Molecules Stretch Research Articles

Simulation of Fountain Flow based on Molecular Dynamics Method

In this paper, numerical simulations of the fountain effect on the flow front of polymer dilute solutions are carried out based on molecular dynamics principles and the FENE dumbbell model. The Euler method is used to solve the constitutive equations of the mechanical model for the simple shear flow field and the dislocation equations of the dumbbell molecules, and subsequently obtain the tracer flow lines and the dumbbell distribution of the flow front. The results are used to calculate the stress field, analyze the rheological evolution law, study the effect of temperature and shear rate and other parameters on the model and analyze the effectiveness of the FENE dumbbell molecular model for the fountain effect. The study shows that due to the fountain effect the dumbbell molecules stretch more with increasing shear rate, the polymer stress at the flow front will show a complex change of stress overshoot and then stabilize, and the dumbbell molecules are oriented along the fountain flow line.

In-Silico Modelling of Transdermal Delivery of Macromolecule Drugs Assisted by a Skin Stretching Hypobaric Device

ObjectivesTo develop a simulation model to explore the interplay between mechanical stretch and diffusion of large molecules into the skin under locally applied hypobaric pressure, a novel penetration enhancement method.MethodsFinite element method was used to model the skin mechanical deformation and molecular diffusion processes, with validation against in-vitro transdermal permeation experiments. Simulations and experimental data were used together to investigate the transdermal permeation of large molecules under local hypobaric pressure.ResultsMechanical simulations resulted in skin stretching and thinning (20%–26% hair follicle diameter increase, and 21%–27% skin thickness reduction). Concentration of dextrans in the stratum corneum was below detection limit with and without hypobaric pressure. Concentrations in viable epidermis and dermis were not affected by hypobaric pressure (approximately 2 μg bullet cm−2). Permeation into the receptor fluid was substantially enhanced from below the detection limit at atmospheric pressure to up to 6 μg bullet cm−2 under hypobaric pressure. The in-silico simulations compared satisfactorily with the experimental results at atmospheric conditions. Under hypobaric pressure, satisfactory comparison was attained when the diffusion coefficients of dextrans in the skin layers were increased from sim 10 μm2bullet s−1 to between 200–500 μm2bullet s−1.ConclusionsApplication of hypobaric pressure induces skin mechanical stretching and enlarges the hair follicle. This enlargement alone cannot satisfactorily explain the increased transdermal permeation into the receptor fluid under hypobaric pressure. The results from the in-silico simulations suggest that the application of hypobaric pressure increases diffusion in the skin, which leads to improved overall transdermal permeation.

Study on the interaction between cinnamic acid and DNA with spectroscopy and molecular docking technique

In mimic physiological conditions, the binding sites and mechanism of cinnamic acid(CA) with calf thymus DNA (ctDNA) were investigated using UV absorption spectroscopy, fluorescence spectroscopy combined with ethidium bromide (EB) fluorescent probe, resonance light scattering (RLS), circular dichroism spectroscopy (CD), surface enhanced Raman spectroscopy (SERS), salt effect, melting point (Tm) experiments and molecular simulation. The results indicate CA may aggregate at the binding sites of ctDNA to form a supramolecularsystem, and can effectively quench the fluorescence of EB-ctDNA system, increase Tm of ctDNA by 6 ℃. The thermodynamic parameters, the binding constant and number of binding sites for CA and ctDNA were calculated in detail. The results of SERS and molecular docking further indicate that the benzene ring and the non-hydroxyl structure of acrylic acid in the CA molecule intercalate between GA base pairs and TC base pairs in the small groove region of ctDNA, respectively, and the hydroxyl structure in the CA molecule stretches outside of ctDNA double helix. This study contributes to the understanding of the interaction mechanism between CA and DNA at the molecular level.

