Designing an Intelligent Controller for a Molecular Valve

Author(s):  
Kasra Momeni ◽  
Aria Alasty

Too much effort has been done for manipulating individual atoms, using nano-manipulators and Scanning Tunneling Microscopes (STM). On the other hand, characterization and manipulation of nano-flows is of great concern. In the current work a molecular valve has been considered, which is made up of six atoms placed on the circumstance of a circle. A fuzzy controller has been designed for controlling the diameter of this molecular valve. The designed fuzzy controller used singleton fuzzifier, Mamdani inference engine, center average defuzzifier and exponential membership functions. A model based on the classical Molecular Dynamics (MD) is used for modeling the nano-system and passing the states to the fuzzy controller. Then the fuzzy controller sets the actuators positions in order to control the diameter of the molecular valve. It has been shown that the designed controller can control the radius with an appropriate accuracy. Dimensionless equations of motion are used for designing the controller; therefore the designed controller is versatile and applicable to all the cases that the interactions between actuators and molecules can be modeled by Lennard-Jones potential. Using such a controller makes the molecular valve become applicable in the real world which has great applications such as drug delivery and controlling nano-flows with single molecule accuracy.

1954 ◽  
Vol 7 (3) ◽  
pp. 219 ◽  
Author(s):  
SD Hamann ◽  
JA Lambert

Theoretical surface tensions at absolute zero have been worked out for liquids whose molecules interact according to the Lennard-Jones potential U = λ/Rn - μ/Rm taking the two sets of exponents : n=12, m=6 and n=28, m=7. The predicted difference between the reduced surface tensions for these two potentials is shown by the experimental surface tensions of monatomic and diatomic liquids on the one hand, and of liquids of polyatomic quasi-spherical molecules on the other hand.


2021 ◽  
Vol 22 (11) ◽  
pp. 5914
Author(s):  
Mengsheng Zha ◽  
Nan Wang ◽  
Chaoyang Zhang ◽  
Zheng Wang

Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis–Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.


1967 ◽  
Vol 47 (7) ◽  
pp. 2491-2494 ◽  
Author(s):  
Bruce Hartmann ◽  
Zaka I. Slawsky

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