Relationship Between Solutions of Helmholtz’s and Laplace’s Equations in Cylindrical and Spherical Coordinates

2015 ◽  
pp. 635-638
Keyword(s):  
Spherical Coordinates

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

2020 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Computational Modelling ◽  
Free Energy Calculations ◽  
Energy Estimates ◽  
Binding Affinities ◽  
Spherical Coordinates ◽  
Collective Variables ◽  
Guest Binding ◽  
Starting Point ◽  
Sampl Challenge

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

The experience of employment of the mathematical cartography methods in cosmology

2017 ◽  
Vol 923 (5) ◽  
pp. 7-16
Author(s):  
A.V. Kavrayskiy
Keyword(s):  
Background Radiation ◽  
Three Dimensional ◽  
Spherical Coordinates ◽  
Linear Element ◽  
Microwave Background ◽  
Euclidian Space ◽  
Microwave Background Radiation ◽  
Rectangular Coordinates ◽  
The Universe ◽  
Length Distortion

The experience of mathematical modeling of the 3D-sphere in the 4D-space and projecting it by mathematical cartography methods in the 3D-Euclidian space is presented. The problem is solved by introduction of spherical coordinates for the 3D-sphere and their transformation into the rectangular coordinates, using the mathematical cartography methods. The mathematical relationship for calculating the length distortion mp(s) of the ds linear element when projecting the 3D-sphere from the 4-dimensional Euclidian space into three-dimensional Euclidian space is derived. Numerical examples, containing the modeling of the ds small linear element by spherical coordinates of 3D-sphere, projecting this sphere into the 3D-Euclidian space and length of ds calculating by means of its projection dL and size of distortion mp(s) are solved. Based on the model of the Universe known in cosmology as the 3D-sphere, the hypothesis of connection between distortion mp(s) and the known observed effects Redshift and Microwave Background Radiation is considered.

Certain problems with the application of stochastic diffusion processes for description of chemical engineering phenomena; Diffusion equations in curvilinear coordinates

1991 ◽  
Vol 56 (3) ◽  
pp. 602-618
Author(s):  
Vladimír Kudrna
Keyword(s):  
Heat Transfer ◽  
Mass Transport ◽  
Probability Density ◽  
Chemical Engineering ◽  
Diffusion Processes ◽  
Curvilinear Coordinates ◽  
Diffusion Equations ◽  
Parabolic Partial Differential Equations ◽  
Spherical Coordinates ◽  
Transformation Procedure

Parabolic partial differential equations used in chemical engineering for the description of mass transport and heat transfer and analogous relationship derived in stochastic processes theory are given. A standard transformation procedure is applied, allowing these relations to be generally written in curvilinear coordinates and particular expressions for cylindrical and spherical coordinates to be derived. The relation between the probability density for the position of a discernible particle and the concentration of a set of such particles is discussed.

Solutions to the Vector Tetrahedron Equation

1965 ◽  
Vol 87 (2) ◽  
pp. 228-234 ◽  
Author(s):  
Milton A. Chace
Keyword(s):  
Closed Form ◽  
Digital Computer ◽  
Three Dimensional ◽  
Dimensional Vector ◽  
Spherical Coordinates ◽  
Tetrahedron Equation ◽  
Position Determination ◽  
Closed Form Solutions

A set of nine closed-form solutions are presented to the single, three-dimensional vector tetrahedron equation, sum of vectors equals zero. The set represents all possible combinations of unknown spherical coordinates among the vectors, assuming the coordinates are functionally independent. Optimum use is made of symmetry. The solutions are interpretable and can be evaluated reliably by digital computer in milliseconds. They have been successfully applied to position determination of many three-dimensional mechanisms.

scholarly journals A NEW FORMULA FOR THE MASS OF A STATIONARY AXISYMMETRIC CONFIGURATION

1995 ◽  
Vol 10 (10) ◽  
pp. 841-844 ◽  
Author(s):  
R. M. AVAKIAN ◽  
G. OGANESSYAN
Keyword(s):  
Pressure Distribution ◽  
Spherical Coordinates ◽  
New Formula ◽  
Axisymmetric Configuration

It has been shown by one of the authors1 that in isotropic spherical coordinates there is a relation between the mass of a static spherical gravitating body and the pressure distribution inside it. In this paper the result is generalized for the case of stationary axisymmetric configurations.

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