• Interatomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space. (wikipedia.org)
  • Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties. (wikipedia.org)
  • Examples of quantitative properties and qualitative phenomena that are explored with interatomic potentials include lattice parameters, surface energies, interfacial energies, adsorption, cohesion, thermal expansion, and elastic and plastic material behavior, as well as chemical reactions. (wikipedia.org)
  • Interatomic potentials can be written as a series expansion of functional terms that depend on the position of one, two, three, etc. atoms at a time. (wikipedia.org)
  • Machine learning (ML) models, if trained to data sets of high-fidelity quantum simulations, produce accurate and efficient interatomic potentials. (nature.com)
  • Predictive molecular simulations require fast, accurate and reactive interatomic potentials. (rsc.org)
  • The approach, uncertainty-driven dynamics for active learning (UDD-AL), modifies the potential energy surface used in molecular dynamics simulations to favor regions of configuration space for which there is large model uncertainty. (nature.com)
  • A particular strength of ML models is a robust representation of the potential energy surfaces of molecular and materials systems when trained to large and diverse data sets of high-fidelity quantum chemistry simulations. (nature.com)
  • Therefore, training sets for ML potentials need to span as much phase (structural) space as possible to perform meaningful simulations. (nature.com)
  • The Molecular Dynamics, Metropolis Monte Carlo and Creutz's Demon Model compares canonical molecular dynamics and Monte Carlo versus microcanonical Creutz's demon simulations. (compadre.org)
  • The Molecular Dynamics, Metropolis Monte Carlo and Creutz's Demon Model was developed using the Easy Java Simulations (EJS) modeling tool. (compadre.org)
  • Inspired by the transient testing experiments we carried out molecular dynamics simulations of stress drops in the regimes similar to those experimentally performed, with the aim to explore the mechanisms responsible for GB accommodation and to verify whether dislocations are still emitted when strain rates after the stress drops are up to 2 or 3 orders of magnitude lower than those usually applied in atomistic deformation simulations. (psi.ch)
  • The development of accurate and efficient molecular dynamics force fields are a crucial step in an overall materials discovery workflow that complements experiments with theoretical simulations. (mrs.org)
  • Molecular modelling and simulations are integral part of biomolecular research. (lu.se)
  • Applications of quantum chemical calculations to investigations of molecular and materials properties, as well as development and applications of classical reaction dynamics simulations. (lu.se)
  • In the former projects atomistic and coarse-grained molecular dynamics and Monte Carlo simulations will be used together with experimental techniques such as scattering and circular dichroism, whereas the third project is focused on atomistic simulations solely. (lu.se)
  • The parameters are evaluated by analyzing the quality of the resulting molecular electrostatic potentials with respect to full QM potentials. (uit.no)
  • Multiscale Modeling & Simulation. (wikipedia.org)
  • We show that a combination of geometry-specific parameters for solvent molecules close to the QM region and averaged parameters for solvent molecules further away allows for efficient polarizable embedding multiscale modeling without compromising the accuracy. (uit.no)
  • As researchers delve deeper into its mechanisms of action and potential benefits, there's a growing realisation that H2 might hold the key to addressing various health challenges. (water-for-health.co.uk)
  • This article aims to provide an in-depth exploration of molecular hydrogen, from its basic properties to its therapeutic potential and mechanisms of action. (water-for-health.co.uk)
  • The aim of this review is to explore the role of glucosinolates derived isothiocyanates in various molecular mechanisms involved in the progression of Alzheimer's disease and their potential in the prevention and treatment of Alzheimer's disease. (frontiersin.org)
  • The project takes advantage of human longitudinal birth cohort data, animal studies and cellular models to test the hypothesis of shared mechanisms and molecular pathways by which ELS shapes an individual's physical and mental health in adulthood. (plos.org)
