scholarly journals Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters

2021 ◽  
Author(s):  
Fabio Falcioni ◽  
Jas Kalayan ◽  
Richard H. Henchman
Keyword(s):  
Partition Coefficients ◽  
Degrees Of Freedom ◽  
Immiscible Liquid ◽  
Vibrational Entropy ◽  
System A ◽  
Energy Entropy ◽  
Liquid Phases ◽  
Large Numbers ◽  
The Mean ◽  
Entropic Contribution

AbstractPartition coefficients quantify a molecule’s distribution between two immiscible liquid phases. While there are many methods to compute them, there is not yet a method based on the free energy of each system in terms of energy and entropy, where entropy depends on the probability distribution of all quantum states of the system. Here we test a method in this class called Energy Entropy Multiscale Cell Correlation (EE-MCC) for the calculation of octanol–water logP values for 22 N-acyl sulfonamides in the SAMPL7 Physical Properties Challenge (Statistical Assessment of the Modelling of Proteins and Ligands). EE-MCC logP values have a mean error of 1.8 logP units versus experiment and a standard error of the mean of 1.0 logP units for three separate calculations. These errors are primarily due to getting sufficiently converged energies to give accurate differences of large numbers, particularly for the large-molecule solvent octanol. However, this is also an issue for entropy, and approximations in the force field and MCC theory also contribute to the error. Unique to MCC is that it explains the entropy contributions over all the degrees of freedom of all molecules in the system. A gain in orientational entropy of water is the main favourable entropic contribution, supported by small gains in solute vibrational and orientational entropy but offset by unfavourable changes in the orientational entropy of octanol, the vibrational entropy of both solvents, and the positional and conformational entropy of the solute.

scholarly journals Entropy of Simulated Liquids Using Multiscale Cell Correlation

Entropy ◽  
2019 ◽  
Vol 21 (8) ◽  
pp. 750
Author(s):  
Hafiz Saqib Ali ◽  
Jonathan Higham ◽  
Richard H. Henchman
Keyword(s):  
Degrees Of Freedom ◽  
Probability Distributions ◽  
Mean Field ◽  
Vibrational Entropy ◽  
Amber Force Field ◽  
Equal Importance ◽  
The Mean ◽  
Dynamics Simulations ◽  
Consistent Treatment ◽  
Better Than

Accurately calculating the entropy of liquids is an important goal, given that many processes take place in the liquid phase. Of almost equal importance is understanding the values obtained. However, there are few methods that can calculate the entropy of such systems, and fewer still to make sense of the values obtained. We present our multiscale cell correlation (MCC) method to calculate the entropy of liquids from molecular dynamics simulations. The method uses forces and torques at the molecule and united-atom levels and probability distributions of molecular coordinations and conformations. The main differences with previous work are the consistent treatment of the mean-field cell approximation to the approriate degrees of freedom, the separation of the force and torque covariance matrices, and the inclusion of conformation correlation for molecules with multiple dihedrals. MCC is applied to a broader set of 56 important industrial liquids modeled using the Generalized AMBER Force Field (GAFF) and Optimized Potentials for Liquid Simulations (OPLS) force fields with 1.14*CM1A charges. Unsigned errors versus experimental entropies are 8.7 J K − 1 mol − 1 for GAFF and 9.8 J K − 1 mol − 1 for OPLS. This is significantly better than the 2-Phase Thermodynamics method for the subset of molecules in common, which is the only other method that has been applied to such systems. MCC makes clear why the entropy has the value it does by providing a decomposition in terms of translational and rotational vibrational entropy and topographical entropy at the molecular and united-atom levels.

The motion of a lunar orbiter

1966 ◽  
Vol 25 ◽  
pp. 373
Author(s):  
Y. Kozai
Keyword(s):  
Degrees Of Freedom ◽  
Dimensional Space ◽  
Artificial Satellite ◽  
Equations Of Motion ◽  
Triaxial Ellipsoid ◽  
The Moon ◽  
Secular Motion ◽  
The Earth ◽  
Close Satellite ◽  
The Mean

The motion of an artificial satellite around the Moon is much more complicated than that around the Earth, since the shape of the Moon is a triaxial ellipsoid and the effect of the Earth on the motion is very important even for a very close satellite.The differential equations of motion of the satellite are written in canonical form of three degrees of freedom with time depending Hamiltonian. By eliminating short-periodic terms depending on the mean longitude of the satellite and by assuming that the Earth is moving on the lunar equator, however, the equations are reduced to those of two degrees of freedom with an energy integral.Since the mean motion of the Earth around the Moon is more rapid than the secular motion of the argument of pericentre of the satellite by a factor of one order, the terms depending on the longitude of the Earth can be eliminated, and the degree of freedom is reduced to one.Then the motion can be discussed by drawing equi-energy curves in two-dimensional space. According to these figures satellites with high inclination have large possibilities of falling down to the lunar surface even if the initial eccentricities are very small.The principal properties of the motion are not changed even if plausible values ofJ3andJ4of the Moon are included.This paper has been published in Publ. astr. Soc.Japan15, 301, 1963.

