Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in a continuum. Although our method is based on a mapping of the particles' dynamics to a regular grid so that discrete Fourier transforms may be taken, it should be emphasized that the introduction of the grid is a purely algorithmic device and that no smoothing, coarse-graining, or mean-field approximations are made. The method thus can be applied to the equations of motion of molecular dynamics (MD) or its Langevin or Brownian variants. For example, in Langevin MD simulations our acceleration technique permits a straightforward spectral decomposition of forces so that the long-wavelength modes are integrated with a longer time step, thereby reducing the time required to reach equilibrium or to decorrelate the system in equilibrium. Speedup factors of up to 30 are observed relative to pure (unaccelerated) Langevin MD. As with acceleration of critical lattice models, even further gains relative to the unaccelerated method are expected for larger systems. Preliminary results for Fourier-accelerated molecular dynamics are presented in order to illustrate the basic concepts. Possible extensions of the method and further lines of research are discussed.
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http://dx.doi.org/10.1103/PhysRevE.64.066704 | DOI Listing |
Chemphyschem
March 2025
Universität Siegen, Physikalische Chemie, Adolf-Reichwein-Str. 2, 57076, Siegen, GERMANY.
Organic-inorganic halocuprates(I) form a promising class of light-emitting materials with high photoluminescence (PL) quantum yield. However, the understanding of their emission properties and the PL mechanism is still limited. Here, we investigate thin films of bis(tetrapropylammonium) hexa-µ-bromo-tetrahedro-tetracuprate(I), [N(C3H7)4]2[Cu4Br6], which has a zero-dimensional (0D) molecular salt structure containing [Cu4Br6]2- ions.
View Article and Find Full Text PDFJ Genet Eng Biotechnol
March 2025
Centre for Bioinformatics, M.D. University, Rohtak, Haryana, India. Electronic address:
The emergence of multidrug resistanceagainst several antifungal drugs and the absence of alternate therapy limits the treatment choices leading to the spread of Candida auris infections, especially inimmunocompromised patients. This work aims to construct the multi-epitope vaccine using an immuno-informatics approachdue to the lack of efficient treatments for C. auris.
View Article and Find Full Text PDFJ Genet Eng Biotechnol
March 2025
Department of Tropical Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; WHO Collaborating Center for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Center, Khon Kaen University, Khon Kaen 40002, Thailand. Electronic address:
Background: Benzimidazole resistance is an emerging challenge among parasitic helminths. It is caused by single nucleotide polymorphisms (SNPs) in specific loci in helminths' β-tubulin genes. Field studies and laboratory investigations reported resistance-associated SNPs in 4 codon locations with 7 allelic variations among hookworms.
View Article and Find Full Text PDFJ Genet Eng Biotechnol
March 2025
Department of Bioinformatics, University of North Bengal, District-Darjeeling, West Bengal 734013, India. Electronic address:
Background: Acquired Immunodeficiency Syndrome (AIDS) is a critical global health issue caused by the human immunodeficiency virus (HIV). It has different strains and subtypes; among these, Subtype C accounts for higher infection rates than others. Despite its high prevalence, the molecular interactions with host receptors, specifically CD4, have not yet been explored.
View Article and Find Full Text PDFJ Genet Eng Biotechnol
March 2025
Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh. Electronic address:
The white spot syndrome virus (WSSV), considered the deadliest pathogen impacting Penaeid shrimp (Penaeus monodon), remains worrisome for the global shrimp industry due to its extreme virulence and mortality rate of up to 100%. To date, there has been no breakthrough in effective antivirals or vaccines that can mitigate the financial damage caused by the pathogen. The distinctive structure of VP28 facilitates its role as a trimer, serving as the primary envelope protein of WSSV.
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