Article
Multidisciplinary Sciences
Jan Kessler, Francesco Calcavecchia, Thomas D. Kuehne
Summary: Inspired by the universal approximation theorem and the widespread adoption of artificial neural network techniques, feed-forward neural networks are proposed as a general purpose trial wave function for quantum Monte Carlo simulations of continuous many-body systems. The accuracy of the trial wave functions was demonstrated by studying an exactly solvable model system of two trapped interacting particles and the hydrogen dimer. The whole many-body wave function can be represented by a neural network for simple model systems, while the antisymmetry condition of non-trivial fermionic systems is incorporated by means of a Slater determinant.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Construction & Building Technology
Nicolas Krattiger, Barbara Lothenbach, Sergey Churakov
Summary: Alkali-silica reaction (ASR) is a significant factor in global concrete durability issues. Research shows that divalent ions can co-adsorb on C-S-H and ASR products under different pH and pore water chemistry conditions.
CEMENT AND CONCRETE RESEARCH
(2021)
Article
Materials Science, Multidisciplinary
Owen Bradley, George G. Batrouni, Richard T. Scalettar
Summary: The Holstein Hamiltonian describes fermions interacting with phonons on a lattice. It predicts the behavior of dressed quasiparticles and the formation of superconducting and charge density wave phases at different densities. Quantum Monte Carlo calculations have been used to determine critical temperatures for these phase transitions in various lattice geometries.
Article
Materials Science, Multidisciplinary
S. Tarat, Bo Xiao, R. Mondaini, R. T. Scalettar
Summary: This paper investigates the two mechanisms for the vanishing of the sign problem in quantum simulations: whether randomly chosen field configurations have negative det[M(h)], or if the specific subset of configurations chosen by the weighting function have a greater preponderance of negative values. By conducting auxiliary field quantum Monte Carlo simulations of interacting fermions, the relative importance of these two mechanisms can be better understood.
Article
Polymer Science
Jiang Zhang, Wenbing Hu
Summary: The effects of specific chain-end hydrogen-bonding interactions on the once-folding crystallization of 16-mers in PEG were investigated. It was found that these interactions have little influence on the kinetics of nucleation and lateral growth, but create a significant gap at the growth front, leading to the double-lamella phenomenon. The chain-end hydrogen-bonding interactions are abundant at the surfaces of once-folded lamellar crystals, enhancing their metastability and hindering their thickening into chain-extended crystals. Additionally, intra- and inter-molecular secondary nucleation at the folded and extended growth fronts exhibit different growth rate dependencies on the interaction strengths. The study reveals the role of specific chain-end interactions in PEG crystallization.
Article
Biochemical Research Methods
Sanmitra Ghosh, Paul J. Birrell, Daniela De Angelis
Summary: In this paper, a computationally efficient method is proposed to quantify the uncertainty in transmission ability during an epidemic. This method does not make assumptions about the timing and magnitude of the impacts of external stimuli on transmission. The proposed approach is valuable for real-time monitoring of epidemics and has been demonstrated through examples of influenza, seasonality, and COVID-19 modeling.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Oncology
Konstantinos P. Chatzipapas, Dimitris Plachouris, Panagiotis Papadimitroulas, Konstantinos A. Mountris, Julien Bert, Dimitris Visvikis, Dimitris Mihailidis, George C. Kagadis
Summary: This study utilized GATE and GGEMS simulation toolkits to estimate dose distribution in Brachytherapy procedures, finding that MC simulations can optimize dose distribution in real time and evaluate therapeutic plans. The study also validated GGEMS as an accurate and efficient MC GPU-based tool for Brachytherapy applications.
Article
Chemistry, Physical
Dilimulati Aierken, Michael Bachmann
Summary: We systematically investigate the effect of bending stiffness on the ground-state conformations of semiflexible polymers. The formation of different conformations depends strongly on the strength of the bending restraint, as observed through detailed analysis of contact and distance maps.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Engineering, Geological
Kunal Gupta, Neelima Satyam, Vaasu Gupta
Summary: Probabilistic modelling is increasingly being used to assess landslide hazard by accounting for spatial and temporal uncertainties in geological, hydrological, geotechnical, seismological, and geomorphological parameters. In this study, a methodology was developed to model the uncertainties in a modified Newmark slope stability analysis model for assessing seismic landslide hazard in Uttarakhand, India. Statistical distributions were used to represent the uncertainties in input parameters, and probability density functions were simulated using the Monte Carlo method to create hazard maps.
Article
Astronomy & Astrophysics
William Detmold, Gurtej Kanwar, Henry Lamm, Michael L. Wagman, Neill C. Warrington
Summary: Path integral contour deformations have been proposed as a solution to sign and signal-to-noise problems in lattice field theories, particularly those related to phase fluctuations. By defining a family of contour deformations suitable for SU(N) lattice gauge theory, these problems associated with complex actions and observables can be significantly reduced. Experimental results show that this approach can achieve a significant reduction in variance.
