UChicago Immunoengineering researchers decode the “cytokine storm” in sepsis
Researchers at the University of Chicago Pritzker School of Molecular Engineering have made a breakthrough in understanding the
Molecular Dynamics
Articles tagged with Molecular Dynamics
Age-related alterations in the oscillatory dynamics serving verbal working memory processing
Researchers investigated the neural mechanisms of verbal working memory processing in healthy aging adults using magnetoencephalography. Age-related increases in theta activity were detected during encoding, and alpha and beta oscillations were stronger in older participants during maintenance and retrieval phases.
Sodium channel investigation
A team of scientists at Kanazawa University used high-speed atomic force microscopy to study the structural dynamics of sodium ion channels in cell membranes. They found that voltage sensor domains can dissociate from pore domains when the channel is in a resting state, leading to dimerization between neighboring channels. These findin...
Elucidating the mechanism of autophagosomes shaping with a flexible web
A research group reconstituted autophagosome formation in vitro, showing that Atg8 protein and enzymes play a central role in shaping the membrane structure. High-speed atomic force microscopy and nuclear magnetic resonance analysis revealed flexible complexes on membranes, which work together to form autophagosomes.
SourceJapan Science and Technology Agency·JournalNature Structural & Molecular Biology·TypeExperimental study·DateDec 19, 2023
First observation of how water molecules move near a metal electrode
Researchers observe changes in water molecule movement near a metal electrode depending on the magnitude and polarity of the applied voltage. The study provides crucial insights into electrochemical reactions and paves the way for designing more efficient battery technologies.
SourceInstitute for Basic Science·JournalProceedings of the National Academy of Sciences·TypeExperimental study·DateDec 18, 2023
Towards next-generation nanocatalysts to revolutionize active electron transfer
Researchers from Japan Advanced Institute of Science and Technology have developed a copolymer-conjugated nanocatalytic system to enhance active electron transfer for increased photoinduced hydrogen generation. The system leverages the advantages of a stimuli-responsive polymer chain to achieve dynamic electron transfer.
SourceJapan Advanced Institute of Science and Technology·JournalChemical Communications·DateDec 13, 2023
Mechanism of pressure-induced glass phase transition leading to advanced phase-change memories
Researchers have found that increasing pressure suppresses a regular atomic arrangement called Peierls-like distortion, which is crucial for phase-change materials. This discovery may lead to the development of new materials for advanced phase-change memory and other applications.
Catalysts of change: Young scientists spearhead breakthrough COVID-19 research in international collaboration
A recent study published in Nature Nanotechnology investigates the coronavirus's ability to attach to human cells under various mechanical stresses. The Alpha variant shows stronger cell adhesion, potentially contributing to its rapid transmission.
SourceAuburn University Department of Physics·JournalNature Nanotechnology·TypeExperimental study·DateNov 29, 2023
Novel machine learning model for molecular simulation under external field
A novel machine learning model, FIREANN, accurately simulates system-field interactions for complex chemical, biological, and material systems. The model correlates response properties like dipole moment and polarizability with potential energy changes under external fields.
Understanding the dynamic behavior of rubber materials
A team of researchers has developed a novel experimental system to simultaneously measure the mechanical properties and internal structure of rubber-like materials. The study found that strain within these materials is non-uniform, depending on the shape and size of composite particles.
SourceWaseda University·JournalMechanical Systems and Signal Processing·TypeImaging analysis·DateNov 9, 2023
Harnessing molecular power: electricity generation on the nanoscale
Researchers have developed a molecular energy harvesting device that can capture the natural motion of molecules in a liquid to generate a stable electric current. The device uses piezoelectric material and can be scaled to full-size generators, offering a game-changing clean energy source.
The fuel economy of a microswimmer
A new model describes microswimmer self-propulsion energy requirements, enabling optimized shape designs and applications in microfluidics, biophysics, and material science. The study reveals surprising similarities between artificial and natural shapes.
SourceMax Planck Institute for Dynamics and Self-Organization·JournalNature Communications·TypeComputational simulation/modeling·DateOct 12, 2023
Making elbow room: Giant molecular rotors operate in solid crystal
A team at Hokkaido University has set a size record for dynamic motion in crystals, demonstrating the largest molecular rotor operational in the solid-state. The rotors consist of a central rotating molecule connected to stationary stator molecules, and can rotate at frequencies of 100–400 kHz.
