A study of the impact of long range interactions on the reactivity of N + N2 using the Grid Empowered Molecular Simulator GEMS

2010 ◽  
Vol 6 (2) ◽  
pp. 196 ◽  
Author(s):  
Sergio Rampino ◽  
Fernando Pirani ◽  
Ernesto Garcia ◽  
Antonio Lagana
Keyword(s):  
Long Range ◽  
Long Range Interactions ◽  
The Impact

scholarly journals Singularities in the gravitational capture of dark matter through long-range interactions

2022 ◽  
Vol 2022 (01) ◽  
pp. 016
Author(s):  
Cristian Gaidau ◽  
Jessie Shelton
Keyword(s):  
Dark Matter ◽  
Long Range ◽  
Capture Rate ◽  
Thermal Motion ◽  
The Sun ◽  
Long Range Interactions ◽  
Population Iii Stars ◽  
Logarithmic Sensitivity ◽  
Gravitational Capture ◽  
The Impact

Abstract We re-examine the gravitational capture of dark matter (DM) through long-range interactions. We demonstrate that neglecting the thermal motion of target particles, which is often a good approximation for short-range capture, results in parametrically inaccurate results for long-range capture. When the particle mediating the scattering process has a mass that is small in comparison to the momentum transfer in scattering events, correctly incorporating the thermal motion of target particles results in a quadratic, rather than logarithmic, sensitivity to the mediator mass, which substantially enhances the capture rate. We quantitatively assess the impact of this finite temperature effect on the captured DM population in the Sun as a function of mediator mass. We find that capture of DM through light dark photons, as in e.g. mirror DM, can be powerfully enhanced, with self-capture attaining a geometric limit over much of parameter space. For visibly-decaying dark photons, thermal corrections are not large in the Sun, but may be important in understanding long-range DM capture in more massive bodies such as Population III stars. We additionally provide the first calculation of the long-range DM self-evaporation rate.

scholarly journals Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1308
Author(s):  
Arvind Ramanathan ◽  
Akash Parvatikar ◽  
Srinivas C. Chennubhotla ◽  
Yang Mei ◽  
Sangita C. Sinha
Keyword(s):  
Long Range ◽  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Dynamic Simulations ◽  
Bh3 Domain ◽  
Long Range Interactions ◽  
Partial Unfolding ◽  
Binding Cleft ◽  
Inference Techniques ◽  
The Impact

Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 μs) of the murine γ-herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. We experimentally validate the role of these hydrophobic interactions by quantifying the impact of mutating these residues on binding to the Beclin1/BECN1 BH3D, demonstrating that these mutations adversely affect both protein stability and binding. To our knowledge, this is the first study detailing the binding-associated conformational changes and presence of long-range interactions within vBCL2s.

scholarly journals Structural Changes in the Acceptor Site of Photosystem II upon Ca2+/Sr2+ Exchange in the Mn4CaO5 Cluster Site and the Possible Long-Range Interactions

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 371
Author(s):  
Koua
Keyword(s):  
Crystal Structure ◽  
Photosystem Ii ◽  
Long Range ◽  
Electron Acceptor ◽  
Structural Changes ◽  
Acceptor Site ◽  
Oxygen Evolving Complex ◽  
Long Range Interactions ◽  
Structural Perturbations ◽  
Oxygen Evolving

The Mn4CaO5 cluster site in the oxygen-evolving complex (OEC) of photosystem II (PSII) undergoes structural perturbations, such as those induced by Ca2+/Sr2+ exchanges or Ca/Mn removal. These changes have been known to induce long-range positive shifts (between +30 and +150 mV) in the redox potential of the primary quinone electron acceptor plastoquinone A (QA), which is located 40 Å from the OEC. To further investigate these effects, we reanalyzed the crystal structure of Sr-PSII resolved at 2.1 Å and compared it with the native Ca-PSII resolved at 1.9 Å. Here, we focus on the acceptor site and report the possible long-range interactions between the donor, Mn4Ca(Sr)O5 cluster, and acceptor sites.

scholarly journals Seasonal streamflow forecasting by conditioning climatology with precipitation indices

