Implementation of the Lees-Edwards boundary condition for shear flow simulation in the ESPResSo M... more Implementation of the Lees-Edwards boundary condition for shear flow simulation in the ESPResSo Molecular Dynamics simulation packages. http://espressomd.org/ This implementation is presented in the article "Lees-Edwards boundary conditions for translation invariant shear flow: implementation and transport properties" by Sebastian Bindgen, Erin Koos, Florian Weik, Rudolf Weeber, and Pierre de Buyl. The article will be available upon publication on the ORCID profile of the authors: Sebastian Bindgen https://orcid.org/0000-0002-5861-0990 Erin Koos https://orcid.org/0000-0002-2468-2312 Pierre de Buyl http://orcid.org/0000-0002-6640-6463
During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environmen... more During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environment of a blastocyst. Embryonic stem cells (ESCs) are derived from the ICM, and mimicking embryogenesis <i>in vitro</i>, mouse ESCs (mESCs) are often cultured in hanging droplets. This promotes the formation of a spheroid as the cells sediment and aggregate owing to increased physical confinement and cell-cell interactions. In contrast, mESCs form two-dimensional monolayers on flat substrates and it remains unclear if the difference in organization is owing to a lack of physical confinement or increased cell-substrate versus cell-cell interactions. Employing microfabricated substrates, we demonstrate that a single geometric degree of physical confinement on a surface can also initiate spherogenesis. Experiment and computation reveal that a balance between cell-cell and cell-substrate interactions finely controls the morphology and organization of mESC aggregates. Physical confinement is thus an important regulatory cue in the three-dimensional organization and morphogenesis of developing cells.
We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacin... more We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the reg...
Submitted for the MAR13 Meeting of The American Physical Society Polymer Translocation Through a ... more Submitted for the MAR13 Meeting of The American Physical Society Polymer Translocation Through a Nanopore from a Crosslinked Gel to Free Solution DAVID SEAN, HENDRICK W. DE HAAN, GARY W. SLATER, University of Ottawa — We present results from a computer simulation study of DNA translocation through a nanopore in a membrane that separates a gel region from free solution. The gel is modeled by a square lattice of fixed poles such that the pore size is set by the lattice spacing. Starting with the DNA on the gel side, we examine how the gel pore size affects the dynamics of translocation. We find that due to entropic and frictional forces, the mean translocation time is affected by gel pore size. Since the spatial restrictions imposed by the gel limit the dynamics to one-dimensional motion on the cis side, variations in the width of the distribution of translocations times are also observed. David Sean University of Ottawa Date submitted: 09 Nov 2012 Electronic form version 1.4
We investigate the chemical equilibria of weak polyelectrolyte nanogels with reaction ensemble Mo... more We investigate the chemical equilibria of weak polyelectrolyte nanogels with reaction ensemble Monte Carlo simulations. With this method, the chemical identity of the nanogel monomers can change between neutral or charged following the acid-base equilibrium reaction HA ⇌ A− + H+. We investigate the effect of changing the chemical equilibria by modifying the dissociation constant K a . These simulations allow for the extraction of static properties like swelling equilibria and the way in which charge—both monomer and ionic—is distributed inside the nanogel. Our findings reveal that, depending on the value of K a , added salt can either increase or decrease the gel size. Using the calculated mean-charge configurations of the nanogel from the reaction ensemble simulation as a quenched input to coupled lattice-Boltzmann molecular dynamics simulations, we investigate dynamical nanogel properties such as the electrophoretic mobility μ and the diffusion coefficient D.
This article recapitulates the state of the art regarding simulations of ionization equilibria of... more This article recapitulates the state of the art regarding simulations of ionization equilibria of weak polyelectrolyte solutions and gels. We start out by reviewing the essential thermodynamics of ionization and...
Langevin dynamics simulations of polymer translocation are performed where the polymer is stretch... more Langevin dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the trans side. Under the influence of stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields a reduced variation in translocation times relative to the mean translocation time. This effect is explored for different ratios of the amplitude of thermal fluctuations to driving forces to control for the relative influence of the thermal path sampled by the polymer. Since the variance in translocation times is due to contributions coming from sampling both thermal noise and initial conformations, our sim...
We present a computer simulation study of polymer translocation in a situation where the chain is... more We present a computer simulation study of polymer translocation in a situation where the chain is initially confined to a closed cylindrical cavity in order to reduce the impact of conformational diversity on the translocation times. In particular, we investigate how the coefficient of variation of the distribution of translocation times can be minimized by optimizing both the volume and the aspect ratio of the cavity. Interestingly, this type of confinement sometimes increases the number and impact of hairpin conformations such that the fluctuations in the translocation process do not follow a power law in time (for instance, these fluctuations can even vary non-monotonically with time). We develop a tension-propagation model for a polymer compressed into such a confining volume and find that its predictions are in good agreement with our simulation results in the experimentally relevant strongly driven limit. Both the theoretical calculations and the simulation data yield a minimu...
