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Three-dimensional Monte Carlo model of the coffee-ring effect in evaporating colloidal droplets.

ABSTRACT: The residual deposits usually left near the contact line after pinned sessile colloidal droplet evaporation are commonly known as a "coffee-ring" effect. However, there were scarce attempts to simulate the effect, and the realistic fully three-dimensional (3D) model is lacking since the complex drying process seems to limit the further investigation. Here we develop a stochastic method to model the particle deposition in evaporating a pinned sessile colloidal droplet. The 3D Monte Carlo model is developed in the spherical-cap-shaped droplet. In the algorithm, the analytical equations of fluid flow are used to calculate the probability distributions for the biased random walk, associated with the drift-diffusion equations. We obtain the 3D coffee-ring structures as the final results of the simulation and analyze the dependence of the ring profile on the particle volumetric concentration and sticking probability.

SUBMITTER: Crivoi A

PROVIDER: S-EPMC3945784 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Three-dimensional Monte Carlo model of the coffee-ring effect in evaporating colloidal droplets.

Crivoi A A Duan Fei F

Scientific reports 20140307

The residual deposits usually left near the contact line after pinned sessile colloidal droplet evaporation are commonly known as a "coffee-ring" effect. However, there were scarce attempts to simulate the effect, and the realistic fully three-dimensional (3D) model is lacking since the complex drying process seems to limit the further investigation. Here we develop a stochastic method to model the particle deposition in evaporating a pinned sessile colloidal droplet. The 3D Monte Carlo model is ...[more]

PMID: 24603647

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Project description:BackgroundLong-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C) and its variant Hi-C are techniques used to measure the interaction frequency (IF) between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization.ResultsWe formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density) were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs) corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH.ConclusionsWe believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional conformations, MCMC5C allows researchers to reliably interpret the result of their assay and contrast conformations under different conditions.Availabilityhttp://Dostielab.biochem.mcgill.ca.

Project description:BackgroundPatients with advanced neuroendocrine tumors (NETs) of the midgut are suitable candidates for 177Lu-DOTATOC therapy. Integrated SPECT/CT systems have the potential to help improve the accuracy of patient-specific tumor dosimetry. Dose estimations to target organs are generally performed using the Medical Internal Radiation Dose scheme. We present a novel Monte Carlo-based voxel-wise dosimetry approach to determine organ- and tumor-specific total tumor doses (TTD).MethodsA cohort of 14 patients with histologically confirmed metastasized NETs of the midgut (11 men, 3 women, 62.3 ± 11.0 years of age) underwent a total of 39 cycles of 177Lu-DOTATOC therapy (mean 2.8 cycles, SD ± 1 cycle). After the first cycle of therapy, regions of interest were defined manually on the SPECT/CT images for the kidneys, the spleen, and all 198 tracer-positive tumor lesions in the field of view. Four SPECT images, taken at 4 h, 24 h, 48 h and 72 h after injection of the radiopharmaceutical, were used to determine their effective half-lives in the structures of interest. The absorbed doses were calculated by a three-dimensional dosimetry method based on Monte Carlo simulations. TTD was calculated as the sum of all products of single tumor doses with single tumor volumes divided by the sum of all tumor volumes.ResultsThe average dose values per cycle were 3.41 ± 1.28 Gy (1.91-6.22 Gy) for the kidneys, 4.40 ± 2.90 Gy (1.14-11.22 Gy) for the spleen, and 9.70 ± 8.96 Gy (1.47-39.49 Gy) for all 177Lu-DOTATOC-positive tumor lesions. Low- and intermediate-grade tumors (G 1-2) absorbed a higher TTD compared to high-grade tumors (G 3) (signed-rank test, p = < 0.05). The pre-therapeutic chromogranin A (CgA) value and the TTD correlated significantly (Pearson correlation: = 0.67, p = 0.01). Higher TTD resulted in a significant decrease of CgA after therapy.ConclusionThese results suggest that Monte Carlo-based voxel-wise dosimetry is a very promising tool for predicting the absorbed TTD based on histological and clinical parameters.

Dataset Information

Three-dimensional Monte Carlo model of the coffee-ring effect in evaporating colloidal droplets.

Publications

Three-dimensional Monte Carlo model of the coffee-ring effect in evaporating colloidal droplets.

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