288 research outputs found
Adaptive Resolution Simulation of Liquid Water
We present a multiscale simulation of liquid water where a spatially adaptive
molecular resolution procedure allows for changing on-the-fly from a
coarse-grained to an all-atom representation. We show that this approach leads
to the correct description of all essential thermodynamic and structural
properties of liquid water.Comment: 4 pages, 3 figures; changed figure
Estimating population size of the cave shrimp Troglocaris anophthalmus (Crustacea, Decapoda, Caridea) using mark–release–recapture data
Estimación del tamaño de la población del camarón cavernícola Troglocaris anophthalmus (Crustacea, Decapoda, Caridea) mediante la utilización de datos de marcaje, liberación y recaptura
Se desconoce el tamaño de la población de numerosos invertebrados acuáticos cavernícolas que son vulnerables a la contaminación de las aguas subterráneas provocada por las actividades antropogénicas. En este estudio estimamos el tamaño de la población del camarón de agua dulce Troglocaris anophthalmus sontica (Crustacea, Decapoda, Caridea) mediante las técnicas de marcaje, liberación y recaptura. La subespecie se estudió en la Vipavaska jama (cueva de Vipava), en Eslovenia, y se calcularon la proporción de sexos y la distribución por edad. Incluso tras considerar el límite inferior de los intervalos de confianza, se halló un gran abundancia de camarones. No obstante, no se encontraron indicios de que haya diferencias en cuanto a la abundancia de camarón entre verano e invierno. La población estaba formada predominantemente por hembras. La facilidad de la captura y las elevadas cifras de población indican que estos camarones podrían utilizarse como bioindicadores en los ecosistemas cavernícolas.Population size estimates are lacking for many small cave–dwelling aquatic invertebrates that are vulnerable to groundwater contamination from anthropogenic activities. Here we estimated the population size of freshwater shrimp Troglocaris anophthalmus sontica (Crustacea, Decapoda, Caridea) based on mark–release–recapture techniques. The subspecies was investigated in Vipavska jama (Vipava cave), Slovenia, with estimates of sex ratio and age distribution. A high abundance of shrimps was found even after considering the lower limit of the confidence intervals. However, we found no evidence of differences in shrimp abundances between summer and winter. The population was dominated by females. Ease of capture and abundant population numbers indicate that these cave shrimps may be useful as a bioindicator in cave ecosystems.Estimación del tamaño de la población del camarón cavernícola Troglocaris anophthalmus (Crustacea, Decapoda, Caridea) mediante la utilización de datos de marcaje, liberación y recaptura
Se desconoce el tamaño de la población de numerosos invertebrados acuáticos cavernícolas que son vulnerables a la contaminación de las aguas subterráneas provocada por las actividades antropogénicas. En este estudio estimamos el tamaño de la población del camarón de agua dulce Troglocaris anophthalmus sontica (Crustacea, Decapoda, Caridea) mediante las técnicas de marcaje, liberación y recaptura. La subespecie se estudió en la Vipavaska jama (cueva de Vipava), en Eslovenia, y se calcularon la proporción de sexos y la distribución por edad. Incluso tras considerar el límite inferior de los intervalos de confianza, se halló un gran abundancia de camarones. No obstante, no se encontraron indicios de que haya diferencias en cuanto a la abundancia de camarón entre verano e invierno. La población estaba formada predominantemente por hembras. La facilidad de la captura y las elevadas cifras de población indican que estos camarones podrían utilizarse como bioindicadores en los ecosistemas cavernícolas
Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly
We present a new adaptive resolution technique for efficient particle-based
multiscale molecular dynamics (MD) simulations. The presented approach is
tailor-made for molecular systems where atomistic resolution is required only
in spatially localized domains whereas a lower mesoscopic level of detail is
sufficient for the rest of the system. Our method allows an on-the-fly
interchange between a given molecule's atomic and coarse-grained level of
description, enabling us to reach large length and time scales while spatially
retaining atomistic details of the system. The new approach is tested on a
model system of a liquid of tetrahedral molecules. The simulation box is
divided into two regions: one containing only atomistically resolved
tetrahedral molecules, the other containing only one particle coarse-grained
spherical molecules. The molecules can freely move between the two regions
while changing their level of resolution accordingly. The coarse-grained and
the atomistically resolved systems have the same statistical properties at the
same physical conditions.Comment: 17 pages, 11 figures, 5 table
Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution
We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a refer- ence system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects
Adaptive Resolution Molecular Dynamics Technique: Down to the Essential
We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region
Capillary filling with wall corrugations] Capillary filling in microchannels with wall corrugations: A comparative study of the Concus-Finn criterion by continuum, kinetic and atomistic approaches
We study the impact of wall corrugations in microchannels on the process of
capillary filling by means of three broadly used methods - Computational Fluid
Dynamics (CFD), Lattice-Boltzmann Equations (LBE) and Molecular Dynamics (MD).
The numerical results of these approaches are compared and tested against the
Concus-Finn (CF) criterion, which predicts pinning of the contact line at
rectangular ridges perpendicular to flow for contact angles theta > 45. While
for theta = 30, theta = 40 (no flow) and theta = 60 (flow) all methods are
found to produce data consistent with the CF criterion, at theta = 50 the
numerical experiments provide different results. Whilst pinning of the liquid
front is observed both in the LB and CFD simulations, MD simulations show that
molecular fluctuations allow front propagation even above the critical value
predicted by the deterministic CF criterion, thereby introducing a sensitivity
to the obstacle heigth.Comment: 25 pages, 8 figures, Langmuir in pres
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