arXiv subjects

Oliver Henrich

Publications and source records attributed to Oliver Henrich.

13 recordsLinked to original sources

arXiv2026

Shape, confinement and inertia effects on the dynamics of a driven spheroid in a viscous fluid

The dynamics of anisotropic particles in viscous flows underpin a wide range of processes in soft matter, microfluidics, and targeted drug delivery. Here, we investigate the motion of externally driven prolate and oblate spheroids suspended in a Newtonian fluid and confined within a square microchannel. Using lattice Boltzmann simulations, complemented by far-field hydrodynamic theory based on superposition of wall interactions, we systematically quantify how particle aspect ratio, strength of confinement, and fluid inertia influence the dynamics of a spheroid. For unconfined spheroids, we show that the translational velocity is maximized not for a sphere but for a prolate (end-on) or oblate (broadside-on) spheroid of a specific aspect ratio. Under confinement, the optimal aspect ratio shifts toward oblate shapes due to the dominant contribution of wall-induced frictional resistance. Off-center positioning introduces strong translation-rotation coupling, giving rise to two families of oscillatory trajectories - glancing and reversing - whose existence and structure are captured as closed orbits in phase space. Weak fluid inertia breaks these closed loops: glancing trajectories spiral outward and merge with reversing trajectories, and new stable fixed points emerge. Together, these results reveal how modest deviations from sphericity or creeping-flow conditions profoundly alter the dynamics of driven particles in confined geometries. The predictions offer guidelines for optimizing particle shape in microfluidic transport and highlight the rich nonlinear behavior accessible in confined suspensions of nonspherical colloids.

cond-mat.soft↗

arXiv2025

Engineering Supercomputing Platforms for Biomolecular Applications

A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an NVIDIA GH200 testbed. The raw performance, power efficiency and data storage requirements of the software was evaluated for each HPC facility, along with qualitative factors such as the user experience and software environment. It was found that the diversity of methods used within computational biology means that there is no single HPC hardware that can optimally run every type of HPC job, and that diverse hardware is the only way to properly support all methods. New hardware, such as AMD GPUs and Nvidia AI chips, are mostly compatible with existing methods, but are also more labour-intensive to support. GPUs offer the most efficient way to run most computational biology tasks, though some tasks still require CPUs. A fast HPC node running molecular dynamics can produce around 10GB of data per day, however, most facilities and research institutions lack short-term and long-term means to store this data. Finally, as the HPC landscape has become more complex, deploying software and keeping HPC systems online has become more difficult. This situation could be improved through hiring/training in DevOps practices, expanding the consortium model to provide greater support to HPC system administrators, and implementing build frameworks/containerisation/virtualisation tools to allow users to configure their own software environment, rather than relying on centralised software installations.

physics.bio-ph↗

arXiv2024

Simulating dynamics of ellipsoidal particles using lattice Boltzmann method

Anisotropic particles are often encountered in different fields of soft matter and complex fluids. In this work, we present an implementation of the coupled hydrodynamics of solid ellipsoidal particles and the surrounding fluid using the lattice Boltzmann method. A standard link-based mechanism is used to implement the solid-fluid boundary conditions. We develop an implicit method to update the position and orientation of the ellipsoid. This exploits the relations between the quaternion which describes the ellipsoid's orientation and the ellipsoid's angular velocity to obtain a stable and robust dynamic update. The proposed algorithm is validated by looking at four scenarios: (i) the steady translational velocity of a spheroid subject to an external force in different orientations, (ii) the drift of an inclined spheroid subject to an imposed force, (iii) three-dimensional rotational motions in a simple shear flow (Jeffrey's orbits), and (iv) developed fluid flows and self-propulsion exhibited by a spheroidal microswimmer. In all cases the comparison of numerical results showed good agreement with known analytical solutions, irrespective of the choice of the fluid properties, geometrical parameters, and lattice Boltzmann model, thus demonstrating the robustness of the proposed algorithm.

cond-mat.soft↗

arXiv2024

Defect-influenced particle advection in highly confined liquid crystal flows

We study the morphology of the Saturn ring defect and director structure around a colloidal particle with normal anchoring conditions and within the flow of the nematic host phase through a rectangular duct of comparable size to the particle. The changes in the defect structures and director profile influence the advection behaviour of the particle, which we compare to that in a simple Newtonian host phase. These effects lead to a non-monotonous dependence of the differential velocity of particle and fluid, also known as retardation ratio, on the Ericksen number.

