Protocols for translocation processes of flexible polymers through a pore using LAMMPS
Summary: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is an open-source, powerful simulator with a customizable platform for extensive Langevin dynamics simulations. Here, we present a protocol for using LAMMPS to develop coarse-grained models of polymeric systems with macromol...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724007330 |
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| author | Vrinda Garg Rejoy Mathew Arindam Chatterjee Surya K. Ghosh |
| author_facet | Vrinda Garg Rejoy Mathew Arindam Chatterjee Surya K. Ghosh |
| author_sort | Vrinda Garg |
| collection | DOAJ |
| description | Summary: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is an open-source, powerful simulator with a customizable platform for extensive Langevin dynamics simulations. Here, we present a protocol for using LAMMPS to develop coarse-grained models of polymeric systems with macromolecular crowding, an integral part of any soft matter or biophysical system. We describe steps for installing software, using LAMMPS basic commands and code, and translocating polymers. This protocol has potential applications in developing mathematical models for DNA sequencing, controlled drug delivery, and cellular transport processes.For complete details on the use and execution of this protocol, please refer to Garg et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-8268315d591843dbbbadf748492dd108 |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-8268315d591843dbbbadf748492dd1082025-01-18T05:05:13ZengElsevierSTAR Protocols2666-16672025-03-0161103568Protocols for translocation processes of flexible polymers through a pore using LAMMPSVrinda Garg0Rejoy Mathew1Arindam Chatterjee2Surya K. Ghosh3Department of Physics, National Institute of Technology, Warangal 506004, IndiaDepartment of Physics, National Institute of Technology, Warangal 506004, IndiaDepartment of Computer Science and Engineering, IIT Patna, Patna, India; Wipro AI Research, Lab45, Bengaluru, IndiaDepartment of Physics, National Institute of Technology, Warangal 506004, India; Corresponding authorSummary: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is an open-source, powerful simulator with a customizable platform for extensive Langevin dynamics simulations. Here, we present a protocol for using LAMMPS to develop coarse-grained models of polymeric systems with macromolecular crowding, an integral part of any soft matter or biophysical system. We describe steps for installing software, using LAMMPS basic commands and code, and translocating polymers. This protocol has potential applications in developing mathematical models for DNA sequencing, controlled drug delivery, and cellular transport processes.For complete details on the use and execution of this protocol, please refer to Garg et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166724007330BiophysicsBiotechnology and bioengineeringPhysics |
| spellingShingle | Vrinda Garg Rejoy Mathew Arindam Chatterjee Surya K. Ghosh Protocols for translocation processes of flexible polymers through a pore using LAMMPS STAR Protocols Biophysics Biotechnology and bioengineering Physics |
| title | Protocols for translocation processes of flexible polymers through a pore using LAMMPS |
| title_full | Protocols for translocation processes of flexible polymers through a pore using LAMMPS |
| title_fullStr | Protocols for translocation processes of flexible polymers through a pore using LAMMPS |
| title_full_unstemmed | Protocols for translocation processes of flexible polymers through a pore using LAMMPS |
| title_short | Protocols for translocation processes of flexible polymers through a pore using LAMMPS |
| title_sort | protocols for translocation processes of flexible polymers through a pore using lammps |
| topic | Biophysics Biotechnology and bioengineering Physics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724007330 |
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