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The force- and flow-induced translocation processes of linear and ring polymers are studied using a combination of multiparticle collision dynamics and molecular dynamics, focusing on the behavior of the polymer translocation time. We compare the force- and flow-induced translocations of linear and ring polymers. It is found that when the translocation time (τ*) is characterized by scaling exponents, δ, δ', and α, via the relations τ* ∼ fδNα and τ* ∼ Jδ'Nα, the scaling exponents are not constants. For long chains tested, α = 1.0 for both force- and flow-induced translocations. The difference between the force- and flow-induced translocations stems from different monomer crowding effects due to distinct flow patterns outside the channel. Furthermore, general relations for polymer translocation time are derived for these two translocation processes, which are in good agreement with the simulation results. Our results provide clear molecular pictures for the force- and flow-induced translocations, which shed light on the understanding of translocation dynamics and provide guidance for practical applications such as molecular sequencing and ultrafiltration.

We construct a segmental scale force level theory for the center-of-mass diffusion constant and corresponding relaxation time for globally compact unconcatenated ring polymer solutions and melts (degree of polymerization

The transport of polymers across nanoscale pores underpins many biological processes, such as the ejection of bacteriophage DNA into a host cell and the transfer of genes between bacteria. The movement of polymers into and out of confinement is also the basis for a wide range of sensing technologies used for single-molecule detection and sequencing. Acquiring an accurate understanding of the translocation dynamics is an essential step in the quantitative analysis of polymer structure, including the localization of binding sites or sequences. Here we use synthetic nanopores and nanostructured DNA molecules to directly measure the velocity profile of driven polymer translocation through synthetic nanopores. Our results reveal a two-stage behaviour in which the translocation initially slows with time before accelerating close to the end of the process. We also find distinct local velocity correlations as the DNA polymer chain passes through the nanopore. Brownian dynamics simulations show that the two-stage behaviour is associated with tension propagation, with correlations arising from the random-walk conformation in which the DNA begins. A study of the dynamics of polymer translocation through synthetic nanopores provides a direct observation of tension propagation—a non-equilibrium description of the process of unfolding that a polymer undergoes during translocation.

Polypropylene (PP) is being considered as a suitable alternative to the cross‐linked polyethylene (XLPE) insulation as the latter is prone to the space charge accumulation when subjected to the voltage polarity reversals in line‐commutated converter high voltage direct current transmission. This novel contribution correlates the space charge accumulation with the trap distribution inside XLPE and PP under the polarity reversal condition. The pulse electro‐acoustic and surface potential decay methods are used to measure the space charge and trap distributions, respectively. These measurements are carried at different poling durations (1 and 6 h at each polarity) and cycles of voltage polarity reversal (one and three cycles) at the electric field of 60 kV/mm. The XLPE shows more homo and hetero charge accumulation than PP. Dominant shallow traps in the XLPE are responsible for the space charge accumulation, whereas deep traps with higher trap density inhibit space charge accumulation within the PP. Furthermore, the positive and negative threshold fields for the space charge accumulation are measured. It is observed that the space charge can be easily accumulated under the negative electric field. Interestingly, the space charge decays rapidly inside the XLPE with the increased number of polarity reversal cycle. A valid theoretical model is developed to explain the space charge accumulation inside the XLPE and PP. The field‐assisted ionization plays a key role in the space charge accumulation inside the XLPE.

The dynamics of adsorption and desorption of counterions on a polyelectrolyte chain in aqueous solution is studied at a single molecular level. The investigation is through the process of fluoresce...

It is now generally agreed that the most dramatic influence of a free surface on local relaxation dynamics occurs over the first 10 nm from the surface. Using the cooperative free volume (CFV) rate...

Although experimental evidence for shear-banding flows in concentrated polymer solutions has accumulated over the last 20 years, the origin of such shear-banding flows is still under heated debate....

