scholarly journals Entropy Dynamics of Phonon Quantum States Generated by Optical Excitation of a Two-Level System

Entropy ◽  
2020 ◽  
Vol 22 (3) ◽  
pp. 286
Author(s):  
Thilo Hahn ◽  
Daniel Wigger ◽  
Tilmann Kuhn
Keyword(s):  
Quantum Physics ◽  
Phonon Mode ◽  
Optical Excitation ◽  
Model Systems ◽  
Lattice Vibrations ◽  
Level System ◽  
Ideal Model ◽  
Wide Range ◽  
Physical Phenomena ◽  
Prototypical Model

In quantum physics, two prototypical model systems stand out due to their wide range of applications. These are the two-level system (TLS) and the harmonic oscillator. The former is often an ideal model for confined charge or spin systems and the latter for lattice vibrations, i.e., phonons. Here, we couple these two systems, which leads to numerous fascinating physical phenomena. Practically, we consider different optical excitations and decay scenarios of a TLS, focusing on the generated dynamics of a single phonon mode that couples to the TLS. Special emphasis is placed on the entropy of the different parts of the system, predominantly the phonons. While, without any decay, the entire system is always in a pure state, resulting in a vanishing entropy, the complex interplay between the single parts results in non-vanishing respective entanglement entropies and non-trivial dynamics of them. Taking a decay of the TLS into account leads to a non-vanishing entropy of the full system and additional aspects in its dynamics. We demonstrate that all aspects of the entropy’s behavior can be traced back to the purity of the states and are illustrated by phonon Wigner functions in phase space.

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

2020 ◽  
Author(s):  
Christian Devereux ◽  
Justin Smith ◽  
Kate Davis ◽  
Kipton Barros ◽  
Roman Zubatyuk ◽  
...  
Keyword(s):  
Drug Development ◽  
Autonomous Vehicles ◽  
Potential Energy Surfaces ◽  
Organic Molecules ◽  
Chemical Elements ◽  
Molecular Potential ◽  
Wide Range ◽  
Energy Surfaces ◽  
New Applications ◽  
Physical Phenomena

<p>Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, S) make up ~90% of drug like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~10<sup>6</sup> factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.</p>

scholarly journals Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  
Keyword(s):  
Biological Systems ◽  
Linear Dichroism ◽  
Quantitative Information ◽  
Living Cells ◽  
Software Tools ◽  
Model Systems ◽  
Membrane Properties ◽  
Polarization Microscopy ◽  
Molecular Processes ◽  
Wide Range

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.

scholarly journals Regulation of Cytochrome c Oxidase by Natural Compounds Resveratrol, (–)-Epicatechin, and Betaine

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1346
Author(s):  
Icksoo Lee
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Model Systems ◽  
Health Improvement ◽  
Published Data ◽  
Mitochondrial Electron Transport Chain ◽  
Naturally Occurring ◽  
Transport Chain ◽  
Wide Range ◽  
Experimental Model Systems

Numerous naturally occurring molecules have been studied for their beneficial health effects. Many compounds have received considerable attention for their potential medical uses. Among them, several substances have been found to improve mitochondrial function. This review focuses on resveratrol, (–)-epicatechin, and betaine and summarizes the published data pertaining to their effects on cytochrome c oxidase (COX) which is the terminal enzyme of the mitochondrial electron transport chain and is considered to play an important role in the regulation of mitochondrial respiration. In a variety of experimental model systems, these compounds have been shown to improve mitochondrial biogenesis in addition to increased COX amount and/or its enzymatic activity. Given that they are inexpensive, safe in a wide range of concentrations, and effectively improve mitochondrial and COX function, these compounds could be attractive enough for possible therapeutic or health improvement strategies.

scholarly journals Microstructure representation of snow in coupled snowpack and microwave emission models

