scholarly journals Coupled Nosé-Hoover equations of motions without time scaling

2016 ◽  
Author(s):  
Ikuo Fukuda ◽  
Kei Moritsugu
Keyword(s):  
Physical System ◽  
Heat Bath ◽  
Bath Temperature ◽  
Model Systems ◽  
Total System ◽  
Canonical Distribution ◽  
Time Scaling ◽  
Original Scheme ◽  
Dynamics Simulations ◽  
Sampling Property

AbstractThe Nosé-Hoover (NH) equation of motion is widely used in molecular dynamics simulations. It enables us to set a constant temperature and produce the canonical distribution for a target physical system. For the purpose of investigating the physical system under fluctuating temperature, we have introduced a coupled Nosé-Hoover equation in our previous work [J. Phys. A 48 455001 (2015)]. The coupled NH equation implements a fluctuating heat-bath temperature in the NH equation of the physical system, and also keeps a statistically complete description via an invariant measure of the total system composed of the physical system and a “temperature system”. However, a difficulty lies in that the time development of the physical system may not correspond to the realistic physical process, because of the need of a scaled time average to compute thermodynamical quantities. The current work gives a solution by presenting a new scheme, which is free from the scaled time but retains the statistical description. By use of simple model systems, we validate the current scheme and compare with the original scheme. The sampling property of the current scheme is also clarified to investigate the effect of function setting used for the distribution of the total system.

TEMPERATURE OF NONEQUILIBRIUM LATTICE SYSTEMS

2006 ◽  
Vol 17 (12) ◽  
pp. 1703-1715 ◽  
Author(s):  
ALBERTO PETRI ◽  
M. J. DE OLIVEIRA
Keyword(s):  
Monte Carlo ◽  
Heat Bath ◽  
Bath Temperature ◽  
Total System ◽  
Local Distribution ◽  
Lattice Systems ◽  
Potts Models ◽  
Monte Carlo Dynamics ◽  
Instantaneous Temperature ◽  
System Energy

We investigate the thermal quench of Ising and Potts models via Monte Carlo dynamics. We find that the local distribution of the site-site interaction energy has the same form as in the equilibrium case, a result that allows us to define an instantaneous temperature θ during the systems relaxation. We also find that, after an undercritical quench, θ equals the heat bath temperature in a finite time, while the total system energy is still decreasing due to the coarsening process.

scholarly journals The thermodynamic theory of black holes

1977 ◽  
Vol 353 (1675) ◽  
pp. 499-521 ◽  
Keyword(s):  
Black Holes ◽  
Black Hole ◽  
Energy Momentum Tensor ◽  
Heat Bath ◽  
Naked Singularity ◽  
Momentum Tensor ◽  
Thermodynamic Theory ◽  
Model Systems ◽  
Quantum Energy ◽  
Third Law Of Thermodynamics

The thermodynamic theory underlying black hole processes is developed in detail and applied to model systems. I t is found that Kerr-Newman black holes undergo a phase transition at a = 0.68 M or Q = 0.86 M , where the heat capacity has an infinite discontinuity. Above the transition values the specific heat is positive, permitting isothermal equilibrium with a surrounding heat bath. Simple processes and stability criteria for various black hole situations are investigated. The limits for entropieally favoured black hole formation are found. The Nernst conditions for the third law of thermodynamics are not satisfied fully for black holes. There is no obvious thermodynamic reason why a black hole may not be cooled down below absolute zero and converted into a naked singularity. Quantum energy-momentum tensor calculations for uncharged black holes are extended to the Reissner-Nordstrom case, and found to be fully consistent with the thermodynamic picture for Q < M . For Q > M the model predicts that ‘naked’ collapse also produces radiation, with such intensity that the collapsing matter is entirely evaporated away before a naked singularity can form.

scholarly journals Quantum Information Remote Carnot Engines and Voltage Transformers

Entropy ◽  
2019 ◽  
Vol 21 (2) ◽  
pp. 127 ◽  
Author(s):  
Jose Diazdelacruz ◽  
Miguel Martin-Delgado
Keyword(s):  
Quantum Information ◽  
Long Range ◽  
Physical System ◽  
Thermal Equilibrium ◽  
Heat Bath ◽  
Magnetic Interactions ◽  
Electrical Network ◽  
Heat Engines ◽  
Different Temperatures ◽  
Available Information