SourceHokkaido University·JournalAngewandte Chemie International Edition·TypeExperimental study·DateSep 28, 2023
New method reveals folding speed limit of helical membrane proteins
A new study published in eLife reveals the folding speed limit of helical membrane proteins using a robust single-molecule tweezer method. The findings provide unprecedented insights into structural states, kinetics, and energy barrier properties, offering valuable guidance for advancing pharmaceutical research and design.
Researchers discover quantum switch for regulating photosynthesis
The study reveals a quantum switching mechanism of LHCII, which regulates energy transfer quantum channel in response to lateral pressure and conformational change. This mechanism enables high efficiency in photosynthesis and balanced photoprotection.
SourceChinese Academy of Sciences Headquarters·JournalNature Plants·TypeExperimental study·DateSep 1, 2023
Unravelling the water dynamics and structure of water-coordinated metal complexes
A team of researchers from Chiba University elucidated the structure and dynamics of Ho-(DBM)3·H2O complex using molecular dynamics simulations. The study revealed unique properties of water in seven-coordinate lanthanide complexes, including characteristic vibrational modes and hydrogen bond dynamics.
Deciphering the molecular dynamics of complex proteins
Complex proteins adopt multiple structural states in solution, making it challenging to determine their three-dimensional structure. A new approach combining NMR spectroscopy and computer simulations reveals the dynamic properties of these proteins.
Exascale revolution: Supercomputers unleash a new era in biophysics discovery
The next generation of supercomputers is revolutionizing biophysics research, allowing researchers to simulate complex biological processes with extraordinary detail. This enables the creation of new proteins and design of novel molecular circuits, challenging longstanding biological assumptions.
SourceAuburn University Department of Physics·JournalBiophysical Journal·TypeComputational simulation/modeling·DateAug 22, 2023
Auburn University hosts the 60th edition of the Renowned Computational Biophysics Workshop
The workshop, under Prof. Rafael Bernardi and Prof. Emad Tajkhorshid's guidance, showcased expertise from NAMD and VMD developers, providing in-depth dives into molecular dynamics simulations and biomolecular visualization.
Accelerating discovery in artificial intelligence for science
The researcher aims to bridge completeness, efficiency, and applications in 3D graphs to solve problems in physics, fluid dynamics, and biotechnology. Geometric graphs can represent molecules, proteins, and drugs, enabling the prediction of their behavior and properties.
Exploring the origins of life
Scientists propose an alternative model to explain the fast onset of chemical reactions required for life. The new paradigm suggests that catalytic clusters can form rapidly and in large numbers, enabling the self-organization of molecules into living structures.
SourceMax Planck Institute for Dynamics and Self-Organization·JournalNature Communications·TypeComputational simulation/modeling·DateAug 4, 2023
Nuclear spin's impact on biological processes uncovered
A new study by Prof. Yossi Paltiel and colleagues reveals that nuclear spin significantly affects oxygen dynamics in chiral environments, particularly in transport. This finding challenges long-held assumptions and opens up possibilities for advancements in biotechnology and quantum biology.
SourceThe Hebrew University of Jerusalem·JournalProceedings of the National Academy of Sciences·TypeExperimental study·DateJul 31, 2023
Observation of refractive index line shape in ultrafast XUV transient absorption spectroscopy
Researchers developed a novel technique to measure the refractive index line shape in ultrafast XUV transient absorption spectroscopy. By controlling the phase of the XUV light field, they can manipulate matter response and explore new physical phenomena.
Biophysicists reveal how three proteins interact to fine-tune cellular movement
Researchers at Emory University have discovered a new paradigm for understanding how actin filaments are formed and fine-tuned in cells. They found that three proteins - formin, twinfilin, and capping protein - work together to regulate the activity of actin filaments, allowing for more precise control of cellular movement.
Unveiling the quantum dance: Experiments reveal nexus of vibrational and electronic dynamics
Researchers discovered a close relationship between nuclear and electron dynamics, challenging the Born-Oppenheimer approximation. This breakthrough could lead to new ways to control and exploit molecular properties for solar energy conversion, quantum information science, and more.
