Soft Matter and Complex Systems Seminar
2006/2007 | 2007/2008 | 2008/2009 | 2009/2010 | 2010/2011 | 2011/2012 | 2012/2013 | 2013/2014 | 2014/2015 | 2015/2016 | 2016/2017 | 2017/2018 | 2018/2019 | 2019/2020 | 2020/2021 | 2021/2022 | 2022/2023 | 2023/2024
2017-06-09 (Friday)
room 17, Pasteura 7 at 09:30 
Łukasz Jasiński (Polish Geological Institute, Wrocław)Flow in a propped fracture – numerical simulations and experiments
Flow patterns in a propped fracture govern transport processes, what is linked to oil/gas extraction or CO2 sequestration effectiveness. Considered fracture is built of two plane walls with one layer of propping agent in between them. The shape of the proppant grains are approximated by circular cylinders.
Firstly, the 2.5D upscaled single phase flow model through such fracture is proposed, solved numerically by means of the Finite Element Method and validated against analytical and 3D numerical solutions. Results of systematic flow calculations are discussed in terms of effective fracture transmissivity as a function of proppant packing fraction, distribution and fracture aperture to proppant diameter ratio.
Secondly, two phase flow experiments are performed as an analogue of flow of supercritical CO2 – H2O through a propped fracture under in-situ conditions.
Firstly, the 2.5D upscaled single phase flow model through such fracture is proposed, solved numerically by means of the Finite Element Method and validated against analytical and 3D numerical solutions. Results of systematic flow calculations are discussed in terms of effective fracture transmissivity as a function of proppant packing fraction, distribution and fracture aperture to proppant diameter ratio.
Secondly, two phase flow experiments are performed as an analogue of flow of supercritical CO2 – H2O through a propped fracture under in-situ conditions.
2017-06-02 (Friday)
room 1.40, Pasteura 5 at 09:30
Paweł R. Dębski (ICHF PAN)Analytical assay for microfluidic diagnostics
Quantitative analytical assays are important in many fields of medical diagnostics and research where they are used to estimate quantitatively the concentration of analytes in samples. In the state of art there are multiple 'analogue' assays [1,2] that use a known correlation between the amplitude of a measured signal (e.g. absorbance of light through a sample cell, electrical conductivity of the sample, time of passage of a sample through a porous bed, intensity of fluorescence, amplitude of force exerted on the sample, etc.) and the concentration of analyte in the sample. In the state of art there are also known 'digital' [3,4] assays in which the concentration of the molecules of analyte, or more generally of target particles being either molecules or colloids, is established with the use of a statistical calculation on the basis of the number of binary (negative or positive) signals recorded from a set of independent partitions of the sample. In the digital assays usually the presence of a single, or a known threshold number of particles, or a threshold concentration of particles in the partition of the sample is amplified to a measurable positive signal.
The method presented here bridges the advantages of the analogue and digital assays in an innovative way to provide for high precision of the estimate of concentration of the analyte while requiring a relatively small number of partitions of the sample. In particular the method relates to quantitation assays that i) provide amplification of a finite number (or concentration) of particles to a measurable signal, and ii) provide a signal, the amplitude of which is related to the number of particles (or their concentration) in the inspected volume. The only requirement for the amplitude is that it is an univocal and monotonically increasing function of the number of particles. The functional dependence may be of many different types, e.g. amplitude being linear in the concentration of particles, square in the concentration of particles, or exponential in the number of particles, or any other kind that satisfies the requirement.
This method is applicable to suitable particles selected from the group comprising or consisting of nucleic acids, peptides, proteins, receptors, enzymes, bacteria, pesticides, drugs, steroids, hormones, lipids, sugars, vitamins or any other suitable particles or combinations thereof.
Here we show the performance of the method for quantitative DNA and RNA assessments based on Polymerase Chain Reaction (PCR) [5]. We propose algorithms of division of the sample into compartments that allow to run such diagnostic tests using tools provided by standard Real Time and digital PCR techniques. Also, we provide analytical tools that synergistically bridge information from analogue and digital signals for improved data analysis.
We show the algorithms for optimal division of the sample and data analysis with experimental and numerical verification, also using Monte Carlo simulations.
REFERENCES:
1. “Real-time PCR in clinical microbiology: applications for routine laboratory testing”, M.J. Espy, et al., Clinical Microbiology Reviews, 19, 165 (2006).
2. “On-Chip, Real-Time, Single-Copy Polymerase Chain Reaction in Picoliter Droplets”, N.R. Beer, et al., Analytical Chemistry, 79, 8471 (2007).
