Abstract During endocytosis of nanoparticles by cells, the cellular membranes engulf particles, thereby forming a closed membrane neck that subsequently undergoes fission. For solid nanoparticles, these endocytic processes have been studied in some detail. Recently, such also found for liquid and condensate droplets, both vitro vivo. These start with spreading droplet onto followed partial or complete engulfment droplet. Here, we use molecular dynamics simulations to study at nanoscale,...

Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, sound absorption coefficient at low concentrations, and positive deviation from Raoult's law for vapor pressure, to mention a few. These anomalies have been attributed different, often contradictory origins, but quantitative understanding is still lacking. We show by computer simulation theoretical analyses that these arise the sudden emergence bicontinuous phase occurs...

We carry out a series of long atomistic molecular dynamics simulations to study the unfolding small protein, chicken villin headpiece (HP-36), in water-ethanol (EtOH) binary mixture. The prime objective this work is explore sensitivity protein toward increasing concentration cosolvent and unravel essential features intermediates formed search dynamical pathway unfolding. In mixtures, HP-36 found unfold partially, under ambient conditions, that otherwise requires temperature as high ∼600 K...

Membrane budding and fission are essential cellular processes that produce new membrane compartments during cell organelle division, for intracellular vesicle trafficking as well endo- exocytosis. Such morphological transformations have also been observed giant lipid vesicles with a size of many micrometers. Here, we report nanovesicles below 50 nm. We use coarse-grained molecular dynamics simulations, by which can visualize the individual vesicles. The induced low concentrations small...

Biomolecular condensates (BCs) are fluid droplets that form in biological cells by liquid-liquid phase separation. Their major components intrinsically disordered proteins. Vast attention has been given recent years to BCs inside the cytosol and nucleus. at cell membrane have not studied same extent so far. However, studies provide increasingly more examples of interfaces between membranes which function as platforms for diverse biomolecular processes. Galectin-3, example, is known mediate...

We find that at a mole fraction 0.05 of DMSO (xDMSO = 0.05) in aqueous solution, linear hydrocarbon chain intermediate length (n 30–40) adopts the most stable collapsed conformation. In pure water, same exhibits an intermittent oscillation between and extended coiled conformations. Even when bulk is 0.05, concentration first hydration layer around 30 30) as large 17%. Formation such hydrophobic environment may be viewed reason for conformation gaining additional stability. second anomalous...

Nanovesicles are closed, bubblelike surfaces with a diameter between 20 and 200 nm, formed by lipid bilayers biomembranes. Electron microscopy (EM) studies have shown that these vesicles can attain both spherical nonspherical shapes. One disadvantage of EM methods is they provide only single snapshot each vesicle. Here, we use molecular dynamics simulations to monitor the morphological transformations individual nanovesicles. We start assembly enclose certain volume water contain total...

Since the time of Kirkwood, observed deviations in magnitude dielectric constant aqueous protein solution from that neat water (∼80) and slower decay polarization have been subjects enormous interest, controversy, debate. Most common proteins large permanent dipole moments (often more than 100 D) can influence structure dynamics even distant molecules, thereby affecting collective fluctuation solution, which turn significantly alter solution's constant. Therefore, distance dependence provide...

Many aqueous binary mixtures, such as water-ethanol, are known to exhibit multiple structural transformations that apparently driven by intermolecular hydrophobic interaction well hydrogen bonding. These interactions often cooperate form special types of self-assembled structures. We study the effect temperature on formation transient ethanol clusters dynamic heterogeneity induced in system due clustering. A major finding work is existence a strong dependence extent heterogeneity. Distinct...

Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations protein myoglobin in aqueous ethanol mixture at various concentrations. The following results particularly striking. (1) Two well-defined regimes, one xEtOH ∼ 0.05 the other 0.25, characterized formation distinct partially...

The protein folding funnel paradigm suggests that and unfolding proceed as directed diffusion in a multidimensional free energy surface where multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even single pathway, with detail chronicling intermediates, is an arduous task. In this work we explore pathway through umbrella sampling, for small globular α-helical chicken-villin headpiece (HP-36) when melting secondary structures...

is an opportunistic and infective bacterium containing orphan DNA methyltransferase (M.BceJIV) with roles in regulating gene expression motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be adenine or thymine) methylates N6 at fifth base position (GTWW

Altering solvent-mediated effective interaction between silica nanoparticles in water through polymer grafting.

Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but also intrinsic to the thermodynamic nature of solution itself (like binary mixtures or at gas-liquid interface). The altered dynamics water presence such diverse surfaces has attracted considerable attention recent years. As these interfaces are quite narrow, only a few molecular layers...

Abstract Stress‐induced changes in energy of the phonons lowest acoustic phonon branch ( q 00 ) direction are investigated Si by using inelastic neutron scattering. Applying uniaxial stress 10 kbar causes order 1%. A change sign is found approximately middle Brillouin zone. Depending on mutual orientation stress, wave vector and polarization phonons, different observed. From observed general mode Grüneisen parameters derived.

In the present study, we investigated magnetic interactions of some dinitrenes by employing broken symmetry-unrestricted density functional theoretical (BS-UDFT) approach along with use three basis sets. The coupling parameter (J) has been calculated, and thereby character molecule strength interaction are explored for these molecules. exchange parameters corresponding unconjugated systems also calculated to see role π-conjugation. Our results suggest that a strong antiferromagnetic exists...

Since the structural transformations observed in water-ethanol binary mixtures are apparently driven by relatively weak intermolecular forces (like hydrophobicity and hydrogen bonding) that often cooperate to form self assembled structures, one expects aggregation properties show strong temperature dependence. We study effect of on formation transient ethanol clusters as well dynamic density heterogeneity induced system due such clustering. The is expected occur small length scales with...

Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding proteins to corresponding partners as well biomolecular organization and phase separation. While such intracellular have a large on structure function, molecular mechanisms driving forces that determine effect dynamics conformations macromolecules are so far not understood. At level, computational methods provide unique lens investigate...