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Fazeli A, Thakore V, Ala-Nissila T, Karttunen M. Non-Stokesian dynamics of magnetic helical nanoswimmers under confinement. PNAS NEXUS 2024; 3:pgae182. [PMID: 38765716 PMCID: PMC11102084 DOI: 10.1093/pnasnexus/pgae182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024]
Abstract
Electromagnetically propelled helical nanoswimmers offer great potential for nanorobotic applications. Here, the effect of confinement on their propulsion is characterized using lattice-Boltzmann simulations. Two principal mechanisms give rise to their forward motion under confinement: (i) pure swimming and (ii) the thrust created by the differential pressure due to confinement. Under strong confinement, they face greater rotational drag but display a faster propulsion for fixed driving frequency in agreement with experimental findings. This is due to the increased differential pressure created by the boundary walls when they are sufficiently close to each other and the particle. We have proposed two analytical relations (i) for predicting the swimming speed of an unconfined particle as a function of its angular speed and geometrical properties, and (ii) an empirical expression to accurately predict the propulsion speed of a confined swimmer as a function of the degree of confinement and its unconfined swimming speed. At low driving frequencies and degrees of confinement, the systems retain the expected linear behavior consistent with the predictions of the Stokes equation. However, as the driving frequency and/or the degree of confinement increase, their impact on propulsion leads to increasing deviations from the Stokesian regime and emergence of nonlinear behavior.
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Affiliation(s)
- Alireza Fazeli
- Department of Mathematics, Western University, London, ON N6A 5B7, Canada
- Center for Advanced Materials and Biomaterials Research, Western University, London, ON N6A 5B7, Canada
| | - Vaibhav Thakore
- Department of Mathematics, Western University, London, ON N6A 5B7, Canada
- Center for Advanced Materials and Biomaterials Research, Western University, London, ON N6A 5B7, Canada
| | - Tapio Ala-Nissila
- Multiscale Statistical and Quantum Physics Group, Quantum Technology Finland Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Espoo, Finland
- Interdisciplinary Centre for Mathematical Modelling, Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK
| | - Mikko Karttunen
- Department of Physics and Astronomy, Western University, London, ON N6A 5B7, Canada
- Department of Chemistry, Western University, London, ON N6A 3K7, Canada
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2
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Afrasiabian N, Wei M, Denniston C. Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces. Biomacromolecules 2023; 24:4103-4112. [PMID: 37417981 PMCID: PMC10498446 DOI: 10.1021/acs.biomac.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.
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Affiliation(s)
- Navid Afrasiabian
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Matthew Wei
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Colin Denniston
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
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3
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Ye H, Shen Z, Li Y. Adhesive rolling of nanoparticles in a lateral flow inspired from diagnostics of COVID-19. EXTREME MECHANICS LETTERS 2021; 44:101239. [PMID: 33644275 PMCID: PMC7897962 DOI: 10.1016/j.eml.2021.101239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Due to the lack of therapeutics and vaccines, diagnostics of COVID-19 emerges as one of the primary tools for controlling the spread of SARS-COV-2. Here we aim to develop a theoretical model to study the detection process of SARS-COV-2 in lateral flow device (LFD), which can achieve rapid antigen diagnostic tests. The LFD is modeled as the adhesion of a spherical nanoparticle (NP) coated with ligands on the surface, mimicking the SARS-COV-2, on an infinite substrate distributed with receptors under a simple shear flow. The adhesive behaviors of NPs in the LFD are governed by the ligand-receptor binding (LRB) and local hydrodynamics. Through energy balance analysis, three types of motion are predicted: (i) firm-adhesion (FA); (ii) adhesive-rolling (AR); and (iii) free-rolling (FR), which correspond to LRB-dominated, LRB-hydrodynamics-competed, and hydrodynamics-dominated regimes, respectively. The transitions of FA-to-AR and AR-to-FR are found to be triggered by overcoming LRB barrier and saturation of LRB torque, respectively. Most importantly, in the AR regime, the smaller NPs can move faster than their larger counterparts, induced by the LRB effect that depends on the radius R of NPs. In addition, a scaling law is found in the AR regime that v ∝ γ ˙ R α (rolling velocity v and shear rate γ ˙ ), with an approximate scaling factor α ∼ - 0 . 2 ± 0 . 05 identified through fitting both theoretical and numerical results. The scaling factor emerges from the energy-based stochastic LRB model, and is confirmed to be universal by examining selections of different LRB model parameters. This size-dependent rolling behavior under the control of flow strength may provide the theoretical guidance for designing efficient LFD in detecting infectious disease.
