Article
Chemistry, Multidisciplinary
Timothee O'Donnell, Frederic Cazals
Summary: Flexible loops play a crucial role in protein function by contributing to the overall energy and structure of the protein. However, generating diverse and low energy loops is challenging. This study introduces a new method for sampling loop conformations by decomposing the loop into tripeptides and identifying necessary conditions for successful closure. The results show that this method outperforms previous approaches in generating diverse conformations.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Timothy Foldes, Antony Lesage, Maria Barbi
Summary: This study reexamines the coil-globule transition of a polymer from a spectral perspective, introducing a new possibility and reintroducing overlooked mature spectral methods. This method not only allows for the determination of the polymer state without information about polymer length or interaction strength, but also proposes an experimental implementation.
PHYSICAL REVIEW LETTERS
(2021)
Article
Mathematics, Applied
Riccardo Tosi, Ramon Amela, Rosa M. Badia, Riccardo Rossi
Summary: The necessity of dealing with uncertainties is increasing in various fields of science and engineering. The proposed asynchronous framework for Monte Carlo and Multilevel Monte Carlo methods aims to improve computational efficiency by introducing a new level of parallelism between batches. This approach maintains the reliability of state-of-the-art techniques while enhancing computational efficiency.
JOURNAL OF SCIENTIFIC COMPUTING
(2021)
Article
Computer Science, Interdisciplinary Applications
DanHua ShangGuan
Summary: The Monte Carlo method is a powerful tool in many research fields, but the increasing complexity of physical models and mathematical models requires efficient algorithms to overcome the computational cost.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Mathematics, Interdisciplinary Applications
Sergio Bacallado, Stefano Favaro, Samuel Power, Lorenzo Trippa
Summary: This paper develops a perfect sampler using the Propp-Wilson algorithm to simulate the posterior distribution of the hierarchical Pitman-Yor process, and evaluates its average running time through extensive simulations. The simulations reveal a significant dependence of running time on the parameters of the model.
Article
Neurosciences
Yu Yao, Klaas E. Stephan
Summary: This article addresses the technical challenges of applying MCMC to hierarchical models for clustering in the space of latent parameters. Specifically focusing on dynamic causal models for fMRI and effective brain connectivity clustering, the study proposes a solution to improve convergence by introducing proposal distributions capturing dependencies between clustering and subject-wise generative model parameters. Validated on synthetic and real-world datasets, the proposed solution shows good convergence performance and superior runtime compared to state-of-the-art Monte Carlo techniques.
HUMAN BRAIN MAPPING
(2021)
Article
Multidisciplinary Sciences
Roland Sandt, Robert Spatschek
Summary: Quantum annealing is an efficient technique for determining ground state configurations of binary optimization problems described by Ising Hamiltonians. In this study, we demonstrate a low-cost computational method for calculating finite temperature properties. The method is particularly effective at low temperatures, where conventional approaches suffer from high rejection rates and significant statistical noise. We validate the approach by applying it to spin glasses and Ising chains.
SCIENTIFIC REPORTS
(2023)
Article
Physics, Multidisciplinary
Indrajit Sau, Arnab Sen, Debasish Banerjee
Summary: Matter-free lattice gauge theories provide an ideal model for studying the confinement to deconfinement transitions at finite temperatures, and the critical exponents can change continuously with varying coupling while maintaining a fixed ratio. This phenomenon, known as weak universality, has been demonstrated for the first time in lattice gauge theories. Using an efficient cluster algorithm, we show that the finite temperature phase transition of U(1) quantum link lattice gauge theory belongs to the 2D XY universality class, and the occurrence of weak universality is observed when higher charged matter fields are added.
PHYSICAL REVIEW LETTERS
(2023)
Article
Mathematics, Applied
Tony Lelievre, Gabriel Stoltz, Wei Zhang
Summary: This study proposes a new MCMC algorithm for sampling probability distributions on submanifolds. Unlike previous methods, this algorithm uses set-valued maps in the proposal step and ensures the correctness of the sampling results through carefully enforced reversibility property.