A physical system out of thermal equilibrium is a resource for obtaining useful work when a heat bath at some temperature is available. Information Heat Engines are the devices which generalize the Szilard cylinders and make use of the celebrated Maxwell demons to this end. In this paper, we consider a thermo-chemical reservoir of electrons which can be exchanged for entropy and work. Qubits are used as messengers between electron reservoirs to implement long-range voltage transformers with neither electrical nor magnetic interactions between the primary and secondary circuits. When they are at different temperatures, the transformers work according to Carnot cycles. A generalization is carried out to consider an electrical network where quantum techniques can furnish additional security.

scholarly journals Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
A Priori ◽  
Model Systems ◽  
Dynamics Simulation ◽  
High Mass ◽  
Mean Square ◽  
Dynamics Simulations

ABSTRACTPredicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2for Cγ, when the sampling was done, for each of these proteins, over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations using AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive toa prioriprediction of crystallographic B-factors of a folded globular protein.

scholarly journals Vibrational couplings and energy transfer pathways of water’s bending mode

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chun-Chieh Yu ◽  
Kuo-Yang Chiang ◽  
Masanari Okuno ◽  
Takakazu Seki ◽  
Tatsuhiko Ohto ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Vibrational Energy ◽  
Heat Bath ◽  
Energy Relaxation ◽  
Ab Initio Molecular Dynamics ◽  
Vibrational Coupling ◽  
Strongly Coupled ◽  
Bending Mode ◽  
Stretch Mode ◽  
Dynamics Simulations

AbstractCoupling between vibrational modes is essential for energy transfer and dissipation in condensed matter. For water, different O-H stretch modes are known to be very strongly coupled both within and between water molecules, leading to ultrafast dissipation and delocalization of vibrational energy. In contrast, the information on the vibrational coupling of the H-O-H bending mode of water is lacking, even though the bending mode is an essential intermediate for the energy relaxation pathway from the stretch mode to the heat bath. By combining static and femtosecond infrared, Raman, and hyper-Raman spectroscopies for isotopically diluted water with ab initio molecular dynamics simulations, we find the vibrational coupling of the bending mode differs significantly from the stretch mode: the intramode intermolecular coupling of the bending mode is very weak, in stark contrast to the stretch mode. Our results elucidate the vibrational energy transfer pathways of water. Specifically, the librational motion is essential for the vibrational energy relaxation and orientational dynamics of H-O-H bending mode.

scholarly journals Glycine in aerosol water droplets: a critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations

2011 ◽  
Vol 11 (2) ◽  
pp. 519-527 ◽  
Author(s):  
X. Li ◽  
T. Hede ◽  
Y. Tu ◽  
C. Leck ◽  
H. Ågren
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Molecular Dynamics Simulations ◽  
Global Climate ◽  
Pure Water ◽  
Model Systems ◽  
Water Droplets ◽  
Cloud Droplets ◽  
Kohler Theory ◽  
Dynamics Simulations

Abstract. Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the Köhler theory which describes the nucleation and the equilibrium growth of cloud droplets, the surface tension of an aerosol droplet is one of the most important factors that determine the critical supersaturation of droplet activation. In this paper, with specific interest to remote marine aerosol, we predict the surface tension of aerosol droplets by performing molecular dynamics simulations on two model systems, the pure water droplets and glycine in water droplets. The curvature dependence of the surface tension is interpolated by a quadratic polynomial over the nano-sized droplets and the limiting case of a planar interface, so that the so-called Aitken mode particles which are critical for droplet formation could be covered and the Köhler equation could be improved by incorporating surface tension corrections.