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Affiliation(s)
- Huilin Ye
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Zhiqiang Shen
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| | - Ying Li
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
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4
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Afrasiabian N, Denniston C. The journey of a single polymer chain to a nanopore. SOFT MATTER 2020; 16:9101-9112. [PMID: 32914157 DOI: 10.1039/d0sm01045f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
For a polymer to successfully thread through a nanopore, it must first find the nanopore. This so-called capture process is typically considered as a two-stage operation consisting of the chain being delivered at the entrance of the nanopore and then insertion of one of the ends. Studying molecular dynamics-lattice Boltzmann simulations of the capture of a single polymer chain under pressure driven hydrodynamic flow, we observe that the insertion can be essentially automatic with no delay for the ends searching for the nanopore. The deformation of the chain within the converging flow area and also, the interplay between the chain elastic forces and the hydrodynamic drag play an important role in the capture of the chain by the nanopore. Along the journey to the nanopore, the chain may form folded shapes. The competition between the elastic and hydrodynamic forces results in unraveling of the folded conformations (hairpins) as the chain approaches the nanopore. Although the ends are not the only monomers that can thread into the nanopore, the unraveling process can result in much higher probability of threading by the ends.
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Affiliation(s)
- Navid Afrasiabian
- Department of Applied Mathematics, University of Western Ontario, London, Canada.
| | - Colin Denniston
- Department of Applied Mathematics, University of Western Ontario, London, Canada. and Department of Physics and Astronomy, University of Western Ontario, London, Canada.
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5
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Parsa MR, Wagner AJ. Large Fluctuations in Nonideal Coarse-Grained Systems. PHYSICAL REVIEW LETTERS 2020; 124:234501. [PMID: 32603140 DOI: 10.1103/physrevlett.124.234501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 03/12/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Using the recently introduced molecular dynamics lattice gas approach, we test fluctuations of coarse-grained quantities. We show that as soon as the system can no longer be considered an ideal gas fluctuations fail to diminish upon coarse graining as is usually expected. These results suggest that current approaches to simulating fluctuating hydrodynamics may have to be augmented to achieve quantitative results for systems with a nonideal equation of state. The molecular dynamics lattice gas method gives a guidance to the exact nature of the fluctuation in such systems.
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Affiliation(s)
- M Reza Parsa
- Department of Applied Mathematics, University of California, Merced, California 95343, USA
| | - Alexander J Wagner
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
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6
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Alcanzare MM, Karttunen M, Ala-Nissila T. Propulsion and controlled steering of magnetic nanohelices. SOFT MATTER 2019; 15:1684-1691. [PMID: 30681686 DOI: 10.1039/c8sm00037a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Externally controlled motion of micro and nanomotors in a fluid environment constitutes a promising tool in biosensing, targeted delivery and environmental remediation. In particular, recent experiments have demonstrated that fuel-free propulsion can be achieved through the application of external magnetic fields on magnetic helically shaped structures. The magnetic interaction between helices and the rotating field induces a torque that rotates and propels them via the coupled rotational-translational motion. Recent works have shown that there exist certain optimal geometries of helical shapes for propulsion. However, experiments show that controlled motion remains a challenge at the nanoscale due to Brownian motion that interferes with the deterministic motion and makes it difficult to achieve controlled steering. In the present work we employ quantitatively accurate simulation methodology to design a setup for which magnetic nanohelices of 30 nm in radius and 180 nm in length (corresponding to previously determined optimal length to radius ratio of 6), with and without cargo, can be accurately propelled and steered in the presence of thermal fluctuations. In particular, we demonstrate fast transport of such nanomotors and devise protocols in manipulating external fields to achieve directionally controlled steering at biologically relevant temperatures.
