We present a simple and general scheme for efficient Boltzmann sampling of conformational space by computer simulation. Multiple replicas of the system differing in temperature T or reaction coordinate λ are simulated independently. In addition, occasional stochastic moves of individual replicas in T or λ space are considered one at a time on the basis of a generalized Hamiltonian containing an extra potential energy term or bias that depends on the distribution of all replicas. The algorithm is inherently suited for shared or heterogeneous computing platforms such as a distributed network.
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http://dx.doi.org/10.1021/ct050302x | DOI Listing |
J Chem Inf Model
January 2025
Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States.
The separation and structural identification of glycans are of great bioanalytical importance. To obtain a good understanding of the structural flexibility of glycans, replica exchange molecular dynamics (REMD) simulations were used based on AMBER force field calculations to create ensembles of glycan structures. Nonpolar surface area (NPSA) calculations based on continuum solvation (CS) models (Dhakal, R.
View Article and Find Full Text PDFBiomimetics (Basel)
November 2024
Department of Dental Laboratory Science, College of Health Science, Catholic University of Pusan, 57 Oryundae-ro, Geumjeong-gu, Busan 46252, Republic of Korea.
DLP printing is a new method for producing zirconia laminates that ensure clinically acceptable gaps in the internal, marginal, and incisal regions. A typical model of a central maxillary incisor was prepped by a dentist and scanned. The laminate was designed using CAD software version 2023.
View Article and Find Full Text PDFPhys Rev E
November 2024
Université Grenoble Alpes, CEA List, 38000 Grenoble, France.
Models for viral populations with high replication error rates (such as RNA viruses) rely on the quasispecies concept, in which mutational pressure beyond the so-called "error threshold" leads to a loss of essential genetic information and population collapse, an effect known as the "error catastrophe." We explain how crossing this threshold, as a result of increasing mutation rates, can be understood as a second-order phase transition, even in the presence of lethal mutations. In particular, we show that, in fitness landscapes with a single peak, this collapse is equivalent to a ferroparamagnetic transition, where the back-mutation rate plays the role of the external magnetic field.
View Article and Find Full Text PDFData Brief
December 2024
Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins gata 6, Göteborg 412 58, Sweden.
A synthetic population is a distribution of synthetic agents that replicates the demographic distribution of a real-world population based on census records. This paper presents an end-to-end model to generate a synthetic population of residents in Gothenburg, Sweden, along with activity schedules and mobility patterns for present and past populations. Using a stochastic modelling approach, we describe the model and present its corresponding dataset.
View Article and Find Full Text PDFSensors (Basel)
December 2024
Department of Mechanical and Aerospace Engineering, Missouri University of Science and Technology, Rolla, MO 65409, USA.
The combination of distributed digital factories (DFs) with sustainable practices has been proposed as a revolutionary technique in modern manufacturing. This review paper explores the convergence of DF with innovative sensor technology, concentrating on the role of Field Programmable Gate Arrays (FPGAs) in promoting this paradigm. A DF is defined as an integrated framework where digital twins (DTs), sensors, laser additive manufacturing (laser-AM), and subtractive manufacturing (SM) work in synchronization.
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