301 research outputs found
Equilibrium free energies from fast-switching trajectories with large time steps
Jarzynski's identity for the free energy difference between two equilibrium
states can be viewed as a special case of a more general procedure based on
phase space mappings. Solving a system's equation of motion by approximate
means generates a mapping that is perfectly valid for this purpose, regardless
of how closely the solution mimics true time evolution. We exploit this fact,
using crudely dynamical trajectories to compute free energy differences that
are in principle exact. Numerical simulations show that Newton's equation can
be discretized to low order over very large time steps (limited only by the
computer's ability to represent resulting values of dynamical variables)
without sacrificing thermodynamic accuracy. For computing the reversible work
required to move a particle through a dense liquid, these calculations are more
efficient than conventional fast switching simulations by more than an order of
magnitude. We also explore consequences of the phase space mapping perspective
for systems at equilibrium, deriving an exact expression for the statistics of
energy fluctuations in simulated conservative systems
Embedded-Cluster Calculations in a Numeric Atomic Orbital Density-Functional Theory Framework
We integrate the all-electron electronic structure code FHI-aims into the
general ChemShell package for solid-state embedding (QM/MM) calculations. A
major undertaking in this integration is the implementation of pseudopotential
functionality into FHI-aims to describe cations at the QM/MM boundary through
effective core potentials and therewith prevent spurious overpolarization of
the electronic density. Based on numeric atomic orbital basis sets, FHI-aims
offers particularly efficient access to exact exchange and second order
perturbation theory, rendering the established QM/MM setup an ideal tool for
hybrid and double-hybrid level DFT calculations of solid systems. We illustrate
this capability by calculating the reduction potential of Fe in the
Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for
(photo-)catalytic water oxidation at TiO2(110).Comment: 12 pages, 4 figure
Thermal and electronic fluctuations of flexible adsorbed molecules : azobenzene on Ag(111)
We investigate the thermal and electronic collective fluctuations that contribute to the finite-temperature adsorption properties of flexible adsorbates on surfaces on the example of the molecular switch azobenzene C12H10N2 on the Ag(111) surface. Using first-principles molecular dynamics simulations, we obtain the free energy of adsorption that accurately accounts for entropic contributions, whereas the inclusion of many-body dispersion interactions accounts for the electronic correlations that govern the adsorbate binding. We find the adsorbate properties to be strongly entropy driven, as can be judged by a kinetic molecular desorption prefactor of 10^24 s−1 that largely exceeds previously reported estimates. We relate this effect to sizable fluctuations across structural and electronic observables. A comparison of our calculations to temperature-programed desorption measurements demonstrates that finite-temperature effects play a dominant role for flexible molecules in contact with polarizable surfaces, and that recently developed first-principles methods offer an optimal tool to reveal novel collective behavior in such complex systems
Equilibrium Sampling From Nonequilibrium Dynamics
We present some applications of an Interacting Particle System (IPS)
methodology to the field of Molecular Dynamics. This IPS method allows several
simulations of a switched random process to keep closer to equilibrium at each
time, thanks to a selection mechanism based on the relative virtual work
induced on the system. It is therefore an efficient improvement of usual
non-equilibrium simulations, which can be used to compute canonical averages,
free energy differences, and typical transitions paths
Adaptive bill morphology for enhanced tool manipulation in New Caledonian crows
Early increased sophistication of human tools is thought to be underpinned by adaptive morphology for efficient tool manipulation. Such adaptive specialisation is unknown in nonhuman primates but may have evolved in the New Caledonian crow, which has sophisticated tool manufacture. The straightness of its bill, for example, may be adaptive for enhanced visually-directed use of tools. Here, we examine in detail the shape and internal structure of the New Caledonian crow’s bill using Principal Components Analysis and Computed Tomography within a comparative framework. We found that the bill has a combination of interrelated shape and structural features unique within Corvus, and possibly birds generally. The upper mandible is relatively deep and short with a straight cutting edge, and the lower mandible is strengthened and upturned. These novel combined attributes would be functional for (i) counteracting the unique loading patterns acting on the bill when manipulating tools, (ii) a strong precision grip to hold tools securely, and (iii) enhanced visually-guided tool use. Our findings indicate that the New Caledonian crow’s innovative bill has been adapted for tool manipulation to at least some degree. Early increased sophistication of tools may require the co-evolution of morphology that provides improved manipulatory skills