Collective Vibrational Strong Coupling Effects on Molecular Vibrational Relaxation and Energy Transfer: Numerical Insights via Cavity Molecular Dynamics Simulations**

AbstractFor a small fraction of hot CO2 molecules immersed in a liquid‐phase CO2 thermal bath, classical cavity molecular dynamics simulations show that forming collective vibrational strong coupling (VSC) between the C=O asymmetric stretch of CO2 molecules and a cavity mode accelerates hot‐molecule relaxation. This acceleration stems from the fact that polaritons can be transiently excited during the nonequilibrium process, which facilitates intermolecular vibrational energy transfer. The VSC effects on these rates 1) resonantly depend on the cavity mode detuning, 2) cooperatively depend on Rabi splitting, and 3) collectively scale with the number of hot molecules. For larger cavity volumes, the average VSC effect per molecule can remain meaningful for up to N≈104 molecules forming VSC. Moreover, the transiently excited lower polariton prefers to relax by transferring its energy to the tail of the molecular energy distribution rather than distributing it equally to all thermal molecules. As far as the parameter dependence is concerned, the vibrational relaxation data presented here appear analogous to VSC catalysis in Fabry–Pérot microcavities.

Collective Vibrational Strong Coupling Effects on Molecular Vibrational Relaxation and Energy Transfer: Numerical Insights via Cavity Molecular Dynamics Simulations*.

For a small fraction of hot CO2 molecules immersed in a liquid-phase CO2 thermal bath, classical cavity molecular dynamics simulations show that forming collective vibrational strong coupling (VSC) between the C=O asymmetric stretch of CO2 molecules and a cavity mode accelerates hot-molecule relaxation. This acceleration stems from the fact that polaritons can be transiently excited during the nonequilibrium process, which facilitates intermolecular vibrational energy transfer. The VSC effects on these rates 1) resonantly depend on the cavity mode detuning, 2) cooperatively depend on Rabi splitting, and 3) collectively scale with the number of hot molecules. For larger cavity volumes, the average VSC effect per molecule can remain meaningful for up to N≈104 molecules forming VSC. Moreover, the transiently excited lower polariton prefers to relax by transferring its energy to the tail of the molecular energy distribution rather than distributing it equally to all thermal molecules. As far as the parameter dependence is concerned, the vibrational relaxation data presented here appear analogous to VSC catalysis in Fabry-Pérot microcavities.

Reactions of OH and OD radicals with simple thiols and sulfides studied by infrared chemiluminescence of isotopic water products: Reaction OH + CH3SH revisited

AbstractVibrational excitation of the H2O, HOD, and D2O product molecules from the reactions of OH and OD radicals with CH3SH, CH3C(O)SH, (CH3)3CSH, H2S, and CH3SCH3 was determined by modeling the infrared emission spectra using a renovated and extended set of model spectroscopic bands. Using the deuterated reactant, CH3SD, it was possible to separate spectra of abstraction from C‐ and S‐sites, which allowed measurement of branching fractions and kinetic isotope effects for individual channels. For the OH + CH3SH reaction, branching fractions of 0.13 ± 0.03 (C─H) and 0.87 ± 0.03 (S─H) were obtained. The vibrational energy released to water from abstraction of H‐atoms from the C─H and S─H sites of the reactant molecules is described. The results reported in this paper take precedence over an earlier study of CH3SH. The vibrational energy partitioning between the stretch and bend modes of water molecules from the reactions of the thiols and related reactions of H2S and CH3SCH3 are discussed. The mechanism for the OH + CH3SSCH3 reaction was confirmed to be addition followed mainly by decomposition to CH3SH and CH3SO.

Selective filling of n-hexane in a tight nanopore

Molecular sieving may occur when two molecules compete for a nanopore. In nearly all known examples, the nanopore is larger than the molecule that selectively enters the pore. Here, we experimentally demonstrate the ability of single-wall carbon nanotubes with a van der Waals pore size of 0.42 nm to separate n-hexane from cyclohexane—despite the fact that both molecules have kinetic diameters larger than the rigid nanopore. This unexpected finding challenges our current understanding of nanopore selectivity and how molecules may enter a tight channel. Ab initio molecular dynamics simulations reveal that n-hexane molecules stretch by nearly 11.2% inside the nanotube pore. Although at a relatively low probability (28.5% overall), the stretched state of n-hexane does exist in the bulk solution, allowing the molecule to enter the tight pore even at room temperature. These insights open up opportunities to engineer nanopore selectivity based on the molecular degrees of freedom.

Breakup Dynamics of Semi-dilute Polymer Solutions in a Microfluidic Flow-focusing Device.

