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Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…

Computational Physics · Physics 2014-10-07 Gareth A. Tribello , Massimiliano Bonomi , Davide Branduardi , Carlo Camilloni , Giovanni Bussi

On behalf of the development team, I review the capabilities of the BAGEL program package in this article. BAGEL is a newly-developed full-fledged program package for electronic-structure computation in quantum chemistry, which is released…

Chemical Physics · Physics 2018-01-30 Toru Shiozaki

Software vulnerabilities are a challenge in cybersecurity. Manual security patches are often difficult and slow to be deployed, while new vulnerabilities are created. Binary code vulnerability detection is less studied and more complex…

Cryptography and Security · Computer Science 2024-04-15 Litao Li , Steven H. H. Ding , Andrew Walenstein , Philippe Charland , Benjamin C. M. Fung

We introduce a novel approach to automatically synthesize a mathematical representation of the control algorithms implemented in industrial cyber-physical systems (CPS), given the embedded system binary. The output model can be used by…

We present a new Python library called vaex, to handle extremely large tabular datasets, such as astronomical catalogues like the Gaia catalogue, N-body simulations or any other regular datasets which can be structured in rows and columns.…

Instrumentation and Methods for Astrophysics · Physics 2018-10-10 Maarten A. Breddels , Jovan Veljanoski

CG-Kit is a new code generation toolkit that we propose as a solution for portability and maintainability for scientific computing applications. The development of CG-Kit is rooted in the urgent need created by the shifting landscape of…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-01-09 Johann Rudi , Youngjun Lee , Aidan H. Chadha , Mohamed Wahib , Klaus Weide , Jared P. O'Neal , Anshu Dubey

DataPix4 (Data Acquisition for Timepix4 Applications) is a new C++ framework for the management of Timepix4 ASIC, a multi-purpose hybrid pixel detector designed at CERN. Timepix4 consists of a matrix of 448x512 pixels that can be connected…

In this report, we introduce DocXChain, a powerful open-source toolchain for document parsing, which is designed and developed to automatically convert the rich information embodied in unstructured documents, such as text, tables and…

Computer Vision and Pattern Recognition · Computer Science 2023-10-20 Cong Yao

We introduce the Computational 2D Materials Database (C2DB), which organises a variety of structural, thermodynamic, elastic, electronic, magnetic, and optical properties of around 1500 two-dimensional materials distributed over more than…

Coherent parity check (CPC) codes are a new framework for the construction of quantum error correction codes that encode multiple qubits per logical block. CPC codes have a canonical structure involving successive rounds of bit and phase…

Quantum Physics · Physics 2018-06-08 Joschka Roffe , David Headley , Nicholas Chancellor , Dominic Horsman , Viv Kendon

Binary embeddings provide efficient and powerful ways to perform operations on large scale data. However binary embedding typically requires long codes in order to preserve the discriminative power of the input space. Thus binary coding…

Data Structures and Algorithms · Computer Science 2015-12-08 Felix X. Yu , Aditya Bhaskara , Sanjiv Kumar , Yunchao Gong , Shih-Fu Chang

Continuous-variable (CV) quantum information processing is a promising candidate for large-scale fault-tolerant quantum computation. However, analysis of CV quantum process relies mostly on direct computation of the evolution of operators…

Generative models for materials have achieved strong performance on periodic bulk crystals, yet their ability to generalize across scale transitions to finite nanostructures remains largely untested. We introduce Crystal-to-Nanoparticle…

Materials Science · Physics 2026-01-28 Can Polat , Erchin Serpedin , Mustafa Kurban , Hasan Kurban

First-principles computational spectroscopy is a critical tool for interpreting experiment, performing structure refinement, and developing new physical understanding. Systematically setting up input files for different simulation codes and…

Inversions of airborne EM data are often an iterative process, not only requiring that the researcher be able to explore the impact of changing components such as the choice of regularization functional or model parameterization, but also…

Geophysics · Physics 2022-03-29 Lindsey J. Heagy , Seogi Kang , Rowan Cockett , Douglas Oldenburg

Contrastive vision-language models such as CLIP have demonstrated strong performance across a wide range of multimodal tasks by learning from aligned image-text pairs. However, their ability to handle complex, real-world web documents…

Computer Vision and Pattern Recognition · Computer Science 2025-10-22 Yiqi Lin , Alex Jinpeng Wang , Linjie Li , Zhengyuan Yang , Mike Zheng Shou

As state-of-the-art quantum computers are capable of running increasingly complex algorithms, the need for automated methods to design and test potential applications rises. Equivalence checking of quantum circuits is an important, yet…

Quantum Physics · Physics 2022-08-30 Tom Peham , Lukas Burgholzer , Robert Wille

Convex polyhedral abstractions of logic programs have been found very useful in deriving numeric relationships between program arguments in order to prove program properties and in other areas such as termination and complexity analysis. We…

Programming Languages · Computer Science 2007-12-18 Kim Henriksen , Gourinath Banda , John Gallagher

Knowledge of the input format of binary executables is important for finding bugs and vulnerabilities, such as generating data for fuzzing or manual reverse engineering. This paper presents an algorithm to recover the structure and semantic…

Cryptography and Security · Computer Science 2024-05-24 Seshagiri Prabhu Narasimha , Arun Lakhotia

Modern software typically performs more than one functionality. These functionalities or features are not always organized in a way for modules representing these features to be used individually. Many software engineering approaches like…

Software Engineering · Computer Science 2021-08-23 Patrick Müller , Krishna Narasimhan , Mira Mezini