2016 ◽  
Author(s):  
Melody Sandells ◽  
Richard Essery ◽  
Nick Rutter ◽  
Leanne Wake ◽  
Leena Leppänen ◽  
...  
Keyword(s):  
Brightness Temperature ◽  
Microstructure Evolution ◽  
Microwave Emission ◽  
Model Systems ◽  
Research Centre ◽  
Emission Model ◽  
Mean Error ◽  
Scale Factors ◽  
Wide Range ◽  
Emission Models

Abstract. This is the first study to encompass a wide range of coupled snow evolution and microwave emission models in a common modelling framework in order to generalise the link between snowpack microstructure predicted by the snow evolution models and microstructure required to reproduce observations of brightness temperature as simulated by snow emission models. Brightness temperatures at 18.7 and 36.5 GHz were simulated by 1323 ensemble members, formed from 63 Jules Investigation Model snowpack simulations, three microstructure evolution functions and seven microwave emission model configurations. Two years of meteorological data from the Sodankylä Arctic Research Centre, Finland were used to drive the model over the 2011–2012 and 2012–2013 winter periods. Comparisons between simulated snow grain diameters and field measurements with an IceCube instrument showed that the evolution functions from SNTHERM simulated snow grain diameters that were too large (mean error 0.12 to 0.16 mm), whereas MOSES and SNICAR microstructure evolution functions simulated grain diameters that were too small (mean error −0.16 to −0.24 mm for MOSES, and −0.14 to −0.18 mm for SNICAR). No model (HUT, MEMLS or DMRT-ML) provided a consistently good fit across all frequencies and polarizations. The smallest absolute values of mean bias in brightness temperature over a season for a particular frequency and polarization ranged from 0.9 to 7.2 K. Optimal scaling factors for the snow microstructure were presented to compare compatibility between snowpack model microstructure and emission model microstructure. Scale factors ranged between 0.3 for the SNTHERM-Empirical MEMLS model combination (2011–2012), and 5.0 or greater when considering non-sticky particles in DMRT-ML in conjunction with MOSES or SNICAR microstructure (2012–2013). Differences in scale factors between microstructure models were generally greater than the differences between microwave emission models, suggesting that more accurate simulations in coupled snowpack-microwave model systems will be achieved primarily through improvements in the snowpack microstructure representation, followed by improvements in the emission models. Other snowpack parameterisations in the snowpack model, mainly densification, led to a mean brightness temperature difference of 11 K when the JIM ensemble was applied to the MOSES microstructure and empirical MEMLS emission model for the 2011–2012 season. Consistency between snowpack microstructure and microwave emission models, and the choice of snowpack densification algorithms should be considered in the design of snow mass retrieval systems and microwave data assimilation systems.

Modeling Food Particle Systems: A Review of Current Progress and Challenges

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lennart Fries
Keyword(s):  
Particle Systems ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Food Particle ◽  
Adequate Model ◽  
Food Powders ◽  
Contact Models ◽  
Physical Phenomena ◽  
The Impact

For many years, food engineers have attempted to describe physical phenomena such as heat and mass transfer in food via mathematical models. Still, the impact and benefits of computer-aided engineering are less established in food than in most other industries today. Complexity in the structure and composition of food matrices are largely responsible for this gap. During processing of food, its temperature, moisture, and structure can change continuously, along with its physical properties. We summarize the knowledge foundation, recent progress, and remaining limitations in modeling food particle systems in four relevant areas: flowability, size reduction, drying, and granulation and agglomeration. Our goal is to enable researchers in academia and industry dealing with food powders to identify approaches to address their challenges with adequate model systems or through structural and compositional simplifications. With advances in computer simulation capacity, detailed particle-scale models are now available for many applications. Here, we discuss aspects that require further attention, especially related to physics-based contact models for discrete-element models of food particle systems. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 12 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

NESTED HIGH-RESOLUTION NOx AND PM SIMULATIONS OVER ZÜRICH

2021 ◽  
Author(s):  
Ivo Suter ◽  
Lukas Emmenegger ◽  
Dominik Brunner
Keyword(s):  
Air Pollution ◽  
Air Quality ◽  
Boundary Conditions ◽  
Meteorological Conditions ◽  
Model Systems ◽  
Multi Scale ◽  
Wide Range ◽  
The Impact ◽  
The City ◽  
Concentration Levels