3. “Digital PCR”, B. Vogelstein, K.W. Kinzler, Proceedings of the National Academy of Sciences, 96, 9236 (1999).
4. “Multiplexed Quantification of Nucleic Acids with Large Dynamic Range Using Multivolume Digital RT-PCR on a Rotational SlipChip Tested with HIV and Hepatitis C Viral Load”, F. Shen, et al., Journal of the American Chemical Society, 133, 17705 (2011).
5. “Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction”, K.B. Mullis, F.A. Faloona, Methods in Enzymology, 155, 335, (1987).
6. “Optimized droplet digital CFU assay (ddCFU) provides precise quantification of bacteria over dynamic range of 6 logs and beyond”, Scheller, O., Pacocha, N., Debski, P.R., Ruszczak, A., Kaminski, T.S., and Garstecki P., Lab on Chip, accepted 26 Apr 2017, first published 28 Apr 2017, DOI: 10.1039/C7LC00206H
7. “Calibration-free assays on standard real-time PCR devices”, Debski, P.R., Gewartowski, K., Bajer, S., and Garstecki, P., Scientific Reports, 2017, 7, 44854
8. “Designing and interpretation of digital assays: Concentration of target in the sample and in the source of sample”, Debski, P.R., and Garstecki, P., Biomolecular Detection and Quantification, 2016, 10, 24-30
9. “Rational design of digital assays”, Debski, P.R., Gewartowski, K., Sulima, M., Kaminski, T.S., and Garstecki, P., Analytical Chemistry, 2015, 87 (16), 8203–8209
The method presented here bridges the advantages of the analogue and digital assays in an innovative way to provide for high precision of the estimate of concentration of the analyte while requiring a relatively small number of partitions of the sample. In particular the method relates to quantitation assays that i) provide amplification of a finite number (or concentration) of particles to a measurable signal, and ii) provide a signal, the amplitude of which is related to the number of particles (or their concentration) in the inspected volume. The only requirement for the amplitude is that it is an univocal and monotonically increasing function of the number of particles. The functional dependence may be of many different types, e.g. amplitude being linear in the concentration of particles, square in the concentration of particles, or exponential in the number of particles, or any other kind that satisfies the requirement.
This method is applicable to suitable particles selected from the group comprising or consisting of nucleic acids, peptides, proteins, receptors, enzymes, bacteria, pesticides, drugs, steroids, hormones, lipids, sugars, vitamins or any other suitable particles or combinations thereof.
Here we show the performance of the method for quantitative DNA and RNA assessments based on Polymerase Chain Reaction (PCR) [5]. We propose algorithms of division of the sample into compartments that allow to run such diagnostic tests using tools provided by standard Real Time and digital PCR techniques. Also, we provide analytical tools that synergistically bridge information from analogue and digital signals for improved data analysis.
We show the algorithms for optimal division of the sample and data analysis with experimental and numerical verification, also using Monte Carlo simulations.
REFERENCES:
1. “Real-time PCR in clinical microbiology: applications for routine laboratory testing”, M.J. Espy, et al., Clinical Microbiology Reviews, 19, 165 (2006).
2. “On-Chip, Real-Time, Single-Copy Polymerase Chain Reaction in Picoliter Droplets”, N.R. Beer, et al., Analytical Chemistry, 79, 8471 (2007).
3. “Digital PCR”, B. Vogelstein, K.W. Kinzler, Proceedings of the National Academy of Sciences, 96, 9236 (1999).
4. “Multiplexed Quantification of Nucleic Acids with Large Dynamic Range Using Multivolume Digital RT-PCR on a Rotational SlipChip Tested with HIV and Hepatitis C Viral Load”, F. Shen, et al., Journal of the American Chemical Society, 133, 17705 (2011).
5. “Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction”, K.B. Mullis, F.A. Faloona, Methods in Enzymology, 155, 335, (1987).
