14 papers · ranked by Valyu relevance
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…
Marco Aldinucci, Cristina Calcagno, Mario Coppo, Ferruccio Damiani + 5 more
'Maurizio Drocco' 'Eva Sciacca' 'Salvatore Spinella' 'Massimo Torquati' 'Angelo Troina'] The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the…
James S. Sims, John G. Hagedorn, Peter M. Ketcham, Steven G. Satterfield + 14 more
'Steven G. Satterfield' 'Terence J. Griffin' 'William L. George' 'Howland A. Fowler' 'Barbara A. am Ende' 'Howard K. Hung' 'Robert B. Bohn' 'John E. Koontz' 'Nicos S. Martys' 'Charles E. Bouldin' 'James A. Warren' 'David L. Feder' 'Charles W. Clark' 'B. James Filla' 'Judith E. Devaney'] The rate of scientific discovery…
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…
Manuel Carrer, Henrique Musseli Cezar, Sigbjørn Løland Bore, Morten Ledum + 1 more
We develop #-HylleraasMD (#-HyMD), a fully end-to-end differentiable molecular dynamics software based on the Hamiltonian hybrid particle-field formalism, and use it to establish a protocol for automated optimization of force field parameters. #-HyMD is templated on the recently established HylleraaasMD software, while…
Carlos Fernandez-Musoles, Daniel Coca, Paul Richmond
In the last decade there has been a surge in the number of big science projects interested in achieving a comprehensive understanding of the functions of the brain, using Spiking Neuronal Network (SNN) simulations to aid discovery and experimentation. Such an approach increases the computational demands on SNN…
Authors not listed
With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs -accelerated implementation within Tinker-HP. For the specific use with the flexible AMOEBA polarizable force field (PFF), we introduce the new "dual–water" GaMD…
Luke Jostins, Johannes Jaeger
Background The use of reverse engineering methods to infer gene regulatory networks by fitting mathematical models to gene expression data is becoming increasingly popular and successful. However, increasing model complexity means that more powerful global optimisation techniques are required for model fitting. The…
Julia L Turner, Scott T Kelley, James S Otto, Faramarz Valafar + 1 more
'Andrew J Bohonak'] Background The Isolation by Distance Web Service (IBDWS) is a user-friendly web interface for analyzing patterns of isolation by distance in population genetic data. IBDWS enables researchers to perform a variety of statistical tests such as Mantel tests and reduced major axis regression (RMA), and…
Patrizio Dazzi
Embarrassingly parallel problems are characterised by a very small amount of information to be exchanged among the parts they are split in, during their parallel execution. As a consequence they do not require sophisticated, low-latency, high-bandwidth interconnection networks but can be efficiently computed in…
Vladislav Skorpil, Vaclav Oujezsky, Arcangelo Castiglione, Gianni D’Angelo
'Gianni D’Angelo'] This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…