𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Collective-variable Monte Carlo simulation of DNA

✍ Scribed by Gabb, H. A.; Pr�vost, C.; Bertucat, G.; Robert, C. H.; Lavery, R.

Publisher
John Wiley and Sons
Year
1997
Tongue
English
Weight
251 KB
Volume
18
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Monte Carlo simulations have been carried out on DNA oligomers using an internal coordinate model associated with a pseudorotational representation of sugar repuckering. It is shown that when this model is combined with the scaled collective variable approach of Noguti and Go, much more efficient simulations are obtained than with simple single variable steps. Application of this method to a DNA oligomer containing a recognition site for the TATA-box binding protein leads to striking similarities with results recently obtained from a 1-ns molecular dynamics simulation using explicit solvent and counterions. In particular, large amplitude bending fluctuations are observed directed toward the major groove. Conformational analysis of the Monte Carlo simulation shows clear base sequence effects on conformational fluctuations and also that the DNA energy hypersurface, like that of proteins, is complex with many local, conformational substates.

📜 SIMILAR VOLUMES

Flexible docking simulations: Scaled col
Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm
✍ Trosset, Jean-Yves; Scheraga, Harold A. 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 155 KB 👁 1 views

An algorithm for docking a flexible ligand onto a flexible or rigid receptor, using the scaled-collective-variables Monte Carlo with energy minimization approach, is presented. Energy minimization is shown to be one of the best techniques for distinguishing between native-and nonnative-generated con

Monte Carlo simulation of diffusion of a
Monte Carlo simulation of diffusion of adsorbed proteins
✍ V.P. Zhdanov; B. Kasemo 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 164 KB 👁 1 views

We present the results of threedimensional lattice Monte Carlo simulations of protein diffusion on the liquid-solid interface in a wide temperature range including the most interesting temperatures (from slightly below T f and up to T c , where T f and T c are the folding and collapse temperatures).

Monte Carlo simulation of denaturation o
Monte Carlo simulation of denaturation of adsorbed proteins
✍ V.P. Zhdanov; B. Kasemo 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 210 KB 👁 1 views

Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 ؋ 3 ؋ 3

Monte Carlo simulation of 4-α-glucanotra
Monte Carlo simulation of 4-α-glucanotransferase reaction
✍ Hiroshi Nakatani 📂 Article 📅 1999 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 123 KB

## 4-␣-Glucanotransferase (GTase, D-enzyme) catalyzes disproportionation between two short polymers of maltooligosaccharides linked by ␣-1,4-glucoside bonds. Using action modes of the potato GTase for the donor and acceptor substrates, the Monte Carlo method was applied to simulate the GTase reac

Vector Monte Carlo for simulation of pol
Vector Monte Carlo for simulation of polarized photons
✍ J. E. Fernández; M. Bastiano; A. Tartari 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 484 KB 👁 1 views

Based on a recent analytical solution of vector transport equations in plane geometry including polarization e †ects, a vector scheme for a Monte Carlo code was worked out. The new code, called MC-SHAPE, was developed both to emphasize the miscalculation in using the scalar approach with average pol

Smart Monte Carlo simulation of a globul
Smart Monte Carlo simulation of a globular protein
✍ Akinori Kidera 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 208 KB 👁 1 views

An algorithm for efficient Monte Carlo simulation of a globular protein is proposed. The algorithm was developed by combining the smart Monte Carlo of Rossky et al. with the scaled-collective-variable Monte Carlo method of Noguti and Go. The results of the simulations demonstrated that the combined