  • Life-course models will integrate the role of modifying factors as sex, socioeconomics, and lifestyle with the goal to better identify groups at risk as well as inform promising strategies to reverse the possible mechanisms and/or reduce the impact of ELS on multi-morbidity development in high-risk individuals. (plos.org)
  • To study deformation mechanisms using molecular dynamics, very high strain rates have to be applied. (psi.ch)
  • However, little is known regarding the potential mechanisms of Cd carcinogenesis. (cdc.gov)
  • Functional enrichment analysis was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and then Gene Set Enrichment Analysis (GSEA) was used to formulate the molecular functions and pathways based on the results of GO and KEGG analyses. (spandidos-publications.com)
  • Statistical potentials have been widely used for modeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between proteins, nucleic acids and small molecules. (nih.gov)
  • Docking with 5EDU, followed by ADMET and TOPKAT analysis of modified ZINC hits provided 9 novel potential HDAC6 inhibitors that possess better docking scores and 2D interactions as compared to the control ZINC hit molecules. (bvsalud.org)
  • The molecules interact in 3D through Lennard-Jones's potential and a wide range of densities, temperatures and energies can be simulated. (compadre.org)
  • Such information on vibration-rotation-electronic quantum states of molecules is critical to the understanding of many branches of chemistry and other fields, including spectroscopy, astronomy, nanotechnology, combustion science, atmospheric science, surface chemistry and molecular modelling. (abdn.ac.uk)
  • A soft ellipsoid contact potential model for a pair of biaxial ellipsoidal molecules is proposed which considers the configuration dependent energy anisotropy explicitly along with their geometrical aspects. (arxiv.org)
  • Computational modelling of functional molecules and materials. (lu.se)
  • Molecular hydrogen, often represented as H2, is a simple diatomic molecule that has garnered significant attention in the realms of science and medicine. (water-for-health.co.uk)
  • At its core, molecular hydrogen is a tasteless, odourless and flammable gas. (water-for-health.co.uk)
  • The importance of molecular hydrogen in the medical and scientific community cannot be understated. (water-for-health.co.uk)
  • The intrigue surrounding molecular hydrogen is not a recent phenomenon. (water-for-health.co.uk)
  • One of the pioneering studies on hydrogen as a medical gas was conducted in 1975 by Dole and colleagues from Baylor University and Texas A&M. Published in the esteemed journal Science , their work highlighted the potential therapeutic applications of hyperbaric hydrogen in treating skin tumours. (water-for-health.co.uk)
  • Over the years, the scope of molecular hydrogen research expanded exponentially. (water-for-health.co.uk)
  • By the turn of the century, molecular hydrogen was being studied in relation to over 170 different human and animal disease models. (water-for-health.co.uk)
  • The establishment of institutions like the Molecular Hydrogen Institute further underscored the importance of this molecule, providing platforms for collaboration, education and advancement of H2 research. (water-for-health.co.uk)
  • Today, molecular hydrogen is not just confined to research labs. (water-for-health.co.uk)
  • What is Molecular Hydrogen? (water-for-health.co.uk)
  • Molecular hydrogen, denoted as H2, might seem deceptively simple at first glance. (water-for-health.co.uk)
  • These are charged species of hydrogen, including the proton (H+) and the hydride ion (H-). They play crucial roles in various chemical and biological processes but are distinct from neutral molecular hydrogen. (water-for-health.co.uk)
  • Machine learning offers a promising approach to construct such potentials by fitting energies and forces to high-level quantum-mechanical data, but doing so typically requires considerable human intervention and data volume. (rsc.org)
  • That is, calculating quantum state energies, wavefunctions and potential energy curves. (abdn.ac.uk)
  • The Monte Carlo computations sample the configuration and velocity spaces similarly to molecular dynamics. (compadre.org)
  • The source code zip archive contains an XML representation of the Molecular Dynamics, Metropolis Monte Carlo and Creutz's Demon Model. (compadre.org)
  • F. Fernandes, Computer Program MOLECULAR DYNAMICS, METROPOLIS MONTE CARLO AND CREUTZ'S DEMON MODEL (2014), WWW Document, ( https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13344&DocID=3915 ). (compadre.org)
