Gary W. Slater
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Diffusive spreading of a polydisperse polymer solution in a channel Open
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
Polymer (imperfect) single-file diffusion: A phase diagram Open
We use Langevin dynamics (LD) simulations to investigate single-file diffusion (SFD) in a dilute solution of flexible linear polymers inside a narrow tube with periodic boundary conditions (a torus). The transition from SFD, where the time…
Methods for separation of polymeric compounds Open
Recently two techniques using free solution electrophoresis to separate charged-uncharged polymer conjugates have proven successful: End Labeled Free Solution Electrophoresis (ELFSE) for DNA sequencing, and Free Solution Conjugate Electrop…
View article: Measurement of proton-carbon forward scattering in a proof-of-principle test of the EMPHATIC spectrometer
Measurement of proton-carbon forward scattering in a proof-of-principle test of the EMPHATIC spectrometer Open
The next generation of long-baseline neutrino experiments will be capable of\nprecision measurements of neutrino oscillation parameters, precision\nneutrino-nucleus scattering, and unprecedented sensitivity to physics beyond\nthe Standard …
Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics Open
We investigate the rod orientation during translocation with electrohydrodynamics included using hybrid Langevin dynamics and lattice Boltzmann simulations.
Estimating the Steady State Diffusion Coefficient Using Data from the\n Transient Anomalous Regime Open
When particles/molecules diffuse in systems that contain obstacles, the\nsteady-state regime (during which the mean-square displacement scales linearly\nwith time, $\\left \\sim t$) is preceded by a transient regime. It\nis common to chara…
Estimating the Steady State Diffusion Coefficient Using Data from the Transient Anomalous Regime Open
When particles/molecules diffuse in systems that contain obstacles, the steady-state regime (during which the mean-square displacement scales linearly with time, $\left \sim t$) is preceded by a transient regime. It is common to characteri…
Ratcheting charged polymers through symmetric nanopores using pulsed fields: Designing a low pass filter for concentrating DNA Open
We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed…
Voltage-driven translocation: Defining a capture radius Open
Analyte translocation involves three phases: (i) diffusion in the loading solution, (ii) capture by the pore, and (iii) threading. The capture process remains poorly characterized because it cannot easily be visualized or inferred from ind…
Random walk on a lattice in the presence of obstacles: The short-time transient regime, anomalous diffusion and crowding Open
The diffusion of a particle in a crowded environment typically proceeds through three regimes: for very short times the particle diffuses freely until it collides with an obstacle for the first time, while for very long times diffusion the…
Reducing the variance in the translocation times by prestretching the polymer Open
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 achi…
Taking stock of avian responses to Puget Sound estuary restoration: inventory and assessment Open
Tidally-influenced estuarine habitats in the Pacific Northwest are ecologically important wintering and migratory stopover habitat for shorebirds, waterfowl and other marine birds, yet there is limited understanding of how estuarine restor…
Rotation-Induced Macromolecular Spooling of DNA Open
This is an Open Access Article. It is published by American Physical Society under the Creative Commons Attribution 4.0 Unported Licence (CC BY). Full details of this licence are available at: http://creativecommons.org/licenses/by/4.0/
Spontaneous Phase Separation of Cocultured Cell Mixtures <i>In vitro</i> Open
During Embryogenesis, cells undergo constant organizational remodelling. Biochemical and biophysical guidance cues act in tandem to guide migration and morphogenesis into distinct cellular patterns. It has been shown that various cell type…
Physical confinement signals regulate the organization of stem cells in three dimensions Open
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 c…
Supplementary material from "Physical confinement signals regulate the organization of stem cells in three dimensions" Open
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 cu…
ESPResSo input parameters from Physical confinement signals regulate the organization of stem cells in three dimensions Open
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 cu…