Podcasts about atomistic

This episode provides an overview of the ancient Greek philosophy of Epicureanism, including its views on ethics, pleasure, friendship, death, and the gods. We explore how Epicurus sought freedom from disturbance and fear through limiting desires, cultivating virtues, and surrounding oneself with friends. We'll also highlight Epicurus' atomic theory of the universe and contrast his views with Christian beliefs about purpose, providence, and the afterlife. Episode Overview Origin of Epicureanism and its founder, Epicurus, in 4th century BC Athens Central goals: freedom from fear (ataraxia), absence of pain (aponia) Path to happiness through limiting desires, seeking simple pleasures Importance of friendship, prudent living, gratitude Withdrawal from politics and public affairs Atomistic theory of matter and metaphysical worldview Views on the gods and lack of an afterlife Life well lived by enjoying earthly delights in the present Discussion Questions How can Christians appreciate Epicurean insights while rejecting its worldview? What critique does Epicureanism offer regarding superstitions and irrational fears? How does the hope we have in Christ differ from the Epicurean view of death? In what ways can an individualistic pursuit of pleasure prove spiritually empty? How can Christians balance earthly joys and sufferings in light of eternity? For other questions and comments, feel free to reach out to Jared at thechurchhistoryproject@gmail.com. For more content, visit the podcast ⁠website ⁠or wherever you find your podcasts. To join The Church History Project Facebook group to engage in more discussion about released episodes and other fascinating nuggets of church history, you can visit the page ⁠here⁠. --- Send in a voice message: https://podcasters.spotify.com/pod/show/church-history-project/message

Well-being and wellness, it should be noted, are not the same. “Well-being” is an aspirational state of life, while “wellness” refers to the interventions humans perform on themselves to improve their health. Our state of living is not always well, and sometimes there is a need for measures that bring us closer to alignment with the universe.Frederick Tsao from the book Dawn of an Era of Well-BeingIn our quest to overcome the challenges that stand in the way of a better future—an era of “well-being” as our program frequently makes reference—we need to consider paths to spiritual betterment which help show us the way. Our guest today is Alberto Villoldo, a trained practitioner of western medicine who has also spent decades studying the shamanic healing practices of the Amazon and Andes. Dr. Villoldo will engage our hosts with a penetrating conversation investigating how shamanic traditions of South America can inform the western thought process. At the nexus of science and spirituality lies the key to our evolution as a species, and the basis of a healing process that will make true well-being accessible. This discussion delves into the evolution of the human brain and its chemistry, and how the shamanic tradition can help reinforce our connection to both nature and a higher level of consciousness.Alberto Villoldo, PhD, is a medical anthropologist and best-selling author who has studied the shamanic healing practices of the Amazon and Andes for over 30 years. He is the founder of the Four Winds Society, and his recent books include The Heart of the Shaman: Stories and Practices of the Luminous Warrior and The Wisdom Wheel: A Mythic Journey through the Four Directions For more information on Shamanic Energy Medicine, please visit this link to Alberto Villoldo's organization The Four Winds Society Dr. Villoldo's latest book The Wisdom Wheel: A Mythic Journey through the Four Directions can purchased here The Heart of the Shaman: Stories and Practices of the Luminous Warrior can be purchased here