We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into ... more We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into a cross-linked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. Thus, this setup combines the mechanics of gel electrophoresis with nanopore translocation. However, contrary to typical gel electrophoresis scenarios, the effect of the field is localized in the immediate vicinity of the nanopore and becomes negligible inside the gel matrix. Thus, we investigate the process by which a semiflexible polymer can be pushed into a gel matrix via a localized field and we describe how the dynamics of gel penetration depends upon the field intensity, polymer stiffness, and gel pore size. Our simulation results show that a semiflexible polymer enters the gel region with two distinct mechanisms depending upon the ratio between the bending length scale and the gel pore size. In both regimes, the gel fibers cause a net increase in the mean translocation time. Interestingly, the translocation rate is found to be constant (a potentially useful feature for many applications) during the predominant part of the translocation process when the polymer is stiff over a length scale comparable to the gel pore size.
Journal of the Royal Society, Interface, Oct 1, 2016
During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environmen... more During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environment of a blastocyst. Embryonic stem cells (ESCs) are derived from the ICM, and mimicking embryogenesis in vitro, mouse ESCs (mESCs) are often cultured in hanging droplets. This promotes the formation of a spheroid as the cells sediment and aggregate owing to increased physical confinement and cell-cell interactions. In contrast, mESCs form two-dimensional monolayers on flat substrates and it remains unclear if the difference in organization is owing to a lack of physical confinement or increased cell-substrate versus cell-cell interactions. Employing microfabricated substrates, we demonstrate that a single geometric degree of physical confinement on a surface can also initiate spherogenesis. Experiment and computation reveal that a balance between cell-cell and cell-substrate interactions finely controls the morphology and organization of mESC aggregates. Physical confinement is thus an im...
Gel electrophoresis separates partially denatured DNA fragments based on chemical sequence. Upon ... more Gel electrophoresis separates partially denatured DNA fragments based on chemical sequence. Upon an increase in temperature, AT-rich regions melt into two strands which is thought to be the main contributor to the rapid reduction of the fragment's mobility. The reduction in mobility is often predicted from the average number of denatured bases regardless of their positions. We re-visit the theoretical basis of this approach and determine that the analysis only holds for denatured domains that occur at the ends. Langevin Dynamics simulations are used to study the effect that the placement of the melted regions has on the mobility by discriminating between denatured domains which occur in the middle of the fragment (bubbles) and at the ends (split-ends). It is found that the split-ends dominate the blocking mechanism. In addition, we find a novel conformation (the ``squid'') which seems to be responsible for the blocking at high fields.
Implementation of the Lees-Edwards boundary condition for shear flow simulation in the ESPResSo M... more Implementation of the Lees-Edwards boundary condition for shear flow simulation in the ESPResSo Molecular Dynamics simulation packages. http://espressomd.org/ This implementation is presented in the article "Lees-Edwards boundary conditions for translation invariant shear flow: implementation and transport properties" by Sebastian Bindgen, Erin Koos, Florian Weik, Rudolf Weeber, and Pierre de Buyl. The article will be available upon publication on the ORCID profile of the authors: Sebastian Bindgen https://orcid.org/0000-0002-5861-0990 Erin Koos https://orcid.org/0000-0002-2468-2312 Pierre de Buyl http://orcid.org/0000-0002-6640-6463
During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environmen... more During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environment of a blastocyst. Embryonic stem cells (ESCs) are derived from the ICM, and mimicking embryogenesis <i>in vitro</i>, mouse ESCs (mESCs) are often cultured in hanging droplets. This promotes the formation of a spheroid as the cells sediment and aggregate owing to increased physical confinement and cell-cell interactions. In contrast, mESCs form two-dimensional monolayers on flat substrates and it remains unclear if the difference in organization is owing to a lack of physical confinement or increased cell-substrate versus cell-cell interactions. Employing microfabricated substrates, we demonstrate that a single geometric degree of physical confinement on a surface can also initiate spherogenesis. Experiment and computation reveal that a balance between cell-cell and cell-substrate interactions finely controls the morphology and organization of mESC aggregates. Physical confinement is thus an important regulatory cue in the three-dimensional organization and morphogenesis of developing cells.
We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacin... more We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the reg...
