• The COSHE theme was formed at CEC in 2023 by the members of Computational Biology and Biological Physics (CBBP, formerly at Astronomy and Theoretical Physics) and the Uncertainty and Evidence Lab. (lu.se)
  • In this work, we test the hypothesis that in a statistical shape model (SSM), the modes that are most relevant for describing anatomy are also most important for determining the output of cardiac electromechanics simulations. (plos.org)
  • This highlights the need to have high fidelity anatomical models in cardiac simulations and demonstrates that subtle changes in cardiac anatomy can have a large impact on cardiac function. (plos.org)
  • Structural, volumetric, and mechanical properties, e.g. geometrical values and density, have been calculated using simulations on these models. (bl.uk)
  • 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 have assessed and used computational tools for this aim, most of them based on molecular dynamics (MD) simulations. (lu.se)
  • In this project we will use molecular dynamics (MD) simulations to investigate local fluctuations in proteins. (lu.se)
  • However, MD simulations of proteins are in practice limited to a few hundred nanoseconds of simulation, if one wants to model all atoms explicitly. (lu.se)
  • It involves two series of molecular dynamics (MD) simulations in which the ligand is artificially transformed to another ligand, for which the binding free energy is known. (lu.se)
  • Much of this research is based on detailed thermodynamic simulations of protein chains in purpose-built software, but we also work with more coarse-grained models. (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)
  • To obtain a molecular understanding of IDPs, a combined approach of experiments and simulations is useful. (lu.se)
  • Models of reactions and molecules are built using special software which can also help in calculations to obtain accurate information on mechanisms of reactions. (edu.gh)
  • Our research aims to invent approaches to engineer new molecules that operate as predicted in biological contexts, and to utilize prediction and engineering to address fundamental questions on the relationship of molecular mechanisms and systems-level function. (ucsf.edu)
  • 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)
  • In the field of computational biophysics, we mainly study the behaviour of large molecules such as proteins, DNA and RNA. (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)
  • Computational Methods in Systems Biology 2011. (crossref.org)
  • The research focus is to develop and employ state-of-the-art computational techniques and synthesis/characterization methods to design and optimise new catalysts and organic semi-conductors for renewable energy applications. (edu.gh)
  • Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories? (ub.edu)
  • Molecular modelling methods are now indispensable tools in chemical, materials, and biomolecular sciences. (elsevier.com)
  • 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)
  • 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)
  • 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)
  • Estimates of evolutionary distances (numbers of substitutions that have occurred since a pair of sequences diverged from a common ancestor) are typically calculated using substitution models (evolutionary distances are used input for distance methods such as neighbor joining ). (wikipedia.org)
  • Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. (biorxiv.org)
  • For the first time, researchers have combined these two methods in order to obtain high-resolution images of molecular structures in either fixed or living cells. (pasteur.fr)
  • To address the many current challenges in the field - from developing more predictive computational design methods to determining the requirements for function in cells - we combine concepts from computer science, physics, chemistry, mathematics, engineering and biology. (ucsf.edu)
  • I. Develop computational methods for modeling & design of proteins, in the program Rosetta ( www.rosettacommons.org ). (ucsf.edu)
  • We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
  • The Master Programme in Applied Computational Science with specialisation in Chemistry will give you detailed knowledge about the underlying methods with respect to chemistry. (lu.se)
  • In this project you will develop computational methods for assembling fragmented (noisy) optical DNA maps into full chromosomal maps for bacteria. (lu.se)
  • In biology, a substitution model , also called models of DNA sequence evolution , are Markov models that describe changes over evolutionary time. (wikipedia.org)
  • For example, branch lengths, especially when those branch lengths are combined with information from the fossil record and a model to estimate the timeframe for evolution. (wikipedia.org)