  • Molecular Dynamics, Metropolis Monte Carlo and Creutz's Demon Model [Computer software]. (compadre.org)
  • Here we explore the translation of biological composites to engineering applications, using a variety of tools including molecular modeling, AI and machine learning, and experimental synthesis and characterization. (mrs.org)
  • We derive a general Bayesian framework for inferring statistically optimized atomic potentials (SOAP) in which the reference state is replaced with data-driven 'recovery' functions. (nih.gov)
  • In this approach, the ML model provides an uncertainty estimate along with its prediction for each new atomic configuration. (nature.com)
  • The course covers theoretical models for the structure and reactions of atomic nuclear, as well as experiments in nuclear physics and their scientific applications. (lu.se)
  • Journal of Physics B: Atomic, Molecular and Optical Physics. (lu.se)
  • 16j) Unsupervised Optimization of Non-Bonded Parameters in Molecular Mechanics Force Fields Using the Particle Swarm Method. (aiche.org)
  • In this work, we describe an automated process for the optimization of non-bonded interactions in molecular mechanics force fields to reproduce selected experimental data, such as vapor-liquid coexistence densities. (aiche.org)
  • We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. (uit.no)
  • are usually modeled with several residues in alternative conforma- basis of elementary statistical mechanics and generic features of tions, each with its own set of AMSDs. (lu.se)
  • Here, we formulate the statistical potentials entirely within a statistical framework, avoiding questionable statistical mechanical assumptions and approximations, including a definition of the reference state. (nih.gov)
  • However, which mutations are most important, which events must occur, and if a specific order is involved in molecular tumorigenesis is unclear. (medscape.com)
  • Using BALB/c-3T3 cell transformation and nude mouse tumorigenesis models, we have investigated the molecular mechanism(s) responsible for cell transformation and tumorigenesis induced by Cd. (cdc.gov)
  • Model of the molecular mechanism for warm and cold IRI. (jci.org)
  • Therefore, an in-depth study of the molecular mechanism underlying the development and/or progression of OA is of particular importance. (spandidos-publications.com)
  • We demonstrate how proteins elevated in the ex vivo model (e.g. (lu.se)
  • Evaluation of different methods to calculated reduction potentials for heme proteins. (lu.se)
  • Message Passing is presently the most widely deployed programming model in massively parallel high performance computing. (lu.se)
  • Data from marketing literature suggested that Ardigen's predictive modeling technology outperformed MoleculeNet, a Stanford-developed large-scale benchmark for molecular machine learning. (genomeweb.com)
  • special topics in mathematical biology including predator-prey models, SI,SIS,SIR epidemic models, competition models of two and three species, Van Der Pol equation, Hodgkin-Huxley and FitzHugh-Nagumo models. (atilim.edu.tr)
  • We had both received training in other aspects of biology (E. coli and Drosophila genetics), where the value of model organisms was well-known. (balzan.org)
  • Thus, when we became interested in plant biology in the late 1970s, we were drawn to the idea of developing a model plant. (balzan.org)
  • This includes cell biology of neurons, coding in neurons by means of electrical potentials, synapse and neurotransmitter function. (lu.se)
  • The journey of H2, from a simple diatomic molecule to a potential therapeutic powerhouse, is a testament to the relentless pursuit of knowledge and the transformative power of scientific research. (water-for-health.co.uk)
  • In the field of molecular modeling , docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex . (wn.com)
  • Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site . (wn.com)
  • Thus, QSAR models in line with computer-aided drug design (CADD) were used for the molecule proposition that became the synthesis target of this work. (usp.br)
  • We can plug that data into models which predict how well each molecule would work for solar cell applications. (eurekalert.org)
  • Based on those results we rank the potential of each molecule - those rankings are part of what we released. (eurekalert.org)
  • The methodology is applied to the optimization of non-bonded Mie potential parameters for three-site water models, ethanol and benzene. (aiche.org)
