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1.
J Chem Theory Comput ; 20(3): 1274-1281, 2024 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-38307009

RESUMO

Methodologies for training machine learning potentials (MLPs) with quantum-mechanical simulation data have recently seen tremendous progress. Experimental data have a very different character than simulated data, and most MLP training procedures cannot be easily adapted to incorporate both types of data into the training process. We investigate a training procedure based on iterative Boltzmann inversion that produces a pair potential correction to an existing MLP using equilibrium radial distribution function data. By applying these corrections to an MLP for pure aluminum based on density functional theory, we observe that the resulting model largely addresses previous overstructuring in the melt phase. Interestingly, the corrected MLP also exhibits improved performance in predicting experimental diffusion constants, which are not included in the training procedure. The presented method does not require autodifferentiating through a molecular dynamics solver and does not make assumptions about the MLP architecture. Our results suggest a practical framework for incorporating experimental data into machine learning models to improve the accuracy of molecular dynamics simulations.

2.
Phys Rev E ; 108(3-1): 034119, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37849133

RESUMO

Many systems in nature are conjectured to exist at a critical point, including the brain and earthquake faults. The primary reason for this conjecture is that the distribution of clusters (avalanches of firing neurons in the brain or regions of slip in earthquake faults) can be described by a power law. Because there are other mechanisms such as 1/f noise that can produce power laws, other criteria that the cluster critical exponents must satisfy can be used to conclude whether or not the observed power-law behavior indicates an underlying critical point rather than an alternate mechanism. We show how a possible misinterpretation of the cluster scaling data can lead one to incorrectly conclude that the measured critical exponents do not satisfy these criteria. Examples of the possible misinterpretation of the data for one-dimensional random site percolation and the one-dimensional Ising model are presented. We stress that the interpretation of a power-law cluster distribution indicating the presence of a critical point is subtle and its misinterpretation might lead to the abandonment of a promising area of research.

3.
Phys Rev E ; 101(2-1): 022103, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32168561

RESUMO

We show that the Olami-Feder-Christensen model exhibits an effective ergodicity breaking transition as the noise is varied. Above the critical noise, the system is effectively ergodic because the time-averaged stress on each site converges to the global spatial average. In contrast, below the critical noise, the stress on individual sites becomes trapped in different limit cycles, and the system is not ergodic. To characterize this transition, we use ideas from the study of dynamical systems and compute recurrence plots and the recurrence rate. The order parameter is identified as the recurrence rate averaged over all sites and exhibits a jump at the critical noise. We also use ideas from percolation theory and analyze the clusters of failed sites to find numerical evidence that the transition, when approached from above, can be characterized by exponents that are consistent with hyperscaling.

4.
Phys Rev E ; 101(2-1): 022102, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32168593

RESUMO

Prediction in complex systems at criticality is believed to be very difficult, if not impossible. Of particular interest is whether earthquakes, whose distribution follows a power-law (Gutenberg-Richter) distribution, are in principle unpredictable. We study the predictability of event sizes in the Olmai-Feder-Christensen model at different proximities to criticality using a convolutional neural network. The distribution of event sizes satisfies a power law with a cutoff for large events. We find that predictability decreases as criticality is approached and that prediction is possible only for large, nonscaling events. Our results suggest that earthquake faults that satisfy Gutenberg-Richter scaling are difficult to forecast.

5.
Ecol Lett ; 22(11): 1817-1827, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31496047

RESUMO

Theory predicts rapid genetic drift during invasions, yet many expanding populations maintain high genetic diversity. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants from the diverse, high-density regions arrive at the expansion edge. When density dependence is weak or negative, the effective population size of the front scales only logarithmically with the carrying capacity. The dependence, however, switches to a sublinear power law and then to a linear increase as the density dependence becomes strongly positive. We develop a unified framework revealing that the transitions between different regimes of diversity loss are controlled by a single, universal quantity: the ratio of the expansion velocity to the geometric mean of dispersal and growth rates at expansion edge. Our results suggest that positive density dependence could dramatically alter evolution in expanding populations even when its contribution to the expansion velocity is small.


Assuntos
Deriva Genética , Variação Genética , Densidade Demográfica , Dinâmica Populacional
6.
Theor Popul Biol ; 127: 102-119, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30981732

RESUMO

Traveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front moving at a constant velocity. This simple picture can break down in structured environments such as tissues, patchy landscapes, and microfluidic devices. Habitat fragmentation can pin the front at a particular location or lock invasion velocities into specific values. Locked velocities are not sensitive to moderate changes in dispersal or growth and are determined by the spatial and temporal periodicity of the environment. The synchronization with the environment results in discontinuous fronts that propagate as periodic pulses. We characterize the transition from continuous to locked invasions and show that it is controlled by positive density-dependence in dispersal or growth. We also demonstrate that velocity locking is robust to demographic and environmental fluctuations and examine stochastic dynamics and evolution in locked invasions.


Assuntos
Modelos Biológicos , Dinâmica Populacional , Algoritmos , Ecossistema , Reprodução
7.
Sci Rep ; 9(1): 713, 2019 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-30679729

RESUMO

The growth of business firms is an example of a system of complex interacting units that resembles complex interacting systems in nature such as earthquakes. Remarkably, work in econophysics has provided evidence that the statistical properties of the growth of business firms follow the same sorts of power laws that characterize physical systems near their critical points. Given how economies change over time, whether these statistical properties are persistent, robust, and universal like those of physical systems remains an open question. Here, we show that the scaling properties of firm growth previously demonstrated for publicly-traded U.S. manufacturing firms from 1974 to 1993 apply to the same sorts of firms from 1993 to 2015, to firms in other broad sectors (such as materials), and to firms in new sectors (such as Internet services). We measure virtually the same scaling exponent for manufacturing for the 1993 to 2015 period as for the 1974 to 1993 period and virtually the same scaling exponent for other sectors as for manufacturing. Furthermore, we show that fluctuations of the growth rate for new industries self-organize into a power law over relatively short time scales.

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