• F. Negri, G. Orlandi, "Electronic and vibronic spectra of molecular systems: models and simulations based on quantum chemically computed molecular parameters'', in Computational Photochemistry, (Theoretical and Computational Chemistry, Volume 16), M. Olivucci Ed., Elsevier, (2005), p 129-169. (unibo.it)
  • In the present work, the adsorption performance and the mechanism of a CO 2 /CH 4 binary mixture in realistic shale kerogen were explored by employing grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations. (mdpi.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)
  • NAMD, GROMACS, LAMMPS, CP2K), for molecular modelling and molecular dynamics simulations, how to create configuration files based on their needs, tuning the models, how to efficiently use the resources based on the simulation details, avoid common mistakes. (prace-ri.eu)
  • Identifying local structure in molecular simulations is of utmost importance. (osti.gov)
  • Using ideas from computer vision, we adapt a specific type of neural network called a PointNet to identify local structural environments in molecular simulations. (osti.gov)
  • article{osti_1542673, title = {A generalized deep learning approach for local structure identification in molecular simulations}, author = {DeFever, Ryan S. and Targonski, Colin and Hall, Steven W. and Smith, Melissa C. and Sarupria, Sapna}, abstractNote = {Identifying local structure in molecular simulations is of utmost importance. (osti.gov)
  • 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)
  • We used all-atom molecular dynamics (MD) simulations to investigate the interactions between dendrimers and hydrocarbons. (confex.com)
  • All-atom MD simulations with explicit water were used to investigate the mechanistic details of association of model aromatic hydrocarbon guest molecules, naphthalene (NPH), and its derivatives, with 3rd - 6th generation (G3-G6) dendrimers. (confex.com)
  • To retain similar guest size and chemistry to NPH, we performed simulations with model compounds that were created by adding two and four hydroxyl groups to NPH. (confex.com)
  • Quantitative predictions of reactive flow dynamics from large-scale simulations of Liquid Rocket Engines (LRE) appear to be model dependent. (sbir.gov)
  • 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)
  • We use molecular dynamics computer simulations to obtain a molecular-level picture of the systems. (lu.se)
  • This year we will also be joined by some members from the European Materials Modelling Council whose focus is to promote modelling and simulations in Europe, especially for experimental and industrial end-users. (lu.se)
  • You can modify this simulation if you have EJS installed by right-clicking within the map and selecting "Open Ejs Model" from the pop-up menu item. (compadre.org)
  • The purpose of this course is to present to existing and potential users of Molecular Dynamics packages the method, the necessary steps for a successful simulation, common practices, common mistakes. (prace-ri.eu)
  • Flow-enhanced nucleation of the crystal phase under shear and uniaxial extension for a monodisperse melt of n -pentacontahectane (C 150 H 302 or C150) chains was studied by nonequilibrium molecular dynamics simulation. (aip.org)
  • New models based on conformational invariants for Kuhn segments are proposed and shown to describe the simulation data more accurately than those based on conformational behavior of entire chains. (aip.org)
  • Recent years have seen significant advances in the accuracy, realism, and predictive capabilities of tools for the theory and simulation of materials. (thomasyoungcentre.org)
  • Predictive, multi-scale modeling and simulation of microstructure evolution in confined granular systems, with an emphasis in manufacturing processes and the relationship between product fabrication and performance. (purdue.edu)
  • Materials and Molecular Design research involves the development and optimisation of molecules and advanced materials for a wide range of applications including pharmaceuticals, catalysts, self-healing, advanced electronics, biomaterials, electrical insulation, nanocomposites, energy storage and generation. (imperial.ac.uk)
  • Then, molecular models are analyzed to visualize molecules' shapes, and 3-D structures are sketched. (flinnsci.com)
  • Students practice drawing Lewis structures of specific molecules, and use these structures to predict their molecular geometry. (flinnsci.com)
  • Students then examine the constructed 11 molecular models to visualize the shapes of molecules and sketch their three-dimensional structures. (flinnsci.com)