Article
Mechanics
M. Beljin-Cavic, I Loncarevic, Lj Budinski-Petkovic, Z. M. Jaksic, S. B. Vrhovac
Summary: This study uses Monte Carlo simulations to investigate the random sequential adsorption of mixtures of objects with varying shapes on a three-dimensional cubic lattice. The research focuses on the influence of geometrical properties of the shapes on the jamming coverage and temporal evolution of density. The results show that the coverage approaches the jamming limit exponentially and the relaxation time is determined by the number of orientations the objects can take on the lattice. The jamming coverage of a mixture can be greater than or in between the jamming coverages of the single-component shapes, depending on the local geometry.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Polymer Science
Matthew J. Williams
Summary: This study investigates the density of states and structural characteristics of helical homopolymers. Through systematic comparisons of results under varying conditions, the study provides valuable insights into the general behavior and structural transformations of helical homopolymers. The findings are effectively showcased through a two-dimensional plot illustrating the relative distribution of different structural types.
Article
Mechanics
V Dossetti, G. M. Viswanathan, V. M. Kenkre
Summary: This article presents numerical investigations on the validity of the Boltzmann prescription in statistical mechanics for large systems. The study focuses on whether the extensivity of energy implies the extensivity of the Boltzmann entropy. Based on simulations considering a large number of states, the results suggest that the systems studied are still too small to conclusively settle the issues raised. However, the new approach outlined in this study represents a first step towards addressing the question of non-extensive statistical mechanics from first principles.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Environmental Sciences
Shannon L. Speir, C. Nathan Jones, Arial J. Shogren, Carla L. Atkinson
Summary: Streamflow and solute concentration are two key variables in watershed science. This study found that the impact of uncertainty in streamflow measurements on estimates of downstream nutrient loading is often overlooked. Any error in estimating streamflow leads to significant unpredictability of annual nutrient loads, which are used as critical benchmarks for governmental nutrient reduction strategies. Moreover, the error in estimates increases with mean streamflow, potentially influencing assessments of water quality success.
ENVIRONMENTAL RESEARCH LETTERS
(2023)
Article
Materials Science, Multidisciplinary
A. Goetz, S. Beyl, M. Hohenadler, F. F. Assaad
Summary: The two-dimensional Su-Schrieffer-Heeger model with electron-phonon coupling is investigated using Langevin dynamics and auxiliary-field quantum Monte Carlo. The efficient method in the challenging adiabatic limit is argued based on an explicit determination of the density of zeros of the fermion determinant. Large-scale simulations establish a transition from a (pi, pi) valence bond solid to an antiferromagnet as the phonon frequency increases. The single-particle spectrum shows renormalization and suggests the presence of a gapped polaronic band, while the particle-hole channels show gapless modes associated with long-range bond and magnetic order.
Article
Endocrinology & Metabolism
Hei Man Fan, Alice L. Mitchell, Elena Bellafante, Saraid McIlvride, Laura Primicheru, Mirko Giorgi, Ivano Eberini, Argyro Syngelaki, Anita Lovgren-Sandblom, Peter Jones, David McCance, Nithya Sukumar, Nishanthi Periyathambi, Yonas Weldeselassie, Katharine F. Hunt, Kypros H. Nicolaides, David Andersson, Stuart Bevan, Paul T. Seed, Gavin A. Bewick, James E. Bowe, Franca Fraternali, Ponnusamy Saravanan, Hanns-Ulrich Marschall, Catherine Williamson
Summary: This study evaluated the role of serum progesterone sulfates in the etiology of gestational diabetes mellitus (GDM). The results showed that concentrations of epiallopregnanolone sulfate (PM5S) were reduced in GDM and in women with higher fasting plasma glucose. PM5S increased glucose-stimulated insulin secretion (GSIS) and this effect was mediated by TRPM3. These findings highlight the importance of progesterone sulfates in the pathogenesis of GDM.
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Immunology
Veerle Somers, Deborah K. Dunn-Walters, Mirjam van der Burg, Judith Fraussen
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Immunology
Samuel Ken-En Gan, Jeremy P. Derrick, Franca Fraternali
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qiongju Qiu, Giancarlo Abis, Florence Mattingly-Peck, Steven Lynham, Franca Fraternali, Maria R. Conte
Summary: Human soluble epoxide hydrolase (hsEH) is a crucial regulator of epoxy fatty acid metabolism. Inhibiting hsEH can ameliorate various pathological conditions. Previous research focused on finding drugs that directly inhibit the enzyme's activity, but the disappointing results of clinical trials have led to the exploration of alternative approaches. This study reveals that endogenous electrophilic lipids and nitro fatty acids can covalently bind to different sites of hsEH, providing insights for the design of new pharmacological agents.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Immunology
Alexander Stewart, Emma Sinclair, Joseph Chi-Fung Ng, Joselli Silva O'Hare, Audrey Page, Ilaria Serangeli, Christian Margreitter, Federica Orsenigo, Katherine Longman, Cecile Frampas, Catia Costa, Holly-May Lewis, Nora Kasar, Bryan Wu, David Kipling, Peter J. M. Openshaw, Christopher Chiu, J. Kenneth Baillie, Janet T. Scott, Malcolm G. Semple, Melanie J. Bailey, Franca Fraternali, Deborah K. Dunn-Walters
Summary: The heterogeneity of immunoglobulin gene reflects the diversity and focus of the immune response. Detailed analysis of samples from different viral infections reveals common responses and unique characteristics. The characteristics of COVID-19 patients vary with age.
