First-passage properties of molecular spiders

Semenov, Oleg; Mohr, David N.; Stefanović, Darko

doi:10.1103/physreve.88.012724

Cited by 15 publications

(7 citation statements)

References 36 publications

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“…An emerging technique to complement BBR studies is the use of coarse-grained simulations that explicitly model interactions between feet and fuel molecules, and the subsequent effects of these interactions on motor transport. ,− These simulations help reveal how molecular-level interactions produce motor-level dynamic behavior and aid in hypothesis generation. However, such simulations have typically focused on small motors with polyvalency on the order of a few tethers.…”

Section: Introductionmentioning

confidence: 99%

Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors

et al. 2022

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Molecular motors, such as myosin and kinesin, perform diverse tasks ranging from vesical transport to bulk muscle contraction. Synthetic molecular motors may eventually be harnessed to perform similar tasks in versatile synthetic systems. The most promising type of synthetic molecular motor, the DNA walker, can undergo processive motion but generally exhibits low speeds and virtually no capacity for force generation. However, we recently showed that highly polyvalent DNA motors (HPDMs) can rival biological motors by translocating at micrometer per minute speeds and generating 100+ pN of force. Accordingly, DNA nanotechnology-based designs may hold promise for the creation of synthetic, force-generating nanomotors. However, the dependencies of HPDM speed and force on tunable design parameters are poorly understood and difficult to characterize experimentally. To overcome this challenge, we present RoloSim, an adhesive dynamics software package for fine-grained simulations of HPDM translocation. RoloSim uses biophysical models for DNA duplex formation and dissociation kinetics to explicitly model tens of thousands of molecular scale interactions. These molecular interactions are then used to calculate the nano- and microscale motions of the motor. We use RoloSim to uncover how motor force and speed scale with several tunable motor properties such as motor size and DNA duplex length. Our results support our previously defined hypothesis that force scales linearly with polyvalency. We also demonstrate that HPDMs can be steered with external force, and we provide design parameters for novel HPDM-based molecular sensor and nanomachine designs.

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Section: Introductionmentioning

confidence: 99%

Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors

et al. 2022

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“…We build on previous models that are based on a class of synthetic molecular walkers known as molecular spiders [20][21][22][23][24]. A spider is composed of an inert chemical body and one or more flexible single-stranded DNAzyme legs.…”

Section: Introductionmentioning

confidence: 99%

“…Experimental data suggest the ratio of dwell time at uncleaved versus cleaved sites could be in the range (0.05, 0.1) [26]. The difference in residence times for legs at visited and unvisited sites has been studied extensively as it relates to first passage properties and directional movement in various simulated environments [20,21,23,24,27]. Notable potential applications of the molecular spider include cargo transport or release of DNA or other product that occurs as a result of the enzymatic action [28].…”

Section: Introductionmentioning

confidence: 99%

Tethered single-legged molecular spiders on independent 1D tracks

Arredondo,

Stefanovic

2019

Preprint

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We study the motion of random walkers with residence time bias between first and subsequent visits to a site, as a model for synthetic molecular walkers composed of coupled DNAzyme legs known as molecular spiders. The mechanism of the transient superdiffusion has been explained via the emergence of a boundary between the new and the previously visited sites, and the tendency of the multi-legged spider to cling to this boundary, provided residence time for a first visit to a site is longer than for subsequent visits. Using both kinetic Monte Carlo simulation and an analytical approach, we model a system that consists of single-legged walkers, each on its own one-dimensional track, connected by a leash, i.e., a kinematic constraint that no two spiders can be more than a certain distance apart. Even though a single one-legged walker does not at all exhibit directional, superdiffusive motion, we find that a team of one-legged walkers on parallel tracks, connected by a flexible tether, does enjoy a superdiffusive transient. Furthermore, the one-legged walker teams exhibit a greater expected number of steps per boundary period and are able to diffuse more quickly through the product sea than two-legged walkers, which leads to longer periods of superdiffusion.

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“…A molecular spider [13], with a rigid body and several flexible legs, moves stochastically on a surface formed by sites containing DNA segments, and can exhibit biased behavior owing to different reactions with fresh sites (catalytic cleavage) and visited sites (dissociation). We extend previous models [3,[14][15][16][17] to implement three basic logic gates (AND, OR, NOT), and cascade the gates to construct logic circuits. Unlike previous models where molecular spiders exhibit biased behaviors, our model uses multiple spiders that are assumed to behave unbiasedly with equal transition rates to all reachable sites.…”

Section: Introductionmentioning

confidence: 99%

Logic circuits based on molecular spider systems

Lakin

Stefanović

2016

Biosystems

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Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity.

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First-passage properties of molecular spiders

Cited by 15 publications

References 36 publications

Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors

Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors

Tethered single-legged molecular spiders on independent 1D tracks

Logic circuits based on molecular spider systems

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