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Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
How do humans move? Advances in reinforcement learning (RL) have produced impressive results in capturing human motion using physics-based humanoid control. However, torque-controlled humanoids fail to model key aspects of human motor…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
Many cellular processes rely on the cell's ability to transport material to and from the nucleus. Networks consisting of many microtubules and actin filaments are key to this transport. Recently, the inhibition of intracellular transport…
We investigate a microscopic motor based on an externally controlled two-level system. One cycle of the motor operation consists of two strokes. Within each stroke, the two-level system is in contact with a given thermal bath and its energy…
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…
The motor part of a crawling eukaryotic cell can be represented schematically as an active continuum layer. The main active processes in this layer are protrusion, originating from non-equilibrium polymerization of actin fibers,…
Retrosynthesis is the task of breaking down a chemical compound recursively step-by-step into molecular precursors until a set of commercially available molecules is found. Consequently, the goal is to provide a valid synthesis route for a…
Non-classical two-step nucleation including preordering and crystal nucleation has been widely proposed to challenge the one-step nucleation framework in diverse materials, while what drives preordering has not been explicitly resolved yet.…
KIF1A, a processive single headed kinesin superfamily motor, hydrolyzes Adenosine triphosphate (ATP) to move along a filamentous track called microtubule. The stochastic movement of KIF1A on the track is characterized by an alternating…
Mixtures of microtubules and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents' molecular properties. We map the non-equilibrium phase diagram of microtubules and tip-accumulating…
We study microscopic engines that use a single active particle as their "working medium". Part of the energy required to drive the directed motion of the particle can be recovered as work, even at constant temperature. A wide class of…
Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or…
Adenosine 5'-triphosphate (ATP) is the nearly ubiquitous "energy currency" of living organisms, and thus is a crucial participant in the majority of enzymatic reactions. The standard models in enzyme kinetics generally ignore the temporal…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
Length-regulation of microtubules (MTs) is essential for many cellular processes. Molecular motors like kinesin 8, which move along MTs and also act as depolymerases, are known as key players in MT dynamics. However, the regulatory…