In the second article of the series, we present the Gibbs2 code, a Fortran90 reimplementation of the original Gibbs program Comput. Phys. Commun. 158 (2004) 57 for the calculation of ...pressure–temperature dependent thermodynamic properties of solids under the quasiharmonic approximation. We have taken advantage of the detailed analysis carried out in the first paper to implement robust fitting techniques. In addition, new models to introduce temperature effects have been incorporated, from the simple Debye model contained in the original article to a full quasiharmonic model that requires the phonon density of states at each calculated volume. Other interesting novel features include the empirical energy corrections, that rectify systematic errors in the calculation of equilibrium volumes caused by the choice of the exchange-correlation functional, the electronic contributions to the free energy and the automatic computation of phase diagrams. Full documentation in the form of a userʼs guide and a complete set of tests and sample data are provided along with the source code.
Program title:Gibbs2
Catalogue identifier: AEJI_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJI_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: GNU General Public License, v3
No. of lines in distributed program, including test data, etc.: 936 087
No. of bytes in distributed program, including test data, etc.: 8 596 671
Distribution format: tar.gz
Programming language: Fortran90
Computer: Any running Unix/Linux
Operating system: Unix, GNU/Linux
Classification: 7.8
External routines: Part of the minpack, pppack and slatec libraries (downloaded from www.netlib.org) are distributed along with the program.
Nature of problem: Given the static E(V) curve, and possibly vibrational information such as the phonon density of states, calculate the equilibrium volume and thermodynamic properties of a solid at arbitrary temperatures and pressures in the framework of the quasiharmonic approximation.
Additional comments: A detailed analysis concerning the fitting of equations of state has been carried out in the first part of this article, and implemented in the code presented here.
Running time: The tests provided only take a few seconds to run.
► Calculation of thermodynamic properties from first principles data. ► Robust fitting of energy versus volume curves using averages of strain polynomials. ► Models for introducing ab initio temperature effects under the quasiharmonic approximation. ► A Fortran90 program implementing the techniques: Gibbs2.
Motivated by the quest for experimental procedures capable of controlled manipulation of single atoms on surfaces, we set up a computational strategy that explores the cyclical vertical manipulation ...of a broad set of single atoms on the GaAs(110) surface. First-principles simulations of atomic force microscope tip–sample interactions were performed considering families of GaAs and Au-terminated tip apexes with varying crystalline termination. We identified a subset of tips capable of both picking up and depositing an adatom (Ga, As, Al, and Au) any number of times via a modify–restore cycle that “resets” the apex of the scanning probe to its original structure at the end of each cycle. Manipulation becomes successful within a certain window of lateral and vertical tip distances that are observed to be different for extracting and depositing each atom. A practical experimental protocol of special utility for potential cyclical manipulation of single atoms on a nonmetallic surface is proposed.
Molecular walkers standing on two or more "feet" on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface-vacuum interface along a ...particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using
ab initio
density functional theory, this molecule moves to the nearest equivalent lattice site
via
the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses
via
a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.
Chiral molecular walkers, standing on their 'feet' on an anisotropic surface, perform preferential unidirectional Brownian motion under the influence of an external oscillating field according to their orientation, conformation and chirality.
The long time dynamics of molecular ratchets on a 1D periodic potential energy surface (PES) subjected to an external stimulus is studied using the rate equation method. The PES consisting of ...repeated waveforms made of two peaks is considered as an example of a spatially symmetric or asymmetric PES. This PES may, for example, correspond to diffusion of a bipedal molecule that moves along an atomic track
via
an inchworm walk mechanism Raval
et al.
,
Angew. Chem., Int. Ed.
, 2015,
54
, 7101. Generalisation to a PES consisting of an arbitrary number of peaks of various heights is straightforward. Assuming the validity of the transition state theory (TST) for the calculation of the transition rates between neighbouring potential wells, the probability of occupying each type of potential well on the PES is obtained analytically, and then the net current for the molecules to move preferentially in a particular direction under application of external fields over a long time is derived. Note that different to methods based on solving numerically the corresponding Fokker-Plank equation, our method is entirely analytical in the limit of weak external fields. The results of the analytical calculations are compared with the exact numerical solution of the derived rate equations. The following external stimuli are considered: constant, sinusoidal and shifted sinusoidal fields due to either a spatially uniform thermal gradient or an electrostatic field. The possible applications of the method for extracting energy from the Brownian motion under load and separating molecules of different chiralities on the surface are also discussed.
