Related papers: Metric tensor as the dynamical variable for variab…
Geometrical methods are extensively applied to thermodynamics including stochastic thermodynamics. In the case of slow-driving linear response regime, a geometrical framework, known as thermodynamic geometry, is established. The key of this…
The novel proposal to invoke the split of the Ricci scalar into bulk and boundary terms in the gravitational action, opens up a new avenue of investigation into stellar dynamics. The Lagrangian contains functional forms of the bulk term…
Adhesive cell-substrate interactions are crucial for cell motility and are responsible for the necessary traction that propels cells. These interactions can also change the shape of the cell, analogous to liquid droplet wetting on adhesive…
The study of cells' dynamical properties is essential to a better understanding of several physiological processes. These properties are directly associated with cells' mechanical parameters experimentally achieved through physical stress.…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
A new anisotropic mesh adaptation strategy for finite element solution of elliptic differential equations is presented. It generates anisotropic adaptive meshes as quasi-uniform ones in some metric space, with the metric tensor being…
This paper introduces coordinate-independent methods for analysing multiscale dynamical systems using numerical techniques based on the transfer operator and its adjoint. In particular, we present a method for testing whether an arbitrary…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
The properties of liquid crystals can be modelled using an order parameter which describes the variability of the local orientation of rod-like molecules. Defects in the director field can arise due to external factors such as applied…
Motivated by a long-standing debate concerning the nature and interrelations of surface-tension variables in fluid membranes, we reformulate the thermodynamics of a membrane vesicle as a generic two-dimensional finite system enclosing a…
This paper proposes a unified approach for dynamic modeling and simulations of general tensegrity structures with rigid bars and rigid bodies of arbitrary shapes. The natural coordinates are adopted as a non-minimal description in terms of…
We present a dynamical framework for modeling the motion of point-like charged particles, with or without mass, in general external electromagnetic fields. A key feature of this formulation is the treatment of time coordinate as a dynamical…
The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…
A new model for biological growth is introduced that couples the geometry of an organism (or part of the organism) to the flow and deposition of material. The model has three dynamical variables (a) a Riemann metric tensor for the geometry,…
The metabolic process in a cell is modeled with the use of the Fourier transformation. The histograms of the invariant measures of chaotic attractors are constructed. In particular, a scenario of adaptation of the metabolic process under a…
A key challenge for molecular dynamics simulations is efficient exploration of free energy landscapes over relevant collective variables (CV). Common methods for enhancing sampling become prohibitively inefficient beyond only a few CVs; in…
Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…
In order to treat tensor force explicitly, we propose a microscopic model for nuclear structure based on antisymmetrized molecular dynamics (AMD). As a result of the present study, it is found that some extentions of the AMD method are…
An intrinsic metric tensor, a flat connexion and the corresponding distance-like function are constructed in the configuration space formed by velocity field {\bf and} the thermodynamic variables of an inviscid fluid. The kinetic-energy…
The phase transition kinetics in three phase systems was investigated using the numerically efficient cell dynamics method. A phasefield model with a simple analytical free energy and single order parameter was used to study the kinetics…