&lt;p&gt;Reducing air pollution, which is the world's largest single environmental health risk, demands better-informed air quality policies. Consequently, multi-scale air quality models are being developed with the goal to resolve cities. One of the major challenges in such model systems is to accurately represent all large- and regional-scale processes that may critically determine the background concentration levels over a given city. This is particularly true for longer-lived species such as aerosols, for which background levels often dominate the concentration levels, even within the city. Furthermore, the heterogeneous local emissions, and complex dispersion in the city have to be considered carefully.&lt;/p&gt;&lt;p&gt;In this study, the impact of processes across a wide range of scales on background concentrations over Switzerland and the city of Zurich was modelled by performing one year of nested European and Swiss national COSMO-ART simulations to obtain adequate boundary conditions for gas-phase chemical, aerosol and meteorological conditions for city-resolving simulations. The regional climate chemistry model COSMO-ART (Vogel et al. 2009) was used in a 1-way coupled mode. The outer, European, domain, which was driven by chemical boundary conditions from the global MOZART model, had a 6.6 km horizontal resolution and the inner, Swiss, domain one of 2.2 km. For the city scale, a catalogue of more than 1000 mesoscale flow patterns with 100 m resolution was created with the model GRAMM, based on a discrete set of atmospheric stabilities, wind speeds and directions, accounting for the influence of land-use and topography. Finally, the flow around buildings was solved with the CFD model GRAL forced at the boundaries by GRAMM. Subsequently, Lagrangian dispersion simulations for a set of air pollutants and emission sectors (traffic, industry, ...) based on extremely detailed building and emission data was performed in GRAL. The result of this nested procedure is a library of 3-dimensional air pollution maps representative of hourly situations in Zurich (Berchet et al. 2017). From these pre-computed situations, time-series and concentration maps can be obtained by selecting situations according to observed or modelled meteorological conditions.&lt;/p&gt;&lt;p&gt;The results were compared to measurements from air quality monitoring network stations. Modelled concentrations of NO&lt;sub&gt;x&lt;/sub&gt; and PM compared well to measurements across multiple locations, provided background conditions were considered carefully. The nested multi-scale modelling system COSMO-ART/GRAMM/GRAL can adequately reproduce local air quality and help understanding the relative contributions of local versus distant emissions, as well as fill the space between precise point measurements from monitoring sites. This information is useful for research, policy-making, and epidemiological studies particularly under the assumption that exceedingly high concentrations become more and more localised phenomenon in the future.&lt;/p&gt;

Planarian Hox genes: novel patterns of expression during regeneration

Development ◽  
1997 ◽  
Vol 124 (1) ◽  
pp. 141-148
Author(s):  
J.R. Bayascas ◽  
E. Castillo ◽  
A.M. Munoz-Marmol ◽  
E. Salo
Keyword(s):  
Hox Genes ◽  
Bilateral Symmetry ◽  
Sister Group ◽  
Model Systems ◽  
Hox Cluster ◽  
Positional Identity ◽  
Wide Range ◽  
Differential Timing ◽  
Anteroposterior Polarity

