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The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the x-ray damage effects observed in x-ray scattering measurements of biological and chemical materials, as well…

Chemical Physics · Physics 2024-06-17 Adam E. A. Fouda , Stephen H. Southworth , Phay J. Ho

The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…

Soft Condensed Matter · Physics 2016-11-03 Gary S. Grest

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…

Soft Condensed Matter · Physics 2009-11-10 D. C. Rapaport

This paper develops a damage model for unfilled cross-linked rubbers based on the concept of scission of polymer chains. The model is built up on the well-known Gent elastic potential complemented by a kinetic equation describing effects of…

Materials Science · Physics 2011-08-03 Alexei Y. Melnikov , A. I. Leonov

This paper presents a physics-based constitutive equation to predict the thermo-chemical aging in elastomers. High-temperature oxidation in elastomers is a complex phenomenon. The macromolecular network of elastomers' microstructures…

Materials Science · Physics 2021-04-20 Maryam Shakiba , Aimane Najmeddine

Shear localization in slowly-driven bulk metallic glasses (BMGs) is typically accompanied by a sharp drop in the bulk stress response as a signature of the plastic yielding transition. It is also observed that the sharpness of this…

Soft Condensed Matter · Physics 2023-09-22 Kamran Karimi , Stefanos Papanikolaou

We have developed a new multiscale simulation technique to investigate history-dependent flow behavior of entangled polymer melt, using a smoothed particle hydrodynamics simulation with microscopic simulators that account for the dynamics…

Soft Condensed Matter · Physics 2011-11-01 Takahiro Murashima , Takashi Taniguchi

We offer an alternative real-space description, based purely on activated processes, for the understanding of relaxation dynamics in hierarchical landscapes. To this end, we use the cluster model, a coarse-grained lattice model of a jammed…

Soft Condensed Matter · Physics 2024-06-27 Mahajabin Rahman , Stefan Boettcher

This paper develops a damage model for unfilled cross-linked rubbers based on the concept of scission of polymer chains. The model is built up on the well-known Gent elastic potential complemented by a kinetic equation describing effects of…

Materials Science · Physics 2011-08-09 Alexei Y. Melnikov , A. I. Leonov

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…

Machine Learning · Computer Science 2022-06-20 Wujie Wang , Minkai Xu , Chen Cai , Benjamin Kurt Miller , Tess Smidt , Yusu Wang , Jian Tang , Rafael Gómez-Bombarelli

Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…

Biological Physics · Physics 2025-04-10 Ryan K. Krueger , Megan C. Engel , Ryan Hausen , Michael P. Brenner

Paints and coatings undergo a variety of physical and chemical changes under environmental exposures. Accurate prediction of these changes is important for the applications of coatings. This work presents a novel approach to modeling…

Soft Condensed Matter · Physics 2024-10-29 Ambesh Gupta , Soumyadipta Maiti , Parvesh Saini , Surabhi Srivastava , Shankar Kausley , Beena Rai

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…

Chemical Physics · Physics 2016-09-13 Flaviu S. Cipcigan , Vlad P. Sokhan , Jason Crain , Glenn J. Martyna

Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…

Condensed Matter · Physics 2009-10-31 Satoru Muto , Hideo Aoki

We study the out-of-equilibrium large time dynamics of a gaussian polymer chain in a quenched random potential. The dynamics studied is a simple Langevin dynamics commonly referred to as the Rouse model. The equations for the two-time…

Disordered Systems and Neural Networks · Physics 2009-11-11 Yadin Y. Goldschmidt

We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…

Statistical Mechanics · Physics 2023-07-12 Marltan O. Wilson , David M. Huang

This paper offers a study of oxygen dissolution into a solid, and its consequences on the mechanical behaviour of the material. In fact, mechanical strains strongly influence the oxidation processes and may be, in some materials,…

Materials Science · Physics 2009-09-17 Nicolas Creton , Virgil Optasanu , Tony Montesin , Sébastien Garruchet

We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…

Machine Learning · Computer Science 2024-07-26 James Koch , Pranab Roy Chowdhury , Heng Wan , Parin Bhaduri , Jim Yoon , Vivek Srikrishnan , W. Brent Daniel

Molecular dynamics simulations were performed for a polymer melt. In quiescent states, the inter-chain interaction energy supported by each particle takes relatively large values persistently for long times if the particle is close to an…

Soft Condensed Matter · Physics 2007-05-23 Ryoichi Yamamoto , Akira Onuki