  • The use of averaged parameters reduces the computational cost to obtain the embedding potential, which can otherwise be a rate-limiting step in calculations involving large environments. (uit.no)
  • Typically, there are five to ten NNs in an ensemble, and these share the same architecture and hyperparameters but, crucially, use a different initial randomization of the model parameters prior to training, as well as different splits of the training/validation data. (nature.com)
  • We review a series of studies focused on the mechanical behavior of materials, especially deformation and fracture, and how these phenomena can be modeled using a combination of molecular dynamics and machine learning, to generate a novel simulated evolutionary process that offers directed adaptation of biomaterial properties. (mrs.org)
  • This model is trained on ~ 30,000 magnetic transition metal oxides retrieved from the Materials Project and in-house calculations, and is able to estimate per-atom magnetic moment within an MAE of 0.33 bohr magnetons. (mrs.org)
  • We see significant speed-ups for spin-polarized DFT calculations initialized with per-atom magnetic moments predicted by our model. (mrs.org)
  • After training this extended model on the transition metal oxides that have been analyzed through a magnetic ordering workflow, we are able to predict the magnitude and sign of the magnetic moment on each atom with high accuracy and thus significantly decrease the number of calculations required to find the ordered magnetic ground state. (mrs.org)
  • Our Bayesian framework may also result in more accurate statistical potentials for additional modeling applications, thus affording better leverage of the experimentally determined protein structures. (nih.gov)
  • The results obtained indicate that DCC in dichloromethane can be efficient for the synthesis of potential new drugs. (usp.br)
  • Epidemiological evidence from systematic research findings and clinical trials suggests that nutritional and functional dietary isothiocyanates interfere with the molecular cascades of Alzheimer's disease pathogenesis and prevent neurons from functional loss. (frontiersin.org)
  • UMass Chan Medical School has established the Translational Institute for Molecular Therapeutics, ushering in the next phase of gene therapy development to accelerate new treatments for rare genetic diseases. (umassmed.edu)
  • The Translational Institute for Molecular Therapeutics was formed to evaluate therapies for rare diseases, where there are few options for seeking treatment. (umassmed.edu)
  • Researchers working with UMass Chan Medical School's Translational Institute for Molecular Therapeutics announced progress in developing a vector to deliver gene replacement therapy in mice models with Cockayne syndrome, a rare and fatal neurodegenerative disease that largely affects children and young adults. (umassmed.edu)
  • Top story: The Translational Institute for Molecular Therapeutics leverages UMass Chan Medical School's extensive experience in researching and developing gene therapies for early-stage clinical trials. (umassmed.edu)
  • In a piece written for The Conversation, Miguel Sena-Esteves, PhD, talks about research leading to the first ever gene therapy for Tay-Sachs disease and the launch of the Translational Institute for Molecular Therapeutics at UMass Chan. (umassmed.edu)
  • The objectives of this program are to accelerate innovative drug discovery, the development of pharmacologic tools for basic and clinical research on mental disorders, or drug or alcohol addiction, and the development and validation of models for evaluating novel therapeutics for mental disorders. (nih.gov)
  • The thermodynamic concept was referred to by Scottish scientist and engineer William Rankine in 1850 with the names thermodynamic function and heat-potential . (wikipedia.org)
  • Pharmacophore-based virtual screening of ZINC database, molecular modeling and designing new derivatives as potential HDAC6 inhibitors. (bvsalud.org)
  • Through this study, we aim to obtain novel HDAC6 selective inhibitors and provide new insights into the detailed structural design of potential HDAC6 inhibitors. (bvsalud.org)
  • Designed novel hits that might act as good HDAC6 inhibitors derived from ZINC database using combined molecular docking and modeling approaches. (bvsalud.org)
  • The method provides a route to routinely generating machine-learned force fields for reactive molecular systems. (rsc.org)