  • This track consists of 15 EC and intersects with the existing specialisations in the physics master ( particle and astrophysics, physics of molecules and materials, neurophysics ), physical chemistry and mathematics . (ru.nl)
  • To better understand the interactions of materials such as cotton fiber with their surroundings, chemists and materials scientists often resort to models of the molecules. (usda.gov)
  • The work is mostly of interest to other scientists who are studying computer models of molecules that contain carbohydrates. (usda.gov)
  • Computational modelling of functional molecules and materials. (lu.se)
  • Currently available projects include computational investigations of functional materials in a broad sense, including organic molecules, transition metal complexes and polymeric systems, nanostructured inorganic materials, as well as surfaces and interfaces. (lu.se)
  • Multiscale Modelling of Materials and Molecules 2017 will take place at the Biomedical Center of Uppsala University from 12th to 14th of June. (lu.se)
  • These calculations were the first step in the combined modeling-experimental study aiming to engineer palladium surfaces with enhanced electrochemical storage of hydrogen. (synopsys.com)
  • AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. (peerj.com)
  • Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. (peerj.com)
  • Predictive modelling has now become a powerful tool which can also deliver real value through application and innovation to the nano, chemical and process industries. (thomasyoungcentre.org)
  • 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)
  • This paper presents the QuantumATK ForceField module and its algorithms, such as molecular dynamics (MD), adaptive kinetic Monte Carlo (AKMC) and nudged elastic band (NEB). (synopsys.com)
  • The series is designed first for graduate students and researchers predominantly in computational and theoretical chemistry as well as materials science and biomolecular science, who are seeking to use and understand molecular modelling methods and approaches for the first time. (elsevier.com)
  • Now in its fifteenth year, the Thomas Young Centre remains a renowned London-based interdisciplinary research network which brings together a range of groups across the capital whose research involves materials and molecular modelling and theoretical chemistry. (thomasyoungcentre.org)
  • To study deformation mechanisms using molecular dynamics, very high strain rates have to be applied. (psi.ch)
  • The pharmacological targets and molecular mechanisms related to risperidone-induced lipogenesis (RIL) remain to be elucidated. (frontiersin.org)
  • Relationships and coupling among the dominant mechanisms most responsible for destabilization are obscured by the complexities of the model and subtle consequences of inherent ad hoc approximations not supported by mathematical rationale. (sbir.gov)
  • Gene expression analysis using microarrays was performed to understand the molecular mechanisms underlying these changes. (aacrjournals.org)
  • Atomistic models of the Spike proteins and the ACE2 receptor are available, with the glycan structures reduced to the first 1-2 sugar residues. (boku.ac.at)
  • By employing a Langmuir trough integrated with X-ray reflectivity and grazing incidence X-ray diffraction techniques, this study examined the molecular packing structure of 1,2-palmitoyl- sn-glycero -3-phosphocholine (DPPC) films before and after enzyme adsorption and enzyme-catalyzed degradation. (rsc.org)
  • They provide insight into structures and interactions at the molecular level, allowing researchers to understand, predict and manipulate characteristics and properties with greater clarity. (elsevier.com)
  • We will create computer models of Spike - ACE2 interactions with different variants of ACE2. (boku.ac.at)
  • We will, for example, hear about how advanced models for intermolecular interactions and clever energy landscape search algorithms can be used to predict crystal structures. (lu.se)
  • MRD is among the few methods that can provide molecular-level informa- tion about protein solvation in native as well as denatured states, and it is used here to simultaneously monitor the interactions of urea and water with the unfolding protein. (lu.se)
  • Moreover, Kennard-Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. (peerj.com)
  • The chemical structures of isoindoles (table.1) were constructed using Hyperchem software (version 7, Hypercube Inc.) .Semi-empirical molecular orbital calculations ( PM3) of the structure were performed using the Hyperchem program and the among all energy minima conformers, the global minimum of compounds were consider in docking calculations. (ispub.com)
