Related papers: From proteins to grains: a journey through simple …

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…

Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…

This is our current research perspective on models providing insight into statistical mechanics. It is necessarily personal, emphasizing our own interest in simulation as it developed from the National Laboratories' work to the worldwide…

Coupled natural systems are generally modeled at multiple abstraction levels. Both structural scale and behavioral complexity of these models are determinants in the kinds of questions that can be posed and answered. As scale and complexity…

With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…

Development of several alternative mathematical models for the biological system in question and discrimination between such models using experimental data is the best way to robust conclusions. Models which challenge existing theories are…

Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…

A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…

The objective of this thesis is to advance the understanding of complex physical phenomena through the lens of statistical physics. Specifically, it addresses two fundamental questions: What types of interactions can induce buckling of…

Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the…

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…

The main subject of the thesis is the study of stationary nonequilibrium states trough the use of microscopic stochastic models that encode the physical interaction in the rules of Markovian dynamics for particles configurations. These…

Granular materials such as sand, powders, and food grains are ubiquitous in civil engineering, geoscience, agriculture, and medicine. While the influence of friction between the grains on the static structure of these systems is well…

In this paper we present recent results on parametric analysis of biological models. The underlying method is based on the algorithms for computing trajectory sets of hybrid systems with polynomial dynamics. The method is then applied to…

Building mathematical models of brains is difficult because of the sheer complexity of the problem. One potential starting point is through basal cognition, which gives abstract representation of a range of organisms without central nervous…

The complexity of biological systems, and the increasingly large amount of associated experimental data, necessitates that we develop mathematical models to further our understanding of these systems. As biological systems are generally not…

First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…

We introduce a system of shallow water-type equations to model laboratory experiments of particle-laden flows. We explore homogeneous liquid-solid suspensions of fine, non-cohesive, monodisperse glass beads which propagate as an equivalent…

In the spirit of the many recent simple models of evolution inspired by statistical physics, we put forward a simple model of the evolution of such models. Like its objects of study, it is (one supposes) in principle testable and capable of…

Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…