 Revealing atomistic structures behind AFM imaginghttps://nanolsi.kanazawa-u.ac.jp/en/achievements/revealing-atomistic-structures-behind-afm-imaging/Atomic force microscopy (AFM) enables the visualization of the dynamics of single biomolecules during their functional activity. However, all observations are restricted to regions that are accessible by a fairly big probing tip during scanning. Hence, the AFM only records images of biomolecular surfaces with limited spatial resolution, thereby missing important information that is required for a detailed understanding of the observed phenomena.To facilitate the interpretation of experimental imaging, Romain Amyot and Holger Flechsig from the Kanazawa NanoLSI have developed the mathematical framework and computational methods to reconstruct 3D atomistic structures from AFM surface scans. ==Transcript of this podcastHello and welcome to the NanoLSI podcast. In this episode we feature the latest research published by Romain Amyot and Holger Flechsig of the Computational Science group at the Kanazawa University NanoLSI.The research described in this podcast was published in the journal PLOS Computational Biology in March 2022. Revealing atomistic structures behind AFM imaginghttps://nanolsi.kanazawa-u.ac.jp/en/achievements/revealing-atomistic-structures-behind-afm-imaging/Atomic force microscopy (AFM) enables the visualization of the dynamics of single biomolecules during their functional activity. However, all observations are restricted to regions that are accessible by a fairly big probing tip during scanning. Hence, the AFM only records images of biomolecular surfaces with limited spatial resolution, thereby missing important information that is required for a detailed understanding of the observed phenomena.To facilitate the interpretation of experimental imaging, Romain Amyot and Holger Flechsig from the Kanazawa NanoLSI have developed the mathematical framework and computational methods to reconstruct 3D atomistic structures from AFM surface scans. In this paper they describe applications for high-speed AFM imaging ranging from single molecular machines, protein filaments, to even large-scale assemblies of protein lattices, and demonstrate how the full atomistic information advances the molecular understanding beyond topographic images.Their approach employs simulation AFM, which was previously established by Amyot and Flechsig and distributed within the free BioAFMviewer software package. Simulation AFM computationally emulates experimental scanning of biomolecules to translate structural data into simulation AFM topographic images that can be compared to real AFM images. The researchers implemented a procedure of automated fitting to identify the high-resolution molecular structure behind a limited-resolution experimental AFM image. It is therefore possible to retrieve full 3D atomistic information from just a scan of the protein surface obtained under AFM observations. To illustrate the potential of this achievement, Flechsig says: “Imagine that instead of just seeing the tip of an iceberg, you are now able to see everything hidden under the sea, to the extent that you can even detect impurities or density differences within its structure, helping you to explain the icebergs' coloration.”To share these developments with the global Bio-AFM community, all computational methods are embedded within the user-friendly BioAFMviewer interactive software interface. The new methods have already been applied in numerous interdisciplinary collaborations to understand expe

In this episode, I'm joined by Prof. Adrian Sutton, Emeritus Professor of Physics at Imperial College London in the UK. Adrian's research in understanding the interplay between processes at the atomic scale and the microstructural behaviour of real material systems has played a critical role in the establishment of the research field of computational materials science. We had an extensive discussion about his many contributions in materials development, his insights into university education and the funding of academic research, and his upcoming book which aims at explaining materials science to a younger audience.The textbooks mentioned during the podcast are available under the following links:Physics of Elasticity and Crystal Defects: https://global.oup.com/academic/product/physics-of-elasticity-and-crystal-defects-9780198860785?cc=de&lang=en&Rethinking the PhD:https://www.amazon.de/-/en/Adrian-P-Sutton/dp/B083XX3LZVInterfaces in Crystalline Materials (with Robert Balluffi):https://www.amazon.de/Interfaces-Crystalline-Materials-Monographs-Chemistry/dp/0198500610Electronic Structure of Materials:https://www.amazon.de/Electronic-Structure-Materials-Science-Publications/dp/0198517548

