Related papers: Oxidative stress response: a proteomic view
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
The pressure dependence of light-induced effects in single-crystalline BiFeO$_3$ is studied by optical spectroscopy. At low pressures, we observe three light-induced absorption features with energies just below the two crystal field…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Biomass gasification procedure is a very complex process and it is influenced by many physical and chemical factors such as biomass gasification temperature and gasifier type. Thermodynamic assessment methodology based on the energy and…
We suggest a geometric approach to modeling biochemical processes, aiming at those processes that occur in humans with food sensitivities or chemical sensitivities.
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…
The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of…
Understanding the consequences of the combined effects of multiple stressors-including stress from man-made chemicals is important for conservation management, the ecological risk assessment of chemicals, and many other ecological…
Quantum chemical studies of reactivity involve calculations on a large number of molecular structures and comparison of their energies. Already the set-up of these calculations limits the scope of the results that one will obtain, because…
Periods of low dissolved oxygen concentration -- hypoxia and anoxia -- threaten the health of aquatic ecosystems and the services they provide.Hypoxia is strongly influenced by temperature, but the different sensitivities and response…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
We present measurements of the stress response of packings formed from a wide range of particle shapes. Besides spheres these include convex shapes such as the Platonic solids, truncated tetrahedra, and triangular bipyramids, as well as…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
We study the interplay of activity, order and flow through a set of coarse-grained equations governing the hydrodynamic velocity, concentration and stress fields in a suspension of active, energy-dissipating particles. We make several…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
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…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Understanding the role of microenvironment in cancer growth and metastasis is a key issue for cancer research. Here, we study the effect of osmotic pressure on the functional properties of primary and metastatic melanoma cell lines. In…
The reversible reactions like A+B <-> C in the many-component diffusive system affect the diffusive properties of the constituents. The effective conjugation of irreversible processes of different dimensionality takes place due to the…