A Hard Constraint Algorithm to Model Particle Interactions in DNA-laden Flows

Journal Article · Tue Aug 01 04:00:00 EDT 2006 · Nanoscale and Microscale Thermophysical Engineering, vol. 11, no. 1, January 1, 2007, pp. 121-128

OSTI ID:940141

Trebotich, D; Miller, G H; Bybee, M D

We present a new method for particle interactions in polymer models of DNA. The DNA is represented by a bead-rod polymer model and is fully-coupled to the fluid. The main objective in this work is to implement short-range forces to properly model polymer-polymer and polymer-surface interactions, specifically, rod-rod and rod-surface uncrossing. Our new method is based on a rigid constraint algorithm whereby rods elastically bounce off one another to prevent crossing, similar to our previous algorithm used to model polymer-surface interactions. We compare this model to a classical (smooth) potential which acts as a repulsive force between rods, and rods and surfaces.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA
• Sponsoring Organization: USDOE
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 940141
• Report Number(s): UCRL-JRNL-223318
• Journal Information: Nanoscale and Microscale Thermophysical Engineering, vol. 11, no. 1, January 1, 2007, pp. 121-128, Journal Name: Nanoscale and Microscale Thermophysical Engineering, vol. 11, no. 1, January 1, 2007, pp. 121-128 Journal Issue: 1 Vol. 11
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
ALGORITHMS
DNA
PARTICLE INTERACTIONS
POLYMERS