Related papers: The chemistry induced by mechanical load
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…
Machine learning is employed at an increasing rate in the research field of quantum chemistry. While the majority of approaches target the investigation of chemical systems in their electronic ground state, the inclusion of light into the…
We consider cooperative reactions and we study the effects of the interaction strength among the system components on the reaction rate, hence realizing a connection between microscopic and macroscopic observables. Our approach is based on…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration…
he manifestation of intra-molecular strains in covalent systems is widely known to accelerate chemical reactions and open alternative reaction paths. This process is moderately understood for isolated molecules and uni-molecular processes.…
Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…
A thermodynamic formulation of jammed matter is reviewed. Experiments and simulations of compressed emulsions and granular materials are then used to provide a foundation for the thermodynamics.
The consequences of source charge and surface modulation are studied within the framework of the Poisson-Boltzmann theory of electrolyte solutions. Through a consideration of various examples, it is found that inherent modulation can lead…
Multiparticle collision dynamics (MPCD) is a relatively new algorithm of fluid flow simulations that has been applied mostly to flows around simple objects. One might ask how it behaves in more complex flows. Therefore, we extend MPCD to…
Probabilistic approach to the description of translational motion of macrobodies indicates the emergence of additional order effects oriented in the direction of motion of the body
We introduce and parameterize a chemomechanical model of microtubule dynamics on the dimer level, which is based on the allosteric tubulin model and includes attachment, detachment and hydrolysis of tubulin dimers as well as stretching of…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
This short article is devoted to the dynamics of controlled (and, therefore, open) systems. The internal forces, which appear only in the presence of external free controls and depend explicitely on them, are considered. Such interactive…
In Part I of this paper series, a theoretical and numerical model for a a driven pendulum filled with liquid was developed. The system was analyzed in the framework of tuned liquid dampers (TLD) and hybrid mass liquid dampers (HMLD) theory.…
A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…
Geometric mechanics is usually studied in applied mathematics and most introductory texts are hence aimed at a mathematically minded audience. The present note tries to provide the intuition of geometric mechanics and to show the relevance…
High speed machining has been improved thanks to considerable advancement on the tools (optimum geometry, harder materials), on machined materials (increased workability and machining capacity for harder workpieces) and finally on the…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…