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Publication# A path integral formalism of DNA looping probability

Abstract

In this thesis we describe a path integral formalism to evaluate approximations to the probability density function for the location and orientation of one end of a continuum polymer chain at thermodynamic equilibrium with a heat bath. We concentrate on those systems for which the associated energy density is at most quadratic in its variables. Our main motivation is to exploit continuum elastic rod models for the approximate computation of DNA looping probabilities. We first re-derive, for a polymer chain system, an expression for the second order correction term due to quadratic fluctuations about a unique minimal energy configuration. The result, originally stated for a quantum mechanical system by G. Papadopoulos (1975), relies on an elegant algebraic argument that carries over to the real-valued path integrals of interest here. The conclusion is that the appropriate expression can be evaluated in terms of the energy of the minimizer and the inverse square root of the determinant of a matrix satisfying a certain non-linear system of differential equations. We then construct a change of variables, which establishes a mapping between the solutions of the aforementioned non-linear Papadopoulos equations and a matrix satisfying an initial value problem for the classic linear system of Jacobi equations associated with the second variation of the energy functional. This conclusion is trivial if no cross-term is present in the second variation, but ceases to be so otherwise. Cross-terms are always present in the application of rod models to DNA. We therefore can conclude that the second order fluctuation correction term to the probability density function for a chain is always given by the inverse square root of the determinant of a matrix of solutions to the Jacobi equations. We believe this conclusion to be original for the real-valued case when the second-variation involves cross-terms. Similar results are known for quantum mechanical systems, and, in this context, a connection between the so called Van-Hove-Morette determinant, which involves partial derivatives of the classical action with respect to the boundary values of the configuration variable, and the Jacobi determinant have also been established. We next apply the formula described above to the specific context of rods, for which the configuration space is that of framed curves, or curves in R3 × SO(3). An immediate application of our theory is possible if the rod model encompasses bend, twist, stretch and shear. However the constrained case, where the rod is considered to be inextensible and unshearable, is more standard in polymer physics. In this last case, our results are more delicate as the Lagrangian description breaks down, and the Hamiltonian formulation must be invoked. It is known that the unconstrained local minimizers approach constrained minimizers as the coefficients in the shear and extension terms of the energy are sent to infinity. Here we observe that the Hamiltonian form of the unconstrained Jacobi system similarly has a limit, so that the fluctuation correction in the path integral can still be expressed as the square root of the determinant of a matrix solution of a set of Jacobi equations appropriate to the constrained problem. As in reality DNA or biological macromolecules are certainly at least slightly shearable and extensible, the limit of the fluctuation correction is undoubtedly physically appropriate. The above theory provides a computationally highly tractable approach to the estimation of the appropriate probability density functions. For application to sequence-dependent models of DNA the associated systems of equations has non-constant coefficients, which is of little consequence for a numerical treatment, but precludes the possibility of finding closed form expressions. On the other hand the theory also applies to simplified homogeneous models. Accordingly, we conclude by applying our approach in a completely analytic and closed-form way to the computation of the approximate probability density function for a uniform, non-isotropic, intrinsically straight and untwisted rod to form a circular loop.

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Deoxyribonucleic acid (diːˈɒksᵻˌraɪboʊnjuːˌkliːᵻk,_-ˌkleɪ-; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic in

In this thesis, we study two distinct problems.
The first problem consists of studying the linear system of partial differential equations which consists of taking a k-form, and applying the exterior derivative 'd' to it and add the wedge product with a 1-form 'a'. The study of this differential operator is linked to the study of the multiplication by a two form, that is the system of linear equations where we take a k-form and apply the exterior wedge product by 'da', the exterior derivative of 'a'. We establish links between the partial differential equation and the linear system.
The second problem is a generalization of the symmetric gradient and the curl equation. The equation of a symmetric gradient consists of taking a vector field, apply the gradient and then add the transpose of the gradient, whereas in the curl equation we subtract the transpose of the gradient. Both can be seen as an equation of the form A * grad u + (grad u)t * A, where A is a symmetric matrix for the case of the symmetric gradient and skew symmetric for the curl equation. We generalize to the case where A verifies no symmetry assumption and more significantly add a Dirichlet condition on the boundary.