Photoswitching in nanoporous, crystalline solids: an experimental and theoretical study for azobenzene linkers incorporated in MOFs
In this article, we use the popular photoswitchable molecule, azobenzene, to demonstrate that the embedding in a nanoporous, crystalline solid enables a precise understanding of light-induced, reversible molecular motion. We investigate two similar azobenzene-containing, pillared-layer metal–organic frameworks (MOFs): Cu2(AzoBPDC)2(BiPy) and Cu2(NDC)2(AzoBiPy). Experimental results from UV-vis spectroscopy and molecular uptake experiments as well as theoretical results based on density-functional theory (DFT) show that in the Cu2(AzoBPDC)2(BiPy) MOF structure, the azobenzene side groups undergo photoisomerization when irradiated with UV or visible light. In a very similar MOF structure, Cu2(NDC)2(AzoBiPy), the experimental studies show an unexpected absence of photoisomerization. The DFT calculations reveal that in both MOFs the initial and final states of the photoswitching process (the trans and the cis conformation) have similar energies, which strongly suggests that the reason for the effective blocking of photoswitching in the AzoBiPy-based MOFs must be related to the switching process itself. More detailed calculations show that in Cu2(NDC)2(AzoBiPy) a naphthalene linker from the molecular framework blocks the photoisomerization trajectory which leads from the trans to the cis conformation. For Cu2(AzoBPDC)2(BiPy), as a result of the different geometry, such a steric hindrance is absent
Review of Modelling Techniques for In Vivo
Background. Knowledge of the musculoskeletal loading conditions during strength training is essential for performance monitoring, injury prevention, rehabilitation, and training design. However, measuring muscle forces during exercise performance as a primary determinant of training efficacy and safety has remained challenging. Methods. In this paper we review existing computational techniques to determine muscle forces in the lower limbs during strength exercises in vivo and discuss their potential for uptake into sports training and rehabilitation. Results. Muscle forces during exercise performance have almost exclusively been analysed using so-called forward dynamics simulations, inverse dynamics techniques, or alternative methods. Musculoskeletal models based on forward dynamics analyses have led to considerable new insights into muscular coordination, strength, and power during dynamic ballistic movement activities, resulting in, for example, improved techniques for optimal performance of the squat jump, while quasi-static inverse dynamics optimisation and EMG-driven modelling have helped to provide an understanding of low-speed exercises. Conclusion. The present review introduces the different computational techniques and outlines their advantages and disadvantages for the informed usage by nonexperts. With sufficient validation and widespread application, muscle force calculations during strength exercises in vivo are expected to provide biomechanically based evidence for clinicians and therapists to evaluate and improve training guidelines
\AA ngstrom depth resolution with chemical specificity at the liquid-vapor interface
The determination of depth profiles across interfaces is of primary
importance in many scientific and technological areas. Photoemission
spectroscopy is in principle well suited for this purpose, yet a quantitative
implementation for investigations of liquid-vapor interfaces is hindered by the
lack of understanding of electron-scattering processes in liquids. Previous
studies have shown, however, that core-level photoelectron angular
distributions (PADs) are altered by depth-dependent elastic electron scattering
and can, thus, reveal information on the depth distribution of species across
the interface. Here, we explore this concept further and show that the
anisotropy parameter characterizing the PAD scales linearly with the average
distance of atoms along the surface normal. This behavior can be accounted for
in the low-collision-number regime. We also show that results for different
atomic species can be compared on the same length scale. We demonstrate that
atoms separated by about 1~\AA~along the surface normal can be clearly
distinguished with this method, achieving excellent depth resolution.Comment: Submitted to Phys. Rev. Let
Convergence Without Hard Criteria: Does EU Soft Law Affect Domestic Unemployment Protection Schemes?
(VLID)177126
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