SourceDOE/Argonne National Laboratory·JournalAngewandte Chemie International Edition·DateJul 19, 2023
DNA organization in real-time
Researchers track the movement of two specific gene elements on a chromosome, finding that they exhibit fast motion and dense packing. This study provides insights into how gene activity is controlled in 3D space, challenging previous assumptions about long-distance communication.
SourceInstitute of Science and Technology Austria·JournalScience·TypeImaging analysis·DateJun 29, 2023
Tracking protein traffic in living cells
Researchers developed TransitID to track protein movement in living cells, revealing new insights into cellular dynamics and protein function. The technique identified unexpected protein presence in stress granules and its role in cancer treatment.
Rensselaer researcher uses pressure to understand RNA dynamics
A Rensselaer Polytechnic Institute researcher used high hydrostatic pressure to examine conformational dynamics of human tRNA, finding excited states that play a role in both normal function and HIV infection. The study suggests new insights into RNA function and potential targets for therapeutics.
SourceRensselaer Polytechnic Institute·JournalProceedings of the National Academy of Sciences·TypeExperimental study·DateJun 22, 2023
Ba2LuAlO5: A new proton conductor for next-generation fuel cells
Scientists at Tokyo Institute of Technology have discovered a new proton conductor, Ba2LuAlO5, which shows high proton conductivity even without modifications. The material's unique structure and water absorption properties make it ideal for protonic ceramic fuel cells, promising a bright future for sustainable energy generation.
SourceTokyo Institute of Technology·JournalCommunications Materials·TypeExperimental study·DateJun 6, 2023
A ribosomal traffic jam that breaks the heart
Researchers found that a mutation in RPL3L, expressed only in heart and skeletal muscle, leads to impaired cardiac contractility by causing ribosomal collisions and protein folding abnormalities. The study aims to develop new treatments for cardiomyopathy and atrial fibrillation.
Elucidating the mysteries of enzyme evolution at the macromolecular level
A research team led by Professor Nicolas Doucet investigated the evolutionary conservation of molecular dynamics in enzymes. They found that specific atomic motions are conserved throughout evolution to preserve biological function.
Chemists tackle the tough challenge of recycling mixed plastics
Researchers at Colorado State University have created a new chemical strategy to deliver universal dynamic crosslinkers into mixed plastic streams, transforming them into viable new polymers that can be turned into higher-value materials. The method makes post-consumer plastics usable as a new kind of material with useful properties.
USTC realizes light-driven programmable colloidal self-assembly
The USTC team has successfully developed a light-driven, programmable system for colloidal self-assembly. Through the cooperative reorganization of nanomotors, they can transport and reconfigure colloidal assemblies in various ways. This breakthrough opens up new possibilities for designing micromachines and smart materials.
SourceUniversity of Science and Technology of China·JournalProceedings of the National Academy of Sciences·DateApr 20, 2023
A new model predicts the flexibility of DNA movement at the molecular scale
A new model of DNA flexibility has been developed, providing results of unprecedented quality and characterizing precision and efficiency at the computational level. The study presents a systematic and comprehensive analysis of DNA movement correlations and introduces a new method to capture them.
SourceInstitute for Research in Biomedicine (IRB Barcelona)·JournalNucleic Acids Research·TypeComputational simulation/modeling·DateMar 31, 2023
Atomic flow of nanojoints in the Ag nanowires interconnect network for flexible electronics and transparent electrode industry
The study investigates the atomic flow behavior during joint formation, exploring processing time, temperature, and stress distribution on nanojoints. The results reveal that local stress and capillary interactions significantly impact joint quality, leading to advances in industrial applications of Ag nanowire interconnect networks.
SourceInternational Journal of Extreme Manufacturing·JournalInternational Journal of Extreme Manufacturing·DateMar 27, 2023
Numerical simulation of materials-oriented ultra-precision diamond cutting: Review and outlook
Researchers review numerical simulations for ultra-precision diamond cutting, exploring properties and microstructures of workpiece materials and their impact on the cutting process. The study provides guidelines for numerical simulations to predict machining responses for various materials.
SourceInternational Journal of Extreme Manufacturing·JournalInternational Journal of Extreme Manufacturing·DateMar 17, 2023
Modelling superfast processes in organic solar cell material
Scientists from the University of Groningen have developed a theoretical framework to explain how charges move through organic solar cells. The study provides insights into the ultrafast charge transfer process, which is crucial for improving the material's efficiency.
