Related papers: Equations of Motion that Recognize Biochemical Pat…
A type of mechanics will be presented that possesses some distinctive properties. On the one hand, its physical description & rules of operation are readily comprehensible & intuitively clear. On the other, it fully satisfies all observable…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…
The electron energy and density matrices in molecular systems are convex in respect of the number of particles. So that, the chemical descriptors based on their derivatives present the hamper of discontinuities for isolated systems and…
Polynomial dynamical systems describing interacting particles in the plane are studied. A method replacing integration of a polynomial multi--particle dynamical system by finding polynomial solutions of a partial differential equations is…
A spatio-temporal evolution of chemicals appearing in a reversible enzyme reaction and modelled by a four component reaction-diffusion system with the reaction terms obtained by the law of mass action is considered. The large time behaviour…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
We investigate the consistency of the fundamental governing equations of motion in continuum mechanics. In the first step, we examine the governing equations for a system of particles, which can be considered as the discrete analog of the…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
One of the molecular properties most intuitive to the human perception is the geometrical shape. However, when exploring a large chemical space the determination of shape needs to be automated. We present a fast and simple approach to…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…
We consider systems of n particles that move with constant velocity between collisions. Their total momentum but not necessarily their kinetic energy is preserved at collisions. As there are no further constraints, these systems are…
Dynamics of systems of structured particles consisting of potentially interacting material points is considered in the framework of classical mechanics. Equations of interaction and motion of structured particles have been derived. The…
A general organizing principle is proposed that can be used to derive the equations of motion describing the near-equilibrium dynamics of causal and thermodynamically stable relativistic systems. The latter are found to display some new…
The dynamics of one species chemical kinetics is studied. Chemical reactions are modelled by means of continuous time Markov processes whose probability distribution obeys a suitable master equation. A large deviation theory is formally…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Living organisms maintain stable functioning amid environmental fluctuations through homeostasis, a property that preserves a system's behavior despite changes in environmental conditions. To elucidate homeostasis in stochastic biochemical…
Extending the famous Model B for the time evolution of a liquid mixture, we derive an approximate expression for the mobility matrix that couples the different mixture components. This approach is based on a single component fluid with…
We present a general approach for the formulation of equations of motion for compact objects in general relativistic theories. The particle is assumed to be moving in a geometric background which in turn is asymptotically flat. Our approach…
The scientific question resolved by this paper is that the continuity equation appears as an equivalent language of the system of first-order linear ODE. The main result characterizes the fact that the continuity equation contains…