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Magill M, Nagel AM, de Haan HW. Parallel computing for mobilities in periodic geometries. Phys Rev E 2022; 106:045304. [PMID: 36397582 DOI: 10.1103/physreve.106.045304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.
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Affiliation(s)
- Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Andrew M Nagel
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
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Li K, Wu J, Guo F, Wang Y, Zhang D, Zhang L. Sliding dynamics of ring on a fixed rod-like block copolymer in rotaxane: Molecular dynamics simulations vs Lifson-Jackson formula. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Haji Abdolvahab R, Niknam Hamidabad M. Pore shapes effects on polymer translocation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:76. [PMID: 33306147 DOI: 10.1140/epje/i2020-12001-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers.
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Wang C, Zhou YL, Sun LZ, Chen YC, Luo MB. Simulation study on the migration of diblock copolymers in periodically patterned slits. J Chem Phys 2019; 150:164904. [PMID: 31042899 DOI: 10.1063/1.5093791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The forced migration of diblock copolymers (ANABNB) in periodically patterned slits was investigated by using Langevin dynamics simulation. The lower surface of the slit consists of stripe α and stripe β distributed in alternating sequence, while the upper one is formed only by stripe β. The interaction between block A and stripe α is strongly attractive, while all other interactions are purely repulsive. Simulation results show that the migration of the diblock copolymer is remarkably dependent on the driving force and there is a transition region at moderate driving force. The transition driving force ft, where the transition region occurs, decreases monotonously with increasing length of block B (NB) but is independent of the polymer length and the periodic length of the slit, which is interpreted from the free energy landscape of diblock copolymer migration. The results also show that periodic slits could be used to separate diblock polymers with different NB by tuning the external driving force.
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Affiliation(s)
- Chao Wang
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Yan-Li Zhou
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Ying-Cai Chen
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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Wang C, Chen YC, Wu F, Luo MB. Simulation on the translocation of homopolymers through sandwich-like compound channels. J Chem Phys 2015; 143:234902. [PMID: 26696074 DOI: 10.1063/1.4937942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The forced translocation of homopolymers through αβα sandwich-like compound channels was investigated by Monte Carlo simulation. The interaction between polymer and part α is strongly attractive, whereas that between polymer and part β is purely repulsive. Simulation results show that the translocation is influenced obviously by the length of part β (Lβ) and the starting position of part β (Lα1). For small Lβ, the translocation is mainly governed by the escaping process, and polymer is trapped near the exit of the channel. However, the translocation time can be tuned by varying Lα1 and the fastest translocation can be achieved at relatively large Lα1. Whereas for large Lβ and small Lα1, the translocation is mainly controlled by the filling process. It is difficult for polymer to enter the channel, and polymer is trapped at the first αβ interface. Finally, the dynamics for the filling process and the escaping process are discussed from the view of free-energy landscape, respectively.
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Affiliation(s)
- Chao Wang
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ying-Cai Chen
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Fan Wu
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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Manneschi C, Fanzio P, Ala-Nissila T, Angeli E, Repetto L, Firpo G, Valbusa U. Stretching of DNA confined in nanochannels with charged walls. BIOMICROFLUIDICS 2014; 8:064121. [PMID: 25553196 PMCID: PMC4265123 DOI: 10.1063/1.4904008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/01/2014] [Indexed: 05/04/2023]
Abstract
There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.
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Affiliation(s)
| | - Paola Fanzio
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Tapio Ala-Nissila
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science , P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland and Department of Physics, Brown University , Providence, Rhode Island 02912-1843, USA
| | - Elena Angeli
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Luca Repetto
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Giuseppe Firpo
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
| | - Ugo Valbusa
- Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy
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