Mode-coupling Smoluchowski dynamics of a double-stranded DNA oligomer

Fausti, Simone; Penna, Giovanni La; Cuniberti, C.; Perico, Angelo

doi:10.1002/(sici)1097-0282(199911)50:6<613::aid-bip6>3.0.co;2-g

Cited by 16 publications

(14 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…DT has already been successfully used to predict properties of both polymers 4 and biological macromolecules. [5][6][7] The main problem of the matrix expansion method used by DT lies in the choice of a finite set of basis functions, while the correct description of all eigenvalues and eigenvectors needs in principle the use of an infinite set. This leads to an approximated evaluation of the eigenstates.…”

Section: Introductionmentioning

confidence: 99%

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods

Gaspari

Rapallo

2008

The Journal of Chemical Physics

View full text Add to dashboard Cite

In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum trajectory, with great savings in computational time required. This offers a theoretical bridge between the experimental static and dynamical properties of polymers.

show abstract

Section: Introductionmentioning

confidence: 99%

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods

Gaspari

Rapallo

2008

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…(27) in the eigenfunctions of L, and then expand these eigenfunction in a finite basis (similar to what is done in quantum chemistry calculations). [56][57][58][59][60][61][62] The basis functions must be chosen with some care for accurate results. Furthermore, in both the continued fraction and eigenfunction expansion methods require equilibrium averages that are difficult to compute for an arbitrary potential, requiring simulations in general.…”

mentioning

confidence: 99%

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

Portman

Takada

Wolynes

2001

The Journal of Chemical Physics

159

196

View full text Add to dashboard Cite

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction coordinates are identified as collective growth modes of the unstable fluctuations about the saddle-points in the free energy surface. The description of the chain dynamics incorporates internal friction (independent of the solvent viscosity) arising from the elementary isomerizations of the backbone dihedral angles. We find that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosity because of internal friction. For λ-repressor, the calculated folding rate prefactor, along with the free energy barrier from the variational theory, gives a folding rate that agrees well with the experimentally determined rate under highly stabilizing conditions, but the theory predicts too large a folding rate at the transition midpoint. This discrepancy obtained using a fairly complete quantitative theory inspires a new set of questions about chain dynamics, specifically detailed motions in individual contact formation.

show abstract

“…Applications of the MCD theory coupled with MD statistics (MCD‐MD) have been performed on synthetic polymers,24 small proteins,25 nucleic acid fragments,26–28 and polysaccharides 29. A fairly good agreement with experimental NMR parameters has been achieved.…”

Section: Introductionmentioning

confidence: 85%

Modeling the dynamics of the solvated SL1 domain of HIV‐1 genomic RNA

2003

View full text Add to dashboard Cite

A mode-coupling solution of the Smoluchowski diffusion equation (MCD theory), designed to describe the dynamics of wobbling macromolecules in water, is applied to a macromolecular bead model including water beads in the nearest layers. The necessary statistical averages are evaluated by time averaging along a molecular dynamics (MD) trajectory where both solute and water are introduced as atomistic models. The cross peaks in (1)H nuclear Overhauser effect spectroscopy (NOESY) NMR spectra that are routinely measured to determine biological structures are here calculated for the mutated 23 nucleotides stem-loop fragment of the SL1 domain in the HIV-1(Lai) genomic RNA. The calculations are in acceptable agreement with experiments without requiring any screening of the hydrodynamic interactions. The screening of hydrodynamics was necessary in previous MCD calculations obtained by using the same full atomistic MD trajectory, but a nonsolvated frictional model.

show abstract

Mode-coupling Smoluchowski dynamics of a double-stranded DNA oligomer

Cited by 16 publications

References 38 publications

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

Modeling the dynamics of the solvated SL1 domain of HIV‐1 genomic RNA

Contact Info

Product

Resources

About