How tethered probes report dynamics of host polymers near the glass transition was investigated by changing the length of the flexible linkers and the number of tethering points via imaging rotational fluorescence correlation microscopy and compared with free probes of different sizes. The results show that tethering did not alter the temperature-dependence of polymer dynamics and the shape of the correlation decay reported by the probe; however, the rotation slowed down up to ≈1 decade when both ends of the probe were restricted with short alkyl chain linkers. Upon comparison with the bigger free probe, the mechanism of the slowdown was attributed to the restricted motion upon tethering for tethered probes compared to averaging over different regions of the dynamic heterogeneity for the bigger probe. If the size of the probe was comparable to that of the dynamic heterogeneity of the system, tethered probes accurately report dynamics relevant to glass transition, regardless of tethering conditions.

The relaxation dynamics of polyisoprene (PI) and nitrile butadiene rubber (NBR) chains at the SiO2 interface were directly probed as a function of distance from the SiO2 surface using time-resolved...

We report a fundamentally new nonlinear dynamic system that couples optical autocatalytic behavior to phase evolution in photoreactive binary polymer blends. Upon exposure to light, the blend undergoes spontaneous patterning into a dense arrangement of microscale polymer filaments. The filaments’ growth in turn induces local spinodal decomposition of the blend along their length, thereby regulating the spatially dynamics of phase separation. This leads to the spontaneous organization of a large-scale binary phase morphology dictated by the filament arrangement. This is a new mechanism for polymer blend organization, which couples nonlinear optical dynamics to chemical phase separation dynamics, and offers a new approach to light-directed patterning and organization of polymer and hybrid blends.

We present molecular dynamics simulations of bead-and-spring polymer chains on chemically heterogeneous, energetically disordered surfaces at near-monolayer coverages. The surfaces consist of random mixtures of weakly (W) and strongly (S) attractive sites. We explore systematically the effect of surface composition on the diffusive dynamics of the chains. The polymer diffusion coefficients have a near-Arrhenius temperature dependence, with activation energies which have a nonmonotonic dependence on the fraction of S sites. In other words, we see a nonmonotonic dependence of the interfacial polymer dynamics on its affinity with the surface, when the latter involves some heterogeneity. The maximum activation energy belongs to the surface containing 75% S and 25% W sites, which combines near-maximum average polymer-surface interactions with near-maximum spread or disorder in these interactions. Our results have interesting implications for polymer adhesion and friction and structure-property relationships in polymer nanocomposites.

Though the strong transformation in mechanical properties of glass-forming materials such as amorphous polymers near the glass transition, Tg, has long been recognized and exploited, efforts to und...

The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments—where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution—seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the “detector” analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion., Journal of Biomolecular NMR, 75 (2-3), ISSN:0925-2738, ISSN:1573-5001

We present the results from an extensive atomistic molecular dynamics simulation study of poly(ethylene oxide) (PEO) doped with various amounts of lithium-bis(trifluoromethane)sulfonimide (LiTFSI) salt under the influence of external electric field strengths up to $1\,$V/nm. The motivation stems from recent experimental reports on the nonlinear response of mobilities to the application of an electric field in such electrolyte systems and arising speculations on field-induced alignment of the polymer chains, creating channel-like structures that facilitate ion passage. Hence, we systematically examine the electric field impact on the lithium coordination environment, polymer structure as well as ionic transport properties and further present a procedure to quantify the susceptibility of both structural and dynamical observables to the external field. Our investigation reveals indeed a coiled-to-stretched transformation of the PEO strands along with a concurrent nonlinear behavior of the dynamic properties. However, from studying the temporal response of the unperturbed electrolyte system to field application we are able to exclude a structurally conditioned enhancement of ion transport and surprisingly observe a slowing down. A microscopic understanding is supplied., Main manuscript comprises 30 pages and 13 figures, supplementary information section comprises 30 pages and 28 figures

