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Memory-induced alignment of colloidal dumbbells.

ABSTRACT: When a colloidal probe is forced through a viscoelastic fluid which is characterized by a long stress-relaxation time, the fluid is excited out of equilibrium. This is leading to a number of interesting effects including a non-trivial recoil of the probe when the driving force is removed. Here, we experimentally and theoretically investigate the transient recoil dynamics of non-spherical particles, i.e., colloidal dumbbells. In addition to a translational recoil of the dumbbells, we also find a pronounced angular reorientation which results from the relaxation of the surrounding fluid. Our findings are in good agreement with a Langevin description based on the symmetries of a director (dumbbell) as well as a microscopic bath-rod model. Remarkably, we find an instability with amplified fluctuations when the dumbbell is oriented perpendicular to the direction of driving. Our results demonstrate the complex behavior of non-spherical objects within a relaxing environment which are of immediate interest for the motion of externally but also self-driven asymmetric objects in viscoelastic fluids.

SUBMITTER: Krishna Kumar K

PROVIDER: S-EPMC10575873 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Memory-induced alignment of colloidal dumbbells.

Krishna Kumar Karthika K Caspers Juliana J Ginot Félix F Krüger Matthias M Bechinger Clemens C

Scientific reports 20231013 1

When a colloidal probe is forced through a viscoelastic fluid which is characterized by a long stress-relaxation time, the fluid is excited out of equilibrium. This is leading to a number of interesting effects including a non-trivial recoil of the probe when the driving force is removed. Here, we experimentally and theoretically investigate the transient recoil dynamics of non-spherical particles, i.e., colloidal dumbbells. In addition to a translational recoil of the dumbbells, we also find a ...[more]

PMID: 37833487

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Project description:Flexible nucleic acid structures can be challenging to accurately resolve with currently available experimental structural determination techniques. As an alternative, molecular dynamics (MD) simulations can provide a window into understanding the unique dynamics and population distributions of these biomolecules. Previously, molecular dynamics simulations of noncanonical (non-duplex) nucleic acids have proven difficult to accurately model. With a new influx of improved nucleic acid force fields, achieving an in-depth understanding of the dynamics of flexible nucleic acid structures may be achievable. In this project, currently available nucleic acid force fields are evaluated using a flexible yet stable model system: the DNA mini-dumbbell. Prior to MD simulations, nuclear magnetic resonance (NMR) re-refinement was accomplished using improved refinement techniques in explicit solvent to yield DNA mini-dumbbell structures with better agreement between the newly determined PDB snapshots, with the NMR data itself, as well as the unrestrained simulation data. Starting from newly determined structures, a total aggregate of over 800 μs of production data between 2 DNA mini-dumbbell sequences and 8 force fields was collected to compare to these newly refined structures. The force fields tested spanned from traditional Amber force fields: bsc0, bsc1, OL15, and OL21 to Charmm force fields: Charmm36 and the Drude polarizable force field, as well as force fields from independent developers: Tumuc1 and CuFix/NBFix. The results indicated slight variations not only between the different force fields but also between the sequences as well. Given our previous experiences with high populations of potentially anomalous structures in RNA UUCG tetraloops and in various tetranucleotides, we expected the mini-dumbbell system to be challenging to accurately model. Surprisingly, many of the recently developed force fields generated structures in good agreement with experiments. Yet, each of the force fields provided a different distribution of potentially anomalous structures.

Dataset Information

Memory-induced alignment of colloidal dumbbells.

Publications

Memory-induced alignment of colloidal dumbbells.

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