Platyhelminthes are widely considered to be the sister group of coelomates (Philippe, H., Chenuil, A. and Adoutte, A. (1994)Development 1994 Supplement, 15–24) and the first organisms to show bilateral symmetry and cephalization. Within this phylum, the freshwater planarians (Turbellaria, Tricladida) have been used as model systems for studying bidirectional regeneration (Slack, J. M. W. (1980) J. Theor. Biol 82, 105–140). We have been attempting to identify potential pattern-control genes involved in the regeneration of planarian heads and tails after amputation. Since Hox cluster genes determine positional identity along the anteroposterior axis in a wide range of animals (Slack, J. M. W., Holland, P. W. H. and Graham, C. F. (1993) Nature 361,490-492), we performed an extensive search for Hox-related genes in the planarian Dugesia(G)tigrina. Sequence analyses of seven planarian Dthox genes (Dthox-A to Dthox-G) reveal high similarities with the homeodomain region of the Hox cluster genes, allowing us to assign planarian Dthox genes to anterior and medial Hox cluster paralogous groups. Whole-mount in situ hybridization studies in regenerating adults showed very early, synchronous and colocalized activation of Dthox-D, Dthox-A, Dthox-C, Dthox-E, Dthox-G and Dthox-F. After one hour of regeneration a clear expression was observed in all Dthox genes studied. In addition, all seemed to be expressed in the same regenerative tissue, although in the last stages of regeneration (9 to 15 days) a differential timing of deactivation was observed. The same Dthox genes were also expressed synchronously and were colocalized during intercalary regeneration, although their expression was delayed. Terminal regeneration showed identical Dthox gene expression in anterior and posterior blastemas, which may prevent these genes from directing the distinction between head and tail. Finally, continuous expression along the whole lateral blastema in sagittal regenerates reflected a ubiquitous Dthox response in all types of regeneration that was not related specifically with the anteroposterior polarity.

scholarly journals Hybrid Dynamic Pharmacophore Models as Effective Tools to Identify Novel Chemotypes for Anti-TB Inhibitor Design: A Case Study With Mtb-DapB

2020 ◽  
Vol 8 ◽  
Author(s):  
Chinmayee Choudhury ◽  
Anshu Bhardwaj
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Chemical Space ◽  
Pharmacophore Model ◽  
Model Systems ◽  
Receptor Interaction ◽  
Hybrid Molecules ◽  
Wide Range ◽  
Binding Pockets ◽  
Pharmacophore Models

Antimicrobial resistance (AMR) is one of the most serious global public health threats as it compromises the successful treatment of deadly infectious diseases like tuberculosis. New therapeutics are constantly needed but it takes a long time and is expensive to explore new biochemical space. One way to address this issue is to repurpose the validated targets and identify novel chemotypes that can simultaneously bind to multiple binding pockets of these targets as a new lead generation strategy. This study reports such a strategy, dynamic hybrid pharmacophore model (DHPM), which represents the combined interaction features of different binding pockets contrary to the conventional approaches, where pharmacophore models are generated from single binding sites. We have considered Mtb-DapB, a validated mycobacterial drug target, as our model system to explore the effectiveness of DHPMs to screen novel unexplored compounds. Mtb-DapB has a cofactor binding site (CBS) and an adjacent substrate binding site (SBS). Four different model systems of Mtb-DapB were designed where, either NADPH/NADH occupies CBS in presence/absence of an inhibitor 2, 6-PDC in the adjacent SBS. Two more model systems were designed, where 2, 6-PDC was linked to NADPH and NADH to form hybrid molecules. The six model systems were subjected to 200 ns molecular dynamics simulations and trajectories were analyzed to identify stable ligand-receptor interaction features. Based on these interactions, conventional pharmacophore models (CPM) were generated from the individual binding sites while DHPMs were created from hybrid-molecules occupying both binding sites. A huge library of 1,563,764 publicly available molecules were screened by CPMs and DHPMs. The screened hits obtained from both types of models were compared based on their Hashed binary molecular fingerprints and 4-point pharmacophore fingerprints using Tanimoto, Cosine, Dice and Tversky similarity matrices. Molecules screened by DHPM exhibited significant structural diversity, better binding strength and drug like properties as compared to the compounds screened by CPMs indicating the efficiency of DHPM to explore new chemical space for anti-TB drug discovery. The idea of DHPM can be applied for a wide range of mycobacterial or other pathogen targets to venture into unexplored chemical space.

