15 papers · ranked by Valyu relevance
Jovan Blanuša, Paolo Ienne, Kubilay Atasu
Enumerating simple cycles has important applications in computational biology, network science, and financial crime analysis. In this work, we focus on parallelising the state-of-the-art simple cycle enumeration algorithms by Johnson and Read-Tarjan along with their applications to temporal graphs. To our knowledge, we…
Meisam Razaviyayn, Mingyi Hong, Zhi‐Quan Luo, Jong‐Shi Pang
Consider the problem of minimizing the sum of a smooth (possibly non-convex) and a convex (possibly nonsmooth) function involving a large number of variables. A popular approach to solve this problem is the block coordinate descent (BCD) method whereby at each iteration only one variable block is updated while the…
Yang Yu
Sequence Authors: ['Yang Yu'] Recent advances in reasoning models have demonstrated significant improvements in accuracy, particularly for complex tasks such as mathematical reasoning, by employing detailed and comprehensive reasoning processes. However, generating these lengthy reasoning sequences is computationally…
Daniel Ruprecht
The paper introduces an OpenMP implementation of pipelined Parareal and compares it to a standard MPI-based implementation. Both versions yield essentially identical runtimes, but, depending on the compiler, the OpenMP variant consumes about 7% less energy. However, its key advantage is a significantly smaller memory…
Ido Ben-Shalom, Charles Lin, Brian Radak, Woody Sherman + 1 more
Molecular dynamics (MD) simulations of proteins are commonly used to sample from the Boltzmann distribution of conformational states, with wide-ranging applications spanning chemistry, biophysics, and drug discovery. However, MD can be inefficient at equilibrating water occupancy for buried cavities in proteins that…
Adrian Jackson, Orestis Agathokleous
—Regions of nested loops are a common feature of High Performance Computing (HPC) codes. In shared memory programming models, such as OpenMP, these structure are the most common source of parallelism. Parallelising these structures requires the programmers to make a static decision on how parallelism should be applied.…
Authors not listed
Cyclic peptides become attractive therapeutic candidates due to their diverse biological activities. However, existing deep learning-based sequence design models, such as ProteinMPNN, are primarily optimized using cross-entropy loss and often overlook the unique topological constraints of cyclic peptides. This limits…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Authors not listed
A significant advancement in Merrifield’s classic solid-phase peptide synthesis (SPPS) that greatly expands the scope of accessible peptide structures is reported here. Building upon the one-bead, one-compound concept, this approach enables the simultaneous synthesis of multiple peptides on a single bead, followed by a…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Temitayo Adefemi
—Parallelization has become a cornerstone of modern computing, influencing everything from high-performance supercomputers to everyday mobile devices. This paper presents a comprehensive guide on the fundamentals of parallelization that every computer scientist should know, beginning with a historical perspective that…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
David Herrmann, Patrick Hodapp, Martin Starman, Pei-Chi Huang + 16 more
Analytical data in chemistry and other disciplines is usually generated in different formats and lacks common data and metadata standards that are necessary for a FAIR handling of research data. In the work presented herein, we describe a workflow that uses non-standardized, in some cases proprietary data formats from…
Frances Smith, Rhys Griffiths, Declan Meehan, Harriet Knowles + 4 more
Synthetic methods that enable the macrocyclisation of peptides facilitate the development of more effective therapeutic and diagnostic tools. Herein we report a peptide cyclisation strategy based on intramolecular interception of visible-light-mediated cysteine desulfurisation. This method allows cyclisation of…
V. Schwambach, S. Cleyet-Merle, Alain Issard, Stéphane Mancini
—Computer vision applications constitute one of the key drivers for embedded multicore architectures. Although the number of available cores is increasing in new architectures, designing an application to maximize the utilization of the platform is still a challenge. In this sense, parallel performance prediction tools…