Articles tagged with Molecular Dynamics
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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'.
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.
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.
A team of researchers has designed in silico molecular probes to track the progress of a misbehaving protein linked to neurodegenerative diseases like ALS and FTD. The probes can detect TDP-43 aggregates at high resolution, paving the way for early diagnosis.
Scientists at Kyushu University have developed organic molecules that align in the same direction, creating a 'giant surface potential' when evaporated onto a surface. This alignment leads to a significant electric field, which can improve OLED efficiency and open new routes for realizing devices that convert vibrations into electricity.
Researchers developed a single-molecule technique to investigate how bacterial proteins form pores in mammalian cells. They tracked the assembly of perfringolysin O protein and found that it forms pores even before complete ring formation is completed.
A new simulation study reveals that molecular clogging affects liquid/solid friction, differing from standard Poiseuille flow observed at the macroscale. The researchers found that strongly confined liquids exhibit unique flow characteristics, including plug and Poiseuille-like flows.
Researchers at Princeton University used artificial intelligence to simulate ice formation by individual atoms and molecules with quantum accuracy. This breakthrough enables tracking of hundreds of thousands of atoms over longer timespans than previous simulations.
Researchers from the Institute of Industrial Science, The University of Tokyo, found that preordering significantly influences crystal growth and nucleation. Their study proposes modifications to address shortcomings in classical nucleation theory.
A research group from Tokyo University of Science has discovered molecular features that govern the filling process at nanoscales, enabling finer resolutions in ultraviolet nanoimprint lithography. The findings provide valuable insights for guiding the selection and design of optimized resists for sub-10 nm resolution.
Researchers observed a novel type of excitation, called a polaron, where collective oscillations of the electron and its screening cloud arise at terahertz frequencies. These oscillations persist for tens of picoseconds and are impulsively triggered by ultrafast electron localization.
The study reveals that TAD boundaries, insulating properties of which are based on the binding of protein CTCF, can vary in strength depending on individual site properties. This finding has implications for understanding genetic diseases and cancer.