scholarly journals The XXL Survey

2018 ◽  
Vol 620 ◽  
pp. A7 ◽  
Author(s):  
V. Guglielmo ◽  
B. M. Poggianti ◽  
B. Vulcani ◽  
C. Adami ◽  
F. Gastaldello ◽  
...  
Keyword(s):  
Mass Function ◽  
Stellar Mass ◽  
X Ray ◽  
Field Versus ◽  
Final Sample ◽  
Wide Range ◽  
The Galaxy ◽  
Halo Masses ◽  
Stellar Masses ◽  
Physical Phenomena

Context. The fraction of galaxies bound in groups in the nearby Universe is high (50% at z ~ 0). Systematic studies of galaxy properties in groups are important in order to improve our understanding of the evolution of galaxies and of the physical phenomena occurring within this environment. Aims. We have built a complete spectrophotometric sample of galaxies within X-ray detected, optically spectroscopically confirmed groups and clusters (G&C), covering a wide range of halo masses at z ≤ 0.6. Methods. In the context of the XXL survey, we analyse a sample of 164 G&C in the XXL-North region (XXL-N), at z ≤ 0.6, with a wide range of virial masses (1.24 × 1013 ≤ M500,scal(M⊙) ≤ 6.63 × 1014) and X-ray luminosities ((2.27 × 1041 ≤ L500,scalXXL(erg s−1) ≤ 2.15 × 1044)). The G&C are X-ray selected and spectroscopically confirmed. We describe the membership assignment and the spectroscopic completeness analysis, and compute stellar masses. As a first scientific exploitation of the sample, we study the dependence of the galaxy stellar mass function (GSMF) on global environment. Results. We present a spectrophotometric characterisation of the G&C and their galaxies. The final sample contains 132 G&C, 22 111 field galaxies and 2225 G&C galaxies with r-band magnitude <20. Of the G&C, 95% have at least three spectroscopic members, and 70% at least ten. The shape of the GSMF seems not to depend on environment (field versus G&C) or X-ray luminosity (used as a proxy for the virial mass of the system). These results are confirmed by the study of the correlation between mean stellar mass of G&C members and L500,scalXXL. We release the spectrophotometric catalogue of galaxies with all the quantities computed in this work. Conclusions. As a first homogeneous census of galaxies within X-ray spectroscopically confirmed G&C at these redshifts, this sample will allow environmental studies of the evolution of galaxy properties.

scholarly journals Quadrature Squeezing and Geometric-Phase Oscillations in Nano-Optics

Nanomaterials ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1391
Author(s):  
Jeong Ryeol Choi
Keyword(s):  
Geometric Phase ◽  
Linear Increase ◽  
Time Behavior ◽  
Squeezed State ◽  
Periodic Oscillations ◽  
Optical Phenomenon ◽  
Dynamical Phase ◽  
Wide Range ◽  
Current Flows ◽  
Physical Phenomena

The geometric phase, as well as the familiar dynamical phase, occurs in the evolution of a squeezed state in nano-optics as an extra phase. The outcome of the geometric phase in that state is somewhat intricate: its time behavior exhibits a combination of a linear increase and periodic oscillations. We focus in this work on the periodic oscillations of the geometric phase, which are novel and interesting. We confirm that such oscillations are due purely to the effects of squeezing in the quantum states, whereas the oscillation disappears when we remove the squeezing. As the degree of squeezing increases in q-quadrature, the amplitude of the geometric-phase oscillation becomes large. This implies that we can adjust the strength of such an oscillation by tuning the squeezing parameters. We also investigate geometric-phase oscillations for the case of a more general optical phenomenon where the squeezed state undergoes one-photon processes. It is shown that the geometric phase in this case exhibits additional intricate oscillations with small amplitudes, besides the principal oscillation. Such a sub-oscillation exhibits a beating-like behavior in time. The effects of geometric-phase oscillations are crucial in a wide range of wave interferences which are accompanied by rich physical phenomena such as Aharonov–Bohm oscillations, conductance fluctuations, antilocalizations, and nondissipative current flows.

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