Droplet microfluidics involving non-Newtonian fluids is of great importance in both fundamental mechanisms and practical applications. In the present study, breakup dynamics in droplet generation of semi-dilute polymer solutions in a microfluidic flow-focusing device were experimentally investigated. We found that the filament thinning experiences a transition from a flow-driven to a capillary-driven regime, analogous to that of purely elastic fluids, while the highly elevated viscosity and complex network structures in the semi-dilute polymer solutions induce the breakup stages with a smaller power-law exponent and extensional relaxation time. It is elucidated that the elevated viscosity of the semi-dilute solution decelerates filament thinning in the flow-driven regime and the incomplete stretch of polymer molecules results in the smaller extensional relaxation time in the capillary-driven regime. These results extend the understanding of breakup dynamics in droplet generation of non-Newtonian fluids and provide guidance for microfluidic synthesis applications involving dense polymeric fluids.

Using water‐miscible nonionic hydrophobic monomer associating HPAM as drag reducing agent

ABSTRACTA water‐miscible nonionic surfmer (AC‐TX100) was synthesized based on Triton X‐100 and acryloyl chloride. Then, a terpolymer P(AM/AA/AC‐TX100) was synthesized by free radical polymerization in aqueous solution and intended to be used as drag reducing agent (DRA). The DRA was defined to be P(AM87.32/AA12.46/AC‐TX1000.22) according to 1H NMR and elemental analysis, the molecular weight was 2.12 × 106 g/mol according to scattering method. DRA shows excellent performance in drag reduction (DR). The highest DR rate of 76% can be obtained when DRA concentration is 0.023% in fresh water; while in brine containing 3% NaCl, DR rate decreases, and it is necessary to increase the concentration to 0.05% to ensure that DR rate is higher than 70%. SEM and cryo‐TEM show that DRA forms a network structure in aqueous solution, and the tightness of this structure has a direct influence on DR performance. Specifically, DRA molecules stretch into the whirlpools generated by water at high flow rates, reducing the quantity and intensity of whirlpools, thereby lowering the energy loss and the friction. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 48362.

Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement

We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD+).

Effect of pH on the adsorption and interactions of Bovine Serum Albumin with functionalized silicon nitride surface.

Force-distance curves between atomic force microscopy (AFM) tip (Si3N4 non-functionalized) and bovine serum Albumin (BSA) immobilized on Si3N4 substrates have been performed with the purpose to understand how multiple interactions between the protein and the tip were favored in different pHs (4, 6 and 10). In this work, 100 silicon wafer samples were used to deposit a layer of Si3N4. Protein immobilization consisted of the silanization of the substrates with 3-aminopropyltriethoxysilane (APTES) and crosslinking with glutaraldehyde (GA). All functionalization steps were evaluated by contact angle, X-Ray electron spectroscopy (XPS) and AFM. AFM images showed increase of roughness following functionalization. At pH 4, it was possible to note that small forces (49.1 ± 2.4 pN) were needed to stretch BSA, with a contour length of CL = (30.0 ± 1.1 nm). At pH 6, the force applied was higher (101.5 ± 5.0 pN) with a higher molecule stretch CL = (75.6 ± 3.8 nm) because the pH is close to the BSA isoelectric point where the folding of the protein is favored as surfaces charges are minimized leading to lower attractive intramolecular forces. Young's Modulus were also calculated and the lowest value (265 kPa) was observed at pH 10.

Adsorption of AgNO3 onto bamboo hemicelluloses in aqueous medium

An insight into the adsorption behavior between hemicellulose biomass and metal ions is important to utilize hemicelluloses as adsorbent. In this study, bamboo hemicelluloses were used as adsorbent for AgNO3 in aqueous medium. The adsorption amount of AgNO3 onto hemicelluloses was determined through an inductively coupled plasma-atomic emission spectrometer (ICP-AES). The morphology and the elemental composition of the recovered hemicelluloses were characterized using atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) techniques, respectively. The filtrate after removing undissolved hemicelluloses was analyzed by ultraviolet-visible spectroscopy (UV–vis). Results demonstrated that the obtained highest adsorption amount of AgNO3 onto hemicelluloses was 42.82 mg/g under the conditions discussed. Some Ag+ was in situ reduced by hemicelluloses to form silver nanoparticles. Ag+ and the formed silver nanoparticles possibly destroyed the hydrogen-bonding network of hemicelluloses, resulting in the stretch of molecules and formed rod-like agglomerates with irregular length. Even an agglomerate with the length of 420 nm was found. The side chains and the newly formed carboxyl groups through oxidation of hemicelluloses by silver ions removed away from the hemicelluloses during adsorption. A part of Ag+ and silver nanoparticles were adsorbed on the unresolved hemicelluloses, and the other part was dispersed in the aqueous solution.