  • Cp2TiCl2: Synthesis, Characterization, Modeling and Catalysis. (acs.org)
  • However, understanding possible approaches, selecting the most appropriate modelling technique for a given application, and accurately interpreting the results can be difficult without understanding the basic principles, benefits and challenges associated with each of the many available methods. (elsevier.com)
  • PCR-based molecular epidemiology approaches, namely mycobacterial interspersed repetitive unit-variable-number tandemrepeat (MIRU-VNTR) are being replaced by genomic epidemiology approaches. (cdc.gov)
  • Unsupervised approaches were initially used to identify classes of materials with similar outcomes followed by supervised learning approaches to identify specific physicochemical characteristics driving toxicity responses. (cdc.gov)
  • We investigate models of Lung Surfactant and TFLL employing combined theoretical and experimental approaches. (lu.se)
  • This is achieved through advances in synthesis and growth, characterisation and theoretical modelling. (imperial.ac.uk)
  • ABSTRACT: Terahertz (THz) spectroscopies offer unmatched non-contact probing of low-energy excitations underlying electronic transport and magnetism in a wide range of novel materials. (sbir.gov)
  • Molecular modeling techniques including Density Functional Theory (DFT) and Molecular Dynamics (MD) techniques are employed to understand methane transport in the pores at typical reservoir conditions. (aiche.org)
  • With the Lewis Structures and Molecular Geometry Guided-Inquiry Chemistry Kit, students draw Lewis structures to predict molecular geometry. (flinnsci.com)
  • Lewis structures and VSEPR theory offer useful models for picturing the structures of covalent compounds. (flinnsci.com)
  • Scaling down material synthesis to crystalline structures only few atoms in size and precisely positioned in device configurations remains highly challenging, but is crucial for new applications e.g., in quantum computing. (lu.se)
  • Molecular modelling methods are now indispensable tools in chemical, materials, and biomolecular sciences. (elsevier.com)
  • The Methods in Molecular and Materials Modelling series seeks to address this issue, providing detailed guidance on available methods and highlighting the pros and cons of different techniques within the context of specific research fields and application areas. (elsevier.com)
  • The Methods in Molecular and Materials Modelling series is a direct response to researcher feedback and seeks to combine foundational background information with practical, step-by-step guidance on the design, development, applications, and interpretation of molecular modelling methods in specific fields of interest. (elsevier.com)
  • Many of today's challenges, such as climate change, energy production and healthcare demand powerful methods for probing the properties of a vast range of materials. (thomasyoungcentre.org)
  • MATERIALS AND METHODS: This article describes the techniques employed at various institutions across the United States to mitigate the risk of misidentified pretransfusion patient specimens. (bvsalud.org)
  • STUDY DESIGN AND METHODS: Model base-case parameter inputs were based on scientific literature, a survey distributed to 27 US hospitals, and transfusion experts' opinion. (bvsalud.org)
  • Materials and methods approach to regulate transgenic expression. (lu.se)
  • IJAACS addresses foundational, engineering and technological aspects of communications systems exhibiting emergent/adaptive behaviour, based on sound theoretical models such as bio-inspired, natural computing, game theory and economic models. (inderscience.com)
  • Following the tradition of the School, the 5th edition will provide training in the basic principles of magnetism and magnetics thorough a broad series of fundamental lectures, while offering the latest insights into up-to-date aspects of magnetism and applications of magnetic materials with lectures focusing on specific topics. (google.com)
  • The 5th edition of the Italian School of Magnetism will be organized by the Nanostructured Magnetic Materials group , nM 2 -Lab (Istituto di Struttura della Materia - CNR and DCCI - University of Genova). (google.com)
  • The second will use remote sensing and imaging to evaluate carbon and nitrogen sources of organic matter at freshwater sites, nearshore sampling of a variety of coastal water properties, and experiments to determine how glacier melt and precipitation change are altering material flux across the Gulf of Alaska coastal margins. (nsf.gov)