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7
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Balasubramanian V, Denniston C. Polymer margination in uniform shear flows. SOFT MATTER 2018; 14:9209-9219. [PMID: 30403255 DOI: 10.1039/c8sm01445k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We address the issue of polymer margination (migration towards surfaces) in uniform shear flows through extensive LBMD (lattice-Boltzmann molecular dynamics) simulations. In particular we consider the effect of monomer size, a on the chain's overall margination tendency for chains of length N = 16, 32 monomers in flows at multiple shear rates [small gamma, Greek, dot above]. We observed higher margination of chains with larger radii monomers in comparison to smaller radii monomer chains of the same length N. We quantify this effect by considering various measures such as the distribution of the maximum extent of the chain into the channel bulk, zm, distribution of its center of mass in the direction normal to the surface, zc and the distributions of the chain's radius of gyration in directions parallel and perpendicular to the surface i.e. Rx, Ry and Rz respectively.
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Affiliation(s)
- Venkat Balasubramanian
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario N6A 5B7, Canada.
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Tan J, Sinno T, Diamond SL. A parallel fluid-solid coupling model using LAMMPS and Palabos based on the immersed boundary method. JOURNAL OF COMPUTATIONAL SCIENCE 2018; 25:89-100. [PMID: 30220942 PMCID: PMC6136258 DOI: 10.1016/j.jocs.2018.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the Jeffery orbits of an ellipsoid particle in shear flow, red blood cell stretching test, and effective blood viscosity flowing in tubes. It demonstrated essentially linear scaling from 512 to 8192 cores for both strong and weak scaling cases. The computing time for the coupling increased with the solid fraction. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code.
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Affiliation(s)
- Jifu Tan
- Department of Mechanical Engineering, Northern Illinois University, DeKalb, IL 60115, USA
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
19104, USA
| | - Scott L Diamond
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
19104, USA
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9
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Blommel T, Wagner AJ. Integer lattice gas with Monte Carlo collision operator recovers the lattice Boltzmann method with Poisson-distributed fluctuations. Phys Rev E 2018; 97:023310. [PMID: 29548240 DOI: 10.1103/physreve.97.023310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Indexed: 06/08/2023]
Abstract
We examine a new kind of lattice gas that closely resembles modern lattice Boltzmann methods. This new kind of lattice gas, which we call a Monte Carlo lattice gas, has interesting properties that shed light on the origin of the multirelaxation time collision operator, and it derives the equilibrium distribution for an entropic lattice Boltzmann. Furthermore these lattice gas methods have Galilean invariant fluctuations given by a Poisson statistics, giving further insight into the properties that we should expect for fluctuating lattice Boltzmann methods.
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Affiliation(s)
- Thomas Blommel
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Alexander J Wagner
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
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10
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Alcanzare MMT, Thakore V, Ollila STT, Karttunen M, Ala-Nissila T. Controlled propulsion and separation of helical particles at the nanoscale. SOFT MATTER 2017; 13:2148-2154. [PMID: 28225092 DOI: 10.1039/c6sm02437h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid. We use a hybrid lattice-Boltzmann molecular dynamics method with full hydrodynamic interactions and thermal fluctuations to demonstrate that controlled propulsion of individual nanohelices in an aqueous environment is possible. We optimize the propulsion velocity and the efficiency of externally driven nanohelices. We quantify the importance of the thermal effects on the directed motion by calculating the Péclet number for various shapes, number of turns and pitch lengths of the helices. Consistent with the experimental microscale separation of chiral objects, our results indicate that in the presence of thermal fluctuations at Péclet numbers >10, chiral particles follow the direction of propagation according to its handedness and the direction of the applied torque making separation of chiral particles possible at the nanoscale. Our results provide criteria for the design and control of helical machines at the nanoscale.
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Affiliation(s)
- Maria Michiko T Alcanzare
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland.
| | - Vaibhav Thakore
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland.