Partition Coefficient Ratios and Tumour Perfusion Studied with 85mKr and 133Xe

1987 ◽  
Vol 26 (06) ◽  
pp. 253-257
Author(s):  
M. Mäntylä ◽  
J. Perkkiö ◽  
J. Heikkonen
Keyword(s):  
Partition Coefficient ◽  
Partition Coefficients ◽  
Regional Blood Flow ◽  
Blood Perfusion ◽  
Compartmental Analysis ◽  
Malignant Tumour ◽  
Mean Value ◽  
Perfusion Rate ◽  
Biological Variables ◽  
The Mean

The relative partition coefficients of krypton and xenon, and the regional blood flow in 27 superficial malignant tumour nodules in 22 patients with diagnosed tumours were measured using the 85mKr- and 133Xe-clearance method. In order to minimize the effect of biological variables on the measurements the radionuclides were injected simultaneously into the tumour. The distribution of the radiotracers was assumed to be in equilibrium at the beginning of the experiment. The blood perfusion was calculated by fitting a two-exponential function to the measuring points. The mean value of the perfusion rate calculated from the xenon results was 13 ± 10 ml/(100 g-min) [range 3 to 38 ml/(100 g-min)] and from the krypton results 19 ± 11 ml/(100 g-min) [range 5 to 45 ml/(100 g-min)]. These values were obtained, if the partition coefficients are equal to one. The equations obtained by using compartmental analysis were used for the calculation of the relative partition coefficient of krypton and xenon. The partition coefficient of krypton was found to be slightly smaller than that of xenon, which may be due to its smaller molecular weight.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

scholarly journals Relaxation Times in Strictly Disk Systems

1971 ◽  
Vol 10 ◽  
pp. 15-19
Author(s):  
George B. Rybicki
Keyword(s):  
Numerical Experiments ◽  
Relaxation Times ◽  
Galactic Structure ◽  
Large Numbers ◽  
Order Of Magnitude ◽  
Vlasov Limit ◽  
The Mean ◽  
Gravitating Systems

AbstractIt is shown that the time of relaxation by particle encounters of self-gravitating systems in the plane interacting by 1/r2 forces is of the same order of magnitude as the mean orbit time. Therefore such a system does not have a Vlasov limit for large numbers of particles, unless appeal is made to some non-zero thickness of the disk. The relevance of this result to numerical experiments on galactic structure is discussed.

GLOBAL FLUCTUATIONS FOR LINEAR STATISTICS OF β-JACOBI ENSEMBLES

2012 ◽  
Vol 01 (04) ◽  
pp. 1250013 ◽  
Author(s):  
IOANA DUMITRIU ◽  
ELLIOT PAQUETTE
Keyword(s):  
Gaussian Process ◽  
Covariance Matrix ◽  
Law Of Large Numbers ◽  
Test Functions ◽  
Linear Statistics ◽  
Jacobi Ensemble ◽  
Large Numbers ◽  
The Mean ◽  
Shifted Chebyshev Polynomial ◽  
Global Fluctuations

We study the global fluctuations for linear statistics of the form [Formula: see text] as n → ∞, for C1 functions f, and λ1, …, λn being the eigenvalues of a (general) β-Jacobi ensemble. The fluctuation from the mean [Formula: see text] turns out to be given asymptotically by a Gaussian process. We compute the covariance matrix for the process and show that it is diagonalized by a shifted Chebyshev polynomial basis; in addition, we analyze the deviation from the predicted mean for polynomial test functions, and we obtain a law of large numbers.

scholarly journals Limit Theorems and Fluctuations for Point Vortices of Generalized Euler Equations

2021 ◽  
Vol 182 (3) ◽  
Author(s):  
Carina Geldhauser ◽  
Marco Romito
Keyword(s):  
Euler Equations ◽  
Mean Field ◽  
Point Vortices ◽  
Positive Temperature ◽  
Field Limit ◽  
Mean Field Limit ◽  
Large Numbers ◽  
The Mean ◽  
Formal Solutions ◽  
2D Torus

AbstractWe prove a mean field limit, a law of large numbers and a central limit theorem for a system of point vortices on the 2D torus at equilibrium with positive temperature. The point vortices are formal solutions of a class of equations generalising the Euler equations, and are also known in the literature as generalised inviscid SQG. The mean-field limit is a steady solution of the equations, the CLT limit is a stationary distribution of the equations.

