Publications by Tyler Shendruk

Multi-particle collision dynamics algorithm for nematic fluids.

Soft matter 11 (2015) 5101-5110

TN Shendruk, JM Yeomans

Research on transport, self-assembly and defect dynamics within confined, flowing liquid crystals requires versatile and computationally efficient mesoscopic algorithms to account for fluctuating nematohydrodynamic interactions. We present a multi-particle collision dynamics (MPCD) based algorithm to simulate liquid-crystal hydrodynamic and director fields in two and three dimensions. The nematic-MPCD method is shown to successfully reproduce the features of a nematic liquid crystal, including a nematic-isotropic phase transition with hysteresis in 3D, defect dynamics, isotropic Frank elastic coefficients, tumbling and shear alignment regimes and boundary condition-dependent order parameter fields.

Simulating the entropic collapse of coarse-grained chromosomes.

Biophysical journal 108 (2015) 810-820

TN Shendruk, M Bertrand, HW de Haan, JL Harden, GW Slater

Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.

Hydrodynamic chromatography and field flow fractionation in finite aspect ratio channels.

Journal of chromatography. A 1339 (2014) 219-223

TN Shendruk, GW Slater

Hydrodynamic chromatography (HC) and field-flow fractionation (FFF) separation methods are often performed in 3D rectangular channels, though ideal retention theory assumes 2D systems. Devices are commonly designed with large aspect ratios; however, it can be unavoidable or desirable to design rectangular channels with small or even near-unity aspect ratios. To assess the significance of finite-aspect ratio effects and interpret experimental retention results, an ideal, analytical retention theory is needed. We derive a series solution for the ideal retention ratio of HC and FFF rectangular channels. Rather than limiting devices' ability to resolve samples, our theory predicts that retention curves for normal-mode FFF are well approximated by the infinite plate solution and that the performance of HC is actually improved. These findings suggest that FFF devices need not be designed with large aspect ratios and that rectangular HC channels are optimal when the aspect ratio is unity.