6. “Optimized droplet digital CFU assay (ddCFU) provides precise quantification of bacteria over dynamic range of 6 logs and beyond”, Scheller, O., Pacocha, N., Debski, P.R., Ruszczak, A., Kaminski, T.S., and Garstecki P., Lab on Chip, accepted 26 Apr 2017, first published 28 Apr 2017, DOI: 10.1039/C7LC00206H
7. “Calibration-free assays on standard real-time PCR devices”, Debski, P.R., Gewartowski, K., Bajer, S., and Garstecki, P., Scientific Reports, 2017, 7, 44854
8. “Designing and interpretation of digital assays: Concentration of target in the sample and in the source of sample”, Debski, P.R., and Garstecki, P., Biomolecular Detection and Quantification, 2016, 10, 24-30
9. “Rational design of digital assays”, Debski, P.R., Gewartowski, K., Sulima, M., Kaminski, T.S., and Garstecki, P., Analytical Chemistry, 2015, 87 (16), 8203–8209
2017-05-19 (Friday)
room 1.40, Pasteura 5 at 09:30
Rafał Ołdziejewski (CFT PAN)Quantum droplets in ultracold dipolar gases, part II
In recent experiments, an ultracold gas of dysprosium atoms (164Dy) was driven into a regime where dipole-dipole interactions are expected to lead to instability and collapse. Unexpectedly, instead of collapsing, the gas formed spatially ordered structure of stable droplets with high density. We will argue that description of the droplet state requires going beyond the mean field theory and show how to incorporate realistic interatomic interactions in the model.
2017-04-21 (Friday)
room 1.40, Pasteura 5 at 09:30
Mark Mineev-Weinstein (Federal University of Rio Grande do Norte, Brazil)Laplacian growth and Selection in Non-Equilibrium Physics
Selecting a single member from continuum of stationary solutions of the nonlinear Laplacian growth equation (LGE), so that the selected member corresponds to the observable asymptotic pattern, is highly non-trivial and has attracted a lot of attention. This problem was solved in 1986 by adding surface tension and using the WKB-like theory, called “Asymptotics beyond all orders”, developed by Kruskal and others.
Finite-parametric exact solutions of LGE, obtained due to its integrability, made possible to challenge this traditional approach by selecting the correct member from a continuous family without surface tension. This was done in 1998 for a relatively simple geometric pattern, namely the finger propagating in a long rectangular Hele-Shaw channel.
After surveying this background, I will demonstrate very recent (and strange) selection results, obtained in 2014-2016 in a multi-connected moving domain. Using exact solutions for this geometry, we obtained that an arbitrary number of moving bubbles reach (after nonlinear interaction) the same asymptotic velocity, which is precisely twice the velocity of a background flow. (In the singular limit this result is reduced to the finger problem mentioned above.)
Finite-parametric exact solutions of LGE, obtained due to its integrability, made possible to challenge this traditional approach by selecting the correct member from a continuous family without surface tension. This was done in 1998 for a relatively simple geometric pattern, namely the finger propagating in a long rectangular Hele-Shaw channel.
After surveying this background, I will demonstrate very recent (and strange) selection results, obtained in 2014-2016 in a multi-connected moving domain. Using exact solutions for this geometry, we obtained that an arbitrary number of moving bubbles reach (after nonlinear interaction) the same asymptotic velocity, which is precisely twice the velocity of a background flow. (In the singular limit this result is reduced to the finger problem mentioned above.)
2017-04-19 (Wednesday)
room 1.40, Pasteura 5 at 09:30
Piotr Morawiecki (Faculty of Physics, UW)Forward and backward evolution of river networks, part II
Water headward erosion is a phenomenon responsible for extending the river valleyinto the hillside and hence creating a ramified drainage networks. Interestingly, thisprocess can be modeled in terms of the geodesic growth of thin lines in a Poissonian field.During seminar I'm going to present results of my bachelor thesis focusing on numericalanalysis of the river network evolution for different growth laws and different bifurcationrules, which determine the moments when the stream bifurcates into two daughterbranches. Investigation includes inverse problem formulated as: can the growth law of ariver be inferred from the analysis of the geometrical structure of its network?
2017-04-07 (Friday)
room 1.40, Pasteura 5 at 09:30
Piotr Morawiecki (Faculty of Physics, UW)Forward and backward evolution of river networks
Water headward erosion is a phenomenon responsible for extending the river valley into the hillside and hence creating a ramified drainage networks. Interestingly, this process can be modeled in terms of the geodesic growth of thin lines in a Poissonian field. During seminar I'm going to present results of my bachelor thesis focusing on numerical analysis of the river network evolution for different growth laws and different bifurcation rules, which determine the moments when the stream bifurcates into two daughter branches. Investigation includes inverse problem formulated as: can the growth law of a river be inferred from the analysis of the geometrical structure of its network?