Maximum Total Point Motion of Five Points Versus All Points in Assessing Tibial Baseplate Stability

2021 ◽  
Author(s):  
Abigail Niesen ◽  
Anna L Garverick ◽  
Maury Hull
Keyword(s):  
Degrees Of Freedom ◽  
Stability Limit ◽  
3D Models ◽  
Six Degrees Of Freedom ◽  
Percent Error ◽  
Model Based ◽  
Point Motion ◽  
The Mean ◽  
The Difference ◽  
Total Point

Abstract Maximum total point motion (MTPM), the point on a baseplate that migrates the most, has been used to assess the risk of tibial baseplate loosening using radiostereometric analysis (RSA). Two methods for determining MTPM for model-based RSA are to use either 5 points distributed around the perimeter of the baseplate or to use all points on the 3D model. The objectives were to quantify the mean difference in MTPM using 5 points vs. all points, compute the percent error relative to the 6-month stability limit for groups of patients, and to determine the dependency of differences in MTPM on baseplate size and shape. A dataset of 10,000 migration values was generated using the mean and standard deviation of migration in six degrees of freedom at 6 months from an RSA study. The dataset was used to simulate migration of 3D models (two baseplate shapes and two baseplate sizes) and calculate the difference in MTPM using 5 virtual points vs. all points and the percent error (i.e. difference in MTPM/stability limit) relative to the 6-month stability limit. The difference in MTPM was about 0.02 mm, or 4% percent relative to the 6-month stability limit, which is not clinically important. Furthermore, results were not affected by baseplate shape or size. Researchers can decide whether to use 5 points or all points when computing MTPM for model-based RSA. The authors recommend using 5 points to maintain consistency with marker-based RSA.

ASYNCHRONOUS UPDATING RESTORES THE LAW OF LARGE NUMBERS IN GLOBALLY COUPLED SYSTEMS

2002 ◽  
Vol 12 (03) ◽  
pp. 663-669 ◽  
Author(s):  
SUDESHNA SINHA
Keyword(s):  
Law Of Large Numbers ◽  
Mean Field ◽  
Coupled Systems ◽  
Large N ◽  
Large Numbers ◽  
Statistical Behavior ◽  
Remarkable Result ◽  
Asynchronous Updating ◽  
The Mean ◽  
The Law

It was observed in earlier studies, that the mean field of globally coupled maps evolving under synchronous updating rules violated the law of large numbers, and this remarkable result generated widespread research interest. In this work we demonstrate that incorporating increasing degrees of asynchronicity in the updating rules rapidly restores the statistical behavior of the mean field. This is clear from the decay of the mean square deviation of the mean field with respect to lattice size N, for varying degrees of asynchronicity, which shows 1/N behavior upto very large N even when the updating is far from fully asynchronous. This is also evidenced through increasing 1/f2 behavior regimes in the power spectrum of the mean field under increasing asynchronicity.

The Connective Tissue Sheath of the Locust Nervous System: A Histochemical Study

1959 ◽  
Vol s3-100 (51) ◽  
pp. 401-412
Author(s):  
DOREEN E. ASHHURST
Keyword(s):  
Nervous System ◽  
Connective Tissue ◽  
Collagen Type ◽  
Histochemical Study ◽  
Locusta Migratoria ◽  
System A ◽  
Large Numbers ◽  
Connective Tissue Sheath ◽  
Cellular Layer ◽  
Sheath Cells

The connective tissue sheath surrounding the nervous system of Locusta migratoria has been studied histochemically. It consists of an outer non-cellular layer, the neural lamella, and an inner layer of cells, the sheath-cells. The neural lamella has been identified as being composed of a collagen-type protein and neutral mucopolysaccharide on the evidence of its histochemical reactions and the identification of hydroxyproline by paper chromatography in a hydrolysate of the neural lamella. The sheath-cells possess large numbers of lipochondria composed of phospholipids and cerebrosides, and small spherical mitochondria. The cytoplasm also contains lipids (some of which may be cerebrosides), glycogen, and RNA.

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