The molecular dynamics simulation using the so-called force field is a computational method to investigate the conformational stability and dynamics of various biomolecules, including proteins and nucleic acids. While a force-balanced force field is necessary for realistic simulations, recent studies revealed that all standard CHARMM and AMBER force fields over-stabilize the protein–DNA interfaces, resulting in abnormally slow diffusion of DNA-binding proteins. To address this issue, we recently developed the CUFIX corrections by calibrating the electrostatic interactions at the protein–DNA interfaces and demonstrated that the CUFIX corrections dramatically improved the diffusion dynamics of DNA-binding proteins. However, whether the improvement was achieved correctly or at the cost of abnormal destabilization of protein–DNA interactions should be validated. Here, we prove that the CUFIX corrections achieved the balance by demonstrating that the CUFIX corrections maintain the complex structure of DNA and a histone-like protein, Hbb.

Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules atta...

Molecular dynamics simulations with many-body polarizable force fields were carried out to investigate the thermodynamic, structural, and dynamic properties of aqueous solutions of 1-butyl-3-methyl...

The lability, dynamics of the first solvation shell, and structure breaking effect properties of Cs+ in liquid ammonia have been evaluated using Quantum Mechanical Charge Field Molecular Dynamics (...

The delocalized exciton on conjugated polymers plays a momentous role in efficient charge generation and transport processes. Because the exciton is delocalized over the conjugated backbone, the ex...

Protein hydration dynamics plays an important role in many physiological processes since protein fluctuations, slow solvation, and the dynamics of hydrating water are all intrinsically related. Red edge excitation shift (REES) is a unique and powerful wavelength-selective (i.e. excitation-energy dependent) fluorescence approach that can be used to directly monitor the environment-induced restriction and dynamics around a polar fluorophore in a complex biological system. This review is mainly focused on recent applications of REES and a novel analysis of REES data to monitor the structural dynamics, functionally relevant conformational transitions and to unmask the structural ensembles in proteins. In addition, the novel utility of REES in imaging protein aggregates in a cellular context is discussed. We believe that the enormous potential of REES approach showcased in this review will engage more researchers, particularly from life sciences.

Dynamics are intricately linked with activity and selectivity when it comes to catalysis, as noted for instance in the enzymatic principles of induced fit and allostery, and yet the range of motions heterogeneous catalytic sites are able to undergo is poorly understood. Solid-state nuclear magnetic resonance (NMR) spectroscopy is perhaps the only tool capable of probing the rapid conformational dynamics found in heterogeneous catalysts but has historically been restricted by its low sensitivity, limiting the detail with which structures can be resolved. Here, we apply solid-state NMR and dynamic nuclear polarization, in combination with density functional theory modeling, to reveal the high-resolution structure and motional freedom of a scandium supported complex in three dimensions. The results are contrasted with the study of the analogous homoleptic complex in the crystalline state, highlighting the impacts that surface structure may have on the dynamics of supported complexes.

The glass transition and dynamics of densely grafted semiflexible polymer brushes are studied by molecular dynamics simulation. The glass transition temperature (Tg) increases with the polymer rigidity. The local glass transition temperature (Tg,local) is estimated from the temperature-dependent dynamics of individual segments including the lateral position fluctuation and lateral mean square displacement. Different from the flexible polymer brush, Tg,local of semiflexible polymer brushes is roughly independent of the segment height. Our simulation reveals that the glass transition is in synchronism with an abrupt change of the chain conformation in semiflexible polymer brushes. When the temperature drops to near Tg, the semiflexible polymer chains elongate, tilt, and become more ordered. Moreover, enhanced segmental dynamics is observed at temperatures just above Tg for the semiflexible polymer brushes.