| | - Santtu T T Ollila
- Varian Medical Systems Finland, Paciuksenkatu 21, 00270 Helsinki, Finland
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum 5600 MB, The Netherlands and Department of Chemistry & Applied Mathematics, Western University, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
| | - Tapio Ala-Nissila
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland. and Department of Physics, Brown University, Box 1843, 182 Hope Street Barus & Holley, Providence, Rhode Island 02912-1843, USA and Department of Mathematical Science and Department of Physics, Loughborough University, Loughborough, LE11 3TU, UK
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11
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Wan Y, Jin K, Ahmad TJ, Black MJ, Xu Z. Energy transfer and motion synchronization between mechanical oscillators through microhydrodynamic coupling. PHYSICS OF FLUIDS 2017; 29. [DOI: 10.1063/1.4978055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Fluidic environment is encountered for mechanical components in many circumstances, which not only damps the oscillation but also modulates their dynamical behaviors through hydrodynamic interactions. In this study, we examine energy transfer and motion synchronization between two mechanical micro-oscillators by performing thermal lattice-Boltzmann simulations. The coefficient of inter-oscillator energy transfer is measured to quantify the strength of microhydrodynamic coupling, which depends on their distance and fluid properties such as density and viscosity. Synchronized motion of the oscillators is observed in the simulations for typical parameter sets in relevant applications, with the formation and loss of stable anti-phase synchronization controlled by the oscillating frequency, amplitude, and hydrodynamic coupling strength. The critical ranges of key parameters to assure efficient energy transfer or highly synchronized motion are predicted. These findings could be used to advise mechanical design of passive and active devices that operate in fluid.
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Affiliation(s)
- Yu Wan
- Tsinghua University 1 Applied Mechanics Laboratory, Department of Engineering Mechanics and Center for Nano and Micro Mechanics, , Beijing 100084, China
| | - Kai Jin
- Tsinghua University 1 Applied Mechanics Laboratory, Department of Engineering Mechanics and Center for Nano and Micro Mechanics, , Beijing 100084, China
| | - Talha J. Ahmad
- EXPEC Advanced Research Center (ARC), Production Technology 2 , Saudi Aramco, Dhahran, Saudi Arabia
| | - Michael J. Black
- EXPEC Advanced Research Center (ARC), Production Technology 2 , Saudi Aramco, Dhahran, Saudi Arabia
| | - Zhiping Xu
- Tsinghua University 1 Applied Mechanics Laboratory, Department of Engineering Mechanics and Center for Nano and Micro Mechanics, , Beijing 100084, China
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12
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Antipova A, Denniston C. Dynamics of disk pairs in a nematic liquid crystal. Phys Rev E 2016; 94:052704. [PMID: 27967038 DOI: 10.1103/physreve.94.052704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 11/07/2022]
Abstract
We use a hybrid lattice Boltzmann method to study the behavior of sets of ferromagnetic colloidal disks in a nematic liquid crystal. When a weak rotating magnetic field acts on the system, the disks rotate following the magnetic field. This leads to a distortion in the liquid crystal that drives translational motion of the disks. If the concentration of disks is high, disks get locked together: a stable chain configuration is created, where each disk lays on the nearest neighbor. For intermediate concentrations of disks, a different behavior is observed. When disks are rotated by the magnetic field by more than 90^{∘} from their initial orientation, the distortion in the liquid crystal leads to a simultaneous flip of both disks. The final disk positions depends only weakly on the initial configuration. Consecutive rotations of magnetic field push disks towards an equidistant configuration. Periodicity of the systems studied and analysis of the flipping motion of a single disk imply that one can use weak rotating magnetic fields to create stable crystal structures of disks.
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Affiliation(s)
- Alena Antipova
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Colin Denniston
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario N6A 5B8, Canada and Department of Physics & Astronomy, The University of Western Ontario, London, Ontario N6A 5B8, Canada
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13
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Wagner AJ, Strand K. Fluctuating lattice Boltzmann method for the diffusion equation. Phys Rev E 2016; 94:033302. [PMID: 27739715 DOI: 10.1103/physreve.94.033302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 06/06/2023]
Abstract
We derive a fluctuating lattice Boltzmann method for the diffusion equation. The derivation removes several shortcomings of previous derivations for fluctuating lattice Boltzmann methods for hydrodynamic systems. The comparative simplicity of this diffusive system highlights the basic features of this first exact derivation of a fluctuating lattice Boltzmann method.