MOLECULAR DYNAMICS STUDY OF THE COALESCENCE OF EQUAL AND UNEQUAL SIZED Cu NANOPARTICLES

2009 ◽  
Vol 20 (02) ◽  
pp. 179-196 ◽  
Author(s):  
H. H. KART ◽  
G. WANG ◽  
I. KARAMAN ◽  
T. ÇAĞIN
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Calculations ◽  
The Other ◽  
Model Systems ◽  
Heat Of Fusion ◽  
Sintering Process ◽  
Melting Temperatures ◽  
Different Temperatures ◽  
Dynamics Simulations ◽  
Good Agreement

Molecular dynamics simulations technique is used to study the consolidation of two nanoparticles of Cu element. We have studied sintering processes of two nanoparticles at different temperatures. Two model systems with 4 and 10 nm diameter of particles are selected to study the sintering process of the two nanoparticles. Orientation effects on the physical properties of consolidation of two nanoparticles with respect to each other are investigated. Temperature effects on the consolidation of two nanoparticles are also studied. The order of the values obtained in the simulation for the constant volume heat capacity and latent heat of fusion is good agreement with the bulk results. Moreover, we have investigated the size effects on the consolidation of two different sizes of nanoparticles, that is, one particle of diameter with 10 nm is fixed while the other one is changing from 1 to 10 nm. Melting temperatures of the copper nanoparticles are found to be decreased as the size of the particle decreases. It is found that simulation results are compatible with the other theoretical calculations.

MASSIVELY DATA-PARALLEL MOLECULAR DYNAMICS

1992 ◽  
Vol 03 (04) ◽  
pp. 709-731
Author(s):  
ERNESTO BONOMI ◽  
MARCO TOMASSINI
Keyword(s):  
Molecular Dynamics ◽  
Heat Bath ◽  
Hard Core ◽  
Parallel Computers ◽  
Particle Systems ◽  
Data Parallel ◽  
Connection Machine ◽  
Large N ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

In light of present day data-parallel computers, an appraisal of molecular dynamics simulations of large N-particle systems, isolated or in contact with a heat-bath, is given. Special attention is focused 011 the Connection Machine CM-2. Particularly the cases of long-range potentials and impulsive hard-core interactions are discussed in detail. Data-parallel strategies including data distribution, communications and computation are presented and compared with well-known sequential approaches. The conclusion offered is that the methods described here are easy to design and offer the possibility of reasonably fast implementations for the reliable simulation of macroscopic samples of matter.

The Impact of Wetting-Heterogeneity Distribution on Capillary Pressure and Macroscopic Measures of Wettability

SPE Journal ◽  
2018 ◽  
Vol 24 (01) ◽  
pp. 200-214 ◽  
Author(s):  
Thomas Hiller ◽  
Julie Ardevol-Murison ◽  
Ann Muggeridge ◽  
Matthias Schröter ◽  
Martin Brinkmann
Keyword(s):  
Capillary Pressure ◽  
The United States ◽  
Model Systems ◽  
United States Bureau ◽  
Length Scale ◽  
Mixed Wettability ◽  
Bead Diameter ◽  
Dynamics Simulations ◽  
Capillary Pressure Curves ◽  
The Impact

Summary We investigate the effect of the length scale of wetting heterogeneities, close to the length scale of a pore, on capillary pressure saturation (CPS) curves and the United States Bureau of Mines (USBM) and Amott-Harvey (AH) wettability indices. These macroscopic wettability indices are used to describe bulk rock wettability, because the local contact angle (the standard physical measure of wettability) in a sample is difficult to access and might vary within and between pores caused by changes in mineralogy and the surface coverage of organic materials. Our study combines laboratory experiments and full-scale fluid-dynamics simulations using the multiphase stochastic-rotation dynamics (SRDmc) model. Four model systems were created using monodisperse glass beads. The surface properties of the beads were modified so that one-half of the surface area in each system was strongly hydrophilic and the other half was hydrophobic. However, each system had a different length scale of wetting heterogeneity, ranging from a fraction of a bead diameter to two bead diameters. There is excellent agreement between the experimental and simulation results. All systems are classified as intermediate-wet on the basis of their AH and USBM indices. An examination of the capillary pressure curves shows that the opening of the stable hysteresis loop decreases monotonically as the length scale of the wetting heterogeneities is increased. Thus, our results suggest that macroscopic wettability indices could be used as indicators of ultimate recovery, but they are not suited to discriminate between the different flows that occur earlier in a mixed-wettability displacement process.

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