  • [4] Other model parameters have been used to gain insights into various aspects of the process of evolution. (wikipedia.org)
  • Most of the work on substitution models has focused on DNA/ RNA and protein sequence evolution. (wikipedia.org)
  • Models of DNA sequence evolution, where the alphabet corresponds to the four nucleotides (A, C, G, and T), are probably the easiest models to understand. (wikipedia.org)
  • Thinking and Modeling Evolution. (lu.se)
  • 2004. Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer's disease . (ub.edu)
  • To further elucidate synaptic mechanisms in humans we are combining these approaches with state-of-the-art biophysically-realistic computational models of cognitive function developed by our collaborators Dr. Xiao-Jing Wang and John D. Murray . (yale.edu)
  • [1] These models describe evolutionary changes in macromolecules (e.g. (wikipedia.org)
  • Multiple sequence alignment (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. (wikipedia.org)
  • It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). (wikipedia.org)
  • The evolutionary distance equation ( d 12 ) is based on the simple model proposed by Jukes and Cantor in 1969. (wikipedia.org)
  • The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). (wikipedia.org)
  • The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. (nih.gov)
  • The global spread of 2019-nCoV: a molecular evolutionary analysis. (cdc.gov)
  • and (i i) to develop (epi)genomic powerful molecular and/or cell biology and close col aboration to create synergies methodologies, profiling strategies, and functional genomics tools, recent progress and better exploit and further expand bioinformatics tools and resources that in understanding of the cancer (epi) unique research tools and expertise. (who.int)
  • Knowledge in theoretical biophysics and computational physics (corresponding to FYTN05/ BERN05 and FYTN03 , respectively) is helpful but not required. (lu.se)
  • The Basel Computational Biology Conference (stylized as [BC]2) is a scientific meeting on the subjects of bioinformatics and computational biology. (wikipedia.org)
  • Combine your biotech major with a master's degree in bioinformatics to prepare for careers where you can tackle complex problems in biology using big data, data mining, machine learning and modeling. (rit.edu)
  • The 2012 Brazilian Symposium on Bioinformatics (BSB 2012) is an international conference which covers all aspects of bioinformatics and computational biology. (wikicfp.com)
  • He also leads the Bioinformatics Activity in the Molecular Epidemiology and Bioinformatics Team of the Division of HIV/AIDS Prevention's Laboratory Branch. (cdc.gov)
  • This paper may help the beginners or researchers who want to continue their research in the field of computational biology and bioinformatics . (bvsalud.org)
  • The complex and heterogeneous genetic background of the patients makes human neurons derived from induced pluripotent stem cells (iPSCs) an attractive model since animal models do not fully reproduce the complex human genetics and behavior. (technion.ac.il)
  • In RIT's biotechnology and molecular biology degree you'll improve human health by harnessing technology advancements and biomolecular processes to research and develop technologies in genetics, agriculture, pharmaceuticals and vaccine development, environment and energy, forensic science, genetic counseling, and more. (rit.edu)
  • Bacterial genetics and molecular pathogenesis in the age of high throughput DNA sequencing. (cdc.gov)
  • Predicting and designing the structures of proteins with biologically useful accuracy has been a key challenge in computational structural biology and molecular engineering. (ucsf.edu)
  • As a first demonstration, we have calculated the structure of proteins in a simple lattice-based model on a quantum computer. (lu.se)
  • Simplified lattice-based models provide a means for exploring the basics of the sequence-structure relationship of proteins. (lu.se)
  • One then needs to solve discrete optimization problems, which, despite the simplicity of the models, become computationally challenging for large proteins. (lu.se)
  • Researchers develop mathematical models that simplify a practical problem so that it can be simulated on a computer, working with systems that range from the molecular scale to simulation of chemical plants. (sc.edu)
  • From these models and using simulation software structural, electronic and physical properties were calculated and compared with experimental data. (bl.uk)
  • Biophysical computational models of the heart provide a quantitative framework for mapping changes in anatomy to whole heart function. (plos.org)