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Alan Brown, Franca Fraternali
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maria-Armineh Tossounian, Maria Baczynska, William Dalton, Charlie Newell, Yilin Ma, Sayoni Das, Jonathan Alexis Semelak, Dario Ariel Estrin, Valeriy Filonenko, Madia Trujillo, Sew Yeu Peak-Chew, Mark Skehel, Franca Fraternali, Christine Orengo, Ivan Gout
Summary: Coenzyme A (CoA) plays a crucial role in metabolism and gene regulation. Recent studies have shown that CoA functions as an important antioxidant by forming a disulfide bond with proteins, called CoAlation. This study identified and classified CoAlated proteins from various organisms under stress conditions, and analyzed the stabilization interactions of CoA segments within the modified cysteines. The findings propose three modes of CoA binding to proteins and provide a comprehensive understanding of CoAlation proteins' functional distribution and CoA-protein stabilization interactions.
Article
Multidisciplinary Sciences
Cecile F. Frampas, Katie Longman, Matt Spick, Holly-May Lewis, Catia D. S. Costa, Alex Stewart, Deborah Dunn-Walters, Danni Greener, George Evetts, Debra J. Skene, Drupad Trivedi, Andy Pitt, Katherine Hollywood, Perdita Barran, Melanie J. Bailey
Summary: Saliva metabolomics, particularly amino acids, can differentiate between high severity and low severity COVID-19 patients, expanding the understanding of COVID-19 metabolic dysregulation and potentially providing a non-invasive means of sampling patients for timely treatment.
Article
Multidisciplinary Sciences
Marius Kausas, Diego Esposito, Katrin Rittinger, Franca Fraternali
Summary: The study uses a combination of small-angle X-ray scattering experiments and molecular dynamics simulations to explore the conformational dynamics of the RBR domain of HOIP, highlighting the importance of interdomain linker flexibility for protein flexibility.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Silvia Crescioli, Isabel Correa, Joseph Ng, Zena N. Willsmore, Roman Laddach, Alicia Chenoweth, Jitesh Chauhan, Ashley Di Meo, Alexander Stewart, Eleni Kalliolia, Elena Alberts, Rebecca Adams, Robert J. Harris, Silvia Mele, Giulia Pellizzari, Anna B. M. Black, Heather J. Bax, Anthony Cheung, Mano Nakamura, Ricarda M. Hoffmann, Manuela Terranova-Barberio, Niwa Ali, Ihor Batruch, Antoninus Soosaipillai, Ioannis Prassas, Antigona Ulndreaj, Miyo K. Chatanaka, Rosamund Nuamah, Shichina Kannambath, Pawan Dhami, Jenny L. C. Geh, Alastair D. MacKenzie Ross, Ciaran Healy, Anita Grigoriadis, David Kipling, Panagiotis Karagiannis, Deborah K. Dunn-Walters, Eleftherios P. Diamandis, Sophia Tsoka, James Spicer, Katie E. Lacy, Franca Fraternali, Sophia N. Karagiannis
Summary: B cells play an important role in the anti-tumor immune response in immunogenic tumors such as melanoma. Tumor-associated B cells undergo clonal expansion, class switch recombination, somatic hypermutation, and receptor revision. Tumor-associated B cells produce antibodies with higher levels of unproductive sequences and distinct complementarity determining region 3 properties. These findings suggest the presence of an active and aberrant autoimmune-like reaction in the tumor microenvironment.
NATURE COMMUNICATIONS
(2023)
Article
Dermatology
Niina K. Hassi, Timir Weston, Giulia Rinaldi, Joseph C. Ng, Asma Smahi, Sophie Twelves, Camilla Davan-Wetton, Dana Fakhreddine, Franca Fraternali, Francesca Capon
Summary: This study systematically investigated the effects of IL36RN sequence changes and identified the structural determinants of IL-36Ra activity. Experimental and machine learning methods were used to identify important amino acids for IL-36Ra stability and IL-36Ra/IL36R engagement. These findings have the potential to facilitate the design of new IL-36 inhibitors and aid in the interpretation of IL36RN variants in diagnostic settings.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Meeting Abstract
Dermatology
A. Onoufriadis, A. Cabezas, J. Ng, J. Canales, M. Costas, J. Ribeiro, J. Rodrigues, M. McAleer, L. Castelo-Soccio, M. Simpson, F. Fraternali, A. Irvine, J. Cameselle, J. McGrath
BRITISH JOURNAL OF DERMATOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Irene Marzuoli, Carlos H. B. Cruz, Christian D. Lorenz, Franca Fraternali
Summary: This study investigates the molecular mechanism, stability, and interaction of antibacterial nanocapsules with model membranes, using Molecular Dynamics and protein design strategies.