The onset of nonrigid dynamics and the melting transition in Ar7

Amar, François G.; Berry, R. Stephen

doi:10.1063/1.451506

Cited by 207 publications

(83 citation statements)

References 31 publications

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“…Much effort has been put forward in establishing a relationship between thermodynamic quantities and MD data 13,42,61,62,63 . The ergoditic theorem ensures in thermodynamics the relation between the observable ensemble averages and the simulated time averaged quantities 13,42 .…”

Section: Transient Inter-layer Atomic Mixing (Tilam)mentioning

confidence: 99%

“…MD studies provides microscopic (atomic) information and an effective temperature can be derived from the individual atomic velocities 13,61 . Another useful quantity, the kinetic temperature of a nanosystem is defined as an averaged kinetic energy per an individual spatial degree of freedom 62,63 . The time averaged temperature of the nanosystem with N number of atoms can be given as…”

Section: Transient Inter-layer Atomic Mixing (Tilam)mentioning

confidence: 99%

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Self-organized transient facilitated atomic transport in Pt∕Al(111)

Süle

2008

The Journal of Chemical Physics

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During the course of atomic transport in a host material, impurity atoms need to surmount an energy barrier driven by thermodynamic bias or at ultra-low temperatures by quantum tunneling. In the present article we demonstrate using atomistic simulations that at ultra-low temperature transient inter-layer atomic transport is also possible without tunneling when the Pt/Al(111) impurity/host system self-organizes itself spontaneously into an intermixed configuration. No such extremely fast athermal concerted process has been reported before at ultra low temperatures. The outlined novel transient atomic exchange mechanism could be of general validity. We find that the source of ultra-low temperature heavy particle barrier crossing is intrinsic and no external bias is necessary for atomic intermixing and surface alloying in Pt/Al although the dynamic barrier height is few eV. The mechanism is driven by the local thermalization of the Al(111) surface in a selforganized manner arranged spontaneously by the system without any external stimulus. The core of the short lived thermalized region reaches the local temperature of ∼ 1000 K (including few tens of Al atoms) while the average temperature of the simulation cell is ∼ 3 K. The transient facilitated intermixing process also takes place with repulsive impurity-host interaction potential leading to negative atomic mobility hence the atomic injection is largely independent of the strength of the impurity-surface interaction. We predict that similar exotic behaviour is possible in other materials as well.

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Section: Transient Inter-layer Atomic Mixing (Tilam)mentioning

confidence: 99%

Section: Transient Inter-layer Atomic Mixing (Tilam)mentioning

confidence: 99%

Self-organized transient facilitated atomic transport in Pt∕Al(111)

Süle

2008

The Journal of Chemical Physics

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“…When applying the superposition formula we collect together the identical contributions for all permutation-inversion isomers of a given minimum, which corresponds to weighting e −β f by 1/o, with o the order of the corresponding point group. 26,30,49 An additional factor that depends on the atomic composition of the system is needed to enumerate the distinct local minima precisely, but cancels from all thermodynamic quantities. Since the point group is C 1 for all the minima considered in the present work, o = 1.…”

Section: Free Energy Of Local Minimamentioning

confidence: 99%

A conformational factorisation approach for estimating the binding free energies of macromolecules

Mochizuki

Whittleston

Somani

et al. 2014

Phys. Chem. Chem. Phys.

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Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. We present a conformational factorization approach. The theory is based on a superposition partition function, where the partition function is written as a sum over contributions from local minima. The factorisation greatly reduces the number of minima that need to be considered, by employing the same local configurations for groups that are sufficiently distant from the binding site. The theory formalises the conditions required to analyse how our definition of the binding site region affects the free energy difference between the apo and holo states. We employ basin-hopping parallel tempering to sample minima that contribute significantly to the partition function, and calculate the binding free energies within the harmonic normal mode approximation. A further significant gain in efficiency is achieved using a recently developed local rigid body framework in both the sampling and the normal mode analysis, which reduces the number of degrees of freedom. We benchmark this approach for human aldose reductase (PDB code 2INE). When varying the size of the rigid region, the free energy difference converges for factorisation of groups at a distance of 14Å from the binding site, which corresponds to 80% of the protein being locally rigidified. This approach is likely to be useful for estimating the binding free energy of protein-ligand complexes.

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“…We first collect an ensemble of 6189 reactive trajectories from PBP to COCT at total energy E = −13.5ε by using the method of Eq. (11). For each of these reactive trajectories, we set the time origin on the PBP side, O PBP , as the last moment at which the trajectory crosses a ′ 1 = −0.1 from below before the trajectory moves into the COCT isomer (see Fig.…”

Section: B Driving Forces For Structural Transitionsmentioning

confidence: 99%

“…For decades, there has been extensive progress in the understanding of structures and dynamics of atomic clusters from the viewpoints of energy landscapes, [1][2][3][4] phase transitions, 5-10 transition rates, [11][12][13][14] saddle crossing dynamics, [15][16][17] and rotational effects. [18][19][20][21] Structures and dynamics of atomic clusters can also provide many insights into the mechanisms for collective motions of even more complex and higher-order systems including molecular clusters 22,23 and self-organized nano-structures.…”

Section: Introductionmentioning

confidence: 99%

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

Oka

Yanao

Koon

2015

The Journal of Chemical Physics

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This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions. C 2015 AIP Publishing LLC. [http://dx

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The onset of nonrigid dynamics and the melting transition in Ar7

Cited by 207 publications

References 31 publications

Self-organized transient facilitated atomic transport in Pt∕Al(111)

Self-organized transient facilitated atomic transport in Pt∕Al(111)

A conformational factorisation approach for estimating the binding free energies of macromolecules

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

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