Related papers: Unified perspective on proteins: A physics approac…
Protein Folding is concerned with the reasons and mechanism behind a protein's tertiary structure. The thermodynamic hypothesis of Anfinsen postulates an universal energy function (UEF) characterizing the tertiary structure, defined…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
One considers geometry with the intransitive equaivalence relation. Such a geometry is a physical geometry, i.e. it is described completely by the world function, which is a half of the squared distance function. The physical geometry…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…
Differentiable physics provides a new approach for modeling and understanding the physical systems by pairing the new technology of differentiable programming with classical numerical methods for physical simulation. We survey the rapidly…
This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time,…
The purpose of this review is to analyze the physics at play in particle resuspension in order to bring insights into the rich complexity of this common but challenging concern. Following the more-is-different vision, this is performed by…
One of the molecular properties most intuitive to the human perception is the geometrical shape. However, when exploring a large chemical space the determination of shape needs to be automated. We present a fast and simple approach to…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Learning is traditionally studied in biological or computational systems. The power of learning frameworks in solving hard inverse-problems provides an appealing case for the development of `physical learning' in which physical systems…
It is generally believed that physical laws, reflecting an inherent order in the universe, are ordained by nature. However, in modern physics the observer plays a central role raising questions about how an observer-centric physics can…
Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish.…
Detecting and exploiting similarities between seemingly distant objects is without doubt an important human ability. This paper develops \textit{from the ground up} an abstract algebraic and qualitative notion of similarity based on the…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
We offer a systematic account of decomposition of quantum systems into parts. Different decompositions (structures) are mutually linked via the proper linear canonical transformations. Different kinds of structures, as well as their…
This work starts with the observation of a certain "rule" (up to now unexplored) in the fundamental laws of Nature. We show some evidence of this, and formulate it as a fundamental principle which exhibits a number physical consequences. In…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…