Related papers: Structural Cellular Hash Chemistry
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems.…
In the context of the concordance cosmology, structure formation in the Universe is the result of the amplification, by gravitational effects, of small perturbations in the primeval density field. This results in the formation of structures…
The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells…
Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich emission line spectra at (sub-)mm wavebands. The observed spectral feature of HMCs such as total number of emission lines and…
This paper describes a new fast and implicitly parallel approach to neighbour-finding in multi-resolution Smoothed Particle Hydrodynamics (SPH) simulations. This new approach is based on hierarchical cell decompositions and sorted…
This paper presents the first results from a model for chemical evolution that can be applied to N-body cosmological simulations and quantitatively compared to measured stellar abundances from large astronomical surveys. This model…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
This paper addresses an open inverse problem at the interface of mathematical analysis and spatial ecology: the unique identification of unknown spatial anomalies -- interpreted as zones of habitat degradation -- and their associated…
The distribution of chemical abundances and their variation in time are important tools to understand the chemical evolution of galaxies: in particular, the study of chemical evolution models can improve our understanding of the basic…
There exist several methods for simulating biological and physical systems as represented by chemical reaction networks. Systems with low numbers of particles are frequently modelled as discrete-state Markov jump processes and are typically…
Performing cell-free expression (CFE) in tailored microfluidic environments is a powerful tool to investigate the organisation of biosystems from molecular to multicellular scales. While cell-free transcription-translation systems simplify…
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…
We begin by reviewing a technique to approximate the dynamics of stochastic programs --written in a stochastic process algebra-- by a hybrid system, suitable to capture a mixed discrete/continuous evolution. In a nutshell, the discrete…
This paper presents an efficient method to perform Structured Matrix Approximation by Separation and Hierarchy (SMASH), when the original dense matrix is associated with a kernel function. Given points in a domain, a tree structure is first…
I discuss the chemical and spectrophotometric evolution of galaxies over cosmological timescales and present a first attempt to treat both aspects in a chemically consistent way. In our evolutionary synthesis approach, we account for the…
We propose and systematically analyze a practical scheme for implementing a one-dimensional non-Hermitian Su-Schrieffer-Heeger model using individually addressable Rydberg atom arrays. Our setup consists of an atomic chain with three-atom…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
We develop an extension of subhalo abundance matching (SHAM) capable of accurately reproducing the real and redshift-space clustering of galaxies in a state-of-the-art hydrodynamical simulation. Our method uses a low-resolution gravity-only…
I review the basic concepts for the spectrophotometric and chemical evolution of galaxies, contrast various approaches and discuss their respective advantages and shortcomings, both for the interpretation of nearby and high redshift…