The long time dynamics of molecular ratchets on a 1D periodic potential energy surface (PES) subjected to an external stimulus is studied using the rate equation method.
Using a toolkit of theoretical techniques comprising ab initio density functional theory calculations, the nudged elastic band method and kinetic Monte Carlo (KMC) modeling, we investigate in great ...detail how para-terphenyl-meta-dicarbonitrile (pTmDC) molecules diffuse and isomerize to self-assemble on the Ag(111) surface. We show that molecules "walk" on the surface via a pivoting mechanism moving each of its two "legs" one at a time. We then identify a peculiar "under-side" isomerization mechanism capable of changing the molecules chirality, and demonstrate that it is fundamental in understanding the growth of hydrogen bonding assembles of ribbons, linkers, clusters and brickwall islands on the Ag(111) surface, as observed in recent scanning tunneling microscopy experiments (ChemPhysChem, 2010, 11, 1446). The discovered underlying atomistic mechanism of self-assembly may be behind the growth of other hydrogen bonding structures of chiral molecules on metal surfaces.
Chiral molecular walkers, standing on their ‘feet’ on an anisotropic surface, perform preferential unidirectional Brownian motion under the influence of an external oscillating field according to ...their orientation, conformation and chirality.
Molecular walkers standing on two or more “feet” on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface–vacuum interface along a particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using
ab initio
density functional theory, this molecule moves to the nearest equivalent lattice site
via
the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses
via
a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.
Correction for 'Controlling the preferential motion of chiral molecular walkers on a surface' by David Abbasi-Pérez
et al.
,
Chem. Sci.
, 2019, DOI:
10.1039/c9sc01135h
.
Using a toolkit of theoretical techniques comprising
ab initio
density functional theory calculations, the nudged elastic band method and kinetic Monte Carlo (KMC) modeling, we investigate in great ...detail how
para
-terphenyl-
meta
-dicarbonitrile (pTmDC) molecules diffuse and isomerize to self-assemble on the Ag(111) surface. We show that molecules "walk" on the surface
via
a pivoting mechanism moving each of its two "legs" one at a time. We then identify a peculiar "under-side" isomerization mechanism capable of changing the molecules chirality, and demonstrate that it is fundamental in understanding the growth of hydrogen bonding assembles of ribbons, linkers, clusters and brickwall islands on the Ag(111) surface, as observed in recent scanning tunneling microscopy experiments (
ChemPhysChem
, 2010,
11
, 1446). The discovered underlying atomistic mechanism of self-assembly may be behind the growth of other hydrogen bonding structures of chiral molecules on metal surfaces.
para
-Terphenyl-
meta
-dicarbonitrile molecules diffuse by pivoting on the Ag(111) surface, and by means of the assisted isomerization mechanism self-assemble to form ribbons, linkers, clusters and brickwall islands.
The last several years have seen intense debate about the issue of transitioning between standard and daylight saving time. In the United States, the annual advance to daylight saving time in spring, ...and fall back to standard time in autumn, is required by law (although some exceptions are allowed under the statute). An abundance of accumulated evidence indicates that the acute transition from standard time to daylight saving time incurs significant public health and safety risks, including increased risk of adverse cardiovascular events, mood disorders, and motor vehicle crashes. Although chronic effects of remaining in daylight saving time year-round have not been well studied, daylight saving time is less aligned with human circadian biology-which, due to the impacts of the delayed natural light/dark cycle on human activity, could result in circadian misalignment, which has been associated in some studies with increased cardiovascular disease risk, metabolic syndrome and other health risks. It is, therefore, the position of the American Academy of Sleep Medicine that these seasonal time changes should be abolished in favor of a fixed, national, year-round standard time.
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