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.09.375691v1?rss=1 Authors: Stadlbauer, P., Islam, B., Otyepka, M., Chen, J., monchaud, d., Zhou, J., Mergny, J.-L., Sponer, J. Abstract: Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics simulations to scrutinize the G4/hemin interaction. We found that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. Importantly, the simulations do not support several mechanistic possibilities (i.e., the wobbling guanine and the iron-bound water molecule) but rather suggest tentative mechanisms in which the external G-quartet itself is responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Our simulations show that once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD simulation technique are also briefly discussed. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249755v1?rss=1 Authors: Patel, D., Barnes, J. E., Davies, W. I. L., Stenkamp, D. L., Patel, J. S. Abstract: For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the {lambda} max value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of {lambda} max values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the {lambda} max of phylogenetically distant Sws2 cone opsins. To build a model that can predict the {lambda} max using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured {lambda} max values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the {lambda} max of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting {lambda} max values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.237008v1?rss=1 Authors: Zheng, W., Dignon, G. L., Xu, X., Regy, R. M., Fawzi, N. L., Kim, Y. C., Best, R., Mittal, J. Abstract: The formation of membraneless organelles in cells commonly occurs via liquid-liquid phase separation (LLPS), and is in many cases driven by multivalent interactions between intrinsically disordered proteins (IDPs). Molecular simulations can reveal the specific amino acid interactions driving LLPS, which is hard to obtain from experiment. Coarse-grained simulations have been used to directly observe the sequence determinants of phase separation but have limited spatial resolution, while all-atom simulations have yet to be applied to LLPS due to the challenges of large system sizes and long time scales relevant to phase separation. We present a novel multiscale computational framework by obtaining initial molecular configurations of a condensed protein-rich phase from equilibrium coarse-grained simulations, and back mapping to an all-atom representation. Using the specialized Anton 2 supercomputer, we resolve microscopic structural and dynamical details of protein condensates through microsecond-scale all-atom explicit-solvent simulations. We have studied two IDPs which phase separate in vitro: the low complexity domain of FUS and the N-terminal disordered domain of LAF-1. Using this approach, we explain the partitioning of ions between phases with low and high protein density, demonstrate that the proteins are remarkably dynamic within the condensed phase, identify the key residue-residue interaction modes stabilizing the dense phase, all while showing good agreement with experimental observations. Our approach is generally applicable to all-atom studies of other single and multi-component systems of proteins and nucleic acids involved in the formation of membraneless organelles. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238485v1?rss=1 Authors: Zerze, G., Stillinger, F., Debenedetti, P. Abstract: Studying the DNA hybridization equilibrium via brute force molecular dynamics (MD) or commonly used advanced sampling approaches is notoriously difficult at the atomistic length scale. However, besides providing more realistic modeling of this microscopic phenomenon, the atomistic resolution is a necessity for some fundamental research questions, such as the ones related to DNA's chirality. Here, we describe an order parameter-based advanced sampling technique to calculate the free energy surface of hybridization and estimate the melting temperature of DNA oligomers at the atomistic resolution, using a native topology-based order parameter. We show that the melting temperatures estimated from our atomistic simulations follow an order consistent with the predictions from melting experiments and those from the nearest neighbor model, for a range of DNA sequences of different GC content. Moreover, free energy surfaces and melting temperatures are calculated to be identical for D- and L-enantiomers of Drew-Dickerson dodecamer. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.23.216341v1?rss=1 Authors: Alavizargar, A., Keller, F., Heuer, A. Abstract: Cholesterol and ergosterol are two dominant sterols in the membranes of eukaryotic and yeast cells, respectively. Although their chemical structure is very similar, their impact on the structure and dynamics of membranes differs.In this work, we have explored the effect of these two sterols on binary mixtures with 1,2-dipalnitoyl-sn-glycerol-3-phosphocholine (DPPC) lipid bilayer at various sterol concentration and temperatures, employing molecular dynamics simulations. The simulations revealed that cholesterol has a stronger impact on the ordering of the lipid chains and leads to more condensed membranes with respect to ergosterol. This difference likely arises from a more planar structure of the ring part as well as the better alignment of cholesterol among the DPPC chains with respect to ergosterol. The degree of the planarity of the ring system affects the orientation of the methyl groups on the rough side and distribute the lipid chains on the two sides of the sterols differently. Similar to the structural observations, cholesterol also has a stronger influence on the dynamics, and consistently, establishes stronger DPPC-sterol interactions when compared to ergosterol. Although our findings are consistent with some previous simulations as well as recent experiments, they are at odds with some other studies. Therefore, the presented results may shed new lights on the impact of sterols on the saturated lipids bilayers with implications for binary mixtures of lipids as well as lipid rafts. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.22.214254v1?rss=1 Authors: Serapian, S., Marchetti, F., Triveri, A., Morra, G., Meli, M., Moroni, E., Sautto, G. A., Rasola, A., Colombo, G. Abstract: Betacoronavirus SARS-CoV-2 is posing a major threat to human health and its diffusion around the world is having dire socioeconomical consequences. Thanks to unprecedented efforts of the scientific community, the atomic structure of several viral proteins has been promptly resolved. As the crucial mediator of host cell infection, the heavily glycosylated trimeric viral Spike protein (S) has been attracting the most attention and is at the center of efforts to develop antivirals, vaccines, and diagnostic solutions. Herein, we use an energy-decomposition approach to identify antigenic domains and antibody binding sites on the fully glycosylated S protein. Crucially, all that is required by our method are unbiased atomistic molecular dynamics simulations; no prior knowledge of binding properties or ad hoc combinations of parameters/measures extracted from simulations is needed. Our method simply exploits the analysis of energy interactions between all intra-protomer aminoacid and monosaccharide residue pairs, and cross-compares them with structural information (i.e., residue-residue proximity), identifying potential immunogenic regions as those groups of spatially contiguous residues with poor energetic coupling to the rest of the protein. Our results are validated by several experimentally confirmed structures of the S protein in complex with anti- or nanobodies. We identify poorly coupled sub-domains: on the one hand this indicates their role in hosting (several) epitopes, and on the other hand indicates their involvement in large functional conformational transitions. Finally, we detect two distinct behaviors of the glycan shield: glycans with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes; those with weaker coupling could themselves be poised for antibody recognition. Predicted Immunoreactive regions can be used to develop optimized antigens (recombinant subdomains, synthetic (glyco)peptidomimetics) for therapeutic applications. Copy rights belong to original authors. Visit the link for more info