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Affiliation(s)
- Alexander J Wagner
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Kyle Strand
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
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14
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The good, the bad and the user in soft matter simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2529-2538. [PMID: 26862882 DOI: 10.1016/j.bbamem.2016.02.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/21/2022]
Abstract
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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15
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Antipova A, Denniston C. Dynamics of a disc in a nematic liquid crystal. SOFT MATTER 2016; 12:1279-1294. [PMID: 26575160 DOI: 10.1039/c5sm02333e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We use lattice Boltzmann simulations to study the dynamics of a disc immersed in a nematic liquid crystal. In the absence of external torques, discs with homeotropic anchoring align with their surface normal parallel to the director of the nematic liquid crystal. In the presence of a weak magnetic field a ferromagnetic disc will rotate to equilibrate the elastic torque due to the distortion of the nematic director and the magnetic torque. When the magnetic field rotates the disc so that the angle θ between normal to the surface of the disc â and director of the liquid crystal n[combining circumflex] becomes greater than π/2, the disc flips around the axis perpendicular to the rotation axis so that â sweeps through π radians. An analysis of this behaviour was performed. In particular, we look at the impact of the disc thickness and edges on defect creation and the flipping transition. We also analyse the importance of backflow.
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Affiliation(s)
- Alena Antipova
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario N6A 5B8, Canada.
| | - Colin Denniston
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario N6A 5B8, Canada. and Department of Physics and Astronomy, The University of Western Ontario, London, Ontario N6A 5B8, Canada.
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16
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How colloid–colloid interactions and hydrodynamic effects influence the percolation threshold: A simulation study in alumina suspensions. J Colloid Interface Sci 2015; 458:241-6. [DOI: 10.1016/j.jcis.2015.07.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 11/23/2022]
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17
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Laganapan AMK, Videcoq A, Bienia M, Ala-Nissila T, Bochicchio D, Ferrando R. Computation of shear viscosity of colloidal suspensions by SRD-MD. J Chem Phys 2015; 142:144101. [PMID: 25877556 DOI: 10.1063/1.4917039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The behaviour of sheared colloidal suspensions with full hydrodynamic interactions (HIs) is numerically studied. To this end, we use the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) method. The shear viscosity of colloidal suspensions is computed for different volume fractions, both for dilute and concentrated cases. We verify that HIs help in the collisions and the streaming of colloidal particles, thereby increasing the overall shear viscosity of the suspension. Our results show a good agreement with known experimental, theoretical, and numerical studies. This work demonstrates the ability of SRD-MD to successfully simulate transport coefficients that require correct modelling of HIs.
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Affiliation(s)
- A M K Laganapan
- SPCTS, UMR 7315, ENSCI, CNRS, Centre Européen de la Céramique, 12 rue Atlantis, 87068 Limoges Cedex, France
| | - A Videcoq
- SPCTS, UMR 7315, ENSCI, CNRS, Centre Européen de la Céramique, 12 rue Atlantis, 87068 Limoges Cedex, France
| | - M Bienia
- SPCTS, UMR 7315, ENSCI, CNRS, Centre Européen de la Céramique, 12 rue Atlantis, 87068 Limoges Cedex, France
| | - T Ala-Nissila
- COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland
| | - D Bochicchio
- Dipartimento di Fisica and CNR-IMEM, via Dodecaneso 33, Genova I-16146, Italy
| | - R Ferrando
- Dipartimento di Fisica and CNR-IMEM, via Dodecaneso 33, Genova I-16146, Italy
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18
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Ollila STT, Denniston C, Karttunen M, Ala-Nissila T. Biopolymer filtration in corrugated nanochannels. PHYSICAL REVIEW LETTERS 2014; 112:118301. [PMID: 24702423 DOI: 10.1103/physrevlett.112.118301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 05/21/2023]
Abstract
We examine pressure-driven nonequilibrium transport of linear, circular, and star polymers through a nanochannel containing a rectangular pit with full hydrodynamic interactions and thermal fluctuations. We demonstrate that with sufficiently small pressure differences, there is contour length-dependent entropic trapping of the polymer in the pit when the pit and the polymer sizes are compatible. This is due to competition between flow and chain relaxation in the pit, which leads to a nonmonotonic dependence of the polymer mobility on its size and should aid in the design of nanofiltration devices based on the polymer size and shape.
