Related papers: Free Energy Transduction in a Chemical Motor Model
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
The diffusion of a molecular motor in the presence of a constant external force is considered on the basis of a simple theoretical model. The motor is represented by a Brownian particle moving in a series of parabolic potentials placed…
Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in…
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
Active gels perform key mechanical roles inside the cell, such as cell division, motion and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
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…
Kinesin and related motor proteins utilize ATP fuel to propel themselves along the external surface of microtubules in a processive and directional fashion. We show that the observed step-like motion is possible through time varying charge…
Enzyme mining is rapidly evolving as a data-driven strategy to identify biocatalysts with tailored functions from the vast landscape of uncharacterized proteins. The integration of machine learning into these workflows enables…
Linear bio-molecular motors move unidirectionally along a track by coordinating several different processes, such as fuel (ATP) capture, hydrolysis, conformational changes, binding and unbinding from a track, and center-of-mass diffusion. A…
Processive molecular motors which drive the traffic of organelles in cells move in a directed way along cytoskeletal filaments. On large time scales, they perform motor walks, i.e., peculiar random walks which arise from the repeated…
Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors…
We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the…
Human-created engines and evolutionarily optimized molecular motors exhibit sophisticated design in order to harvest chemical or thermal energy for generating unidirectional motion. The complexity of these motors makes their random…
An equilibrium reversible cycle with a certain engine to transduce the energy of any chemical reaction into mechanical energy is proposed. The efficiency for chemical energy transduction is also defined so as to be compared with Carnot…
Biological functions in each animal cell depend on coordinated operations of a wide variety of molecular motors. Some of the these motors transport cargo to their respective destinations whereas some others are mobile workshops which…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
We present a theoretical treatment of energy transfer in a molecular motor described in terms of overdamped Brownian motion on a multidimensional tilted periodic potential. The tilt acts as a thermodynamic force driving the system out of…