Related papers: Energy-momentum conserving integration schemes for…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
We analyze the convergence rate of various momentum-based optimization algorithms from a dynamical systems point of view. Our analysis exploits fundamental topological properties, such as the continuous dependence of iterates on their…
In this paper we consider unconditionally energy stable numerical schemes for the nonstationary 3D magneto-micropolar equations that describes the microstructure of rigid microelements in electrically conducting fluid flow under some…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
Space-time modulation systems have garnered significant attention due to their resemblance to moving-matter systems and promising applications. Unlike conventional moving-matter systems, modulation systems do not involve net motion of…
We analyse three time integration schemes for unfitted methods in fluid structure interaction. In Alghorithm 1 we propose a fully discrete monolithic algorithm with P1 P1 stabilized finite elements for the fluid problem; for this alghorithm…
Understanding electron energy dynamics in low-temperature plasmas such as capacitively coupled plasmas (CCPs), including energy absorption, conversion, transport, and dissipation, is essential for interpreting discharge physics and process…
We derive an expression for the energy-momentum tensor in the discrete lattice formulation of pure glue QCD. The resulting expression satisfies the continuity equation for energy conservation up to numerical errors with a symmetric…
Structure-preserving integrators are in the focus of ongoing research because of their distinguished features of robustness and long time stability. In particular, their formulation for coupled problems that include dissipative mechanisms…
A new energy and enstrophy conserving scheme is evaluated using a suite of test cases over the global spherical domain or bounded domains. The evaluation is organized around a set of pre-defined properties: accuracy of individual opeartors,…
This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal…
We address the problem of constructing numerical integrators for nonholonomic Lagrangian systems that enjoy appropriate discrete versions of the geometric properties of the continuous flow, including the preservation of energy. Building on…
Variational integrators are a special kind of geometric discretisation methods applicable to any system of differential equations that obeys a Lagrangian formulation. In this thesis, variational integrators are developed for several…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
We present a class of non-standard numerical schemes which are modifications of the discrete gradient method. They preserve the energy integral exactly (up to the round-off error). The considered class contains locally exact discrete…
We present a mathematically rigorous method suitable for solving three-body bound state and scattering problems when the inter-particle interaction is of a hard-core nature. The proposed method is a variant of the Boundary Condition Model…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Since the expense of the numerical integration of large scale dynamical systems is often computationally prohibitive, model reduction methods, which approximate such systems by simpler and much lower order ones, are often employed to reduce…
This paper formulates variational integrators for finite element discretizations of deformable bodies with heat conduction in the form of finite speed thermal waves. The cornerstone of the construction consists in taking advantage of the…