Submitted for the MAR13 Meeting of The American Physical Society Polymer Translocation Through a ... more Submitted for the MAR13 Meeting of The American Physical Society Polymer Translocation Through a Nanopore from a Crosslinked Gel to Free Solution DAVID SEAN, HENDRICK W. DE HAAN, GARY W. SLATER, University of Ottawa — We present results from a computer simulation study of DNA translocation through a nanopore in a membrane that separates a gel region from free solution. The gel is modeled by a square lattice of fixed poles such that the pore size is set by the lattice spacing. Starting with the DNA on the gel side, we examine how the gel pore size affects the dynamics of translocation. We find that due to entropic and frictional forces, the mean translocation time is affected by gel pore size. Since the spatial restrictions imposed by the gel limit the dynamics to one-dimensional motion on the cis side, variations in the width of the distribution of translocations times are also observed. David Sean University of Ottawa Date submitted: 09 Nov 2012 Electronic form version 1.4
We investigate the chemical equilibria of weak polyelectrolyte nanogels with reaction ensemble Mo... more We investigate the chemical equilibria of weak polyelectrolyte nanogels with reaction ensemble Monte Carlo simulations. With this method, the chemical identity of the nanogel monomers can change between neutral or charged following the acid-base equilibrium reaction HA ⇌ A− + H+. We investigate the effect of changing the chemical equilibria by modifying the dissociation constant K a . These simulations allow for the extraction of static properties like swelling equilibria and the way in which charge—both monomer and ionic—is distributed inside the nanogel. Our findings reveal that, depending on the value of K a , added salt can either increase or decrease the gel size. Using the calculated mean-charge configurations of the nanogel from the reaction ensemble simulation as a quenched input to coupled lattice-Boltzmann molecular dynamics simulations, we investigate dynamical nanogel properties such as the electrophoretic mobility μ and the diffusion coefficient D.
This article recapitulates the state of the art regarding simulations of ionization equilibria of... more This article recapitulates the state of the art regarding simulations of ionization equilibria of weak polyelectrolyte solutions and gels. We start out by reviewing the essential thermodynamics of ionization and...
Langevin dynamics simulations of polymer translocation are performed where the polymer is stretch... more Langevin dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the trans side. Under the influence of stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields a reduced variation in translocation times relative to the mean translocation time. This effect is explored for different ratios of the amplitude of thermal fluctuations to driving forces to control for the relative influence of the thermal path sampled by the polymer. Since the variance in translocation times is due to contributions coming from sampling both thermal noise and initial conformations, our sim...
We present a computer simulation study of polymer translocation in a situation where the chain is... more We present a computer simulation study of polymer translocation in a situation where the chain is initially confined to a closed cylindrical cavity in order to reduce the impact of conformational diversity on the translocation times. In particular, we investigate how the coefficient of variation of the distribution of translocation times can be minimized by optimizing both the volume and the aspect ratio of the cavity. Interestingly, this type of confinement sometimes increases the number and impact of hairpin conformations such that the fluctuations in the translocation process do not follow a power law in time (for instance, these fluctuations can even vary non-monotonically with time). We develop a tension-propagation model for a polymer compressed into such a confining volume and find that its predictions are in good agreement with our simulation results in the experimentally relevant strongly driven limit. Both the theoretical calculations and the simulation data yield a minimu...
We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into ... more We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into a cross-linked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. Thus, this setup combines the mechanics of gel electrophoresis with nanopore translocation. However, contrary to typical gel electrophoresis scenarios, the effect of the field is localized in the immediate vicinity of the nanopore and becomes negligible inside the gel matrix. Thus, we investigate the process by which a semiflexible polymer can be pushed into a gel matrix via a localized field and we describe how the dynamics of gel penetration depends upon the field intensity, polymer stiffness, and gel pore size. Our simulation results show that a semiflexible polymer enters the gel region with two distinct mechanisms depending upon the ratio between the bending length scale and the gel pore size. In both regimes, the gel fibers cause a net increase in the mean translocation time. Interestingly, the translocation rate is found to be constant (a potentially useful feature for many applications) during the predominant part of the translocation process when the polymer is stiff over a length scale comparable to the gel pore size.
Journal of the Royal Society, Interface, Oct 1, 2016
During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environmen... more During embryogenesis, the spherical inner cell mass (ICM) proliferates in the confined environment of a blastocyst. Embryonic stem cells (ESCs) are derived from the ICM, and mimicking embryogenesis in vitro, mouse ESCs (mESCs) are often cultured in hanging droplets. This promotes the formation of a spheroid as the cells sediment and aggregate owing to increased physical confinement and cell-cell interactions. In contrast, mESCs form two-dimensional monolayers on flat substrates and it remains unclear if the difference in organization is owing to a lack of physical confinement or increased cell-substrate versus cell-cell interactions. Employing microfabricated substrates, we demonstrate that a single geometric degree of physical confinement on a surface can also initiate spherogenesis. Experiment and computation reveal that a balance between cell-cell and cell-substrate interactions finely controls the morphology and organization of mESC aggregates. Physical confinement is thus an im...
Gel electrophoresis separates partially denatured DNA fragments based on chemical sequence. Upon ... more Gel electrophoresis separates partially denatured DNA fragments based on chemical sequence. Upon an increase in temperature, AT-rich regions melt into two strands which is thought to be the main contributor to the rapid reduction of the fragment's mobility. The reduction in mobility is often predicted from the average number of denatured bases regardless of their positions. We re-visit the theoretical basis of this approach and determine that the analysis only holds for denatured domains that occur at the ends. Langevin Dynamics simulations are used to study the effect that the placement of the melted regions has on the mobility by discriminating between denatured domains which occur in the middle of the fragment (bubbles) and at the ends (split-ends). It is found that the split-ends dominate the blocking mechanism. In addition, we find a novel conformation (the ``squid'') which seems to be responsible for the blocking at high fields.
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