Related papers: Free Energy Transduction in a Chemical Motor Model
We analyze an autonomous micro-engine as a closed quantum mechanical system, including the work it performs and the fuel it consumes. Our model system shows by example that it is possible to transfer energy steadily and spontaneously…
Two simple (rotator and one-particle) mechanistic models are suggested to describe simultaneously at a minimal level of sophistication two basic functions of F$_1$-ATPase: a motor regime driven by ATP hydrolysis and its inverted function as…
The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
A mathematical model for chemical reactions in electrolytes is developed using an Energy variational method consistent with classical thermodynamics. Electrostatics and chemical reactions are included in properly defined energetic and…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…
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…
Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
Chemical reaction engineering is key to industrial might and sustainable chemistry. This will be enabled using smart, efficient catalysts or catalysis ecosystems. This is possible with advanced artificial intelligence and machine learning…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Recent experiments demonstrate that molecular motors from the Myosin II family serve as cross-links inducing active tension in the cytoskeletal network. Here we revise the Brownian ratchet model, previously studied in the context of active…
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…
Understanding the operation of biological molecular motors, nanoscale machines that transduce electrochemical energy into mechanical work, is enhanced by bottom-up strategies to synthesize novel motors.
We have developed a novel method to evaluate the potential profile of a molecular motor at each chemical state from only the probe's trajectory and applied it to a rotary molecular motor F$_1$-ATPase. By using this method, we could also…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…