SourceUniversity of Groningen·JournalThe Journal of Physical Chemistry·TypeComputational simulation/modeling·DateMar 16, 2023
Theory sorts order from chaos in complex quantum systems
A new mathematical theory developed by Peter Wolynes and David Logan predicts the nature of motions in a chlorophyll molecule when it absorbs energy from sunlight. The findings suggest that there are exceptions where simple motions persist for long times, influencing processes like photosynthesis.
SourceUniversity of Illinois at Urbana-Champaign, News Bureau·JournalProceedings of the National Academy of Sciences·TypeComputational simulation/modeling·DateFeb 27, 2023
Tame heat with pressure
A Chinese research team has developed a barocaloric thermal battery concept that extracts thermal energy from low-temperature waste heat sources by controlling pressure. The system, materialized in ammonium thiocyanate, releases up to 11 times more heat than the mechanical energy input.
SourceChinese Academy of Sciences Headquarters·JournalScience Advances·TypeExperimental study·DateFeb 17, 2023
Mapping molecular funnels with X-rays: precise timings of non-adiabatic excited state dynamics
Scientists at Stockholm University propose a nonlinear spectroscopic technique to investigate coupled nuclear electronic dynamics in photo-excited molecules. This approach allows for the observation of conical intersections, which are 'funnels' connecting different electronic states, and provides insight into non-adiabatic dynamics.
Can clay capture carbon dioxide?
Researchers are exploring how a kind of clay can soak up carbon dioxide and store it, potentially reducing the impact of climate change. The study found that carbon dioxide is more stable in wet clay nanopores than in plain water.
SourceDOE/Sandia National Laboratories·JournalThe Journal of Physical Chemistry Letters·TypeComputational simulation/modeling·DateFeb 9, 2023
New research computes first step toward predicting lifespan of electric space propulsion systems
New research computes first step toward predicting lifespan of electric space propulsion systems by developing a model that bridges scales between molecular dynamics simulations and experiments. The model resolves limitations and uncertainties in experimental data, gaining insight into critical phenomenon and surface morphology over time.
Rice lab uncovers dynamics behind protein crucial in breast cancer
Researchers at Rice University have discovered a new way protein structures communicate with each other to regulate hormone activity. This finding could lead to improved therapies for breast cancer and other diseases.
SourceRice University·JournalProceedings of the National Academy of Sciences·TypeComputational simulation/modeling·DateJan 30, 2023
Simulations and experiments reveal unprecedented detail about water’s motion in salt water
Researchers at New York University captured extremely fast dynamics of water molecules moving around salt ions at a scale of over a trillion times per second. The findings allow for more reliable models of ion dynamics, which could improve rechargeable batteries and MRIs.
CityU unravels interfacial interactions of the lead-free perovskite for efficient hydrogen production
Researchers at City University of Hong Kong have developed a lead-free perovskite photocatalyst for highly efficient solar energy-to-hydrogen conversion. The study uncovers the interfacial dynamics between halide perovskite molecules and electrolytes, enabling better photoelectrochemical hydrogen generation.
SourceCity University of Hong Kong·JournalAdvanced Materials·TypeExperimental study·DateJan 13, 2023
Unraveling the selective transport of sugar and hormone that underlies male fertility in plants
The study reveals that SWEET13 transporter is necessary for pollen production, highlighting the importance of sucrose transport. Researchers used molecular docking and simulation to understand how SWEET13 selectively transports sucrose over gibberellin.
SourceInstitute of Transformative Bio-Molecules (ITbM), Nagoya University·JournalProceedings of the National Academy of Sciences·TypeExperimental study·DateDec 25, 2022
Plants between light and darkness
Researchers discovered two ion transport proteins, VCCN1 and KEA3, that dynamically adjust photosynthetic performance in response to light fluctuations. The study found that these proteins play a crucial role in protecting plants from excessive sunlight and optimizing growth under varying light conditions.
Combining snapshot ultrafast imaging with 3D atomistic simulation: A new approach to explore laser ablation
Researchers combined ultrafast imaging with 3D atomistic simulation to study femtosecond laser ablation. The technique revealed the ablation mechanism of bulky gold at different excitation energy flow densities, providing guidance for material fabrication.
