Related papers: Universal relations in the self-assembly of protei…
We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
Biological approximations, which are universal for diverse species, are well known. With no other experimental data, their invariance to transformations from one species to another yields exact conservation (with respect to biological…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
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…
The discovery of two fundamental laws concerning cellular dynamics with recursive growth is reported. First, the chemical abundances measured over many cells are found to obey a log-normal distribution and second, the relationship between…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
All physical systems in equilibrium obey the laws of thermodynamics. In other words, whatever the precise nature of the interaction between the atoms and molecules at the microscopic level, at the macroscopic level, physical systems exhibit…
The physical models of a successful unified theory about the Universe must operate in different phase of matter evolution and different fields of physics. The attempts to build such wide range theory as a bunch of theories developed for…
Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the last decades the life sciences have succeeded in…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
A universal framework is proposed, where all laws are regularities of relations between things or agents. Parts of the world at one or all times are modeled as networks called SYSTEMS with a minimum of axiomatic properties. A notion of…
Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of…
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To…