IMA JOURNAL OF NUMERICAL ANALYSIS
(2023)
Article
Spectroscopy
Shaohui Yu, Jing Liu
Summary: This paper proposes an ensemble calibration model FDA-EM-PLS (functional data analysis-ensemble learning-partial least squares) for near-infrared spectroscopy, based on the functional data analysis method. By dividing the near-infrared spectroscopy into intervals and conducting functional data analysis, clustering, and Monte Carlo sampling, this model achieves accurate detection of corn and soil data.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Astronomy & Astrophysics
Cagin Yunus, William Detmold
Summary: In Monte Carlo calculations of lattice quantum field theories, the variance of the sampling procedure defines the precision of the calculation. If the variance of an estimator is infinite or significantly larger than the square of the mean, the quantity cannot be reliably estimated. The Gross-Neveu model provides an example where the variances of estimators involving fermion fields are divergent, and alternative sampling methods are proposed.
Article
Mathematics, Applied
Alexander D. Gilbert, Frances Y. Kuo, Ian H. Sloan
Summary: This paper analyzes a method for approximating the distribution function and density of a random variable that depends on a possibly high number of independent random variables. The method involves smoothing the original integrand by preintegration with respect to one chosen variable, and then computing the integral of the resulting smoother function using a suitable quasi-Monte Carlo method. Interpolation is used to reconstruct the distribution or density on an interval. The preintegration technique is a special case of conditional sampling, which has previously been applied to various problems in statistics and computational finance.
SIAM JOURNAL ON NUMERICAL ANALYSIS
(2023)
Article
Computer Science, Theory & Methods
Yiolanda Englezou, Timothy W. Waite, David C. Woods
Summary: This study focuses on comparing various methods for approximating expected Shannon information gain in common nonlinear models, with ALIS being up to 70% cheaper than LIS and sometimes being both cheaper and more accurate.
STATISTICS AND COMPUTING
(2022)
Article
Statistics & Probability
Nathan Robertson, James M. Flegal, Dootika Vats, Galin L. Jones
Summary: This article discusses the simultaneous estimation of means and quantiles in Monte Carlo experiments, providing a multivariate central limit theorem and a fast algorithm for constructing confidence regions. These methods are incorporated into standard visualization techniques for Monte Carlo results, making it easier for practitioners to assess the reliability of the outcomes.
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2021)
Review
Environmental Sciences
Olivera Stojanovic, Bastian Siegmann, Thomas Jarmer, Gordon Pipa, Johannes Leugering
Summary: Researchers use Bayesian hierarchical models to predict complex phenomena from heterogeneous datasets. They find that this approach helps mitigate the problems caused by heterogeneity and improves the robustness and interpretability of predictive models. One application is the estimation of leaf area index, an important indicator in agronomical modeling.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Yangjie Huang, Ning Zhao, Yung-hua Wang, Charles Truillet, Junnian Wei, Matthew F. L. Parker, Joseph E. Blecha, Christopher R. Drake, Henry F. VanBrocklin, Diego Garrido-Ruiz, Matthew P. Jacobson, Rahul Aggarwal, Spencer C. Behr, Robert R. Flavell, David M. Wilson, Youngho Seo, Michael J. Evans
Summary: The research conducted on the compound (+/-)-C-11-YJH08 demonstrates the high-affinity and high selectivity ligand-receptor interaction, supporting its use for the first measurements of GR expression in human subjects via PET imaging.