Customarily, the studies of dynamics of hydrated proteins are focused on the fast hydration water ν-relaxation, the slow structural α-relaxation responsible for a single glass transition, and the protein dynamic transition (PDT). Guided by the analogy with the dynamics of highly asymmetric mixtures of molecular glass-formers, we explore the possibility that the dynamics of hydrated proteins are richer than presently known. By providing neutron scattering, dielectric relaxation, calorimetry, and deuteron NMR data in two hydrated globular proteins, myoglobin and BSA, and the fibrous elastin, we show the presence of two structural α-relaxations, α1 and α2, and the hydration water ν-relaxation, all coupled together with interconnecting properties. There are two glass transition temperatures Tgα1and Tgα2 corresponding to vitrification of the α1 and α2 processes. Relaxation time τα2(T) of the α2-relaxation changes its Arrhenius temperature dependence to super-Arrhenius on crossing Tgα1 from below. The ν-relaxation responds to the two vitrifications by changing the T-dependence of its relaxation time τν(T) on crossing consecutively Tgα2 and Tgα1. It generates the PDT at Td where τν(Td) matches about five times the experimental instrument timescale τexp, provided that Td > Tgα1. This condition is satisfied by the hydrated globular proteins considered in this paper, and the ν-relaxation is in the liquid state with τν(T) having the super-Arrhenius temperature dependence. However, if Td < Tgα1, the ν-relaxation fails to generate the PDT because it is in the glassy state and τν(T) has Arrhenius T-dependence, as in the case of hydrated elastin. Overall, the dynamics of hydrated proteins are the same as the dynamics of highly asymmetric mixtures of glass-formers. The results from this study have expanded the knowledge of the dynamic processes and their properties in hydrated proteins, and impact on research in this area is expected.

Dendronized polymers (denpols) are thick polymers comprising a linear backbone with grafted treelike structures (dendrons). The latter give rise to a molecular thickness that is a function of dendr...

Well-dispersed polymer-tethered silica nanoparticles exhibit soft glassy rheology and caging behaviors due to chain interpenetration driven by entropic attraction and geometric confinement. In this...

Twisted internal charge transfer (TICT) states are of fundamental importance during the photo-physical processes of dyes and sensors. In this contribution, excited-state dynamics of an Al3+ fluorescence sensor 1-{[(2-hydroxyphenyl)-imino]methyl}naphthalen-2-ol based on the turn-on signal is clarified. Two different dark TICT states are observed by exploring the excited-state potential energy surface. With the twist of the C2-N bond, the two dark states can be reached facilely, which induce the experimentally observed weak fluorescence of the sensor. The sensing mechanism is then uncovered by investigating the electronic coupling between the sensor and analyte. Al3+ is proved to form strong coordination bonds with the sensor, which restricts the motion of the C2-N bond. Consequently, the TICT states are eliminated, which generate the turn-on signal. This sensing mechanism is trustworthy and intrinsically different from the previously proposed one, which would shed some light on the design of turn-on sensors.

Retrieving information about the molecular motion of polymer chain in melt from the FID is based on the theoretical assumptions in which the heterogeneity of segmental dynamics and its anisotropy along chain are ignored. This article—the second and conclusive in the series—demonstrates, in detail, the FID calculation for various length chains considering these peculiarities revealed in the previous article. The experimentally observed FID components are assigned to the corresponding fragments of the entangled chain, and reasons for the deviation from theoretical values defined by the chain structure are proposed.

In this study, we investigated the structural dynamic features of the [NH3(CH2)2NH3]ZnCl4 crystal as a function of temperature through magic angle spinning (MAS) 1H nuclear magnetic resonance (NMR), MAS 13C NMR, and static 14N NMR. From the chemical shifts, changes in the structural environments of 13C and 14N were evident. The 1H spin–lattice relaxation time (T1ρ) values at high temperatures undergo molecular motion according to the Bloembergen–Purcell–Pound theory, and the 13C T1ρ value also varied abruptly with increasing temperature. Although the phase-transition temperature was not detected from the differential scanning calorimetry result, the chemical shifts and T1ρ results showed discontinuities around 300 K. Herein, the activation energies of molecular motion for 1H and 13C obtained from T1ρ are discussed. In addition, we compare the structural dynamics of diammonium-type [NH3(CH2)2NH3]ZnCl4 obtained in this study and monoammonium-type [CH3NH3]2ZnCl4 previously reported. The findings reported herein can provide important insights for potential applications of [NH3(CH2)2NH3]ZnCl4 crystals.