This thesis is devoted to the derivation of error estimates for partial differential equations with random input data, with a focus on a posteriori error estimates which are the basis for adaptive strategies. Such procedures aim at obtaining an approximation of the solution with a given precision while minimizing the computational costs. If several sources of error come into play, it is then necessary to balance them to avoid unnecessary work. We are first interested in problems that contain small uncertainties approximated by finite elements. The use of perturbation techniques is appropriate in this setting since only few terms in the power series expansion of the exact random solution with respect to a parameter characterizing the amount of randomness in the problem are required to obtain an accurate approximation. The goal is then to perform an error analysis for the finite element approximation of the expansion up to a certain order. First, an elliptic model problem with random diffusion coefficient with affine dependence on a vector of independent random variables is studied. We give both a priori and a posteriori error estimates for the first term in the expansion for various norms of the error. The results are then extended to higher order approximations and to other sources of uncertainty, such as boundary conditions or forcing term. Next, the analysis of nonlinear problems in random domains is proposed, considering the one-dimensional viscous Burgers' equation and the more involved incompressible steady-state Navier-Stokes equations. The domain mapping method is used to transform the equations in random domains into equations in a fixed reference domain with random coefficients. We give conditions on the mapping and the input data under which we can prove the well-posedness of the problems and give a posteriori error estimates for the finite element approximation of the first term in the expansion. Finally, we consider the heat equation with random Robin boundary conditions. For this parabolic problem, the time discretization brings an additional source of error that is accounted for in the error analysis. The second part of this work consists in the analysis of a random elliptic diffusion problem that is approximated in the physical space by the finite element method and in the stochastic space by the stochastic collocation method on a sparse grid. Considering a random diffusion coefficient with affine dependence on a vector of independent random variables, we derive a residual-based a posteriori error estimate that controls the two sources of error. The stochastic error estimator is then used to drive an adaptive sparse grid algorithm which aims at alleviating the so-called curse of dimensionality inherent to tensor grids. Several numerical examples are given to illustrate the performance of the adaptive procedure.

Ludovica Cotta-Ramusino, John Maddocks

We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit continuum mechanics models for the computation of DNA looping probabilities, but here we focus on explaining the novel analytical aspects in the derivation of our approximation formula. Accordingly, and for simplicity, the current presentation is limited to the illustrative case of planar configurations. A path integral formalism is adopted, and, in the standard way, the first approximation to the looping pdf is obtained from a minimal energy configuration satisfying prescribed end conditions. Then we compute an additional factor in the pdf which encompasses the contributions of quadratic fluctuations about the minimum energy configuration along with a simultaneous evaluation of the partition function. The original aspects of our analysis are twofold. First, the quadratic Lagrangian describing the fluctuations has cross-terms that are linear in first derivatives. This, seemingly small, deviation from the structure of standard path integral examples complicates the necessary analysis significantly. Nevertheless, after a nonlinear change of variable of Riccati type, we show that the correction factor to the pdf can still be evaluated in terms of the solution to an initial value problem for the linear system of Jacobi ordinary differential equations associated with the second variation. The second novel aspect of our analysis is that we show that the Hamiltonian form of these linear Jacobi equations still provides the appropriate correction term in the inextensible, unshearable limit that is commonly adopted in polymer physics models of, e. g. DNA. Prior analyses of the inextensible case have had to introduce nonlinear and nonlocal integral constraints to express conditions on the relative displacement of the end points. Our approximation formula for the looping pdf is of quite general applicability as, in contrast to most prior approaches, no assumption is made of either uniformity of the elastic chain, nor of a straight intrinsic shape. If the chain is uniform the Jacobi system evaluated at certain minimum energy configurations has constant coefficients. In such cases our approximate pdf can be evaluated in an entirely explicit, closed form. We illustrate our analysis with a planar example of this type and compute an approximate probability of cyclization, i.e., of forming a closed loop, from a uniform elastic chain whose intrinsic shape is an open circular arc.

2010