Variable soft sphere molecular model for inverse‐power‐law or Lennard‐Jones potential

1991 ◽  
Vol 3 (10) ◽  
pp. 2459-2465 ◽  
Author(s):  
Katsuhisa Koura ◽  
Hiroaki Matsumoto

The methods of determining molecular fields, described in previous papers, are here applied with certain modifications to the cases of helium and neon. There is considerable observational material available in the case of helium, both as regards its isotherms and as regards its viscosity over a large range of temperature, but it has not as yet been used with any success to yield satisfactory information about its outer field. Keesom, who obtained a number of theoretical formulæ for the second virial coefficient of the equation of state, was unable to find any which would satisfactorily explain the temperature variation of this coefficient in the case of helium, as determined experimentally by Kamerlingh Onnes; in fact, the experimental coefficient showed at the higher temperatures a distinct maximum, and this property none of his theoretical formulæ possessed. The maximum property has, moreover, been confirmed by the later experimental work of Holborn and Otto. The formula, given in a recent paper, is, however, more successful in this direction, and the method of using it, there described, leads to the conclusion that the field of helium can well be represented by the superposition of repulsive and attractive fields, each according to an inverse power law. Furthermore, the values of the force constants are here determined. It has long been recognised that the temperature variation of the viscosity of helium cannot adequately be represented by the theoretical Sutherland formula, with the obvious inference that helium cannot be regarded (even roughly) as a rigid sphere with a superimposed attractive field. This is perhaps not surprising in view of the comparatively simple electronic structure of helium. Kamerlingh Onnes has shown that the variation can best be represented by the simple law, in which the viscosity varies as a power of the temperature. This formula, although first given as an empirical result, corresponds theoretically to a molecular model, in which the molecules are regarded as point centres of force repelling according to an inverse power law. The information available concerning the viscosity of helium is here used, for the first time, to determine the actual value of the repulsive force constant. It is further shown that the result is consistent with that found by the other (entirely independent) method, above described. The field thus determined is one of repulsion according to an inverse 14th power of the distance and a very weak attraction according to an inverse 5th power.


2006 ◽  
Author(s):  
Gerardo Ramirez ◽  
Sonia Perez ◽  
John G. Holden

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.


The investigation of a preceding paper has shown that the temperature variation of viscosity, as determined experimentally, can be satisfactorily explained in many gases on the assumption that the repulsive and attractive parts of the molecular field are each according to an inverse power of the distance. In some cases, in argon, for example, it was further shown that the experimental facts can be explained by more than one molecular model, from which we inferred that viscosity results alone are insufficient to determine precisely the nature of molecular fields. The object of the present paper is to ascertain whether a molecular model of the same type will also explain available experimental data concerning the equation of state of a gas, and if so, whether the results so obtained, when taken in conjunction with those obtained from viscosity, will definitely fix the molecular field. Such an investigation is made possible by the elaborate analysis by Kamerlingh Onnes of the observational material. He has expressed the results in the form of an empirical equation of state of the type pv = A + B/ v + C/ v 2 + D/ v 4 + E/ v 6 + F/ v 8 , where the coefficients A ... F, called by him virial coefficients , are determined as functions of the temperature to fit the observations. Now it is possible by various methods to obtain a theoretical expression for B as a function of the temperature and a strict comparison can then be made between theory and experiment. Unfortunately the solution for B, although applicable to any molecular model of spherical symmetry, is purely formal and contains an integral which can be evaluated only in special cases. This has been done up to now for only two simple models, viz., a van der Waals molecule, and a molecule repelling according to an inverse power law (without attraction), but it is shown in this paper that it can also be evaluated in the case of the model, which was successful in explaining viscosity results. As the two other models just mentioned are particular cases of this, the appropriate formulæ for B are easily deduced from the general one given here.


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