Related papers: Unified perspective on proteins: A physics approac…
A physical theory of the world is presented under the unifying principle that all of nature is laid out before us and experienced through the passage of time. The one-dimensional progression in time is opened out into a multi-dimensional…
Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Both metamathematics and physics are posited to emerge from samplings by observers of the unique ruliad structure that corresponds to the entangled limit of all possible computations. The possibility of higher-level mathematics accessible…
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any given geometry, and thus to any given type…
The present paper presents a new general conception of interaction between physical systems, differing significantly from that of both classical physics and quantum physics as generally understood. We believe this conception could provide…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The process of cognition is analysed to adjust the set theory to physical description. Postulates and basic definitions are revised. The specific sets of predicates, called presets, corresponding to the physical objects identified by an…
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
The reader surely knows what particles physics is about: finding building blocks of nature that appear elementary at a given time and study their interactions - so why in the world this essay? The problem is how to arrive at a fundamental…
When we work with information from multiple sources, the formalism each employs to handle uncertainty may not be uniform. In order to be able to combine these knowledge bases of different formats, we need to first establish a common basis…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…