  • Under these studies, the mechanisms and molecular level details of industrially relevant chemical reactions that are difficult, if not impossible to obtain experimentally, are investigated with the aid of computers. (edu.gh)
  • Available projects also include computational investigations of reaction mechanisms and reaction dynamics for solar energy conversion and catalysis/photocatalysis. (lu.se)
  • 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)
  • This new imaging technique could become a key tool in the study of numerous microbial complexes and their interactions with host cells at the molecular level. (pasteur.fr)
  • Computational molecular modeling for the assessment of nanoparticle toxicity: interactions with biomolecules. (cdc.gov)
  • 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)
  • Recently we have shown that a coarse-grained model based on the primitive model, that has been used for modelling polyelectrolytes for over 30 years, works well for a range of IDPs where electrostatics governs the intra- and intermolecular interactions [1]. (lu.se)
  • 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)
  • This project housed in the Chemistry Department, KNUST by the Computational and Molecular Modeling laboratory. (edu.gh)
  • 70% of the biotechnology and molecular bioscience elective courses have a hands-on laboratory component. (rit.edu)
  • 1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany [email protected]. (nih.gov)
  • 3 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany. (nih.gov)
  • These laboratories include: (1) computational neurobiology Laboratory: The goal of their research is to build bridges between brain levels from the biophysical properties of synapses to the function of neural systems. (hopkinsmedicine.org)
  • Although considerable progress has been made in using experimental and computational techniques to determine start and final structural states, we have a limited understanding of what happens in between. (lu.se)
  • Using tools from statistical and computational physics, we construct models and investigate biomolecular processes and properties. (lu.se)
  • Recommended knowledge: Computational physics corresponding to FYTN03 and programming experience. (lu.se)
  • not unique for the embryonic system but are shared by other ogenesis regulation must consider different scales of multi-cellular modeling areas. (lu.se)
  • The K a /K s ratio (also called ω in codon substitution models) is a parameter of interest in many studies. (wikipedia.org)
  • Computational models used in biology are rapidly increasing in complexity, size, and numbers. (biorxiv.org)
  • It is observed that finding out the most suitable and efficient optimization technique for the accurate inference of all kinds of networks, i.e., in-silico, in-vivo, etc., with less computational complexity is still an open research problem to all. (bvsalud.org)
  • This means, they will use computer generated models to find suitable and cost effective ways to obtain such polymers. (edu.gh)
  • However, this approach is limited by its low resolving power, which only helps distinguish cellular and molecular structures at a scale of 200-300 nanometres (nm). (pasteur.fr)
  • This in-person 5-day EMBO Workshop will gather early-career researchers and field leaders at the crossroads of single-cell omics, modelling and HPC to pave the way for realistic, scalable human digital twins of cells, tissues and organs. (bsc.es)
  • To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. (biorxiv.org)
  • Researchers from the Institut Pasteur and CNRS have set up a new optical microscopy approach that combines two recent imaging techniques in order to visualize molecular assemblies without affecting their biological functions, at a resolution 10 times better than that of traditional microscopes. (pasteur.fr)
  • The development of a new optical microscopy approach by the researchers of the Institut Pasteur and CNRS offers unique perspectives for molecular biology. (pasteur.fr)
  • Applied computational science can be divided into several components: mathematics, modelling, statistics, and programming. (lu.se)
  • CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. (blogspot.com)
  • In fact, substitution models can be developed for any biological characters that can be encoded using a specific alphabet (e.g., amino acid sequences combined with information about the conformation of those amino acids in three-dimensional protein structures [7] [8] ). (wikipedia.org)
  • To overcome this problem we develop a method that combines a computational structural modeling (which delivers atomic-resolution structures) with experimental data (which provides information about the population of different states). (lu.se)
  • In chapter 5 atomistic molecular models have been developed with the help of molecular mechanics and semi-empirical quantum mechanical calculations. (bl.uk)
  • Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. (wikipedia.org)
  • The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. (nih.gov)
  • Our delight is in the use of these external funding from the Royal Society to continue building local physical and human resource capacity in molecular and materials modeling in a developing country that is integrated into the global scientific research community. (edu.gh)
  • This will change the landscape of chemical research in KNUST and the quest to be recognized globally as a center of computational scientific research. (edu.gh)
  • Our cutting-edge research centres promote interdisciplinary collaborations in nano-, molecular and life sciences. (concordia.ca)
  • The overarching objective of this research arm is to bridge levels of explanation to mechanistically understand human psychiatric symptoms by combining computational, pharmacological and clinical neuroimaging. (yale.edu)
  • 2) computational Principles of Natural Sensory Processing: Research in this lab focuses on the computational principles of how the brain processes information. (hopkinsmedicine.org)
  • His primary research interests are related to agent-based modeling of infectious diseases, transmission network analysis, and data visualization. (cdc.gov)
  • Computational research is very suitable for master projects and shorter student projects (such as Fördjupningskurs ), because it's possible to reach far into the research process in a fairly short time. (lu.se)
  • The focus of this course is on the reasons for doing science, the intellectual and instrumental tools used, the models developed to solve new problems, and the assertion that chemistry has a tremendous effect on your personal life and on the decisions made by society. (beloit.edu)
  • Building on a core of biology, chemistry, math, and the liberal arts, the courses in the bachelor of science in biotechnology are taught from a molecular bioscience perspective with a focus on the central genetic dogma of molecular biology. (rit.edu)
  • In addition to knowledge of theory of computational science, there will be an emphasis on obtaining knowledge about the practical tools that are used by professionals in the field and you will amongst several things train your skills in programming. (lu.se)
  • The second year includes two compulsory courses: Computational Science, and Reproducible Data Science and Statistical Learning. (lu.se)
  • The group is part of COSHE, the Computational Science for Health and Environment theme at CEC. (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)
  • 2004. Synthesis, biological evaluation and molecular modelling of diversely functionalized heterocyclic derivatives as inhibitors of acetylcholinesterase/butyrylcholinesterase and modulators of Ca2+ channels and nicotinic receptors . (ub.edu)
  • In this thesis the developments of detailed atomistic molecular models for poly(phenylene), substituted and unsubstituted polypyrrole and their corresponding oligomers has been outlined. (bl.uk)
  • 2013 "Genetic Variation + Human Health" 2012 "ECCB'12, 11th European Conference on Computational Biology" in association with the 10th Basel Computational Biology conference. (wikipedia.org)
  • By observing the value of kinetic parameters of S-system model, it is possible to extract the regulatory relationships among genes . (bvsalud.org)
  • The object of our study aimed to review and to correlate genes involved in ASD and those related to ultrasonic communication in animal model studies of language-based social behavior at the PubMed database. (bvsalud.org)
  • El objetivo de nuestro estudio tuvo como objetivo revisar y correlacionar genes involucrados en TEA y aque- llos relacionados con la comunicación ultrasónica en estudios con modelos animales de comportamiento social basado en el lenguaje en la base de datos PubMed. (bvsalud.org)
  • [2] Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree. (wikipedia.org)
  • Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users' intuition about model similarity, and to support complex model searches in databases. (biorxiv.org)
  • The aim of this course is to introduce students to common deep learnings architectues such as multi-layer perceptrons, convolutional neural networks and recurrent models such as the LSTM. (lu.se)
  • exposures and lifestyle alter critical advances as well as the uniqueness and These developments have also led to molecular pathways and promote cancer strengths of IARC. (who.int)
  • By enabling both time resolution and structural detail Time-Resolved Small Angle X-ray/Neutron Scattering (TR-SAXS/TR-SANS) is uniquely suited to interrogate complex self-assembly reactions and to provide a molecular understanding of self-assembly pathways. (lu.se)