相关论文: Using a Fast Adaptive Function Approximator to cal…
Self organization mechanisms are essential for the cytoskeleton to adapt to the requirements of living cells. They rely on the intricate interplay of cytoskeletal filaments, crosslinking proteins and molecular motors. Here we present an in…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
We introduce a mathematical model for the mechanical behaviour of the eukaryotic cell cytoskeleton. This discrete model involves a regular array of pre-stressed protein filaments that exhibit resistance to enthalpic stretching, joined at…
The cytoskeleton is an inhomogeneous network of semi-flexible filaments, which are involved in a wide variety of active biological processes. Although the cytoskeletal filaments can be very stiff and embedded in a dense and cross-linked…
The composite cytoskeleton, comprising interacting networks of semiflexible actin and rigid microtubules, actively generates forces and restructures using motor proteins such as myosins to enable key mechanical processes including cell…
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…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
The cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. Its versatile reconfigurability, programmed by interactions…
The cytoskeleton is a model active matter system that controls diverse cellular processes from division to motility. While both active actomyosin dynamics and actin-microtubule interactions are key to the cytoskeleton's versatility and…
The formation, maintenance and reorganization of the cytoskeletal filament network is essential for a number of cellular processes. While the crucial role played by active forces generated by motor proteins has been studied extensively,…
The mechanical properties of cells are dominated by the cytoskeleton, an interconnected network of long elastic filaments. The connections between the filaments are provided by crosslinking proteins, which constitute, next to the filaments,…
The cytoplasm is a heterogeneous mixture containing many types of proteins that self-assemble into a wide variety of complexes. The accuracy and speed of cytoplasmic self-assembly is astonishing because it involves the correct…
Accurate prediction of protein-ligand interactions is essential for computer-aided drug discovery. However, existing methods often fail to capture solvent-dependent conformational changes and lack the ability to jointly learn multiple…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
The cytoskeleton provides eukaryotic cells with mechanical support and helps them perform their biological functions. It is a network of semiflexible polar protein filaments and many accessory proteins that bind to these filaments, regulate…
In this paper, we develop and analyze a minimal model for a 2D network of cross-linked actin filaments and myosin motors, representing the cortical cytoskeleton of eukaryotic cells. We implement coarse-grained representations of force…
Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of ATP or GTP hydrolysis. The same is…