Implicit implementation of the nonlocal operator method: an open source code

In this paper, we present an open-source code for the first-order and higher-order nonlocal operator method (NOM) including a detailed description of the implementation. The NOM is based on so-called support, dual-support, nonlocal operators, and an operate energy functional ensuring stability. The nonlocal operator is a generalization of the conventional differential operators. Combined with the method of weighed residuals and variational principles, NOM establishes the residual and tangent stiffness matrix of operate energy functional through some simple matrix without the need of shape functions as in other classical computational methods such as FEM. NOM only requires the definition of the energy drastically simplifying its implementation. The implementation in this paper is focused on linear elastic solids for sake of conciseness through the NOM can handle more complex nonlinear problems. The NOM can be very flexible and efficient to solve partial differential equations (PDEs), it’s also quite easy for readers to use the NOM and extend it to solve other complicated physical phenomena described by one or a set of PDEs. Finally, we present some classical benchmark problems including the classical cantilever beam and plate-with-a-hole problem, and we also make an extension of this method to solve complicated problems including phase-field fracture modeling and gradient elasticity material.

Collective chemotaxis in a Voronoi model for confluent clusters

Collective chemotaxis, where single cells cannot climb a biochemical signaling gradient but clusters of cells can, has been observed in different biological contexts, including confluent tissues where there are no gaps or overlaps between cells. Although particle-based models have been developed that predict important features of collective chemotaxis, the mechanisms in those models depend on particle overlaps, and so it remains unclear if they can explain behavior in confluent systems. Here, we develop an open-source code that couples a 2D Voronoi simulation for confluent cell mechanics to a dynamic chemical signal that can diffuse, advect, and/or degrade, and use the code to study potential mechanisms for collective chemotaxis in cellular monolayers. We first study the impact of advection on collective chemotaxis, and delineate a regime where advective terms are important. Next, we investigate two possible chemotactic mechanisms, contact inhibition of locomotion and heterotypic interfacial tension, and demonstrate that both can drive collective chemotaxis in certain parameter regimes. We further demonstrate that the scaling behavior of cluster motion is well-captured by simple analytic theories.

Comparison of Open Source Code when Updating using the Damerau-Levenshtein Distance

The paper describes a text comparison problem that arises during the update of open source programs in the presence of user changes. An algorithm based on calculating the Damerau — Levenshtein distance is used to correctly match the lines of two texts. The main difference between the proposed algorithm and the classical one is that the weights of such operations as insert, delete, replace, and permute are not constants, but depend on the values of individual text elements and their location. The paper also describes the functionality that allows the programmer to simplify the task of analyzing changes in program texts. The functionality is based on dynamic control of the comparison process, during which the programmer can manually establish correspondences between the compared texts. The effectiveness of the proposed method is checked when updating modules in the 1C:Enterprise system.

Finding Software License Violations Through Binary Code Clone Detection - A Retrospective

Ten years ago, we published the article Finding software license violations through binary code clone detection at the MSR 2011 conference. Our paper was motivated by the tendency of em- bedded hardware vendors to only release binary blobs of their rmware, often violating the licensing terms of open-source soft- ware present inside those blobs. The techniques presented in our paper were designed to accurately identify open-source code hid- den inside binary blobs. Here, we give our perspectives on the impact of our work, both industrially and academically, and re- visit the original problem statement to see what has happened in the eld of open-source compliance in the intervening decade.