Related papers: Oxidative stress response: a proteomic view
The aim of the present work is to introduce a thermodynamic model to describe the growth of an oxide layer on a metallic substrate. More precisely, this paper offers a study of oxygen dissolution into a solid, and its consequences on the…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
This short review covers a wide selection of topics from a multidisciplinary area of dynamics of nonequilibrium systems in physics, chemistry, biology. Theoretical models of colloid particle and protein deposition and adhesion at surfaces,…
This paper offers a study of oxygen dissolution into a solid, and its consequences on the mechanical behaviour of the material. In fact, mechanical strains strongly influence the oxidation processes and may be, in some materials,…
Strain relaxations of a p(1x2) ordered oxygen layer on W(110) are measured as a function of temperature across the disordering transition using low-energy electron diffraction. The measured strains approach values of 0.027 in the [1-10] and…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions. One example is the immune system signalling, where infected tissues release chemokines…
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…
The complexity of the cells can be described and understood by a number of networks such as protein-protein interaction, cytoskeletal, organelle, signalling, gene transcription and metabolic networks. All these networks are highly dynamic…
This paper introduces a novel approach to quantifying ecological resilience in biological systems, particularly focusing on noisy systems responding to episodic disturbances with sudden adaptations. Incorporating concepts from…
Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint.…
The importance of molecular-scale forces in sculpting biological form and function has been acknowledged for more than a century. Accounting for forces in biology is a problem that lies at the intersection of soft condensed matter physics,…
Protein biologics hold immense potential in therapeutic applications, but their ephemeral nature has hindered their widespread application. The effects of different stressors on protein folding have long been studied, but whether these…
Organogenesis involves large deformations and complex shape changes that require elaborate mechanical regulation. Models of tissue biomechanics have been introduced to account for the coupling between mechanical response and biochemical…
The recent advancements in mathematical modeling of biochemical systems have generated increased interest in sensitivity analysis methodologies. There are two primary approaches for analyzing these mathematical models: the stochastic…
Dramatic rise of mutators has been found to accompany adaptation of bacteria in response to many kinds of stress. Two views on the evolutionary origin of this phenomenon emerged: the pleiotropic hypothesis positing that it is a byproduct of…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…