Measuring times in billionths of a billionth of a second
Researchers use novel interferometric technique to measure time delay between H2 and D2 isotopes, finding phase shift of nearly 3 attoseconds caused by nuclear motion. The study uses high harmonic generation and advanced theoretical modeling to validate the method.
USTC make breakthroughs in atomistic neural network representations for chemical dynamics simulations
A USTC team has made significant advancements in atomistic neural network (AtNN) representations for chemical dynamics simulations. By decomposing system properties into atomic contributions, AtNN can satisfy different symmetries and periodicities, achieving accurate and efficient molecular dynamics simulations of complex systems.
SourceUniversity of Science and Technology of China·JournalWiley Interdisciplinary Reviews Computational Molecular Science·DateDec 14, 2022
Molecular shape-shifting
Researchers at Max Planck Institute developed a new model describing the autonomous remodeling of molecular structures. This concept sheds light on self-organization in living matter and could inspire engineering strategies for designing molecular robotic shape-shifters.
SourceMax Planck Institute for Dynamics and Self-Organization·JournalNature Nanotechnology·DateDec 13, 2022
Simulations are starting to gel
By incorporating hydrodynamics into their models, the researchers improved predictions of final structures compared to conventional computational models. This work may lead to the development of smart materials with controllable properties in response to external conditions.
SourceInstitute of Industrial Science, The University of Tokyo·JournalPhysical Review Letters·DateDec 12, 2022
Study by RIT scientists indicates SARS-CoV-2 variants are still transmissible between species
Researchers used computer simulations to show that SARS-CoV-2 variants can attach to host cells in both bats and humans using their spike proteins. The study's findings suggest a significant risk of mammalian cross-species infectivity, contradicting initial expectations of reduced transmission.
Cryptic drug-binding sites discovered in the dance
Scientists at KAUST have identified dynamic regions, called cryptic binding sites, that can be targeted by drugs to treat cancer. The study reveals how molecular motion influences ligand binding to BTB domains, a critical part of many proteins involved in disease.
SourceKing Abdullah University of Science & Technology (KAUST)·JournalNature Communications·DateNov 21, 2022
Legacy of a molecular dynamics trailblazer
Molecular dynamics simulation pioneer Martin Karplus and his team pioneered the simulation of protein motion, impacting biology and physics. This breakthrough enabled scientists to study protein function through dynamic simulations, leading to a deeper understanding of biological processes.
Rice refines analysis of MRI contrast agents
A Rice-led team developed molecular simulations that reveal distinct differences in how inner and outer shells of water molecules around gadolinium respond to thermal excitation. Temperature affects the self-diffusivity of molecules, influencing relaxation rates in MRI scans.
SourceRice University·JournalPhysical Chemistry Chemical Physics·TypeComputational simulation/modeling·DateNov 17, 2022
Sticking together without stickiness
Enzymatic reactions induce phase separation and autoregulation of enzyme activity, creating dynamic environments for cellular processes. This novel mechanism provides an alternative to traditional understanding of cellular organelle function.
SourceMax Planck Institute for Dynamics and Self-Organization·JournalPhysical Review Letters·TypeComputational simulation/modeling·DateOct 27, 2022
Quantum computers in action in chemistry
Researchers at Paderborn University developed a new algorithm for quantum computing in chemistry, reducing qubit count and increasing parallelisation. This allows for the simulation of larger molecules and improved accuracy despite 'quantum noise'.
Magnesium ions slow down water dynamics on short length scales
Researchers from the Max Born Institute found that magnesium ions reduce ultrafast fluctuations in water's hydration shell, slowing solvation dynamics. The study reveals a short-range effect of individual ion pairs on dilute aqueous systems.
SourceMax Born Institute for Nonlinear Optics and Short Pulse Spectroscopy (MBI)·JournalACS Physical Chemistry Au·TypeExperimental study·DateOct 12, 2022
An unstable, flake-like network in the making
A team of researchers from MPI-CBG discovered that thousands of short-lived droplet-like condensates made up of actin filaments generate a first cortex in C. elegans after fertilization. This finding provides new insights into the formation and control of subcellular structures, crucial for cellular and developmental processes.
SourceMax Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)·JournalNature·TypeExperimental study·DateSep 16, 2022