Associate Professor in the Department of Mechanical Engineering and Director of the Atomistic Simulation & Energy Group at MIT, Asegun Henry, discusses his research and how it may hold the key to moving the needle on climate change. In this episode, you will learn: How heat is transferred between atoms, what factors heat transfer mechanisms are dependent upon, and what happens at extremely hot temperatures    How electricity can be stored as heat in the “sun in a box” technology being developed by Henry and his group What benefits are conferred by liquid metals for transferring heat When you heat a pot of water, what's actually happening? What's behind those boiling bubbles…what processes and principles lead to your observations? It may sound like a rather simple question, but there's probably more to it than you think. In fact, this was one of the questions that led Professor Asegun Henry into the field of research involving heat transfer, high temperatures, and energy. For Henry, it took awhile for him to get a straight answer to these questions, but today's show begins with exactly that. Also discussed are the two projects Henry and his group are currently working on, which include an energy storage technology that involves storing heat rather than electricity in order to achieve extremely low costs, and a CO2-free technological approach to hydrogen production. He provides an in-depth explanation of the physics and chemistry involved, and the solar energy and other commercial applications of this research. Learn more by visiting https://ase.mit.edu/. Available on Apple Podcasts: apple.co/2Os0myK

From predicting the properties of nanotechnological devices to the structural stability of small proteins and dynamics of water. Atomistic computer simulations of matter based on solving quantum mechanical equations is an interdisciplinary area that touches physics, chemistry, and a part of biology. By calculating the electronic structure of an arrangement of atoms, and at the same time predicting the forces acting on the individual nuclei (which are themselves quantum particles), it is possible to calculate a range of properties of known and unknown materials and molecules in a computer. I will illustrate some of the successes of these theories, from predicting the properties of nanotechnological devices to the structural stability of small proteins and dynamics of water.

From predicting the properties of nanotechnological devices to the structural stability of small proteins and dynamics of water. Atomistic computer simulations of matter based on solving quantum mechanical equations is an interdisciplinary area that touches physics, chemistry, and a part of biology. By calculating the electronic structure of an arrangement of atoms, and at the same time predicting the forces acting on the individual nuclei (which are themselves quantum particles), it is possible to calculate a range of properties of known and unknown materials and molecules in a computer. I will illustrate some of the successes of these theories, from predicting the properties of nanotechnological devices to the structural stability of small proteins and dynamics of water.