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Affiliation(s)
- Santtu T T Ollila
- COMP Centre of Excellence, Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland and Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada N6A 5B8
| | - Colin Denniston
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada N6A 5B8
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada N6A 5B8 and Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Tapio Ala-Nissila
- COMP Centre of Excellence, Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland and Department of Physics, Brown University, Providence, Rhode Island 02912-1843, USA
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Mökkönen H, Ikonen T, Jónsson H, Ala-Nissila T. Polymer escape from a confining potential. J Chem Phys 2014; 140:054907. [PMID: 24511979 DOI: 10.1063/1.4863920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were calculated using the path integral hyperdynamics method to evaluate the escape rate. A minimum is found in the rate for self-avoiding polymers of intermediate length while the escape rate decreases monotonically with polymer length for ideal polymers. The increase in the rate for long, self-avoiding polymers is ascribed to crowding in the potential well which reduces the free energy escape barrier. An effective potential curve obtained using the centroid as an independent variable was evaluated by thermodynamic averaging and Kramers rate theory then applied to estimate the escape rate. While the qualitative features are well reproduced by this approach, it significantly overestimates the rate, especially for the longer polymers. The reason for this is illustrated by constructing a two-dimensional effective energy surface using the radius of gyration as well as the centroid as controlled variables. This shows that the description of a transition state dividing surface using only the centroid fails to confine the system to the region corresponding to the free energy barrier and this problem becomes more pronounced the longer the polymer is. A proper definition of a transition state for polymer escape needs to take into account the shape as well as the location of the polymer.
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Affiliation(s)
- Harri Mökkönen
- Department of Applied Physics and COMP CoE, Aalto University School of Science, P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland
| | - Timo Ikonen
- Department of Applied Physics and COMP CoE, Aalto University School of Science, P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland
| | - Hannes Jónsson
- Department of Applied Physics and COMP CoE, Aalto University School of Science, P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics and COMP CoE, Aalto University School of Science, P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland
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Kaehler G, Wagner AJ. Fluctuating ideal-gas lattice Boltzmann method with fluctuation dissipation theorem for nonvanishing velocities. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:063310. [PMID: 23848809 DOI: 10.1103/physreve.87.063310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/12/2012] [Indexed: 06/02/2023]
Abstract
Current implementations of fluctuating ideal-gas descriptions with the lattice Boltzmann methods are based on a fluctuation dissipation theorem, which, while greatly simplifying the implementation, strictly holds only for zero mean velocity and small fluctuations. We show how to derive the fluctuation dissipation theorem for all k, which was done only for k=0 in previous derivations. The consistent derivation requires, in principle, locally velocity-dependent multirelaxation time transforms. Such an implementation is computationally prohibitively expensive but, with a small computational trick, it is feasible to reproduce the correct FDT without overhead in computation time. It is then shown that the previous standard implementations perform poorly for non vanishing mean velocity as indicated by violations of Galilean invariance of measured structure factors. Results obtained with the method introduced here show a significant reduction of the Galilean invariance violations.
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Affiliation(s)
- G Kaehler
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
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Ollila STT, Denniston C, Ala-Nissila T. One- and two-particle dynamics in microfluidic T-junctions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:050302. [PMID: 23767470 DOI: 10.1103/physreve.87.050302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Indexed: 06/02/2023]
Abstract
Advances in precise focusing of colloidal particles in microfluidic systems open up the possibility of using microfluidic junctions for particle separation and filtering applications. We present a comprehensive numerical study of the dynamics of solid and porous microparticles in T-shaped junctions. Good agreement with experimental data is obtained on the location of particle-separating streamlines for single solid particles with realistic parameters corresponding to the experiments. We quantify the changes in the position of the separating line for porous, partially penetrable colloids. A prediction of the full phase diagram for particle separation is presented in the case of two successive particles entering a T-junction. Our results suggest the intriguing possibility of using the one- and two-particle T-junctions as logic gates.
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Affiliation(s)
- Santtu T T Ollila
- COMP Centre of Excellence, Department of Applied Physics, Aalto University School of Science and Technology, P.O. Box 11000, FIN-00076 Aalto, Espoo, Finland.
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Tomilov A, Videcoq A, Chartier T, Ala-Nissilä T, Vattulainen I. Tracer diffusion in colloidal suspensions under dilute and crowded conditions with hydrodynamic interactions. J Chem Phys 2012; 137:014503. [DOI: 10.1063/1.4731661] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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