Coarse-grained lattice model simulations of sequence-structure fitness of a ribosome-inactivating protein

Biopolymers ◽  
2008 ◽  
Vol 89 (2) ◽  
pp. 153-159 ◽  
Author(s):  
Mark A. Olson ◽  
In-Chul Yeh ◽  
Michael S. Lee
Keyword(s):  
Lattice Model ◽  
Coarse Grained ◽  
Ribosome Inactivating Protein ◽  
Sequence Structure ◽  
Model Simulations

Lattice model simulations of the stacking/unstacking behaviour in thylakoid membranes

1990 ◽  
Vol 145 (1) ◽  
pp. 65-81 ◽  
Author(s):  
D. Nicholson ◽  
S.J. Zara ◽  
N.G. Parsonage ◽  
J. Barber
Keyword(s):  
Lattice Model ◽  
Thylakoid Membranes ◽  
Model Simulations

Interlocking order parameter fluctuations in structural transitions between adsorbed polymer phases

2016 ◽  
Vol 18 (3) ◽  
pp. 2143-2151 ◽  
Author(s):  
Paulo H. L. Martins ◽  
Michael Bachmann
Keyword(s):  
Lattice Model ◽  
Order Parameter ◽  
Thermal Conditions ◽  
Coarse Grained ◽  
Chain Growth ◽  
Structural Transitions ◽  
Contact Density ◽  
Adsorbed Polymer

By means of contact-density chain-growth simulations of a simple coarse-grained lattice model for a polymer grafted at a solid homogeneous substrate, we investigate the complementary behavior of the numbers of surface–monomer and monomer–monomer contacts under various solvent and thermal conditions.

scholarly journals DNA brick self-assembly with an off-lattice potential

Soft Matter ◽  
2016 ◽  
Vol 12 (29) ◽  
pp. 6253-6260 ◽  
Author(s):  
Aleks Reinhardt ◽  
Daan Frenkel
Keyword(s):  
Lattice Model ◽  
Self Assembly ◽  
Coarse Grained ◽  
Lattice Potential

We show that many-component addressable self-assembly of DNA bricks is possible to achieve with a coarse-grained but realistic off-lattice model.

scholarly journals Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding

2020 ◽  
Author(s):  
Kevin Tsai ◽  
Samuel Britton ◽  
Ali Nematbakhsh ◽  
Roya Zandi ◽  
Weitao Chen ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Cell Surface ◽  
Vegetative Reproduction ◽  
Bending Stiffness ◽  
Small Gtpase ◽  
Coarse Grained ◽  
Surface Model ◽  
Bud Formation ◽  
Model Simulations ◽  
Dimensionless Ratio

AbstractThe budding yeast, Saccharomyces cerevisiae, is a prime biological model to study mechanisms underlying asymmetric growth. Previous studies have shown that, prior to yeast bud emergence, polarization of a conserved small GTPase, Cdc42, must be established. Additionally, hydrolase changes the mechanical properties of the cell wall and plasma membrane with the periplasm between them (cell surface). However, how the surface mechanical properties in the emerging bud are different from the properties of the mother cell and their role in bud formation are not well understood. We hypothesize that the polarized chemical signal alters the local dimensionless ratio of stretching to bending stiffness of the cell surface of the emerging yeast bud. To test this hypothesis, a novel three-dimensional coarse-grained particle-based model has been developed which describes inhomogeneous mechanical properties of the cell surface. Model simulations suggest that regulation of the dimensionless ratio of stretching to bending stiffness of the cell surface is necessary to initiate bud formation. Furthermore, model simulations predict that bud shape depends strongly on the experimentally observed molecular distribution of the polarized signaling molecule Cdc42, while the neck shape of the emerging bud is strongly impacted by the properties of the chitin and septin ring. This 3D model of asymmetric cell growth can also be used for studying viral budding and other vegetative reproduction processes performed via budding.

scholarly journals Coarse-Grained Lattice Model for Molecular Recognition

2006 ◽  
Vol 97 (12) ◽  
Author(s):  
Hans Behringer ◽  
Andreas Degenhard ◽  
Friederike Schmid
Keyword(s):  
Molecular Recognition ◽  
Lattice Model ◽  
Coarse Grained

scholarly journals A Lattice Model on the Rate of DNA Hybridization

2021 ◽  
Author(s):  
R Murugan
Keyword(s):  
Numerical Analysis ◽  
Lattice Model ◽  
Dna Hybridization ◽  
Translational Diffusion ◽  
Internal Displacement ◽  
Radius Of Gyration ◽  
Average Radius ◽  
Collision Rate ◽  
Reaction Volume ◽  
Model Simulations

We develop a lattice model on the rate of hybridization of the complementary single-stranded DNAs (c-ssDNAs). Upon translational diffusion mediated collisions, c-ssDNAs interpenetrate each other to form correct (cc), incorrect (icc) and trap-correct contacts (tcc) inside the reaction volume. Correct contacts are those with exact registry matches which leads to nucleation and zipping. Incorrect contacts are the mismatch contacts which are less stable compared to tcc which can occur in the repetitive c-ssDNAs. Although tcc possess registry match within the repeating sequences, they are incorrect contacts in the view of the whole c-ssDNAs. The nucleation rate (kN) is directly proportional to the collision rate and the average number of correct-contacts (<ncc>) formed when both the c-ssDNAs interpenetrate each other. Detailed lattice model simulations suggest that 〈n_cc 〉∝L⁄V where L is the length of c-ssDNAs and V is the reaction volume. Further numerical analysis revealed the scaling for the average radius of gyration of c-ssDNAs (Rg) with their length as R_g∝√L. Since the reaction space will be approximately a sphere with radius equals to 2Rg and V∝L^(3⁄2), one obtains k_N∝1/√L. When c-ssDNAs are nonrepetitive, then the overall renaturation rate becomes as k_R∝k_N L and one finally obtains k_R∝√L in line with the experimental observations. When c-ssDNAs are repetitive with a complexity of c, then earlier models suggested the scaling k_R∝√L/c which breaks down at c = L. This clearly suggested the existence of at least two different pathways of renaturation in case of repetitive c-ssDNAs viz. via incorrect contacts and trap correct contacts. The trap correct contacts can lead to the formation of partial duplexes which can keep the complementary strands in the close vicinity for a prolonged timescale. This is essential for the extended 1D slithering, inchworm movements and internal displacement mechanisms which can accelerate the searching for the correct contacts. Clearly, the extent of slithering dynamics will be inversely proportional to the complexity. When the complexity is close to the length of c-ssDNAs, then the pathway via incorrect contacts will dominate. When the complexity is much lesser than the length of c-ssDNA, then pathway via trap correct contacts would be the dominating one.

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