Related papers: Frustration in Biomolecules
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for…
Geometrically frustrated assemblies where building blocks misfit have been shown to generate intriguing phenomena from self-limited growth, fiber formation, to structural complexity. We introduce a graph theory formulation of geometrically…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Evidence accumulated over the past decade provides support for liquid-liquid phase separation as the mechanism underlying the formation of biomolecular condensates, which include not only membraneless organelles such as nucleoli and RNA…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
As Phil Anderson noted long ago, frustration can be generally defined by measuring the fluctuations in the coupling energy across a plane boundary between two large blocks of material. Since that time, a number of groups have studied the…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Topological frustration arises when boundary conditions impose geometric frustration in a quantum system, creating delocalized defects in the ground states and profoundly altering the low-energy properties. While previous studies have been…
Artificially engineered light-matter systems constitute a novel, versatile architecture for the quantum simulation of driven, dissipative phase transitions and non-equilibrium quantum many-body systems. Here, we review recent experimental…
The cells and tissues that make up our body juggle contradictory mechanical demands. It is crucial for their survival to be able to withstand large mechanical loads, but it is equally crucial for them to produce forces and actively change…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
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…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…