Stretch and Dynamics of Single Chromatin Molecules Confined in Nanofluidic Channels

Inside the nucleus of eukaryotic cells, chromatin is compacted into a condensed state without compromising its accessibility for the machinery of life. The high degree of compaction in tandem with accessibility are key factors in the complex regulation of the genome. In this study, we report the static and dynamic properties of bacteriophage T4 DNA (165.6kbp) reconstituted with recombinant human histone octamers and confined inside nanochannels of various cross-sectional diameter (100 - 250 nm). The reconstituted chromatin complex is thought to be a good model for long segments of heterogeneous human chromatin. We measured the mean stretch and its fluctuations for various environmental conditions and histone loading fractions. Two relaxation modes are observed, with the slowest one pertaining to partial opening up of the complex. The efficiency of chromatin compaction by various multivalent ions and condensing agents is explored and discussed in terms of nucleosome-nucleosome interaction.

Insight into Water Structure at the Surfactant Surfaces and in Microemulsion Confinement.

Interactions with surfactant molecules can significantly alter the structure of interfacial water. We present a comparative study of water-surfactant interactions using two different spectroscopic approaches: water at planar surfactant monolayers by sum frequency generation (SFG) spectroscopy and interfacial water confined in reverse micelles formed by the same surfactants using IR absorption spectroscopy. We report spectral features in the OH-stretching region (3200-3700 cm-1) that are observed in both IR and SFG spectra, albeit with different relative amplitudes, for ionic surfactant sodium 1,4-bis-2-ethylhexylsulfosuccinate (AOT) and nonionic surfactant polyoxyethylene(4)lauryl ether (Brij L-4) reverse micelles in hexane and the corresponding monolayers at the air/water interface. A prominent feature in the SFG spectra of the OH stretch at 3560 cm-1 is attributed to water molecules that have a weak donor hydrogen bond to the surfactant headgroup. The same feature is observed in the IR spectra of reverse micelles after deconvoluting the interfacial versus bulk spectral contributions. We performed an orientational analysis of these water molecules utilizing the polarization-dependent SFG spectra, which shows an average tilt angle of the OH stretch of surfactant-bound water molecules of ∼155° with respect to the surface normal.

First Evidence of Vibrationally Driven Bimolecular Reactions in Solution: Reactions of Br Atoms with Dimethylsulfoxide and Methanol.

We present evidence for vibrational enhancement of the rate of bimolecular reactions of Br atoms with dimethylsulfoxide (DMSO) and methanol (CH3OH) in the condensed phase. The abstraction of a hydrogen atom from either of these solvents by a Br atom is highly endoergic: 3269 cm-1 for DMSO and 1416 or 4414 cm-1 for CH3OH, depending on the hydrogen atom abstracted. Thus, there is no thermal abstraction reaction at room temperature. Broadband electronic transient absorption shows that following photolysis of bromine precursors Br atoms form van der Waals complexes with the solvent molecules in about 5 ps and this Br•-solvent complex undergoes recombination. To explore the influence of vibrational energy on the abstraction reactions, we introduce a near-infrared (NIR) pump pulse following the photolysis pulse to excite the first overtone of the C-H (or O-H) stretch of the solvent molecules. Using single-wavelength detection, we observe a loss of the Br•-solvent complex that requires the presence of both photolysis and NIR pump pulses. Moreover, the magnitude of this loss depends on the NIR wavelength. Although this loss of reactive Br supports the notion of vibrationally driven chemistry, it is not concrete evidence of the hydrogen-abstraction reaction. To verify that the loss of reactive Br results from the vibrationally driven bimolecular reaction, we examine the pH dependence of the solution (as a measure of the formation of the HBr product) following long-time irradiation of the sample with both photolysis and NIR pump beams. We observe that when the NIR beam is on-resonance, the hydronium ion concentration increases fourfold as compared to that when it is off-resonance, suggesting the formation of HBr via a vibrationally driven hydrogen-abstraction reaction in solution.