The dynamic heterogeneity of polymer chains is characterized by the lower correlation times of its end Kuhn segments with respect to those of the middle segments. In this study, the heterogeneity was investigated using molecular dynamics simulation of freely jointed chains of various lengths in the melt. Our characterization of the segmental dynamics along the chain additionally revealed the heterogeneity of rotational anisotropy, which was also lower for chain-end segments compared to those for chain-middle ones. This heterogeneity can be quantitatively characterized by intra-segmental residual dipolar coupling, which influences the transverse magnetic relaxation rate of the various chain segments and, ultimately, defines the free induction decay shape for chains of any length. Further, in the second part of this report, the origin of this relationship is discussed in detail.

Adefovir is regarded as a potential antiviral agent. However, it cannot be considered as a valuable drug candidate due to its high polarity that limits its permeability across the human intestinal mucosa. When the ribose phosphate group of adefovir is replaced by the isopolar phosphonomethyl ether functionality, it neutralizes the negative charge of the drug. This makes the drug lipid-soluble and potent to diffuse across the cell membrane. The prodrug adefovir dipivoxil is regarded as a potent antiviral drug against hepatitis B virus (HBV), human immunodeficiency virus (HIV), Rauscher murine leukemia virus (R-MuLV), murine cytomegalovirus (MCMV), herpes simplex virus (HSV), simian immunodeficiency virus (SIV), and feline immunodeficiency virus (FIV). The correlation between the structure and the dynamics of adefovir dipivoxil is determined by measuring the principal components of chemical shift anisotropy (CSA) tensor, site-specific spin–lattice relaxation time, and molecular correlation time at crystallographically different carbon nuclei sites. The CSA parameters, spin–lattice relaxation time, and molecular correlation time of phosphorous nucleus of the organophosphate group of adefovir dipivoxil molecule are also determined. The spin–lattice relaxation time of carbon nuclei varies from 1 to 107 s. The range of molecular correlation time also varies from 10–4 to 10–8 s. These remarkable diversities of motional dynamics of the molecules imply that there exist various motional degrees of freedom within this valuable drug and these motional degrees of freedom are independent of each other, which may be the reason for the biological activities exhibited by the drug. The correlation between structure and dynamics of such an important antiviral drug adefovir dipivoxil can be visualized by these types of extensive spectroscopic measurements, which will enlighten the path of inventing advanced medicine in the pharmaceutical industry, and it will also illuminate the understanding of the structure–activity relationships of antiviral drug.

We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk‐like behavior. The application of this computational protocol to magnesium chloride (MgCl2) solutions at different concentrations (0.6–2.8 mol kg−1) gives h values in excellent agreement with experimental hydration numbers obtained using GHz‐to‐THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well‐defined criterion for the definition of hydration number and provides a link with the molecular‐level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water‐water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl2 has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg‐water interaction rather than the Cl‐water interaction., Ab initio molecular dynamics simulations are used to characterize the structural, vibrational, and dynamical properties of water in aqueous magnesium chloride (MgCl2) solutions, and to develop a methodology to compute the hydration number (h) of aqueous electrolytes from water reorientation dynamics. The application of this protocol gives h values of MgCl2 solutions in excellent agreement with experimental hydration numbers obtained using GHz‐to‐THz dielectric relaxation spectroscopy.

