Related papers: Allostery and Kinetic Proofreading
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 study of free piston Stirling engine (FPSE) requires both accurate thermodynamic and dynamic modelling to predict its performances. The steady state behaviour of the engine partly relies on non linear dissipative phenomena such as…
Actomyosin networks are major structural components of the cell. They provide mechanical integrity and allow dynamic remodeling of eukaryotic cells, self-organizing into the diverse patterns essential for development. We provide a…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Flow-based generative models can be viewed through a physics lens: sampling transports a particle from noise to data by integrating a time-varying velocity field, and each sample corresponds to a trajectory with its own dynamical effort.…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
T cell receptor signaling must operate reliably under tight time constraints. While assuming quite different mechanisms, two prominent models of T cell receptor activation, kinetic segregation and kinetic proofreading, both introduce a…
Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For…
The origin of biological motion can be traced back to the function of molecular motor proteins. Cytoplasmic dynein and kinesin transport organelles within our cells moving along a polymeric filament, the microtubule. The motion of the…
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination…
Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical…
Cortical actin networks are highly dynamic and play critical roles in shaping the mechanical properties of cells. The actin cytoskeleton undergoes significant reorganization over the course of the cell cycle, when cortical actin transitions…