  • In order to facilitate the ongoing development of automated machine-learned force fields using tools like FLARE++ and Nequip, we have generated a benchmarking dataset of molten single-element bulk structures with a vacancy defect in order to study the interplay between many body behavior and model performance. (mrs.org)
  • To demonstrate this general approach, we computed statistical potentials for protein-protein docking (SOAP-PP) and loop modeling (SOAP-Loop). (nih.gov)
  • We demonstrate applications to a range of molecular systems with relevance to computational organic chemistry: ranging from bulk solvents, a solvated metal ion and a metallocage onwards to chemical reactivity, including a bifurcating Diels-Alder reaction in the gas phase and non-equilibrium dynamics (a model S N 2 reaction) in explicit solvent. (rsc.org)
  • Systematic molecular/genomic epidemiology studies for tuberculosis surveillance cannot be implemented in many countries. (cdc.gov)
  • Rational integration of MIRU-VNTR, WGS, and tailored strain-specific PCRs could be a new model for tuberculosis surveillance in countries without molecular/genomic epidemiology programs. (cdc.gov)
  • New genotyping strategies in Mycobacterium tuberculosis have led to development of molecular epidemiology strategies that enable clarification of TB transmission dynamics ( 1 - 4 ). (cdc.gov)
  • PCR-based molecular epidemiology approaches, namely mycobacterial interspersed repetitive unit-variable-number tandemrepeat (MIRU-VNTR) are being replaced by genomic epidemiology approaches. (cdc.gov)
  • The national TB-control programs of many resource-constrained countries with a high TB prevalence lack systematic molecular epidemiology analysis ( 7 ). (cdc.gov)
  • Panama is an example of a country that, despite recently being classified in the upper-income category, has not implemented a systematic molecular/genomic epidemiology-based surveillance program ( 7 ). (cdc.gov)
  • LCMD is a computational/theoretical laboratory, focusing on electronic structure theory in the area of method development and conceptual work applied to the field of homogeneous catalysis and organic molecular material s . (epfl.ch)
  • Survey of the anaerobic biodegradation potential of organic chemicals in digesting sludge. (cdc.gov)
  • While its basic structure might suggest simplicity, the therapeutic potential and diverse applications of H2 have made it a focal point of research and exploration. (water-for-health.co.uk)
  • These studies span a wide range of human and animal disease models, suggesting that H2's influence is vast and its potential applications are expansive. (water-for-health.co.uk)
  • This groundbreaking study laid the foundation for subsequent research, hinting at the vast potential of H2 in medical applications. (water-for-health.co.uk)
  • Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore be used to create new or extend existing functionality associated with those applications. (eyesopen.com)
  • This has far reaching implications for plant science at both the fundamental level and in potential applications. (balzan.org)
  • The present study aims to prepare a polyherbal formulation (PHF) of Azadirachta indica (Neem), Aloe barbadensis (Aloe vera), Allium sativum (garlic), Acacia arabica (Babul), and Aegle marmelos (Bel) and evaluation of antidiabetic and antioxidant activity utilizing the in vitro model. (hindawi.com)
  • An Example of a result obtained from a combination about modeling toolkits: conformers from Omega TK were overlayed using Shape TK while surfaces and coloring were generated by Spicoli TK. (eyesopen.com)
  • Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
  • From initial studies focusing on its potential anti-tumor properties, the research spectrum broadened to explore H2's role in combating oxidative stress, inflammation and various other pathological conditions. (water-for-health.co.uk)
  • Feature papers represent the most advanced research with significant potential for high impact in the field. (mdpi.com)
  • The Committee agreed that, despite the considerable progress that had been made in investigating variola virus, significant components of this research, most notably the refinement and use of an animal model developed in 2001 and the development of antiviral drugs, were unlikely to be completed by the end of 2002. (who.int)
  • Further, during extensive discussion about the potential availability of an animal model, additional research was identified that would necessitate access to live variola virus stocks after the expected 2002 destruction date. (who.int)
  • Additionally, the authors built a prediction model including 28 SNPs which classified 37 percent of men enrolled in PCPT to have reduced risk of high-grade cancer when taking finasteride. (aacr.org)