Collective excitations in liquid dimethyl sulfoxide (DMSO): FIR spectrum, low frequency vibrational density of states, and ultrafast dipolar solvation dynamics.

Valuable dynamical and structural information about neat liquid DMSO at ambient conditions can be obtained through a study of low frequency vibrations in the far infrared (FIR), that is, terahertz regime. For DMSO, collective excitations as well as single molecule stretches and bends have been measured by different kinds of experiments such as OHD-RIKES and terahertz spectroscopy. In the present work, we investigate the intermolecular vibrational spectrum of DMSO through three different computational techniques namely (i) the far-infrared spectrum obtained through the Fourier transform of total dipole moment auto-time correlation function, (ii) from the Fourier transform of the translational and angular velocity time autocorrelation functions, and (iii) a quenched normal mode analysis of the parent liquid at 300 K. The three spectra, although exhibit differences among each other, reveal similar features which are in good, semi-quantitative, agreement with experimental results. The study of participation ratio of the density of states obtained from the normal mode analysis shows that the broad spectrum around 100 cm-1 involves collective oscillations of 300-400 molecules. Dipolar solvation dynamics exhibit ultrafast energy relaxation with an initial time constant around 157 fs which can be attributed to the coupling to the collective excitations. We compare the properties of DMSO with those of water vis-a-vis the existence of the low frequency collective modes. Last, we find that the collective excitation spectrum exhibits strong temperature dependence.

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide.

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).

Spectroscopy and Ultrafast Vibrational Dynamics of Strongly Hydrogen Bonded OH Species at the α-Al2O3(112̅0)/H2O Interface

Frequency and time-resolved vibrational sum frequency generation (vSFG) are used to investigate the behavior of water at the α-Al2O3(1120) surface. In addition to the typical water OH peaks (∼3200 and ∼3400 cm–1), the α-Al2O3(1120)/H2O interface shows an additional red-shifted feature at ∼3000 cm–1. Addition of ions (0.1 M NaCl) largely attenuates the water OH peaks but has little effect on the 3000 cm–1 peak. The 3000 cm–1 feature is assigned to the O–H stretch of surface aluminol groups and/or interfacial water molecules that are strongly hydrogen bonded to the alumina surface. Density functional theory calculations were performed to test this assignment, revealing the presence of both associated and dissociated H2O configurations (chemisorbed surface OH group) with frequencies at 3155 and 3190 cm–1, respectively, at a hydrated α-Al2O3(1120) surface. IR pump–vSFG probe measurements reveal that the interfacial OH species show very fast (<200 fs; bulk waterlike) vibrational relaxation dynamics, which i...

Molecular dynamics simulation on volume swelling of CO2–alkane system

The microscopic mechanism of the volume swelling of CO2–alkane (decane, octane, hexane and cyclohexane) systems and the effects of temperature, pressure and alkane structure on the volume swelling of CO2–alkane systems are investigated by performing molecular dynamics simulation. It is shown that the increase in pressure, the reduction in temperature and the straight-chain structure of the alkane are of benefit to the volume swelling of CO2–alkane systems by calculating the volume swelling coefficient; CO2 in supercritical state plays a dominant role in the volume swelling of CO2–alkane systems. The microscopic process of the volume swelling of CO2–decane system shows that the increase in the average separation distance between decane molecules and the stretch of decane molecules result in the volume swelling of decane as CO2 dissolve into decane. The calculations of interaction energies in CO2–decane system indicate that the interaction between CO2 and decane molecules is responsible for the volume swelling of CO2–alkane system. Further study on the interaction between CO2 and decane molecules shows that the dispersion interaction, resulting in the different solubility of CO2 in alkanes, is the essence of the volume swelling for CO2–alkane system. This work is a good start on understanding the mechanism of alkane swelling influenced by CO2 at the molecular level and provides useful information for guiding CO2 enhancing oil recovery.