Articles tagged with Molecular Dynamics
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.
Physicists at University of Münster successfully reveal dynamic interaction of molecular shuttles using molecular-dynamic simulations. The study provides detailed insight into how embedded machines function and interact, enabling targeted control of transport properties and catalytic processes.
Scientists successfully measured the attosecond-scale Wigner time delay in molecular photoionization, providing insights into the timing of the photoemission process. The 'double-pointer attoclock' scheme was used to disentangle the orientation-dependent behavior of molecular Coulomb interaction and molecular orbital structure.
A team from Tokyo Tech has developed a new methodology to observe dynamic bonding between atoms, revealing transient structures resulting from atomic assembly. They used video tracking and ADF-STEM to directly visualize metallic dimers and trimers, achieving high atom discrimination accuracy.
Researchers at the Beckman Institute for Advanced Science and Technology observed structural chirality in achiral conjugated polymers, which can enhance solar cells' charge capacity. This discovery introduces new opportunities for research at the convergence of biology and electronics.
Scientists found that certain dynamical defects help explain the allowed vibrational modes inside amorphous solids, like glasses. These findings may lead to controlling the properties of amorphous materials.
Researchers at Massachusetts General Hospital developed scission-accelerated fluorophore exchange (SAFE) to visualize molecules in living cells without disrupting normal physiological processes. The method uses immunofluorescence tags and fast chemical reactions to remove tags, creating a multi-color movie-like continuous stream of ima...
A new time-resolved instrument measures circular dichroism changes in fractions of a picosecond, enabling the capture of photoexcited molecules' chirality and conformational motion. This resolves the deactivation mechanism of iron-based spin-crossover complexes, crucial for magnetic data storage.
A research team led by Professor Youdong Mao has developed a new method using time-resolved cryo-electron microscopy and machine learning-based 4D reconstruction to visualize the USP14-proteasome system in atomic detail. This reveals a 'multiverse' of parallel reality pathways, allowing for targeted inhibition of cancer cells.
A joint research team investigated the generation of low-energy protons in dissociative ionization of H2 using time-energy-resolved spectroscopy. They found that low-energy protons are produced via dipole-transition at large bond lengths, contrary to the expected bond-softening scenario.
Researchers used Frontera supercomputer to model coronavirus-receptor interactions, discovering a 'one-two punch' combo that primes virus for fusion. The study provides new understanding of the mechanism behind increased virulence of variants such as delta and omicron.
Researchers successfully measured the wettability of graphene and other 2D materials using VSFG, a surface-selective tool that connects macroscopic and molecular-level properties. The study found that graphene's 'wetting transparency' diminishes with increasing layers, becoming hydrophobic at a certain point.
A team led by Osamu Takahashi developed a procedure to reproduce the double peak feature of x-ray emission spectroscopy spectra in liquid water. They used molecular dynamics calculations and first principles quantum mechanical calculations to estimate XES spectra, reproducing features such as the double peaks.
Researchers developed mpH^2 MM to analyze fluctuating molecular signals, enabling predictions of shape changes. The framework was applied to DNA and proteins, revealing distinct mechanisms for binding molecules.
Researchers developed a vortex microscope that captures detailed motion and rotation of molecules in liquid. The technique provides unprecedented insight into molecular dynamics, enabling the study of diseases like Alzheimer's.
Researchers at the University of Eastern Finland used molecular modeling to investigate nano-plastic transport into cell membranes. The study found that some microplastics can passively penetrate the membrane, potentially causing adverse health effects.
Researchers have solved atomic-level structures of the muscle-type nicotinic acetylcholine receptor, a crucial step in understanding its function. The new findings could lead to breakthroughs in treating neurological disorders such as congenital myasthenic syndrome and myasthenia gravis.
Researchers from the University of Amsterdam have found that ice can heal itself by forming a new layer of ice to cover scratches and cuts. This discovery could potentially extend breaks between skating races, but careful control of moisture in the air is still necessary.
Scientists have characterized thousands of small molecules in coral reef ecosystems, providing insights into food web dynamics and chemical ecology. The study found that corals and seaweeds release diverse compounds that influence nutrient concentrations and availability in the ecosystem.
Janus particles, with two distinct physical chemical properties, exhibit unique behavior in simulations. Their shape significantly influences their orientation at interfaces and mobility, impacting rheology and processing schemes.
Researchers at Waseda University discovered a new protein isoform called Senp5S, which helps regulate Drp1 and mitochondrial dynamics during brain development. The study suggests a novel and vital role for post-translational SUMOylation in neuronal differentiation.
Researchers at Duke University have discovered paddlewheel-like molecular dynamics that help push sodium ions through a quickly evolving class of solid-state batteries. The insights will guide researchers in their pursuit of a new generation of sodium-ion batteries to replace lithium-ion technology.
Researchers developed a novel computer simulation method that can analyze key proteins in the reproductive cycle of SARS-CoV-2, promising to accelerate the search for bioactive compounds against COVID-19. The method estimates a reduction in research time from two to three years to under a year.
A team of researchers used the X-ray laser European XFEL to study the detailed dynamics of how water molecules break apart when exposed to high-energy radiation. The study reveals that the disintegration process is more complicated than expected, with the oxygen atom not being flung away hard when the molecule breaks up.
Recent study uses advanced spectroscopy techniques to observe water molecules in superconcentrated salt solutions and identifies heterogeneity in solvation structure. This finding explains the unexpected fast lithium-ion transport in highly viscous electrolytes.
Researchers at Arizona State University have developed a new microscopy method that can track 100 single molecules simultaneously in three dimensions. The technique uses surface plasmon resonance (SPR) technology to precisely image molecular binding events and study their dynamic activities in real time.
