A stochastic approximation scheme and convergence theorem for particle interactions with perfectly reflecting boundaries

We prove the existence of a solution to an equation governing the number density within a compact domain of a discrete particle system for a prescribed class of particle interactions taking into account the effects of the diffusion and drift of the set of particles. Each particle carries a number of internal coordinates which may evolve continuously in time, determined by what we will refer to as the internal drift, or discretely via the interaction kernels. Perfectly reflecting boundary conditions are imposed on the system and all the processes may be spatially and temporally inhomogeneous. We use a relative compactness argument to construct a sequence of measures that converge weakly to a solution of the governing equation. Since the proof of existence is a constructive one, it provides a stochastic approximation scheme that can be used for the numerical study of molecular dynamics.Comment: 43 page

Properties of the solutions of delocalised coagulation and inception problems with outflow boundaries

Well posedness is established for a family of equations modelling particle populations undergoing delocalised coagulation, advection, inflow and outflow in a externally specified velocity field. Very general particle types are allowed while the spatial domain is a bounded region of $d$-dimensional space for which every point lies on exactly one streamline associated with the velocity field. The problem is formulated as a semi-linear ODE in the Banach space of bounded measures on particle position and type space. A local Lipschitz property is established in total variation norm for the propagators (generalised semi-groups) associated with the problem and used to construct a Picard iteration that establishes local existence and global uniqueness for any initial condition. The unique weak solution is shown further to be a differentiable or at least bounded variation strong solution under smoothness assumptions on the parameters of the coagulation interaction. In the case of one spatial dimension strong differentiability is established even for coagulation parameters with a particular bounded variation structure in space. This one dimensional extension establishes the convergence of the simulation processes studied in [Patterson, Stoch. Anal. Appl. 31, 2013] to a unique and differentiable limit

DNA-Protein Binding Rates: Bending Fluctuation and Hydrodynamic Coupling Effects

We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory focuses on two competing effects: polymer shape fluctuations, which speed up association, and the hydrodynamic coupling between the diffusing particle and the chain, which slows down association. Polymer bending fluctuations are described using a mean field dynamical theory, while the hydrodynamic coupling between polymer and particle is incorporated through a simple heuristic approximation. Both of these we validate through comparison with Brownian dynamics simulations. Neither of the effects has been fully considered before in the biophysical context, and we show they are necessary to form accurate estimates of reaction processes. The association rate depends on the stiffness of the polymer and the particle size, exhibiting a maximum for intermediate persistence length and a minimum for intermediate particle radius. In the parameter range relevant to DNA-protein binding, the rate increase is up to 100% compared to the Smoluchowski result for simple center-of-mass motion. The quantitative predictions made by the theory can be tested experimentally.Comment: 21 pages, 11 figures, 1 tabl

On the Inversion of High Energy Proton

Inversion of the K-fold stochastic autoconvolution integral equation is an elementary nonlinear problem, yet there are no de facto methods to solve it with finite statistics. To fix this problem, we introduce a novel inverse algorithm based on a combination of minimization of relative entropy, the Fast Fourier Transform and a recursive version of Efron's bootstrap. This gives us power to obtain new perspectives on non-perturbative high energy QCD, such as probing the ab initio principles underlying the approximately negative binomial distributions of observed charged particle final state multiplicities, related to multiparton interactions, the fluctuating structure and profile of proton and diffraction. As a proof-of-concept, we apply the algorithm to ALICE proton-proton charged particle multiplicity measurements done at different center-of-mass energies and fiducial pseudorapidity intervals at the LHC, available on HEPData. A strong double peak structure emerges from the inversion, barely visible without it.Comment: 29 pages, 10 figures, v2: extended analysis (re-projection ratios, 2D