arXiv subjects

Adrian Diaz

Publications and source records attributed to Adrian Diaz.

5 recordsLinked to original sources

arXiv2025

A Finite Element Method for Simulation of Coupled Dynamics of Dislocations and Fracture

This work presents a finite element method for simulating dynamic processes that involve the coupled evolution of dislocation motion and crack propagation. The method numerically solves the Concurrent Atomistic-Continuum (CAC) formulation of the conservation of linear momentum. A crystalline material is discretized at the unit-cell level using 6-node prism elements whose geometry allows dislocations and cracks to nucleate and propagate along element facets. Nanoscale simulations of single-crystal Cu, Fe, and Si demonstrate the initiation and propagation of dislocations and cracks, and these results are reproduced by the finite element method in excellent agreement with fully atomistic molecular dynamics simulations. Mesoscale simulations of single-crystal Cu further demonstrate the ability of the method to capture size-dependent brittle and ductile behavior. Under plane-strain conditions the Cu model fractures in a brittle manner, while a fully three-dimensional model exhibits curved and intersecting dislocations that blunt the crack tip and prevent crack propagation, resulting in ductile behavior. The accuracy, efficiency, and applicability of the method are discussed.

cond-mat.mtrl-sci↗

arXiv2025

Effect of Misfit and Threading Dislocations on Surface Energies of PbTe-PbSe Interfaces

This work quantifies the effect of misfit and threading dislocations on the surface energies of PbTe-PbSe interfaces, with the defect structures of the interfaces being obtained from atomistic and multiscale simulations of their manufacturing processes. Simulation results show that direct bonding produces semi-coherent interfaces with two-dimensional misfit dislocation networks, while heteroepitaxial processes produce complex three-dimensional dislocation structures with both misfit and threading dislocations. Surface energies at these interfaces were determined by computing the interaction energies across these interfaces. Compared with coherent interfaces, directly bonded interfaces exhibit up to ~23% lower surface energy, while the surface energies of epitaxially grown interfaces can be nearly 50% lower. The results demonstrate the significant effects of dislocations on interfacial energy.

cond-mat.mtrl-sci↗

arXiv2024

bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties

We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics, incorporating predictors for backbone and sidechain dynamics, local secondary structure propensities, early folding, long disorder, beta-sheet aggregation and FUS-like phase separation. Our package significantly eases the integration and execution of these tools, enhancing accessibility for both computational and experimental researchers.

q-bio.QM↗

arXiv2017

Recent Progress in the Concurrent Atomistic-Continuum (CAC) Method and its Application in Phonon Transport

This work presents recent the progress in the development of the Concurrent Atomistic-Continuum (CAC) method for coarse-grained space- and time-resolved atomistic simulations of phonon transport. Application examples, including heat pulses propagating across grain boundaries and phase interfaces, as well as the interactions between phonons and moving dislocations, are provided to demonstrate the capabilities of CAC. The simulation results provide visual evidence and reveal the underlying physics of a variety of phenomena including: phonon focusing, wave interference, dislocation drag, interfacial Kapitza resistance caused by quasi-ballistic phonon transport, etc. A new method to quantify fluxes in transient transport processes is also introduced.

cond-mat.mes-hall↗

arXiv2017

Passing Waves from Atomistic to Continuum

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This then permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

cond-mat.mtrl-sci↗