Related papers: Mechanics, Energetics, Entropy and Kinetics of a B…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
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 molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors "transduce" input energy into mechanical work. All the nano-motors considered here operate…
Multibody systems usually give rise to complex nonlinear dynamics, and the bicycle is not an exception. Even a simple model as the Two-Mass-Skate presents a long expression of the kinetic energy, making difficult to write explicitly the…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Multi-component molecular machines are ubiquitous in biology. We review recent progress on describing their thermodynamic properties using autonomous bipartite Markovian dynamics. The first and second laws can be split into local versions…
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In…
Purpose: From the myofibrils to the whole muscle scale, muscle micro-constituents exhibit passive and active mechanical properties, potentially coupled to electrical, chemical, and thermal properties. Experimental characterization of some…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
The extension of thermodynamic principles to active matter remains a challenge due to the non-equilibrium nature inherent to active systems. In this study, we introduce a framework to assess entropy in our minimal macroscopic experiment…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they…
The equilibrium behavior of binary mixtures can be understood through the competition of energy scales, which classifies their corresponding phase diagrams into distinct topological regimes (Types I-IV). However, in many soft-matter…