Fluids with internal degrees of freedom. I. Extended thermodynamics approach

1987 ◽  
Vol 86 (7) ◽  
pp. 4208-4215 ◽  
Author(s):  
R. F. Rodríguez ◽  
L. S. García‐Colín ◽  
L. F. del Castillo
Keyword(s):  
Degrees Of Freedom ◽  
Extended Thermodynamics ◽  
Internal Degrees Of Freedom

scholarly journals Molecular Extended Thermodynamics of Rarefied Polyatomic Gases with a New Hierarchy of Moments

Fluids ◽  
2021 ◽  
Vol 6 (2) ◽  
pp. 62
Author(s):  
Takashi Arima ◽  
Tommaso Ruggeri
Keyword(s):  
Degrees Of Freedom ◽  
Maximum Entropy Principle ◽  
Extended Thermodynamics ◽  
Moment Equations ◽  
Field Equations ◽  
Polyatomic Gases ◽  
Moment System ◽  
Rarefied Polyatomic Gases ◽  
Entropy Principle ◽  
Internal Degrees Of Freedom

The aim of this paper is to construct the molecular extended thermodynamics for classical rarefied polyatomic gases with a new hierarchy, which is absent in the previous procedures of moment equations. The new hierarchy is deduced recently from the classical limit of the relativistic theory of moments associated with the Boltzmann–Chernikov equation. The field equations for 15 moments of the distribution function, in which the internal degrees of freedom of a molecule are taken into account, are closed with the maximum entropy principle. It is shown that the theory contains, as a principal subsystem, the previously polyatomic 14 fields theory, and in the monatomic limit, in which the dynamical pressure vanishes, the differential system converges, instead of to the Grad 13-moment system, to the Kremer 14-moment system.

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 A novel class of translationally invariant spin chains with long-range interactions

2020 ◽  
Vol 2020 (8) ◽  
Author(s):  
B. Basu-Mallick ◽  
F. Finkel ◽  
A. González-López
Keyword(s):  
Long Range ◽  
Degrees Of Freedom ◽  
Spin Chains ◽  
Open Chain ◽  
New Class ◽  
Spin Interactions ◽  
Long Range Interactions ◽  
Spin Reversal ◽  
Twisted Yangian ◽  
Internal Degrees Of Freedom

Abstract We introduce a new class of open, translationally invariant spin chains with long-range interactions depending on both spin permutation and (polarized) spin reversal operators, which includes the Haldane-Shastry chain as a particular degenerate case. The new class is characterized by the fact that the Hamiltonian is invariant under “twisted” translations, combining an ordinary translation with a spin flip at one end of the chain. It includes a remarkable model with elliptic spin-spin interactions, smoothly interpolating between the XXX Heisenberg model with anti-periodic boundary conditions and a new open chain with sites uniformly spaced on a half-circle and interactions inversely proportional to the square of the distance between the spins. We are able to compute in closed form the partition function of the latter chain, thereby obtaining a complete description of its spectrum in terms of a pair of independent su(1|1) and su(m/2) motifs when the number m of internal degrees of freedom is even. This implies that the even m model is invariant under the direct sum of the Yangians Y (gl(1|1)) and Y (gl(0|m/2)). We also analyze several statistical properties of the new chain’s spectrum. In particular, we show that it is highly degenerate, which strongly suggests the existence of an underlying (twisted) Yangian symmetry also for odd m.

scholarly journals Dissipative dynamics of a particle coupled to a field via internal degrees of freedom

2021 ◽  
Vol 103 (5) ◽  
Author(s):  
Kanupriya Sinha ◽  
Adrián Ezequiel Rubio López ◽  
Yiğit Subaşı
Keyword(s):  
Degrees Of Freedom ◽  
Dissipative Dynamics ◽  
Internal Degrees Of Freedom

scholarly journals Optimal Relabeling of Water Molecules and Single-Molecule Entropy Estimation

Biophysica ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 279-296
Author(s):  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Water Molecules ◽  
Maximum Information ◽  
Nearest Neighbours ◽  
Biomolecular Simulations ◽  
Solvent Molecules ◽  
Solvation Entropy ◽  
Dynamics Simulations ◽  
Internal Degrees Of Freedom

Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degrees of freedom in biomolecular simulations, and for the rigorous computation of positional-orientational entropy of one and two molecules. The mutual information expansion (MIE) and the maximum information spanning tree (MIST) methods were proposed and used to deal with a large number of non-independent degrees of freedom, providing estimates or bounds on the global entropy, thus complementing the kNN method. The application of the combination of such methods to solvent molecules appears problematic because of the indistinguishability of molecules and of their symmetric parts. All indistiguishable molecules span the same global conformational volume, making application of MIE and MIST methods difficult. Here, we address the problem of indistinguishability by relabeling water molecules in such a way that each water molecule spans only a local region throughout the simulation. Then, we work out approximations and show how to compute the single-molecule entropy for the system of relabeled molecules. The results suggest that relabeling water molecules is promising for computation of solvation entropy.

Multi-arm grasp and manipulation of objects with internal degrees of freedom

1990 ◽  
Author(s):  
A. Jain ◽  
G. Rodriguez ◽  
K. Kreutz-Delgado
Keyword(s):  
Degrees Of Freedom ◽  
Internal Degrees Of Freedom

scholarly journals Counting Statistics for Mesoscopic Conductors with Internal Degrees Of Freedom

2010 ◽  
Vol 105 (2) ◽  
Author(s):  
Christopher Birchall ◽  
Henning Schomerus
Keyword(s):  
Degrees Of Freedom ◽  
Mesoscopic Conductors ◽  
Counting Statistics ◽  
Internal Degrees Of Freedom
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