A new process has been identified to accelerate the use of low-cost materials, transforming the energy sector with potential to replace silicone-based solar panels. The dynamic dimeric copper complexes offer a novel combination of fast charge transport and efficient redox mechanisms.
Researchers developed a new method to predict stress at atomic scale using machine learning, enabling accurate predictions of grain boundary stresses in actual metal specimens. This breakthrough advances the field of mechanics of materials and enables scientists to engineer stronger and more heat-resistant metals.
Researchers have developed Mass-Sensitive Particle Tracking (MSPT) to analyze proteins on biological membranes in real-time. The method enables the determination of protein location and size changes without labeling, providing valuable insights into dynamic processes at the membrane.
The study assesses how temperature influences droplet size in elastic matrices, providing insights into biological molecule arrangement and condensate formation. It also explores the role of phase separation and its effect on droplet growth.
Researchers have discovered the molecular mechanisms behind stem cell rolling in blood vessels, a complex process that slows down cells using long tethers. The findings offer new insights into improving stem cell transplantations and developing treatments for metastasizing cancers.
The study models biomolecular condensates using oil droplets and polymer mesh, revealing temperature modulation's impact on droplet growth and size distribution. The results provide insights into the formation of microscopic patterns in biological systems.
Researchers develop new theory for attosecond transient absorption spectroscopy of polyatomic molecules, revealing electron-nuclear dynamics. The technique provides sufficient resolution to study decoherence of electron motion caused by nuclear rearrangement.
Researchers reveal stable phosphatidylglycerol-DNA complex formation with strong van der Waals and hydrophobic interactions. The complex's structural parameters are determined, providing insight into the differences between DNA-phospholipid interaction and fatty acid binding.
Researchers used complex computer simulations to study the attachment of SARS-CoV-2 and its variants to human cells. They found that the virus has two main locations where it grabs onto the host cell receptor ACE2, with early strains having a slippery interaction at one region that becomes less slippery as variants evolve.
Researchers found that the stability of an amorphous metal alloy's structure is disrupted by mechanical influences, leading to crystalline inclusions. The alloy retains useful properties at pressures below 400 gigapascals before experiencing rapid crystallization and loss of structural integrity.
Scientists have successfully visualized the molecular motion of a highly unstable compound, 10-mesityl-1,8-bis(trifluoromethyl)-9-phosphaanthracene, using novel spectroscopic techniques. The study revealed unprecedented molecular motions and structure information, shedding light on its radical reactivity and potential applications.
Researchers have developed a way to precisely control defects within active liquid crystals by changing the gradient of activity around them. This can be achieved through pulses of light or chemical composition changes, enabling controlled movement and behavior of these materials.
The study reveals that lysine residues in the RNA polymerase act as a 'bucket brigade', transporting drugs and nucleotides to the binding site through electrostatic interactions. Favipiravir is found to be taken up more efficiently than ATP, while remdesivir outperforms favipiravir.
A new study combines experimental data and molecular dynamics simulations to study the conformation of an RNA fragment involved in protein synthesis. The research led to a new method for defining biomolecule structures in their physiological environments.
Researchers develop parallel optical-soliton reactors to study multi-soliton dynamics, unveiling statistical rules that resemble classic chemical kinetics. The system enables on-demand synthesis and dissociation of soliton molecules, promoting a collective-level insight into soliton dynamics.
Researchers create ab initio NAMD method to investigate spin-valley exciton dynamics in MoS2, revealing e-h exchange interaction plays a crucial role. The new method provides a powerful tool for studying exciton relaxation, lifetime, dissociation, and defect interactions in solid materials.
Researchers studied how modern immunotherapeutic anti-cancer drugs interact with the immune system, finding that tiny molecular motions are key to their effectiveness. The study, published in Cancers, reveals how these drugs bind to specific receptors on killer cells without activating them.
Scientists at Kanazawa University developed a new method to study the neutralization of excess charges during mass spectrometry, which can lead to more accurate results. The team used a combination of continuum and molecular dynamics simulations to model the effect of adding molecules of the opposite charge to neutralize excess charge.
Scientists at the University of Graz successfully transfer single organic molecules along a specific direction on a silver surface, demonstrating precise control over their movement. The experiment uses electrostatic forces to move molecules up to 150nm with high precision and speed.
A team of researchers has introduced Deep Potential Molecular Dynamics (DPMD), a new machine learning-based protocol that can simulate over 100 million atoms per day. The protocol achieves ab initio accuracy and was recognized with the ACM Gordon Bell Prize for its achievement in high-performance computing.
Researchers use a new method to extract information from cryo-EM data, enabling the visualization of minimum free-energy pathways during simulations. This study demonstrates the potential of cryo-EM in understanding biological functions and has implications for drug discovery.
Researchers at the Max Born Institute have developed a method to record high-resolution movies of molecular dynamics using electrons ejected from a molecule by an intense laser field. This technique allows for the observation of ultrafast nuclear rearrangement with both high temporal and spatial resolution.
Biological condensates, previously known as membrane-less organelles, have been found to play a crucial role in DNA repair and aging. Researchers used the Frontera supercomputer to study their behavior and recruitment of molecules.
A team of scientists used THz pulses to study the intermolecular motion of liquid water, revealing a hydrogen bond harmonic oscillator model and polarizability anisotropy on sub-picosecond scales. The results provide insights into the transient structure of liquid water and its interaction with solvent molecules.
Researchers have discovered that LHCII trimer acts as a molecular machine responding to environmental conditions like temperature and acidity. This mechanism enables the protein to switch between efficient light collection and photoprotection, promoting energy dissipation when necessary.
A European research team developed a photographic film at the atomic level to track the motion of a molecular building block. The result shows a light-controlled 'pedalo-type motion', moving forward and backward, which could help control material properties with molecular switches.