Perovskites are widely utilized either as a primary component or as a substrate in which the dynamics of charged oxygen vacancy defects play an important role. Current knowledge regarding the dynamics of vacancy mobility in perovskites is solely based upon volume- and/or time-averaged measurements. This impedes our understanding of the basic physical principles governing defect migration in inorganic materials. Here, we measure the ergodic and nonergodic dynamics of vacancy migration at the relevant spatial and temporal scales using time-resolved atomic force microscopy techniques. Our findings demonstrate that the time constant associated with oxygen vacancy migration is a local property and can change drastically on short length and time scales, such that nonergodic states lead to a dramatic increase in the migration barrier. This correlated spatial and temporal variation in oxygen vacancy dynamics can extend hundreds of nanometers across the surface in inorganic perovskites.

Changes in the glass transition dynamics caused by nanoconfinement reveal pronounced out-of-equilibrium features. Therefore, the confinement effects weaken with time. Using dielectric spectroscopy, we have investigated the impact of molecular weight on the equilibration kinetics of the studied polymer embedded within anodic aluminum oxide nanoporous templates. For our research, we have used poly(phenylmethyl siloxane) (PMPS) with low (Mw = 2530 g/mol) and high (Mw = 27,800 g/mol) molecular weight. We have found that the observed faster dynamics of the nanopore-confined systems weakens with time, and ultimately it is possible to regain the bulk-like mobility. The equilibration time increases by reducing the pore size and lowering the annealing temperature much below the glass transition temperature of the interfacial layer, Tg_interface. The experimental data analysis has also revealed that the molecular weight of the nanopore-confined polymer influences the recovery of the bulk segmental relaxation time, τα. Low-molecular-weight PMPS rearrange and reach denser packing of the polymer chains with greater ease than the high-molecular-weight one. Finally, we have also demonstrated that the molecular weight affects the relationship between the time constant characterizing the equilibration kinetics and the characteristic time of viscous flow in cylindrical channels of nanometer size.

Relaxation dynamics of unentangled polymer melts (with a chain length below N = 100 for polyethylene) can be studied by performing either Rouse mode or relaxation mode analysis, such as proper orth...

The coupling between electrons and protons and the long-range transport of protons play important roles throughout biology. Biomimetic systems derived from benzimidazole-phenol (BIP) constructs have been designed to undergo proton-coupled electron transfer (PCET) upon electrochemical or photochemical oxidation. Moreover, these systems can transport protons along hydrogen-bonded networks or proton wires through multiproton PCET. Herein, the nonequilibrium dynamics of both single and double proton transfer in BIP molecules initiated by oxidation are investigated with first-principles molecular dynamics simulations. Although these processes are concerted in that no thermodynamically stable intermediate is observed, the simulations predict that they are predominantly asynchronous on the ultrafast time scale. For both systems, the first proton transfer typically occurs ∼100 fs after electron transfer. For the double proton transfer system, typically the second proton transfer occurs hundreds of femtoseconds after the initial proton transfer. A machine learning algorithm was used to identify the key molecular vibrational modes essential for proton transfer: a slow, in-plane bending mode that dominates the overall inner-sphere reorganization, the proton donor–acceptor motion that leads to vibrational coherence, and the faster donor–hydrogen stretching mode. The asynchronous double proton transfer mechanism can be understood in terms of a significant mode corresponding to the two anticorrelated proton donor–acceptor motions, typically decreasing only one donor–acceptor distance at a time. Although these PCET processes appear concerted on the time scale of typical electrochemical experiments, attaching these BIP constructs to photosensitizers may enable the detection of the asynchronicity of the electron and multiple proton transfers with ultrafast two-dimensional spectroscopy. Understanding the fundamental PCET mechanisms at this level will guide the design of PCET systems for catalysis and energy conversion processes., Neural networks help predict important motions in bioinspired molecules when they undergo proton-coupled electron transfer comprising one or two proton transfers along a proton wire.

We investigate the photodissociation of CH3Cl at 193.3 nm using the velocity map imaging technique in (CH3Cl)n clusters in comparison with isolated molecules. Our results for the isolated molecules...