cond-mat.soft↗

arXiv2022

Controllable particle migration in liquid crystal flows

We observe novel positional control of a colloidal particle in microchannel flow of a nematic liquid crystal. Lattice Boltzmann simulations show multiple equilibrium particle positions, the existence and position of which are tunable using the driving pressure, in direct contrast to the classical Segre-Silberberg effect in isotropic liquids. In addition, particle migration in nematic flow occurs an order of magnitude faster. These new equilibria are determined through a balance of elastic forces, hydrodynamic lift and drag as well as order-flow interactions through the defect structure around the particle.

cond-mat.soft↗

arXiv2021

Shear-enhanced elasticity in the cubic blue phase I

We present results of the linear and non-linear rheology of cubic blue phase I (BPI). The elasticity of BPI is dominated by double-twist cylinders assembled in a body-centered cubic lattice, which can be specified by disclination lines. We find that the elasticity of BPI is enhanced by an order of magnitude by applying pre-shear. The shear-enhanced elasticity is attributed to a rearrangement of the disclination lines that are arrested in a metastable state. Our results are relevant for the understanding of the dynamics of disclinations in cubic blue phases.

cond-mat.soft↗

arXiv2021

A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results

The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of -- and feed into our understanding of -- less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.

q-bio.BM↗

arXiv2019

A Numerical Study of Three-Armed DNA Hydrogel Structures

We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both simulations with the oxDNA2 model and experiments and find excellent agreement. The morphology of the Y-DNA molecules is investigated when several alterations in the design are made. Adding inert nucleotides to the central core region of the Y-DNA molecules has a very minor effect on their overall geometry, whereas palindromic sequences in the sticky ends via which the individual Y-DNA molecules hybridize, have a profound influence on their relative twisting and bending angles.

cond-mat.soft↗

arXiv2018

Coarse-Grained Simulation of DNA using LAMMPS

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

cond-mat.soft↗

arXiv2017

Mesoscopic Modelling and Simulation of Soft Matter

The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance computing and community codes for soft matter simulation.

cond-mat.soft↗

arXiv2016

Microfluidic Flow of Cholesteric Liquid Crystals

We explore the rheology and flow-induced morphological changes of cholesteric liquid crystal patterns subject to Poiseuille flow within a slab geometry, and under different anchoring conditions at the wall. Our focus is particularly on the behaviour of Cholesteric Fingers of the first kind and of Blue Phase II. Depending on the applied pressure gradient, we observe a number of dynamic regimes with different rheological properties. Our results provide the first insight into the flow response of cholesteric phases with fully two- or three-dimensional director field patterns and normal and planar degenerate anchoring conditions as commonly realised in experiments. They are also of high relevance for a fundamental understanding of complex liquid crystals in confinement and an important step towards future microfluidic applications that are based on cholesteric liquid crystals.

cond-mat.soft↗

arXiv2013

Rheology of Cubic Blue Phases

We study the behaviour of cubic blue phases under shear flow via lattice Boltzmann simulations. We focus on the two experimentally observed phases, Blue Phase I (BPI) and Blue Phase II (BPII). The disclination network of Blue Phase II continuously breaks and reforms under steady shear, leading to an oscillatory stress response in time. For larger shear rates, the structure breaks up into a Grandjean texture with a cholesteric helix lying along the flow gradient direction. Blue Phase I leads to a very different response. Here, oscillations are only possible for intermediate shear rates -- very slow flow causes a transition of the initially ordered structure into an amorphous network with an apparent yield stress. Larger shear rates lead to another amorphous state with different structure of the defect network. For even larger flow rates the same break-up into a Grandjean texture as for Blue Phase II is observed. At the highest imposed flow rates both cubic blue phases adopt a flow-aligned nematic state. Our results provide the first theoretical investigation of sheared blue phases in large systems, and are relevant to understanding the bulk rheology of these materials.

cond-mat.soft↗

arXiv2005

Yield Stress Discontinuity in a Simple Glass

Large scale molecular dynamics simulations are performed to study the steady state yielding dynamics of a well established simple glass. In contrast to the supercooled state, where the shear stress, $σ$, tends to zero at vanishing shear rate, $\gammadot$, a stress plateau forms in the glass which extends over about two decades in shear rate. This strongly suggests the existence of a finite dynamic yield stress in the glass, $σ^+ (T) \equiv σ(T; \gammadot \to 0) >0$. Furthermore, the temperature dependence of $σ^+$ suggests a yield stress discontinuity at the glass transition in agreement with recent theoretical predictions. We scrutinize and support this observation by testing explicitly for the assumptions (affine flow, absence of flow induced ordering) inherent in the theory. Also, a qualitative change of the flow curves enables us to bracket the glass transition temperature $T_c$ of the theory from above and (for the first time in simulations) {\it from below}. Furthermore, the structural relaxation time in the steady state behaves quite similar to the system viscosity at all studied shear rates and temperatures.

cond-mat.soft↗