scholarly journals Molecular Learning of a Soft-Disks Fluid

2021 ◽  
Author(s):  
Luca Zammataro

This work is based on the Equivalence between Molecular Dynamics and Neural networks. It provides learning proofs in a Lennard-Jones (LJ) fluid, presented as a network of particles having non-bonded interactions. I describe the fluid's learning as the property of an order that emerges as an adaptation in establishing equilibrium with energy and thermal conservation. The experimental section demonstrates the fluid can be trained with logic-gates patterns. The work goes beyond Molecular Computing's application, explaining how this model uses its intrinsic minimizing properties in learning and predicting outputs. Finally, it gives hints for a theory on real chemistry's computational universality.

Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ximing Li ◽  
Luna Rizik ◽  
Valeriia Kravchik ◽  
Maria Khoury ◽  
Netanel Korin ◽  
...  

AbstractComplex biological systems in nature comprise cells that act collectively to solve sophisticated tasks. Synthetic biological systems, in contrast, are designed for specific tasks, following computational principles including logic gates and analog design. Yet such approaches cannot be easily adapted for multiple tasks in biological contexts. Alternatively, artificial neural networks, comprised of flexible interactions for computation, support adaptive designs and are adopted for diverse applications. Here, motivated by the structural similarity between artificial neural networks and cellular networks, we implement neural-like computing in bacteria consortia for recognizing patterns. Specifically, receiver bacteria collectively interact with sender bacteria for decision-making through quorum sensing. Input patterns formed by chemical inducers activate senders to produce signaling molecules at varying levels. These levels, which act as weights, are programmed by tuning the sender promoter strength Furthermore, a gradient descent based algorithm that enables weights optimization was developed. Weights were experimentally examined for recognizing 3 × 3-bit pattern.


1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.


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