JOURNAL OF NUCLEAR MEDICINE
(2021)
Article
Chemistry, Multidisciplinary
Mosavverul Hassan, Evangelos A. Coutsias
Summary: The study discusses the kinematic geometry of protein backbone structures constrained by hydrogen bonds, showing simple geometrical correlations and introducing a new classification of ideal helices with an analytical expression for backbone dihedrals. The addition of a second parameter allows for a generalization of previous expressions, providing an efficient parametrization of structures consistent with H-bond parameters. An analogs parametrization of beta-turns using inverse kinematic methods is also presented, offering potential applications in protein and peptide design.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Medicine, Research & Experimental
Mausam Kalita, Javier Villanueva-Meyer, Yuki Ohkawa, Chakrapani Kalyanaraman, Katharine Chen, Esraa Mohamed, Matthew F. L. Parker, Matthew P. Jacobson, Joanna J. Phillips, Michael J. Evans, David M. Wilson
Summary: Aberrant biosynthesis of GAGs in glioma contributes to malignant growth, and disrupting GAGs with small molecule inhibitors shows potential therapeutic benefits in blocking rogue signaling and proliferation in glioblastoma.
MOLECULAR PHARMACEUTICS
(2021)
Article
Biochemistry & Molecular Biology
Wan-Chen Tsai, Ansari Mukhtar Aleem, Chris Whittington, Wilian A. Cortopassi, Chakrapani Kalyanaraman, Angel Baroz, Anthony T. Iavarone, Ewa Skrzypczak-Jankun, Matthew P. Jacobson, Adam R. Offenbacher, Theodore Holman
Summary: Through computational modeling, experimental mutagenesis, and hydrogen-deuterium exchange (HDX) investigations, this study reveals the dimeric structure of human platelet 12S-lipoxygenase (h12-LOX). Experimental results demonstrate that mutations in specific amino acid residues affect dimer formation of h12-LOX, further validating the accuracy of the computational model.
Article
Biochemistry & Molecular Biology
Wan-Chen Tsai, Chakrapani Kalyanaraman, Adriana Yamaguchi, Michael Holinstat, Matthew P. Jacobson, Theodore R. Holman
Summary: This study investigated the reactions of human platelet 12-lipoxygenase, human reticulocyte 15-lipoxygenase-1, and human epithelial 15-lipoxygenase-2 with docosahexaenoic acid to produce 17S-HpDHA. The enzymes showed varying efficiencies and product distributions, with 15-LOX isozymes producing higher levels of 17S-HpDHA. The differences in the effective k(cat)/K-M values for 17S-HpDHA suggest distinct reactivity patterns among the enzymes.
Article
Biochemistry & Molecular Biology
Wan-Chen Tsai, Ansari M. Aleem, Jennyfer Tena, Mirella Rivera-Velazquez, Harman Singh Brah, Sarvind Tripathi, Melinee D'silva, Jerry L. Nadler, Chakrapani Kalyanaraman, Matthew P. Jacobson, Theodore Holman
Summary: Human platelet 12-(S)-Lipoxygenase (12-LOX) plays a crucial role in platelet activation and cardiometabolic disease. ML355, a specific 12-LOX inhibitor, has shown promising effects in reducing thrombosis and protecting human pancreatic islets. By proposing a binding model and synthesizing a derivative called Lox12Slug001, researchers have been able to enhance the potency and selectivity of the inhibitor for potential therapeutic applications.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Wan-Chen Tsai, Nathan C. Gilbert, Amanda Ohler, Michelle Armstrong, Steven Perry, Chakrapani Kalyanaraman, Adam Yasgar, Ganesha Rai, Anton Simeonov, Ajit Jadhav, Melissa Standley, Hsiau-Wei Lee, Phillip Crews, Anthony T. Iavarone, Matthew P. Jacobson, David B. Neau, Adam R. Offenbacher, Marcia Newcomer, Theodore R. Holman
Summary: This study reported newly discovered molecules that are more potent and structurally distinct from previous inhibitors, along with the development of binding models for three imidazole inhibitors and the synthesis of novel inhibitors of the imidazole scaffold. Additionally, the study demonstrated the activity of these inhibitors in an h15-LOX-2/HEK293 cell assay, suggesting their potential as important tool compounds for understanding h15-LOX-2's role in human biology and development as therapeutic agents.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Neurosciences
Swetha Mohan, Paul J. Sampognaro, Andrea R. Argouarch, Jason C. Maynard, Mackenzie Welch, Anand Patwardhan, Emma C. Courtney, Jiasheng Zhang, Amanda Mason, Kathy H. Li, Eric J. Huang, William W. Seeley, Bruce L. Miller, Alma Burlingame, Mathew P. Jacobson, Aimee W. Kao
Summary: This study identifies multiple lysosomal proteases that can process PGRN into multi- and single-granulin fragments in a pH-dependent manner and implicates AEP and granulin F in the neurobiology of FTLD-TDP-Pgrn. Modulating progranulin cleavage and granulin production may be a potential therapeutic strategy for FTLD-Pgrn and other progranulin-related diseases.
