Finite-Temperature Quasi-Continuum

2013 ◽  
Vol 65 (1) ◽  
Author(s):  
E. B. Tadmor ◽  
F. Legoll ◽  
W. K. Kim ◽  
L. M. Dupuy ◽  
R. E. Miller
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Finite Temperature ◽  
Theoretical Background ◽  
Review Article ◽  
Test Cases ◽  
Loading Conditions ◽  
Atomistic Region ◽  
Quasistatic Loading ◽  
The Continuum

A generalization of the quasi-continuum (QC) method to finite temperature is presented. The resulting “hot-QC” formulation is a partitioned domain multiscale method in which atomistic regions modeled via molecular dynamics coexist with surrounding continuum regions. Hot-QC can be used to study equilibrium properties of systems under constant or quasistatic loading conditions. Two variants of the method are presented which differ in how continuum regions are evolved. In “hot-QC-static” the free energy of the continuum is minimized at each step as the atomistic region evolves dynamically. In “hot-QC-dynamic” both the atomistic and continuum regions evolve dynamically in tandem. The latter approach is computationally more efficient, but introduces an anomalous “mesh entropy” which must be corrected. Following a brief review of related finite-temperature methods, this review article provides the theoretical background for hot-QC (including new results), discusses the implementational details, and demonstrates the utility of the method via example test cases including nanoindentation at finite temperature.

ON THE DIMERIZATION OF LINEAR POLYMERS

1989 ◽  
Vol 03 (02) ◽  
pp. 125-133 ◽  
Author(s):  
C. ARAGÃO DE CARVALHO
Keyword(s):  
Free Energy ◽  
Effective Potential ◽  
Ground State ◽  
Finite Temperature ◽  
Continuum Limit ◽  
Linear Polymers ◽  
Renormalization Condition ◽  
Loop Approximation ◽  
The One ◽  
The Continuum

We use the continuum limit of the Su-Schrieffer-Heeger model for linear polymers to construct its effective potential (Gibbs free energy) both at zero and finite temperature. We study both trans and cis-polymers. Our results show that, depending on a renormalization condition to be extracted from experiment, there are several possibilities for the minima of the dimerized ground state of cis-polymers. All calculations are done in the one-loop approximation.

The Heterogeneous Multiscale Method for Dynamics of Solids with Applications to Brittle Cracks

2009 ◽  
Vol 1229 ◽  
Author(s):  
Jerry Yang ◽  
Xiantao Li
Keyword(s):  
Elastic Waves ◽  
Crack Opening ◽  
Multiscale Method ◽  
Atomic Scale ◽  
Special Treatment ◽  
Loading Conditions ◽  
Coupling Condition ◽  
Atomistic Region ◽  
Heterogeneous Multiscale ◽  
The Continuum

AbstractWe present a multiscale method for the modeling of dynamics of crystalline solids. The method employs the continuum elastodynamics model to introduce loading conditions and capture elastic waves, and near isolated defects, molecular dynamics (MD) model is used to resolve the local structure at the atomic scale. The coupling of the two models is achieved based on the framework of the heterogeneous multiscale method (HMM) and a consistent coupling condition with special treatment of the MD boundary condition. Application to the dynamics of a brittle crack under various loading conditions is presented. Elastic waves are observed to pass through the interface from atomistic region to the continuum region and reversely. Thresholds of strength and duration of shock waves to launch the crack opening are quantitatively studied and related to the inertia effect of crack tips.

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

Thermodynamics of Flowing Systems: with Internal Microstructure

1994 ◽  
Author(s):  
Antony N. Beris ◽  
Brian J. Edwards
Keyword(s):  
Free Energy ◽  
Theoretical Study ◽  
Flow Behavior ◽  
Irreversible Thermodynamics ◽  
Hamiltonian Mechanics ◽  
Complex Interplay ◽  
Microscopic Models ◽  
Flow Phenomena ◽  
The Subject ◽  
The Continuum

This much-needed monograph presents a systematic, step-by-step approach to the continuum modeling of flow phenomena exhibited within materials endowed with a complex internal microstructure, such as polymers and liquid crystals. By combining the principles of Hamiltonian mechanics with those of irreversible thermodynamics, Antony N. Beris and Brian J. Edwards, renowned authorities on the subject, expertly describe the complex interplay between conservative and dissipative processes. Throughout the book, the authors emphasize the evaluation of the free energy--largely based on ideas from statistical mechanics--and how to fit the values of the phenomenological parameters against those of microscopic models. With Thermodynamics of Flowing Systems in hand, mathematicians, engineers, and physicists involved with the theoretical study of flow behavior in structurally complex media now have a superb, self-contained theoretical framework on which to base their modeling efforts.

A molecular dynamics study on liquid 1-octanol. Part 3. Evaluating octanol/water partition coefficients of novel thrombin inhibitors via free-energy perturbations

2005 ◽  
Vol 102 (5) ◽  
pp. 542-553 ◽  
Author(s):  
César Augusto Fernandes De Oliveira ◽  
Cristiano Ruch Werneck Guimarães ◽  
Heloisa De Mello ◽  
Aurea Echevarria ◽  
Ricardo Bicca De Alencastro
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Partition Coefficients ◽  
Thrombin Inhibitors ◽  
Free Energy Perturbations

scholarly journals Debye-Hückel Free Energy of an Electric Double Layer with Discrete Charges Located at a Dielectric Interface

Membranes ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 129
Author(s):  
Guilherme Volpe Bossa ◽  
Sylvio May
Keyword(s):  
Free Energy ◽  
Double Layer ◽  
Electric Double Layer ◽  
Low Dielectric Constant ◽  
Surface Charges ◽  
Dielectric Interface ◽  
Charge Densities ◽  
Low Dielectric ◽  
Poisson Boltzmann ◽  
The Continuum

Poisson–Boltzmann theory provides an established framework to calculate properties and free energies of an electric double layer, especially for simple geometries and interfaces that carry continuous charge densities. At sufficiently small length scales, however, the discreteness of the surface charges cannot be neglected. We consider a planar dielectric interface that separates a salt-containing aqueous phase from a medium of low dielectric constant and carries discrete surface charges of fixed density. Within the linear Debye-Hückel limit of Poisson–Boltzmann theory, we calculate the surface potential inside a Wigner–Seitz cell that is produced by all surface charges outside the cell using a Fourier-Bessel series and a Hankel transformation. From the surface potential, we obtain the Debye-Hückel free energy of the electric double layer, which we compare with the corresponding expression in the continuum limit. Differences arise for sufficiently small charge densities, where we show that the dominating interaction is dipolar, arising from the dipoles formed by the surface charges and associated counterions. This interaction propagates through the medium of a low dielectric constant and alters the continuum power of two dependence of the free energy on the surface charge density to a power of 2.5 law.

scholarly journals Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

2021 ◽  
Author(s):  
Lorenzo Casbarra ◽  
Piero Procacci
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Drug Discovery ◽  
Binding Free Energy ◽  
Cost Ratio ◽  
Benefit Cost Ratio ◽  
Docking Program ◽  
Benefit Cost ◽  
Overall Reliability ◽  
Absolute Binding Free Energy

AbstractWe systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.

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