Zannoni, C (Università di Bologna) Friday 22 March 2013, 11:00-11:50

Muccioli, L (Università di Bologna) Wednesday 20 March 2013, 14:50-15:40

The interactions between biomolecules and their environment can be studied by experiments and simulations. Results from experiments and simulations are often interpretations based on the raw data. For an accurate comparison of both approaches, the interpretation of the raw data from experiments and simulation have to be in compliance. The design of such simulations and interpretation of raw data is demonstrated in this thesis for two examples; fluorescence resonance energy transfer (FRET) experiments and surface adsorption of biomolecules on inorganic surfaces like gold. FRET experiments allow to probe molecular distances via the distance-dependent energy transfer efficiency from an excited donor dye to its acceptor counterpart. In single molecule settings, not only average distances, but also distance distributions or even fluctuations can be probed, providing a powerful tool to study flexibilities and structural changes in biomolecules. However, the measured energy transfer efficiency does not only depend on the distance between the two dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages have to be employed, which severely limit the accuracy of the distance distributions extracted from FRET experiments alone. In this work, I combined efficiency distributions from FRET experiments with dye orientation statistics from molecular dynamics (MD) simulations to calculate improved estimates of the distance distributions. From the time-dependent mutual dye orientations, the FRET efficiency was calculated and the statistics of individual photo-absorption, FRET, and photo-emission events were determined from subsequent Monte Carlo (MC) simulations. All recorded emission events were then collected to bursts from which efficiencies were calculated in close resemblance to the actual FRET experiment. The feasibility of this approach has been tested by direct comparison to experimental data. As my test system, I chose a poly-proline chain with Alexa 488 and Alexa 594 dyes attached. Quantitative agreement of calculated efficiency distributions from simulations with the experimental ones was obtained. In addition, the presence of cis-isomers and specific dye conformations were identified as the sources of the experimentally observed heterogeneity. This agreement of in silico FRET with experiments allows employment of the dye orientation dynamics from simulations in the distance reconstruction. For multiple levels of approximation, the dye orientation dynamics was used in dye orientation models. At each level, fewer assumptions were applied to the dye orientation model. Each model was then used to reconstruct distance distributions from experimental efficiency distributions. Comparison of reconstructed distance distributions with those from simulations revealed a systematically improved accuracy of the reconstruction in conjunction with a reduction of model assumptions. This result demonstrates that dye orientations from MD simulations, combined with MC photon generation, can indeed be used to improve the accuracy of distance distribution reconstruction from experimental FRET efficiencies. A second example of simulations and interpretation in compliance with experiments are the studies of protein adsorption on gold surfaces. Interactions between biomolecules and inorganic surfaces, e.g. during the biomineralization of bone, are fundamental for multicellular organisms. Moreover, understanding these interactions is the basis for biotechnological applications such as biochips or nano-sensing. In the framework of the PROSURF project, a multi-scale approach for the simulation of biomolecular adsorption was implemented. First, parameters for MD simulations were derived from ab initio calculations. These parameters were then applied to simulate the adsorption of single amino acids and to calculate their adsorption free energy profiles. For the screening of adsorbed protein conformations, rigid body Brownian dynamics (BD) docking on surfaces was benchmarked with the free energy profiles from the MD simulations. Comparison of the protein adsorption rate from surface plasmon resonance experiments and BD docking yielded good agreement and therefore justifies the multi-scale approach. Additionally, MD simulations of protein adsorption on gold surfaces revealed an unexpected importance of positively charged residues on the surface for the initial adsorption steps. The multi-scale approach presented here allows the study of biomolecular interactions with inorganic surfaces consistently at multiple levels of theory: Atomistic details of the adsorption process can be studied by MD simulations whereas BD allows the extensive screening of protein libraries or adsorption geometries. In summary, compliance of simulation and experimental setup allows benchmarking of the simulation accuracy by comparison to experiments. In contrast to employing experiments alone, the combination of experiments and simulations enhances the accuracy of interpreted results from experimental raw data.

This presentation demonstrates the OMEN capabilities to perform a multi-scale simulation of advanced InAs-based high mobility transistors.Learning Objectives:Quantum Transport Simulator Full-Band and Atomistic III-V HEMTs Performance Analysis Good Agreement with Experiment Some Open Issues Outlook Improve Models (Contact) Investigate Scaling of Gate Length Scattering?

This presentation demonstrates the OMEN capabilities to perform a multi-scale simulation of advanced InAs-based high mobility transistors.Learning Objectives:Quantum Transport Simulator Full-Band and Atomistic III-V HEMTs Performance Analysis Good Agreement with Experiment Some Open Issues Outlook Improve Models (Contact) Investigate Scaling of Gate Length Scattering?

Lecture on electrocatalysis with discrete metal complexes. This lecture is part of the Energy Seminar, an interdisciplinary series of talks primarily by Stanford experts on a broad range of energy topics. (May 21, 2008)

Atomistic theoretical descriptions of thermal chemical recations in complex environments are well achieved by combined quantum and molecular mechanical (QM/MM) methods. The goal of this work is to extend such techniques to enable the description of photochemical reactions and to carry out case studies subsequently. In order to tackle the enormous computational demand due to the involvement of excited electronic states, we (i) largely speed up the individually selecting multi-refernce configuration interaction (IS/MRCI) scheme by Tavan and Schulten (1980) by a new grahical algorithm and (ii) take use of recently developed semimempirical valence shell models (Thiel 1997) which are well suited for excited electronic states. The efficiency and accuracy of the resulting IS/MRCI-algorithm is demonstrated by its application to the first electronic excited states of butadiene. The new QM/MM method is used to calculate absorption energies along a molecular dynamics trajectory of a small Schiff base in isotonic solution.