  • It draws on potential energy models to gain insight into the behavior of minima and transition states. (routledge.com)
  • We anticipate the use of our model to screen materials for interesting magnetic behavior and for the inverse design of novel materials with desired magnetic properties. (mrs.org)
  • Main methods: Anticancer activity of the I. obliquus extract was examined in mouse models of Lewis lung carcinoma growth and spontaneous metastasis after 3 weeks of continuous extract intake at the dose of 6 mg/kg/day, which corresponded to that ingested daily with Chaga infusion in Japan. (researchgate.net)
  • Key findings: The extract of I. obliquus caused significant tumor suppressive effects in both models. (researchgate.net)
  • Overall, compound 8, is a permeable potent and selective dual AChEI that can be considered as a good candidate with potential impact for further pharmacological development in Alzheimer's therapy. (uaeu.ac.ae)
  • A reasonable model is based on colon cancer development. (medscape.com)
  • Although the exact process has not been elucidated, the sum of these mutations is believed to lead to cancer development in this model. (medscape.com)
  • The concept will be rapidly prototyped for a proof-of-concept experiment, for feasibility evaluation, and for providing a preliminary design and demonstration plan for Phase II, which will involve development, building, and testing of a brass-board model of the optical security system. (nsf.gov)
  • This includes the anatomy of invertebrate and vertebrate nervous systems, important model animals, and the development and regeneration of nervous systems. (lu.se)
  • We independently settled on Arabidopsis because preliminary experiments by George Redei and others indicated that it had the kinds of properties that were desirable in a model plant. (balzan.org)
  • You can find the genome of a frog online, or the genome of a worm, but you cannot do that for the quantum properties of molecular materials. (eurekalert.org)
  • For each injury cause, alcohol-attributable fractions across studies were synthesized by meta-analysis of single proportions using generalized linear mixed models. (cdc.gov)
  • These experiments are closely linked to epigenetic analysis and gene editing experiments performed in cell culture models of glioma. (lu.se)
  • A HypoGen-based 3D QSAR HDAC6 pharmacophore was built and used as a query model to screen approximately 8 million ZINC database compounds. (bvsalud.org)
  • Here we show that, by leveraging hierarchical and active learning, accurate Gaussian Approximation Potential (GAP) models can be developed for diverse chemical systems in an autonomous manner, requiring only hundreds to a few thousand energy and gradient evaluations on a reference potential-energy surface. (rsc.org)
  • Overtones and combination bands observed in vibrational predissociation spectra of cold ions can often be anticipated by expanding the potential energy surface to third order. (osu.edu)
  • Note that in case the pair potential is given per atom pair, in the two-body term the potential should be multiplied by 1/2 as otherwise each bond is counted twice, and similarly the three-body term by 1/6. (wikipedia.org)
  • Similarly, for modeling 12-residue loops in the PLOP benchmark, the average main-chain root mean square deviation of the best scored conformations by SOAP-Loop is 1.5 Å, close to the average root mean square deviation of the best sampled conformations (1.2 Å) and significantly better than that selected by Rosetta (2.1 Å), DFIRE (2.3 Å), DOPE (2.5 Å) and PLOP scoring functions (3.0 Å). (nih.gov)
  • The discovery of the structure of DNA by Francis Crick and James Watson in the early 1950s ushered in a new era in molecular biologic science. (medscape.com)
  • In preclinical models utilizing human lung cancer cells and specific NSCLC mutational subsets, the researchers found that tumor growth was enhanced by anti-PD-1 treatment but not by anti-PD-1 F(ab) 2 fragments, which lack the Fc portion of the antibody. (aacr.org)
  • Molecular modeling and rational planning optimize the search for new potential drugs. (usp.br)
  • The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. (eyesopen.com)
  • However, these methods usually require training of a separate Gaussian process model and rely on the structural representation in latent space. (nature.com)
  • Thirteen studies were identified comparing the HS-RDT and conventional RDT (co-RDT) to molecular methods to detect malaria in pregnancy. (cdc.gov)