Related papers: High-order WENO scheme for Polymerization-type equ…
In this paper, we provide a detailed theoretical analysis of the numerical scheme introduced in J. Comput. Phys. 436 (2021) 110253 for the reaction kinetics of a class of chemical reaction networks that satisfies detailed balance condition.…
A modified Weighted Essentially Non-Oscillatory (WENO) reconstruction technique preventing accuracy loss near critical points (regardless of their order) of the underlying data is presented. This approach only uses local data from the…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
A new, high-order slope-limiting procedure for the Piecewise Parabolic Method (PPM) and the Piecewise Quartic Method (PQM) is described. Following a Weighted Essentially Non-Oscillatory (WENO)-type paradigm, the proposed slope-limiter seeks…
Central WENO schemes are a natural candidate for higher-order schemes for non-local conservation laws, since the underlying reconstructions do not only provide single point values of the solution but a complete (high-order) reconstruction…
Mathematical models of protein-protein dynamics, such as the heterodimer model, play a crucial role in understanding many physical phenomena. This model is a system of two semilinear parabolic partial differential equations describing the…
The Chemical Master Equation (CME) is well known to provide the highest resolution models of a biochemical reaction network. Unfortunately, even simulating the CME can be a challenging task. For this reason more simple approximations to the…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Each and every biological function in living organism happens as a result of protein-protein interactions.The diseases are no exception to this. Identifying one or more proteins for a particular disease and then designing a suitable…
Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…
In our previous work [29], we proposed a class of high-order asymptotic preserving (AP) finite difference weighted essentially non-oscillatory (WENO) schemes for solving the shallow water equations (SWEs) with bottom topography and Manning…
A novel central weighted essentially non-oscillatory (central WENO; CWENO)-type scheme for the construction of high-resolution approximations to discontinuous solutions to hyperbolic systems of conservation laws is presented. This procedure…
We present the first high order one-step ADER-WENO finite volume scheme with Adaptive Mesh Refinement (AMR) in multiple space dimensions. High order spatial accuracy is obtained through a WENO reconstruction, while a high order one-step…
The aim of this paper is to study a whole class of first order differential inclusions, which fit into the framework of perturbed sweeping process by uniformly prox-regular sets. After obtaining well-posedness results, we propose a…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
The advantage of WENO-JS5 scheme [ J. Comput. Phys. 1996] over the WENO-LOC scheme [J. Comput. Phys.1994] is that the WENO-LOC nonlinear weights do not achieve the desired order of convergence in smooth monotone regions and at critical…
In this paper we present a class of high order accurate cell-centered Arbitrary-Eulerian-Lagrangian (ALE) one-step ADER-WENO finite volume schemes for the solution of nonlinear hyperbolic conservation laws on two-dimensional unstructured…
In this paper, a simple and efficient third-order weighted essentially non-oscillatory (WENO) reconstruction is developed for three-dimensional flows, in which the idea of two-dimensional WENO-AO scheme on unstructured meshes…
In this paper we propose the first better than second order accurate method in space and time for the numerical solution of the resistive relativistic magnetohydrodynamics (RRMHD) equations on unstructured meshes in multiple space…
In this article, the construction and implementation of a seventh order weighted essentially non-oscillatory scheme is reported for hyperbolic conservation laws. Local smoothness indicators are constructed based on $L_{1}$-norm, where a…