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The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
We present multiscale models of cancer tumor invasion with components at the molecular, cellular, and tissue levels. We provide biological justifications for the model components, present computational results from the model, and discuss…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
Quantum collision models allow for the dynamics of open quantum systems to be described by breaking the environment into small segments, typically consisting of non-interacting harmonic oscillators or two-level systems. This work introduces…
We consider a calculus of resources and processes as a basis for modelling decision-making in multi-agent systems. The calculus represents the regulation of agents' choices using utility functions that take account of context. Associated…
We describe a type system for the linear-algebraic lambda-calculus. The type system accounts for the part of the language emulating linear operators and vectors, i.e. it is able to statically describe the linear combinations of terms…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as…
An agent-based model (ABM) is a computational model in which the local interactions of autonomous agents with each other and with their environment give rise to global properties within a given domain. As the detail and complexity of these…
A new mathematical model for non-equilibrium evaporation/condensation including boiling effect is proposed. A simplified differential-algebraic system of equations is obtained. A code to solve numerically this differential-algebraic system…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
At present it is still quite difficult to match the vast knowledge on the behavior of individual tumor cells with macroscopic measurements on clinical tumors. On the modeling side, we already know how to deal with many molecular pathways…
The authors propose new additive models for binary outcomes, where the components are copula-based regression models (Noh et al, 2013), and designed such that the model may capture potentially complex interaction effects. The models do not…
Dynamics in correlated quantum matter is a hard problem, as its exact solution generally involves a computational effort that grows exponentially with the number of constituents. While a remarkable progress has been witnessed in recent…
Quantum computations operate in the quantum world. For their results to be useful in any way, there is an intrinsic necessity of cooperation and communication controlled by the classical world. As a consequence, full formal descriptions of…
The virial expansion provides a non-perturbative view into the thermodynamics of quantum many-body systems in dilute regimes. While powerful, the expansion is challenging as calculating its coefficients at each order $n$ requires analyzing…
In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells,…
Quantum collision models normally consist of a system interacting with a set of ancillary units representing the environment. While these ancillary systems are usually assumed to be either two level systems (TLS) or harmonic oscillators, in…
In this paper, we present a physically informed neural network representation of the effective interactions associated with coupled-cluster downfolding models to describe chemical systems and processes. The neural network representation not…