4,217 research outputs found
Mechanochemical enzymes and protein machines as hydrodynamic force dipoles: The active dimer model
Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium fluctuating flows collectively generated by the enzymes, mixing in the solution and diffusion of passive particles within it are expected to get enhanced. Here, we investigate the intensity and statistical properties of such force dipoles in the minimal active dimer model of a mechanochemical enzyme. In the framework of this model, novel estimates for hydrodynamic collective effects in solution and in lipid bilayers under rapid rotational diffusion are derived, and available experimental and computational data is examined
Oscillation-based methods for actuation and manipulation of nano-objects
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in AIP Conference Proceedings 1882, 020056 (2017) and may be found at https://doi.org/10.1063/1.5001635.We discuss how oscillations can be used for fixation or manipulation of nano-objects or producing nano-drives. The underlying principles are scale-invariant and principally can be scaled down up to the molecular scale. The main underlying principle of fixation and actuation occurs to be symmetry breaking of an oscillating system. From this unifying standpoint, a series of actuation principles are discussed as dragging, ratchets, micro walking, friction-inertia actuators, oscillation tweezers, flagella motors for propulsion in liquids as well as some recently proposed actuation principles
Dynamic entanglement in oscillating molecules and potential biological implications
We demonstrate that entanglement can persistently recur in an oscillating
two-spin molecule that is coupled to a hot and noisy environment, in which no
static entanglement can survive. The system represents a non-equilibrium
quantum system which, driven through the oscillatory motion, is prevented from
reaching its (separable) thermal equilibrium state. Environmental noise,
together with the driven motion, plays a constructive role by periodically
resetting the system, even though it will destroy entanglement as usual. As a
building block, the present simple mechanism supports the perspective that
entanglement can exist also in systems which are exposed to a hot environment
and to high levels of de-coherence, which we expect e.g. for biological
systems. Our results furthermore suggest that entanglement plays a role in the
heat exchange between molecular machines and environment. Experimental
simulation of our model with trapped ions is within reach of the current
state-of-the-art quantum technologies.Comment: Extended version, including supplementary information. 9 pages, 8
figure
Modeling the thermal evolution of enzyme-created bubbles in DNA
The formation of bubbles in nucleic acids (NAs) are fundamental in many
biological processes such as DNA replication, recombination, telomeres
formation, nucleotide excision repair, as well as RNA transcription and
splicing. These precesses are carried out by assembled complexes with enzymes
that separate selected regions of NAs. Within the frame of a nonlinear dynamics
approach we model the structure of the DNA duplex by a nonlinear network of
coupled oscillators. We show that in fact from certain local structural
distortions there originate oscillating localized patterns, that is radial and
torsional breathers, which are associated with localized H-bond deformations,
being reminiscent of the replication bubble. We further study the temperature
dependence of these oscillating bubbles. To this aim the underlying nonlinear
oscillator network of the DNA duplex is brought in contact with a heat bath
using the Nos-Hoover-method. Special attention is paid to the
stability of the oscillating bubbles under the imposed thermal perturbations.
It is demonstrated that the radial and torsional breathers, sustain the impact
of thermal perturbations even at temperatures as high as room temperature.
Generally, for nonzero temperature the H-bond breathers move coherently along
the double chain whereas at T=0 standing radial and torsional breathers result.Comment: 19 pages, 7 figure
Timing molecular motion and production with a synthetic transcriptional clock
The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of āloadā processes such as the operation of a DNA-based nanomechanical device (āDNA tweezersā) or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an āinsulator circuitā was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems
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