  • Modeling shows good agreement with experiments and further indicates how SPPs can be tailored with high spatiotemporal precision using the shape of the 2D TMDs with thicknesses down to single molecular layers. (lu.se)
  • Our research covers many aspects of modern physics, and we conduct both basic and applied research, which includes both experiments and theoretical modeling. (lu.se)
  • Tapping into both AlphaFold and RoseTTAFold, they tweaked the programs to predict which proteins are likely to tag-team and sketched up the resulting complexes into a 3D models. (singularityhub.com)
  • 1995), the molecular mechanism and the peptide group, suggesting that urea-peptide inter- whereby urea unfolds proteins has not been established. (lu.se)
  • Many researchers worldwide have attempted to elucidate the molecular mechanism underlying muscle wasting using the two models ( 5 - 16 ). (spandidos-publications.com)
  • We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. (nature.com)
  • This in silico model, which is based on biochemical rate equations, does not describe a specific organism, but the magnitudes of its parameters are chosen to match realistic values. (lu.se)
  • The general conclusions of the analysis suggest that the class of materials, carbon nanotubes and nanofibers, can be subdivided based on specific endpoints, some aspects of in vitro outcomes predict in vivo toxicity, and the methodological approach can possibly be adapted beyond the finite scope of this study. (cdc.gov)
  • One research thrust involves remotely imaging and sensing active wildfires to generate models and other tools that predict fire risk and behavior in fire-prone sites of the Alaskan Boreal forest. (nsf.gov)
  • In addition, there is not a mathemati- cal model to predict the distribution of variability of individual repertoire in an analogue of Hardy-Weinberg Law. (bvsalud.org)
  • Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
  • We used 7 multiwalled carbon nanotubes and 2 carbon nanofibers (CNT/F) from U.S facilities to evaluate predictability, sensitivity, and the relationship of physicochemical characteristics to key molecular initiating events and functional responses following exposure. (cdc.gov)
  • They are used increasingly together with experiment and a large and growing proportion of experimentally based studies make use of modelling techniques to help analyze and interpret data. (elsevier.com)
  • Dr. Zoe Cournia (female) is a Researcher - Assistant Professor level at the Biomedical Research Foundation, Academy of Athens, where she works on anticancer drug design, design of drug delivery systems and biomolecular modeling using computational techniques. (prace-ri.eu)
  • To explore this potential and advance our knowledge of the role of sPLA 2 in related diseases, it is necessary to systematically investigate the molecular interaction of the enzyme with lipids. (rsc.org)
  • We have created a complete model of the Spike-ACE2 interaction, with full glycosylation. (boku.ac.at)
  • The model confirms that the glycans can play a significant role in the interaction. (boku.ac.at)
  • Molecular docking revealed that compounds 13 , 5 and 28 exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding, π - π stacking and hydrophobic interaction inside the binding pocket. (peerj.com)
  • Molecular interaction of sPLA 2 (from bee venom) with the DPPC monolayer exhibited Ca 2+ dependence. (rsc.org)
  • With a minimalist model of metabolism, cell growth and transcriptional regulation in a microorganism, we explore how the interaction between environmental conditions and gene regulation set the growth rate of cells in the phase of exponential growth. (lu.se)
  • Frontiers in Molecular Biosciences. (lu.se)
  • 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)
  • We offer a synergy track Computational and Data Science in the master Physics and Astronomy and use the synergy of different disciplines in the science faculty that are engaged in computational modeling and data science. (ru.nl)
  • The INSTM (National Interuniversity Consortium of Materials Science and Technology) will offer a grant covering the registration fee for three young researchers (max 7 years after the PhD) affiliated to a research unit of the INSTM consortium. (google.com)
  • Our research areas include subatomic physics, molecular physics, condensed matter physics, materials science, biophysics, accelerators and advanced light sources, such as lasers and synchrotron light systems. (lu.se)
  • Almost every aspect of modern life involves materials and benefits from advances in materials modelling. (thomasyoungcentre.org)