2017 ◽  
Vol 21 (3) ◽  
pp. 1573-1591 ◽  
Author(s):  
Louise Crochemore ◽  
Maria-Helena Ramos ◽  
Florian Pappenberger ◽  
Charles Perrin
Keyword(s):  
Long Range ◽  
Precipitation Forecast ◽  
Low Flow ◽  
Drought Risk ◽  
Streamflow Forecasting ◽  
Streamflow Forecasts ◽  
Precipitation Indices ◽  
Seasonal Streamflow ◽  
Prediction Approach ◽  
The Impact

Abstract. Many fields, such as drought-risk assessment or reservoir management, can benefit from long-range streamflow forecasts. Climatology has long been used in long-range streamflow forecasting. Conditioning methods have been proposed to select or weight relevant historical time series from climatology. They are often based on general circulation model (GCM) outputs that are specific to the forecast date due to the initialisation of GCMs on current conditions. This study investigates the impact of conditioning methods on the performance of seasonal streamflow forecasts. Four conditioning statistics based on seasonal forecasts of cumulative precipitation and the standardised precipitation index were used to select relevant traces within historical streamflows and precipitation respectively. This resulted in eight conditioned streamflow forecast scenarios. These scenarios were compared to the climatology of historical streamflows, the ensemble streamflow prediction approach and the streamflow forecasts obtained from ECMWF System 4 precipitation forecasts. The impact of conditioning was assessed in terms of forecast sharpness (spread), reliability, overall performance and low-flow event detection. Results showed that conditioning past observations on seasonal precipitation indices generally improves forecast sharpness, but may reduce reliability, with respect to climatology. Conversely, conditioned ensembles were more reliable but less sharp than streamflow forecasts derived from System 4 precipitation. Forecast attributes from conditioned and unconditioned ensembles are illustrated for a case of drought-risk forecasting: the 2003 drought in France. In the case of low-flow forecasting, conditioning results in ensembles that can better assess weekly deficit volumes and durations over a wider range of lead times.

scholarly journals Detecting long-range interactions between migrating cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
C. Metzner ◽  
F. Hörsch ◽  
C. Mark ◽  
T. Czerwinski ◽  
A. Winterl ◽  
...  
Keyword(s):  
Nk Cells ◽  
Tumor Cells ◽  
Long Range ◽  
Cooperative Behavior ◽  
Simulated Data ◽  
Movement Direction ◽  
Repulsive Interaction ◽  
Collagen Gels ◽  
Long Range Interactions ◽  
A Cell

AbstractChemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories: For each movement step of a cell relative to the position of a potential target, we compute a p value that quantifies the likelihood of the movement direction under the null-hypothesis of blind migration. The resulting distribution of p values, pooled over all recorded cell trajectories, is then compared to an ensemble of reference distributions in which the positions of targets are randomized. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of our p value method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.

scholarly journals A novel class of translationally invariant spin chains with long-range interactions

2020 ◽  
Vol 2020 (8) ◽  
Author(s):  
B. Basu-Mallick ◽  
F. Finkel ◽  
A. González-López
Keyword(s):  
Long Range ◽  
Degrees Of Freedom ◽  
Spin Chains ◽  
Open Chain ◽  
New Class ◽  
Spin Interactions ◽  
Long Range Interactions ◽  
Spin Reversal ◽  
Twisted Yangian ◽  
Internal Degrees Of Freedom

Abstract We introduce a new class of open, translationally invariant spin chains with long-range interactions depending on both spin permutation and (polarized) spin reversal operators, which includes the Haldane-Shastry chain as a particular degenerate case. The new class is characterized by the fact that the Hamiltonian is invariant under “twisted” translations, combining an ordinary translation with a spin flip at one end of the chain. It includes a remarkable model with elliptic spin-spin interactions, smoothly interpolating between the XXX Heisenberg model with anti-periodic boundary conditions and a new open chain with sites uniformly spaced on a half-circle and interactions inversely proportional to the square of the distance between the spins. We are able to compute in closed form the partition function of the latter chain, thereby obtaining a complete description of its spectrum in terms of a pair of independent su(1|1) and su(m/2) motifs when the number m of internal degrees of freedom is even. This implies that the even m model is invariant under the direct sum of the Yangians Y (gl(1|1)) and Y (gl(0|m/2)). We also analyze several statistical properties of the new chain’s spectrum. In particular, we show that it is highly degenerate, which strongly suggests the existence of an underlying (twisted) Yangian symmetry also for odd m.

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