which is not a correct semiclassical limit. We point out errors in two derivations of the latter. Finally we show how the semiclassical coherent state propagators lead to WKB-type quantization rules and to approximations for the Husimi distributions of stationary states.Comment: 80 pages, 4 figure

The nowcasting SAF products and services: recent improvements in the new SW packages PPS v2018 and GEO v2018 and future plans

Presentación realizada en la 3rd European Nowcasting Conference, celebrada en la sede central de AEMET en Madrid del 24 al 26 de abril de 2019

Light-Induced Responses of Slow Oscillatory Neurons of the Rat Olivary Pretectal Nucleus

Background: The olivary pretectal nucleus (OPN) is a small midbrain structure responsible for pupil constriction in response to eye illumination. Previous electrophysiological studies have shown that OPN neurons code light intensity levels and therefore are called luminance detectors. Recently, we described an additional population of OPN neurons, characterized by a slow rhythmic pattern of action potentials in light-on conditions. Rhythmic patterns generated by these cells last for a period of approximately 2 minutes. Methodology: To answer whether oscillatory OPN cells are light responsive and whether oscillatory activity depends on retinal afferents, we performed in vivo electrophysiology experiments on urethane anaesthetized Wistar rats. Extracellular recordings were combined with changes in light conditions (light-dark-light transitions), brief light stimulations of the contralateral eye (diverse illuminances) or intraocular injections of tetrodotoxin (TTX). Conclusions: We found that oscillatory neurons were able to fire rhythmically in darkness and were responsive to eye illumination in a manner resembling that of luminance detectors. Their firing rate increased together with the strength of the light stimulation. In addition, during the train of light pulses, we observed two profiles of responses: oscillationpreserving and oscillation-disrupting, which occurred during low- and high-illuminance stimuli presentation respectively. Moreover, we have shown that contralateral retina inactivation eliminated oscillation and significantly reduced the firin