Related papers: Acceleration of enzymatic reaction-diffusion kinet…
The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced…
Like their larger micron-scale counterparts, {\AA}ngstr\"om-scale chemically self-propelled motors use asymmetric catalytic activity to produce self-generated concentration gradients that lead to directed motion. Unlike their micron-scale…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
The collective dynamics of $N$ weakly coupled processive molecular motors are considered theoretically. We show, using a discrete lattice model, that the velocity-force curves strongly depend on the effective dynamic interactions between…
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…
The molecular motor protein kinesin plays a key role in fundamental cellular processes such as intracellular transport, mitotic spindle formation, and cytokinesis, with important implications for neurodegenerative and cancer disease…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Self-propelled chemically powered synthetic micron and nano-scale motors are being intensively studied because of the wide range of potential applications that exploit their directed motion. This paper considers even smaller…
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…
In a single molecule assay, the motion of a molecular motor is often inferred from measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic set-up taking into account…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
We investigate the efficiency of systems of molecular motors operating at maximum power. We consider two models of kinesin motors on a microtubule: for both the simplified and the detailed model, we find that the many-body exclusion effect…
Simulated sliding between an oxidized silicon tip and surface over six decades of velocity using accelerated molecular dynamics reproduces the experimentally observed velocity dependence of the friction force. Unlike in the crystalline…
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…
Molecular motors do not work in isolation {\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like…
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 this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
Several enzymes exhibit enhanced diffusion in the presence of a substrate. One explanation of this enhancement arises from fluctuating dimer models, which suggest that enzymes have a higher diffusion constant when interacting with…
The generation of unidirectional motion has been a long-standing challenge in engineering of molecular motors and, more generally, machines. A molecular motor is characterized by a set of low energy states that differ in their…
Molecular motors are in charge of almost every process in the life cycle of cells, such as protein synthesis, DNA replication, and cell locomotion, hence being of crucial importance for understanding the cellular dynamics. However, given…