2017-03-31 (Friday)
room 1.40, Pasteura 5 at 09:30
Gustavo C. Abade 1 and Wojciech W. Grabowski 1,2 (1. Institute of Geophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland; 2. National Center for Atmospheric Research NCAR Boulder, Colorado, USA)Diffusional growth of cloud droplets in turbulent clouds
This talk will discuss spectral broadening of droplet size distributions in turbulent clouds through a mechanism referred to as the eddy hopping. The key idea, suggested a quarter century ago, is that droplets arriving at a given location within a turbulent cloud follow different trajectories and thus experience different growth histories, and that this leads to a significant spectral broadening. In this study, the adiabatic parcel model with super-droplets is used to contrast droplet growth with and without turbulence. Turbulence inside the parcel is described by two parameters: i) the dissipation rate of the turbulent kinetic energy, and ii) the linear extent of the parcel. As expected, adiabatic parcel without turbulence produces extremely narrow droplet spectra. In the turbulent parcel, a stochastic scheme is used to account for vertical velocity fluctuations that lead to local supersaturation fluctuations for each super-droplet. These fluctuations mimic the impact of droplets hopping turbulent eddies in a natural cloud. The representation of eddy hopping developed here can be included in a straightforward way in the subgrid-scale scheme of a Lagrangian large-eddy simulation cloud model and may lead to a significant acceleration of simulated rain development through collision/coalescence.
2017-03-24 (Friday)
room 0.03a, Pasteura 5 at 09:30
Jan Chwedeńczuk (IFT UW)Violation of Bell inequalities in a many-body system of massive particles, part II
Entanglement between two separate systems is a necessary resource to violate a Bell inequality in a test of local realism. We demonstrate that to overcome the Bell bound, this correlation must be accompanied by the entanglementbetween the constituent particles. This happens whenever a super-selection rule imposes a constraint on feasible local operations. Next, we propose an experiment, where the violation of the Bell inequality occurs between two distant parts of a many-body system of massive particles. The source of correlated atoms is a spinor Bose-Einstein condensate residing in an optical lattice, as in: M. Bonneau, et al., Phys. Rev. A 87, 061603 (2013). We characterize the complete experimental procedure, together with the local operations and the measurements, necessary to run the Bell test. We show how the amplitude of the violation of the Bell inequality depends on the strengths of the two-body correlations and on the number of scattered pairs.
2017-03-17 (Friday)
room 1.40, Pasteura 5 at 09:30
Jan Chwedeńczuk (IFT UW)Violation of Bell inequalities in a many-body system of massive particles
Entanglement between two separate systems is a necessary resource to violate a Bell inequality in a test of local realism. We demonstrate that to overcome the Bell bound, this correlation must be accompanied by the entanglementbetween the constituent particles. This happens whenever a super-selection rule imposes a constraint on feasible local operations. Next, we propose an experiment, where the violation of the Bell inequality occurs between two distant parts of a many-body system of massive particles. The source of correlated atoms is a spinor Bose-Einstein condensate residing in an optical lattice, as in: M. Bonneau, et al., Phys. Rev. A 87, 061603 (2013). We characterize the complete experimental procedure, together with the local operations and the measurements, necessary to run the Bell test. We show how the amplitude of the violation of the Bell inequality depends on the strengths of the two-body correlations and on the number of scattered pairs.
2017-03-10 (Friday)
room 1.40, Pasteura 5 at 09:30
Paweł Kondratiuk (IFT UW)Weakly nonlinear analysis of the reactive-infiltration instability
Alteration of a rock composition can be caused by external fluids, which infiltrate the rock and dissolve some of its minerals. The dissolution does not proceed uniformly in the whole volume of the rock. Instead, a dissolution front forms, which is a quasi-2D surface between the altered (dissolved) and unaltered parts of the rock. All the chemical activity concentrates in the vicinity of the front. Linear stability analysis (LSA) of such a dissolution front was already studied in the 1980s. It was shown that whenever the altered rock is more permeable than the primary rock, a flat dissolution front is unstable and spontaneously breaks up into an array of protrusions. The characteristic distance between these protrusions was predicted. The further evolution of the system is dominated by strong nonlinear couplings between the fluid flow, reactant transport, and the porous matrix evolution. Therefore it was mostly studied by numerical simulations, and apart from the LSA, very few strict analytical results were obtained. In our research we aim to fill a part of this gap. We derive a weakly nonlinear theory of reactive infiltration, which goes one step further than the traditional LSA. Analyzing nonlinear couplings between two most important harmonic modes of the front perturbation, we study the first effects of nonlinearities: competition between the protrusions, and a symmetry breakup between the leading and the trailing parts of the dissolution front. We estimate the moment when the linear description of the process becomes inappropriate.