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The effects of molecularly targeted drug perturbations on cellular activities and fates are difficult to predict using intuition alone because of the complex behaviors of cellular regulatory networks. An approach to overcoming this problem…
Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…
We present a multiphase mathematical model for tumor growth which incorporates the remodeling of the extracellular matrix and describes the formation of fibrotic tissue by tumor cells. We also detail a full qualitative analysis of the…
We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the…
The construction of coarse-grained descriptions of a system's kinetics is well established in biophysics. One prominent example is Markov state models in protein folding dynamics. In this paper, we develop a coarse-grained, discrete state…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
A classical example of a mathematical model for oscillations in a biological system is the Selkov oscillator, which is a simple description of glycolysis. It is a system of two ordinary differential equations which, when expressed in…
Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the…
A coagulation process is studied in a set of random masses, in which two randomly chosen masses and the smallest mass of the set multiplied by some fixed parameter $\omega\in [-1,1]$ are iteratively added. Besides masses (or primary…
We apply a recently developed unsupervised machine learning scheme for local atomic environments to characterize large-scale, disordered aggregates formed by sequence-defined macromolecules. This method provides new insight into the…
Self-propelled particles that are subject to noise are a well-established generic model system for active matter. A homogeneous alignment field can be used to orient the direction of the self-propulsion velocity and to model systems like…
The problem of geometric phase for an open quantum system is reinvestigated in a unifying approach. Two of existing methods to define geometric phase, one by Uhlmann's approach and the other by kinematic approach, which have been considered…
Modeling of polymer oxidative aging has been actively studied since the 1990s. Insights from these studies suggest that the transport of oxygen and radicals significantly influences aging heterogeneity, alongside chemical reaction kinetics.…
In this paper, we analyse a model for the growth of three-dimensional walled cells. In this model the biomechanical expansion of the cell is coupled with the geometry of its wall. We consider that the density of building material depends on…
Identifying structural parameters in linear simultaneous-equation models is a longstanding challenge. Recent work exploits information in higher-order moments of non-Gaussian data. In this literature, the structural errors are typically…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
This paper presents a mathematical framework for optimizing drug delivery in cancer treatment using a nonlocal model of solid tumor growth. We present a coupled system of partial differential equations that incorporate long-range cellular…
In this paper we analyse a differential system related to a Glioblastoma growth. Using numerical simulations, we prove that model captures different kind of growth changing adequately the parameters of the model. Firstly, we make an…
Size segregation in bedload transport is studied numerically with a coupled fluid-discrete element model. Starting from an initial deposit of small spherical particles on top of a large particle bed, the segregation dynamics of the bed is…
We study the adiabatic limit in the density matrix approach for a quantum system coupled to a weakly dissipative medium. The energy spectrum of the quantum model is supposed to be non-degenerate. In the absence of dissipation, the geometric…