Related papers: Conformational selection or induced fit? New insig…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic…
We study the population genetics of Evolution in the important special case of weak selection, in which all fitness values are assumed to be close to one another. We show that in this regime natural selection is tantamount to the…
Understanding the role of non-equilibrium driving in self-organization is crucial for developing a predictive description of biological systems, yet it is impeded by their complexity. The actin cytoskeleton serves as a paradigm for how…
The mechanical environment of a substrate plays a key role in influencing the behavior of adherent biological cells. Traditional tunable substrates have limitations as their mechanical properties cannot be dynamically altered in-situ during…
Actin and myosin drive many instances of force generation, deformation, and shape change in cells, tissues, and organisms. In particular, cytoskeletal actomyosin is remarkable in its adaptive architecture, responding to a host of…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
The actin cytoskeleton is a key component in the machinery of eukaryotic cells, and it selfassembles out of equilibrium into a wide variety of biologically crucial structures. While the molecular mechanisms involved are well characterized,…
A new class of micromechanically motivated chain network models for soft biological tissues is presented. On the microlevel, it is based on the statistics of long chain molecules. A wormlike chain model is applied to capture the behavior of…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
The role of thermal fluctuations on the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular aggregates may undergo…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
This paper demonstrates that simple yet important characteristics of coevolution can occur in evolutionary algorithms when only a few conditions are met. We find that interaction-based fitness measurements such as fitness (linear) ranking…
Associative learning is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was early recognized to be a general trait of complex multicellular organisms but also found in "simpler"…
We study in this paper certain properties of the responses of dynamical systems to external inputs. The motivation arises from molecular systems biology. and, in particular, the recent discovery of an important transient property, related…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
The quasi-equilibrium approximation is acceptable when molecular interactions are fast enough compared to circuit dynamics, but is no longer allowed when cellular activities are governed by rare events. A typical example is the lactose…
Conformal field theories (CFTs) feature prominently in high-energy physics, statistical mechanics, and condensed matter. For example, CFTs govern emergent universal properties of systems tuned to quantum phase transitions, including their…