  • The primary focus of this recommendation service is molecular organic compounds. (nist.gov)
  • Additionally, the predictability of in vitro model systems to in vivo outcomes from a complementary study was determined. (cdc.gov)
  • To complement the in vivo system of chick embryos, we employ patient omics data, single cell RNA sequencing, human and mouse embryos, human cancer cell cultures, human pluripotent stem cells, chick embryo neural crest-derived in vitro crestosphere cultures, and zebrafish and mouse in vivo models. (lu.se)
  • 2003). The therapeutic effects of different genes delivered by ment of the hGFAP promoter used here has been extensively studied and lentiviral vectors have been documented in a number of animal found to be up-regulated after several different stimuli both in vitro and models, both in rodents and primates, and examples include delivery in vivo in transgenic mice (Brenner et al. (lu.se)
  • The projects target high priority research areas for NSF including next-generation power grids, the mitigation of wildfires, the prevention of water contamination, understanding the rules of life, and discovery and development of new materials for future technologies. (nsf.gov)
  • An interdisciplinary and collaborative environment at the cutting-edge of materials and molecular modelling research, providing an opportunity to build networks of contacts, broaden collaborative efforts and develop research to new levels. (thomasyoungcentre.org)
  • 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)
  • Models of full parts allow researchers to quickly examine AM effects such as distortion and residual stress. (sandia.gov)
  • In order to better understand the driving forces of NPH association with dendrimers, we studied the association of increasingly hydrophilic model compounds. (confex.com)
  • In this study, we investigated the additional effect of impaired glucose tolerance (IGT), an essential component of MetS, on retinal degeneration using the WNIN/GR-Ob rat model. (molvis.org)
  • In the present study, we established models of ECC and late cancer cachexia (LCC) and compared different stages of cancer cachexia using two cancer cachectic mouse models induced by colon-26 (C26) adenocarcinoma or Lewis lung carcinoma (LLC). (spandidos-publications.com)
  • Intersecting analysis, molecular docking, and pathway validation analysis showed that risperidone influences the adipocytokine signaling pathway by targeting MAPK14 (mitogen-activated protein kinase 14), MAPK8 (mitogen-activated protein kinase 8), and RXRA (retinoic acid receptor RXR-alpha), thereby inhibiting long-chain fatty acid β-oxidation by decreasing STAT3 (signal transducer and activator of transcription 3) expression and phosphorylation. (frontiersin.org)
  • 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)
  • 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)
  • Our main model organism is the chick embryo , ideal for functional and translational studies on neural crest development. (lu.se)
  • RILs were systematically analyzed by integrating multiple databases through integrated network pharmacology, transcriptomics, molecular docking, and molecular experiment analysis. (frontiersin.org)
  • Modeling the influence of carbon nanotube and nanofiber physicochemical properties on key molecular initiating events and functional endpoints using epithelial, macrophage, and fibroblast cell models. (cdc.gov)
  • Military applications for CBRNE/GWTO and C4ISR require R&D for materials to protect personnel and equipment. (sbir.gov)
  • The web applications provides utilities for the assessment of specific property measurements for pure and binary chemical systems, the broader data needs of pure systems, and recommendations for binary mixture measurements that could extend the current UNIFAC model. (nist.gov)
  • The meeting will be a mix of method/model-oriented contributions and timely applications. (lu.se)
  • However, challenges remain in experimental synthesis and characterization of new materials, such as providing insight into observed properties for further advancement. (sbir.gov)
  • iii) performance of pharmaceutical solid products (e.g., tensile strength, stiffness, swelling and disintegration), biomaterials (e.g., transport and feeding of corn stover) and energetic materials (e.g., deformation and heat generation under quasi-static, near-resonant and impact conditions, and formation and growth of hot spots) materials. (purdue.edu)
  • This interface is created as it simulates a shale model which in reality is made up of clay (kaolinite) and quartz-like (silica) materials. (aiche.org)