MOLECULAR NEURODEGENERATION
(2021)
Article
Chemistry, Medicinal
Mosavverul Hassan, Evangelos A. Coutsias
Summary: QBKR (Quaternary Backbone Kinematic Reconstruction) is a fast analytical method for reconstructing protein and linear or cyclic peptide chains' all-atom backbones from C-a coordinate traces, with a unique kinematic model that incorporates noncanonical geometry. It can handle perturbations in geometry, optimize spring-based objective functions, and enrich conformational ensembles. The method can also be used to speed up the process of all-atom description from large experimental data or subpar electron density maps.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Xiaoxiao Sun, Jake M. Bieber, Heinz Hammerlindl, Robert J. Chalkley, Kathy H. Li, Alma L. Burlingame, Matthew P. Jacobson, Lani F. Wu, Steven J. Altschuler
Summary: By modulating environmental signals, cellular mechanisms that promote and eliminate cancer persistence can be identified and targeted. Interferon and protein arginine methyltransferase play pivotal roles in this process.
Article
Chemistry, Physical
Ajeet Kumar Yadav, Pradipta Bandyopadhyay, Evangelos A. Coutsias, Ken A. Dill
Summary: Crustwater is a fast computational statistical mechanical model that describes the behavior of nonpolar solvation in water. It provides new insights into the hydrophobic effect by introducing a solvation shell and explaining the role of solute-water interactions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Diego Garrido Ruiz, Angelica Sandoval-Perez, Amith Vikram Rangarajan, Emma L. Gunderson, Matthew P. Jacobson
Summary: The oxidation states of cysteine side chains are determined by the pH and redox potential of the environment, and their effects on protein structure and function are still poorly understood compared to other post-translational modifications. This article analyzes the regulatory role of cysteine reactivity in proteins, highlighting the interplay between electrostatics and redox potential. It also identifies underdeveloped areas in the computational study of cysteine reactivity through molecular simulations.
Article
Chemistry, Physical
Angelica Sandoval-Perez, Beth Apsel Winger, Matthew P. Jacobson
Summary: This study proposes a method based on molecular dynamics and free energy calculations to predict the functional effect of KIT mutations. It has important clinical implications by defining the functional significance of previously uncharacterized KIT mutations and guiding targeted therapy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Sergei Kotelnikov, Ryota Ashizawa, Konstantin I. Popov, Omeir Khan, Mikhail Ignatov, Stan Xiaogang Li, Mosavverul Hassan, Evangelos A. Coutsias, Gennady Poda, Dzmitry Padhorny, Alexander Tropsha, Sandor Vajda, Dima Kozakov
Summary: In the ligand prediction category of CASP15, the challenge was to predict the positions and conformations of small molecules binding to proteins. Template-based docking methods were found to be more suitable for the AlphaFold2-generated models, although direct docking methods were used in some cases.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Mathematical & Computational Biology
Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, Burak Ogan Mancarci, Jordan Sicherman, Matthew Jacobson, Justin Leong, Patrick Tan, Paul Pavlidis
Summary: Despite the vast amount of transcriptomic data in public repositories, effective reuse remains challenging due to issues such as unstructured metadata, inconsistent data processing, and varying probe-gene mappings. The Gemma bioinformatics system was created to address these issues by providing curated transcriptomic datasets, analytical software, and a web interface. With over 10,000 manually curated datasets and hundreds of curated transcriptomic platforms, Gemma offers broad coverage of conditions and tissues, particularly focusing on brain-related datasets. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service, and an R package.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)